2009
Durham, Elizabeth; Dorr, Brent; Woetzel, Nils; Staritzbichler, René; Meiler, Jens
Solvent accessible surface area approximations for rapid and accurate protein structure prediction Journal Article
In: J Mol Model, vol. 15, no. 9, pp. 1093–1108, 2009, ISSN: 0948-5023.
Abstract | Links | BibTeX | Tags:
@article{pmid19234730,
title = {Solvent accessible surface area approximations for rapid and accurate protein structure prediction},
author = {Elizabeth Durham and Brent Dorr and Nils Woetzel and René Staritzbichler and Jens Meiler},
doi = {10.1007/s00894-009-0454-9},
issn = {0948-5023},
year = {2009},
date = {2009-09-01},
journal = {J Mol Model},
volume = {15},
number = {9},
pages = {1093--1108},
abstract = {The burial of hydrophobic amino acids in the protein core is a driving force in protein folding. The extent to which an amino acid interacts with the solvent and the protein core is naturally proportional to the surface area exposed to these environments. However, an accurate calculation of the solvent-accessible surface area (SASA), a geometric measure of this exposure, is numerically demanding as it is not pair-wise decomposable. Furthermore, it depends on a full-atom representation of the molecule. This manuscript introduces a series of four SASA approximations of increasing computational complexity and accuracy as well as knowledge-based environment free energy potentials based on these SASA approximations. Their ability to distinguish correctly from incorrectly folded protein models is assessed to balance speed and accuracy for protein structure prediction. We find the newly developed "Neighbor Vector" algorithm provides the most optimal balance of accurate yet rapid exposure measures.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The burial of hydrophobic amino acids in the protein core is a driving force in protein folding. The extent to which an amino acid interacts with the solvent and the protein core is naturally proportional to the surface area exposed to these environments. However, an accurate calculation of the solvent-accessible surface area (SASA), a geometric measure of this exposure, is numerically demanding as it is not pair-wise decomposable. Furthermore, it depends on a full-atom representation of the molecule. This manuscript introduces a series of four SASA approximations of increasing computational complexity and accuracy as well as knowledge-based environment free energy potentials based on these SASA approximations. Their ability to distinguish correctly from incorrectly folded protein models is assessed to balance speed and accuracy for protein structure prediction. We find the newly developed "Neighbor Vector" algorithm provides the most optimal balance of accurate yet rapid exposure measures.
Koehler, Julia; Woetzel, Nils; Staritzbichler, René; Sanders, Charles R; Meiler, Jens
A unified hydrophobicity scale for multispan membrane proteins Journal Article
In: Proteins, vol. 76, no. 1, pp. 13–29, 2009, ISSN: 1097-0134.
Abstract | Links | BibTeX | Tags:
@article{pmid19089980,
title = {A unified hydrophobicity scale for multispan membrane proteins},
author = {Julia Koehler and Nils Woetzel and René Staritzbichler and Charles R Sanders and Jens Meiler},
doi = {10.1002/prot.22315},
issn = {1097-0134},
year = {2009},
date = {2009-07-01},
journal = {Proteins},
volume = {76},
number = {1},
pages = {13--29},
abstract = {The concept of hydrophobicity is critical to our understanding of the principles of membrane protein (MP) folding, structure, and function. In the last decades, several groups have derived hydrophobicity scales using both experimental and statistical methods that are optimized to mimic certain natural phenomena as closely as possible. The present work adds to this toolset the first knowledge-based scale that unifies the characteristics of both alpha-helical and beta-barrel multispan MPs. This unified hydrophobicity scale (UHS) distinguishes between amino acid preference for solution, transition, and trans-membrane states. The scale represents average hydrophobicity values of amino acids in folded proteins, irrespective of their secondary structure type. We furthermore present the first knowledge-based hydrophobicity scale for mammalian alpha-helical MPs (mammalian hydrophobicity scale--MHS). Both scales are particularly useful for computational protein structure elucidation, for example as input for machine learning techniques, such as secondary structure or trans-membrane span prediction, or as reference energies for protein structure prediction or protein design. The knowledge-based UHS shows a striking similarity to a recent experimental hydrophobicity scale introduced by Hessa and coworkers (Hessa T et al., Nature 2007;450:U1026-U1032). Convergence of two very different approaches onto similar hydrophobicity values consolidates the major differences between experimental and knowledge-based scales observed in earlier studies. Moreover, the UHS scale represents an accurate absolute free energy measure for folded, multispan MPs--a feature that is absent from many existing scales. The utility of the UHS was demonstrated by analyzing a series of diverse MPs. It is further shown that the UHS outperforms nine established hydrophobicity scales in predicting trans-membrane spans along the protein sequence. The accuracy of the present hydrophobicity scale profits from the doubling of the number of integral MPs in the PDB over the past four years. The UHS paves the way for an increased accuracy in the prediction of trans-membrane spans.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The concept of hydrophobicity is critical to our understanding of the principles of membrane protein (MP) folding, structure, and function. In the last decades, several groups have derived hydrophobicity scales using both experimental and statistical methods that are optimized to mimic certain natural phenomena as closely as possible. The present work adds to this toolset the first knowledge-based scale that unifies the characteristics of both alpha-helical and beta-barrel multispan MPs. This unified hydrophobicity scale (UHS) distinguishes between amino acid preference for solution, transition, and trans-membrane states. The scale represents average hydrophobicity values of amino acids in folded proteins, irrespective of their secondary structure type. We furthermore present the first knowledge-based hydrophobicity scale for mammalian alpha-helical MPs (mammalian hydrophobicity scale--MHS). Both scales are particularly useful for computational protein structure elucidation, for example as input for machine learning techniques, such as secondary structure or trans-membrane span prediction, or as reference energies for protein structure prediction or protein design. The knowledge-based UHS shows a striking similarity to a recent experimental hydrophobicity scale introduced by Hessa and coworkers (Hessa T et al., Nature 2007;450:U1026-U1032). Convergence of two very different approaches onto similar hydrophobicity values consolidates the major differences between experimental and knowledge-based scales observed in earlier studies. Moreover, the UHS scale represents an accurate absolute free energy measure for folded, multispan MPs--a feature that is absent from many existing scales. The utility of the UHS was demonstrated by analyzing a series of diverse MPs. It is further shown that the UHS outperforms nine established hydrophobicity scales in predicting trans-membrane spans along the protein sequence. The accuracy of the present hydrophobicity scale profits from the doubling of the number of integral MPs in the PDB over the past four years. The UHS paves the way for an increased accuracy in the prediction of trans-membrane spans.
Lindert, Steffen; Staritzbichler, René; Wötzel, Nils; Karakaş, Mert; Stewart, Phoebe L; Meiler, Jens
EM-fold: De novo folding of alpha-helical proteins guided by intermediate-resolution electron microscopy density maps Journal Article
In: Structure, vol. 17, no. 7, pp. 990–1003, 2009, ISSN: 1878-4186.
Abstract | Links | BibTeX | Tags:
@article{pmid19604479,
title = {EM-fold: De novo folding of alpha-helical proteins guided by intermediate-resolution electron microscopy density maps},
author = {Steffen Lindert and René Staritzbichler and Nils Wötzel and Mert Karakaş and Phoebe L Stewart and Jens Meiler},
doi = {10.1016/j.str.2009.06.001},
issn = {1878-4186},
year = {2009},
date = {2009-07-01},
journal = {Structure},
volume = {17},
number = {7},
pages = {990--1003},
abstract = {In medium-resolution (7-10 A) cryo-electron microscopy (cryo-EM) density maps, alpha helices can be identified as density rods whereas beta-strand or loop regions are not as easily discerned. We are proposing a computational protein structure prediction algorithm "EM-Fold" that resolves the density rod connectivity ambiguity by placing predicted alpha helices into the density rods and adding missing backbone coordinates in loop regions. In a benchmark of 11 mainly alpha-helical proteins of known structure a native-like model is identified in eight cases (rmsd 3.9-7.9 A). The three failures can be attributed to inaccuracies in the secondary structure prediction step that precedes EM-Fold. EM-Fold has been applied to the approximately 6 A resolution cryo-EM density map of protein IIIa from human adenovirus. We report the first topological model for the alpha-helical 400 residue N-terminal region of protein IIIa. EM-Fold also has the potential to interpret medium-resolution density maps in X-ray crystallography.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
In medium-resolution (7-10 A) cryo-electron microscopy (cryo-EM) density maps, alpha helices can be identified as density rods whereas beta-strand or loop regions are not as easily discerned. We are proposing a computational protein structure prediction algorithm "EM-Fold" that resolves the density rod connectivity ambiguity by placing predicted alpha helices into the density rods and adding missing backbone coordinates in loop regions. In a benchmark of 11 mainly alpha-helical proteins of known structure a native-like model is identified in eight cases (rmsd 3.9-7.9 A). The three failures can be attributed to inaccuracies in the secondary structure prediction step that precedes EM-Fold. EM-Fold has been applied to the approximately 6 A resolution cryo-EM density map of protein IIIa from human adenovirus. We report the first topological model for the alpha-helical 400 residue N-terminal region of protein IIIa. EM-Fold also has the potential to interpret medium-resolution density maps in X-ray crystallography.
Stepanovic, Svetlana Z; Potet, Franck; Petersen, Christina I; Smith, Jarrod A; Meiler, Jens; Balser, Jeffrey R; Kupershmidt, Sabina
The evolutionarily conserved residue A653 plays a key role in HERG channel closing Journal Article
In: J Physiol, vol. 587, no. Pt 11, pp. 2555–2566, 2009, ISSN: 1469-7793.
Abstract | Links | BibTeX | Tags:
@article{pmid19406877,
title = {The evolutionarily conserved residue A653 plays a key role in HERG channel closing},
author = {Svetlana Z Stepanovic and Franck Potet and Christina I Petersen and Jarrod A Smith and Jens Meiler and Jeffrey R Balser and Sabina Kupershmidt},
doi = {10.1113/jphysiol.2008.166694},
issn = {1469-7793},
year = {2009},
date = {2009-06-01},
journal = {J Physiol},
volume = {587},
number = {Pt 11},
pages = {2555--2566},
abstract = {Human ether-a-go-go-related gene (HERG) encodes the rapid, outwardly rectifying K(+) current I(Kr) that is critical for repolarization of the cardiac action potential. Congenital HERG mutations or unintended pharmaceutical block of I(Kr) can lead to life-threatening arrhythmias. Here, we assess the functional role of the alanine at position 653 (HERG-A653) that is highly conserved among evolutionarily divergent K(+) channels. HERG-A653 is close to the 'glycine hinge' implicated in K(+) channel opening, and is flanked by tyrosine 652 and phenylalanine 656, which contribute to the drug binding site. We substituted an array of seven (I, C, S, G, Y, V and T) amino acids at position 653 and expressed individual variants in heterologous systems to assess changes in gating and drug binding. Substitution of A653 resulted in negative shifts of the V(1/2) of activation ranging from -23.6 (A653S) to -62.5 (A653V) compared to -11.2 mV for wild-type (WT). Deactivation was also drastically altered: channels with A653I/C substitutions exhibited delayed deactivation in response to test potentials above the activation threshold, while A653S/G/Y/V/T failed to deactivate under those conditions and required hyperpolarization and prolonged holding potentials at -130 mV. While A653S/G/T/Y variants showed decreased sensitivity to the I(Kr) inhibitor dofetilide, these changes could not be correlated with defects in channel closure. Homology modelling suggests that in the closed state, A653 forms tight contacts with several residues from the neighbouring subunit in the tetramer, playing a key role in S6 helix packing at the narrowest part of the vestibule. Our study suggests that A653 plays an important functional role in the outwardly rectifying gating behaviour of HERG, supporting channel closure at membrane potentials negative to the channel activation threshold.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Human ether-a-go-go-related gene (HERG) encodes the rapid, outwardly rectifying K(+) current I(Kr) that is critical for repolarization of the cardiac action potential. Congenital HERG mutations or unintended pharmaceutical block of I(Kr) can lead to life-threatening arrhythmias. Here, we assess the functional role of the alanine at position 653 (HERG-A653) that is highly conserved among evolutionarily divergent K(+) channels. HERG-A653 is close to the 'glycine hinge' implicated in K(+) channel opening, and is flanked by tyrosine 652 and phenylalanine 656, which contribute to the drug binding site. We substituted an array of seven (I, C, S, G, Y, V and T) amino acids at position 653 and expressed individual variants in heterologous systems to assess changes in gating and drug binding. Substitution of A653 resulted in negative shifts of the V(1/2) of activation ranging from -23.6 (A653S) to -62.5 (A653V) compared to -11.2 mV for wild-type (WT). Deactivation was also drastically altered: channels with A653I/C substitutions exhibited delayed deactivation in response to test potentials above the activation threshold, while A653S/G/Y/V/T failed to deactivate under those conditions and required hyperpolarization and prolonged holding potentials at -130 mV. While A653S/G/T/Y variants showed decreased sensitivity to the I(Kr) inhibitor dofetilide, these changes could not be correlated with defects in channel closure. Homology modelling suggests that in the closed state, A653 forms tight contacts with several residues from the neighbouring subunit in the tetramer, playing a key role in S6 helix packing at the narrowest part of the vestibule. Our study suggests that A653 plays an important functional role in the outwardly rectifying gating behaviour of HERG, supporting channel closure at membrane potentials negative to the channel activation threshold.
Friedland, Gregory D; Lakomek, Nils-Alexander; Griesinger, Christian; Meiler, Jens; Kortemme, Tanja
A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family Journal Article
In: PLoS Comput Biol, vol. 5, no. 5, pp. e1000393, 2009, ISSN: 1553-7358.
Abstract | Links | BibTeX | Tags:
@article{pmid19478996,
title = {A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family},
author = {Gregory D Friedland and Nils-Alexander Lakomek and Christian Griesinger and Jens Meiler and Tanja Kortemme},
doi = {10.1371/journal.pcbi.1000393},
issn = {1553-7358},
year = {2009},
date = {2009-05-01},
journal = {PLoS Comput Biol},
volume = {5},
number = {5},
pages = {e1000393},
abstract = {Conformational ensembles are increasingly recognized as a useful representation to describe fundamental relationships between protein structure, dynamics and function. Here we present an ensemble of ubiquitin in solution that is created by sampling conformational space without experimental information using "Backrub" motions inspired by alternative conformations observed in sub-Angstrom resolution crystal structures. Backrub-generated structures are then selected to produce an ensemble that optimizes agreement with nuclear magnetic resonance (NMR) Residual Dipolar Couplings (RDCs). Using this ensemble, we probe two proposed relationships between properties of protein ensembles: (i) a link between native-state dynamics and the conformational heterogeneity observed in crystal structures, and (ii) a relation between dynamics of an individual protein and the conformational variability explored by its natural family. We show that the Backrub motional mechanism can simultaneously explore protein native-state dynamics measured by RDCs, encompass the conformational variability present in ubiquitin complex structures and facilitate sampling of conformational and sequence variability matching those occurring in the ubiquitin protein family. Our results thus support an overall relation between protein dynamics and conformational changes enabling sequence changes in evolution. More practically, the presented method can be applied to improve protein design predictions by accounting for intrinsic native-state dynamics.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Conformational ensembles are increasingly recognized as a useful representation to describe fundamental relationships between protein structure, dynamics and function. Here we present an ensemble of ubiquitin in solution that is created by sampling conformational space without experimental information using "Backrub" motions inspired by alternative conformations observed in sub-Angstrom resolution crystal structures. Backrub-generated structures are then selected to produce an ensemble that optimizes agreement with nuclear magnetic resonance (NMR) Residual Dipolar Couplings (RDCs). Using this ensemble, we probe two proposed relationships between properties of protein ensembles: (i) a link between native-state dynamics and the conformational heterogeneity observed in crystal structures, and (ii) a relation between dynamics of an individual protein and the conformational variability explored by its natural family. We show that the Backrub motional mechanism can simultaneously explore protein native-state dynamics measured by RDCs, encompass the conformational variability present in ubiquitin complex structures and facilitate sampling of conformational and sequence variability matching those occurring in the ubiquitin protein family. Our results thus support an overall relation between protein dynamics and conformational changes enabling sequence changes in evolution. More practically, the presented method can be applied to improve protein design predictions by accounting for intrinsic native-state dynamics.
Lindert, Steffen; Stewart, Phoebe L; Meiler, Jens
Hybrid approaches: applying computational methods in cryo-electron microscopy Journal Article
In: Curr Opin Struct Biol, vol. 19, no. 2, pp. 218–225, 2009, ISSN: 1879-033X.
Abstract | Links | BibTeX | Tags:
@article{pmid19339173,
title = {Hybrid approaches: applying computational methods in cryo-electron microscopy},
author = {Steffen Lindert and Phoebe L Stewart and Jens Meiler},
doi = {10.1016/j.sbi.2009.02.010},
issn = {1879-033X},
year = {2009},
date = {2009-04-01},
journal = {Curr Opin Struct Biol},
volume = {19},
number = {2},
pages = {218--225},
abstract = {Recent advances in cryo-electron microscopy have led to an increasing number of high (3-5A) to medium (5-10A) resolution cryoEM density maps. These density maps contain valuable information about the protein structure but frequently require computational algorithms to aid their structural interpretation. It is these hybrid approaches between cryoEM and computational protein structure prediction algorithms that will shape protein structure elucidation from density maps.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Recent advances in cryo-electron microscopy have led to an increasing number of high (3-5A) to medium (5-10A) resolution cryoEM density maps. These density maps contain valuable information about the protein structure but frequently require computational algorithms to aid their structural interpretation. It is these hybrid approaches between cryoEM and computational protein structure prediction algorithms that will shape protein structure elucidation from density maps.
Kaufmann, Kristian W; Dawson, Eric S; Henry, L Keith; Field, Julie R; Blakely, Randy D; Meiler, Jens
In: Proteins, vol. 74, no. 3, pp. 630–642, 2009, ISSN: 1097-0134.
Abstract | Links | BibTeX | Tags:
@article{pmid18704946,
title = {Structural determinants of species-selective substrate recognition in human and Drosophila serotonin transporters revealed through computational docking studies},
author = {Kristian W Kaufmann and Eric S Dawson and L Keith Henry and Julie R Field and Randy D Blakely and Jens Meiler},
doi = {10.1002/prot.22178},
issn = {1097-0134},
year = {2009},
date = {2009-02-01},
journal = {Proteins},
volume = {74},
number = {3},
pages = {630--642},
abstract = {To identify potential determinants of substrate selectivity in serotonin (5-HT) transporters (SERT), models of human and Drosophila serotonin transporters (hSERT, dSERT) were built based on the leucine transporter (LeuT(Aa)) structure reported by Yamashita et al. (Nature 2005;437:215-223), PBDID 2A65. Although the overall amino acid identity between SERTs and the LeuT(Aa) is only 17%, it increases to above 50% in the first shell of the putative 5-HT binding site, allowing de novo computational docking of tryptamine derivatives in atomic detail. Comparison of hSERT and dSERT complexed with substrates pinpoints likely structural determinants for substrate binding. Forgoing the use of experimental transport and binding data of tryptamine derivatives for construction of these models enables us to critically assess and validate their predictive power: A single 5-HT binding mode was identified that retains the amine placement observed in the LeuT(Aa) structure, matches site-directed mutagenesis and substituted cysteine accessibility method (SCAM) data, complies with support vector machine derived relations activity relations, and predicts computational binding energies for 5-HT analogs with a significant correlation coefficient (R = 0.72). This binding mode places 5-HT deep in the binding pocket of the SERT with the 5-position near residue hSERT A169/dSERT D164 in transmembrane helix 3, the indole nitrogen next to residue Y176/Y171, and the ethylamine tail under residues F335/F327 and S336/S328 within 4 A of residue D98. Our studies identify a number of potential contacts whose contribution to substrate binding and transport was previously unsuspected.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
To identify potential determinants of substrate selectivity in serotonin (5-HT) transporters (SERT), models of human and Drosophila serotonin transporters (hSERT, dSERT) were built based on the leucine transporter (LeuT(Aa)) structure reported by Yamashita et al. (Nature 2005;437:215-223), PBDID 2A65. Although the overall amino acid identity between SERTs and the LeuT(Aa) is only 17%, it increases to above 50% in the first shell of the putative 5-HT binding site, allowing de novo computational docking of tryptamine derivatives in atomic detail. Comparison of hSERT and dSERT complexed with substrates pinpoints likely structural determinants for substrate binding. Forgoing the use of experimental transport and binding data of tryptamine derivatives for construction of these models enables us to critically assess and validate their predictive power: A single 5-HT binding mode was identified that retains the amine placement observed in the LeuT(Aa) structure, matches site-directed mutagenesis and substituted cysteine accessibility method (SCAM) data, complies with support vector machine derived relations activity relations, and predicts computational binding energies for 5-HT analogs with a significant correlation coefficient (R = 0.72). This binding mode places 5-HT deep in the binding pocket of the SERT with the 5-position near residue hSERT A169/dSERT D164 in transmembrane helix 3, the indole nitrogen next to residue Y176/Y171, and the ethylamine tail under residues F335/F327 and S336/S328 within 4 A of residue D98. Our studies identify a number of potential contacts whose contribution to substrate binding and transport was previously unsuspected.
Fallen, Katherine; Banerjee, Sreedatta; Sheehan, Jonathan; Addison, Daniel; Lewis, L Michelle; Meiler, Jens; Denton, Jerod S
The Kir channel immunoglobulin domain is essential for Kir1.1 (ROMK) thermodynamic stability, trafficking and gating Journal Article
In: Channels (Austin), vol. 3, no. 1, pp. 57–68, 2009, ISSN: 1933-6969.
Abstract | Links | BibTeX | Tags:
@article{pmid19221509,
title = {The Kir channel immunoglobulin domain is essential for Kir1.1 (ROMK) thermodynamic stability, trafficking and gating},
author = {Katherine Fallen and Sreedatta Banerjee and Jonathan Sheehan and Daniel Addison and L Michelle Lewis and Jens Meiler and Jerod S Denton},
doi = {10.4161/chan.3.1.7817},
issn = {1933-6969},
year = {2009},
date = {2009-01-01},
journal = {Channels (Austin)},
volume = {3},
number = {1},
pages = {57--68},
abstract = {The renal inward rectifying potassium channel Kir1.1 plays key roles in regulating electrolyte homeostasis and blood pressure. Loss-of-function mutations in the channel cause a life-threatening salt and water balance disorder in infants called antenatal Bartter syndrome (ABS). Of more than 30 ABS mutations identified, approximately half are located in the intracellular domain of the channel. The mechanisms underlying channel dysfunction for most of these mutations are unknown. By mapping intracellular mutations onto an atomic model of Kir1.1, we found that several of these are localized to a phylogenetically ancient immunoglobulin (Ig)-like domain (IgLD) that has not been characterized previously, prompting us to examine this structure in detail. The IgLD is assembled from two beta-pleated sheets packed face-to-face, creating a beta-sheet interface or core, populated by highly conserved side chains. Thermodynamic calculations on computationally mutated channels suggest that IgLD core residues are among the most important residues for determining cytoplasmic domain stability. Consistent with this notion, we show that two ABS mutations (A198T and Y314C) located within the IgLD core impair channel biosynthesis and trafficking in mammalian cells. A fraction of core mutant channels reach the cell surface, but are electrically silent due to closure of the helix-bundle gate. Compensatory mutation-induced rescue of channel function revealed that IgLD core mutants fail to rectify. Our study sheds new light on the pathogenesis of ABS and establishes the IgLD as an essential structure within the Kir channel family.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The renal inward rectifying potassium channel Kir1.1 plays key roles in regulating electrolyte homeostasis and blood pressure. Loss-of-function mutations in the channel cause a life-threatening salt and water balance disorder in infants called antenatal Bartter syndrome (ABS). Of more than 30 ABS mutations identified, approximately half are located in the intracellular domain of the channel. The mechanisms underlying channel dysfunction for most of these mutations are unknown. By mapping intracellular mutations onto an atomic model of Kir1.1, we found that several of these are localized to a phylogenetically ancient immunoglobulin (Ig)-like domain (IgLD) that has not been characterized previously, prompting us to examine this structure in detail. The IgLD is assembled from two beta-pleated sheets packed face-to-face, creating a beta-sheet interface or core, populated by highly conserved side chains. Thermodynamic calculations on computationally mutated channels suggest that IgLD core residues are among the most important residues for determining cytoplasmic domain stability. Consistent with this notion, we show that two ABS mutations (A198T and Y314C) located within the IgLD core impair channel biosynthesis and trafficking in mammalian cells. A fraction of core mutant channels reach the cell surface, but are electrically silent due to closure of the helix-bundle gate. Compensatory mutation-induced rescue of channel function revealed that IgLD core mutants fail to rectify. Our study sheds new light on the pathogenesis of ABS and establishes the IgLD as an essential structure within the Kir channel family.
Koehler, Julia; Mueller, Ralf; Meiler, Jens
Improved prediction of trans-membrane spans in proteins using an Artificial Neural Network Journal Article
In: IEEE Symp Comput Intell Bioinforma Comput Biol Proc, vol. 2009, pp. 68–74, 2009.
Abstract | Links | BibTeX | Tags:
@article{pmid27747315,
title = {Improved prediction of trans-membrane spans in proteins using an Artificial Neural Network},
author = {Julia Koehler and Ralf Mueller and Jens Meiler},
doi = {10.1109/CIBCB.2009.4925709},
year = {2009},
date = {2009-01-01},
journal = {IEEE Symp Comput Intell Bioinforma Comput Biol Proc},
volume = {2009},
pages = {68--74},
abstract = {Tools for the identification of trans-membrane spans from the protein sequence are widely used in the experimental community. Computational structural biology seeks to increase the prediction accuracy of such methods since they represent a first step towards membrane protein tertiary structure prediction from the amino acid sequence. We introduce a predictor that is able to identify trans-membrane spans from the sequence of a protein. The novelty of the approach presented here is the simultaneous prediction of trans-membrane spanning α-helices and β-strands within a single tool. An artificial neural network was trained on databases of 102 membrane proteins and 3499 soluble proteins. Prediction accuracies of up to 92% for soluble residues, 75% for residues in the interface, and 73% for TM residues are achieved. On average the algorithm predicts 79% of the residues correctly which is a substantial improvement from a previously published implementation which achieved 57% accuracy (Koehler , , 2008). The algorithm was applied to four membrane proteins to illustrate the applicability to both α-helical bundles and β-barrels.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Tools for the identification of trans-membrane spans from the protein sequence are widely used in the experimental community. Computational structural biology seeks to increase the prediction accuracy of such methods since they represent a first step towards membrane protein tertiary structure prediction from the amino acid sequence. We introduce a predictor that is able to identify trans-membrane spans from the sequence of a protein. The novelty of the approach presented here is the simultaneous prediction of trans-membrane spanning α-helices and β-strands within a single tool. An artificial neural network was trained on databases of 102 membrane proteins and 3499 soluble proteins. Prediction accuracies of up to 92% for soluble residues, 75% for residues in the interface, and 73% for TM residues are achieved. On average the algorithm predicts 79% of the residues correctly which is a substantial improvement from a previously published implementation which achieved 57% accuracy (Koehler , , 2008). The algorithm was applied to four membrane proteins to illustrate the applicability to both α-helical bundles and β-barrels.
2008
Lakomek, Nils-Alexander; Lange, Oliver F; Walter, Korvin F A; Farès, Christophe; Egger, Dalia; Lunkenheimer, Peter; Meiler, Jens; Grubmüller, Helmut; Becker, Stefan; de Groot, Bert L; Griesinger, Christian
Residual dipolar couplings as a tool to study molecular recognition of ubiquitin Journal Article
In: Biochem Soc Trans, vol. 36, no. Pt 6, pp. 1433–1437, 2008, ISSN: 1470-8752.
Abstract | Links | BibTeX | Tags:
@article{pmid19021570,
title = {Residual dipolar couplings as a tool to study molecular recognition of ubiquitin},
author = {Nils-Alexander Lakomek and Oliver F Lange and Korvin F A Walter and Christophe Farès and Dalia Egger and Peter Lunkenheimer and Jens Meiler and Helmut Grubmüller and Stefan Becker and Bert L de Groot and Christian Griesinger},
doi = {10.1042/BST0361433},
issn = {1470-8752},
year = {2008},
date = {2008-12-01},
journal = {Biochem Soc Trans},
volume = {36},
number = {Pt 6},
pages = {1433--1437},
abstract = {RDCs (residual dipolar couplings) in NMR spectroscopy provide information about protein dynamics complementary to NMR relaxation methods, especially in the previously inaccessible time window between the protein correlation time tau(c) and 50 micros. For ubiquitin, new modes of motion of the protein backbone could be detected using RDC-based techniques. An ensemble of ubiquitin based on these RDC values is found to comprise all different conformations that ubiquitin adopts upon binding to different recognition proteins. These conformations in protein-protein complexes had been derived from 46 X-ray structures. Thus, for ubiquitin recognition by other proteins, conformational selection rather than induced fit seems to be the dominant mechanism.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
RDCs (residual dipolar couplings) in NMR spectroscopy provide information about protein dynamics complementary to NMR relaxation methods, especially in the previously inaccessible time window between the protein correlation time tau(c) and 50 micros. For ubiquitin, new modes of motion of the protein backbone could be detected using RDC-based techniques. An ensemble of ubiquitin based on these RDC values is found to comprise all different conformations that ubiquitin adopts upon binding to different recognition proteins. These conformations in protein-protein complexes had been derived from 46 X-ray structures. Thus, for ubiquitin recognition by other proteins, conformational selection rather than induced fit seems to be the dominant mechanism.
Dong, Elizabeth; Smith, Jarrod; Heinze, Sten; Alexander, Nathan; Meiler, Jens
BCL::Align-sequence alignment and fold recognition with a custom scoring function online Journal Article
In: Gene, vol. 422, no. 1-2, pp. 41–46, 2008, ISSN: 0378-1119.
Abstract | Links | BibTeX | Tags:
@article{pmid18601985,
title = {BCL::Align-sequence alignment and fold recognition with a custom scoring function online},
author = {Elizabeth Dong and Jarrod Smith and Sten Heinze and Nathan Alexander and Jens Meiler},
doi = {10.1016/j.gene.2008.06.006},
issn = {0378-1119},
year = {2008},
date = {2008-10-01},
journal = {Gene},
volume = {422},
number = {1-2},
pages = {41--46},
abstract = {BCL::Align is a multiple sequence alignment tool that utilizes the dynamic programming method in combination with a customizable scoring function for sequence alignment and fold recognition. The scoring function is a weighted sum of the traditional PAM and BLOSUM scoring matrices, position-specific scoring matrices output by PSI-BLAST, secondary structure predicted by a variety of methods, chemical properties, and gap penalties. By adjusting the weights, the method can be tailored for fold recognition or sequence alignment tasks at different levels of sequence identity. A Monte Carlo algorithm was used to determine optimized weight sets for sequence alignment and fold recognition that most accurately reproduced the SABmark reference alignment test set. In an evaluation of sequence alignment performance, BCL::Align ranked best in alignment accuracy (Cline score of 22.90 for sequences in the Twilight Zone) when compared with Align-m, ClustalW, T-Coffee, and MUSCLE. ROC curve analysis indicates BCL::Align's ability to correctly recognize protein folds with over 80% accuracy. The flexibility of the program allows it to be optimized for specific classes of proteins (e.g. membrane proteins) or fold families (e.g. TIM-barrel proteins). BCL::Align is free for academic use and available online at http://www.meilerlab.org/.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
BCL::Align is a multiple sequence alignment tool that utilizes the dynamic programming method in combination with a customizable scoring function for sequence alignment and fold recognition. The scoring function is a weighted sum of the traditional PAM and BLOSUM scoring matrices, position-specific scoring matrices output by PSI-BLAST, secondary structure predicted by a variety of methods, chemical properties, and gap penalties. By adjusting the weights, the method can be tailored for fold recognition or sequence alignment tasks at different levels of sequence identity. A Monte Carlo algorithm was used to determine optimized weight sets for sequence alignment and fold recognition that most accurately reproduced the SABmark reference alignment test set. In an evaluation of sequence alignment performance, BCL::Align ranked best in alignment accuracy (Cline score of 22.90 for sequences in the Twilight Zone) when compared with Align-m, ClustalW, T-Coffee, and MUSCLE. ROC curve analysis indicates BCL::Align's ability to correctly recognize protein folds with over 80% accuracy. The flexibility of the program allows it to be optimized for specific classes of proteins (e.g. membrane proteins) or fold families (e.g. TIM-barrel proteins). BCL::Align is free for academic use and available online at http://www.meilerlab.org/.
Kang, Congbao; Tian, Changlin; Sönnichsen, Frank D; Smith, Jarrod A; Meiler, Jens; George, Alfred L; Vanoye, Carlos G; Kim, Hak Jun; Sanders, Charles R
Structure of KCNE1 and implications for how it modulates the KCNQ1 potassium channel Journal Article
In: Biochemistry, vol. 47, no. 31, pp. 7999–8006, 2008, ISSN: 1520-4995.
Abstract | Links | BibTeX | Tags:
@article{pmid18611041,
title = {Structure of KCNE1 and implications for how it modulates the KCNQ1 potassium channel},
author = {Congbao Kang and Changlin Tian and Frank D Sönnichsen and Jarrod A Smith and Jens Meiler and Alfred L George and Carlos G Vanoye and Hak Jun Kim and Charles R Sanders},
doi = {10.1021/bi800875q},
issn = {1520-4995},
year = {2008},
date = {2008-08-01},
journal = {Biochemistry},
volume = {47},
number = {31},
pages = {7999--8006},
abstract = {KCNE1 is a single-span membrane protein that modulates the voltage-gated potassium channel KCNQ1 (K V7.1) by slowing activation and enhancing channel conductance to generate the slow delayed rectifier current ( I Ks) that is critical for the repolarization phase of the cardiac action potential. Perturbation of channel function by inherited mutations in KCNE1 or KCNQ1 results in increased susceptibility to cardiac arrhythmias and sudden death with or without accompanying deafness. Here, we present the three-dimensional structure of KCNE1. The transmembrane domain (TMD) of KCNE1 is a curved alpha-helix and is flanked by intra- and extracellular domains comprised of alpha-helices joined by flexible linkers. Experimentally restrained docking of the KCNE1 TMD to a closed state model of KCNQ1 suggests that KCNE1 slows channel activation by sitting on and restricting the movement of the S4-S5 linker that connects the voltage sensor to the pore domain. We postulate that this is an adhesive interaction that must be disrupted before the channel can be opened in response to membrane depolarization. Docking to open KCNQ1 indicates that the extracellular end of the KCNE1 TMD forms an interface with an intersubunit cleft in the channel that is associated with most known gain-of-function disease mutations. Binding of KCNE1 to this "gain-of-function cleft" may explain how it increases conductance and stabilizes the open state. These working models for the KCNE1-KCNQ1 complexes may be used to formulate testable hypotheses for the molecular bases of disease phenotypes associated with the dozens of known inherited mutations in KCNE1 and KCNQ1.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
KCNE1 is a single-span membrane protein that modulates the voltage-gated potassium channel KCNQ1 (K V7.1) by slowing activation and enhancing channel conductance to generate the slow delayed rectifier current ( I Ks) that is critical for the repolarization phase of the cardiac action potential. Perturbation of channel function by inherited mutations in KCNE1 or KCNQ1 results in increased susceptibility to cardiac arrhythmias and sudden death with or without accompanying deafness. Here, we present the three-dimensional structure of KCNE1. The transmembrane domain (TMD) of KCNE1 is a curved alpha-helix and is flanked by intra- and extracellular domains comprised of alpha-helices joined by flexible linkers. Experimentally restrained docking of the KCNE1 TMD to a closed state model of KCNQ1 suggests that KCNE1 slows channel activation by sitting on and restricting the movement of the S4-S5 linker that connects the voltage sensor to the pore domain. We postulate that this is an adhesive interaction that must be disrupted before the channel can be opened in response to membrane depolarization. Docking to open KCNQ1 indicates that the extracellular end of the KCNE1 TMD forms an interface with an intersubunit cleft in the channel that is associated with most known gain-of-function disease mutations. Binding of KCNE1 to this "gain-of-function cleft" may explain how it increases conductance and stabilizes the open state. These working models for the KCNE1-KCNQ1 complexes may be used to formulate testable hypotheses for the molecular bases of disease phenotypes associated with the dozens of known inherited mutations in KCNE1 and KCNQ1.
Lakomek, Nils-Alexander; Walter, Korvin F A; Farès, Christophe; Lange, Oliver F; de Groot, Bert L; Grubmüller, Helmut; Brüschweiler, Rafael; Munk, Axel; Becker, Stefan; Meiler, Jens; Griesinger, Christian
Self-consistent residual dipolar coupling based model-free analysis for the robust determination of nanosecond to microsecond protein dynamics Journal Article
In: J Biomol NMR, vol. 41, no. 3, pp. 139–155, 2008, ISSN: 0925-2738.
Abstract | Links | BibTeX | Tags:
@article{pmid18523727,
title = {Self-consistent residual dipolar coupling based model-free analysis for the robust determination of nanosecond to microsecond protein dynamics},
author = {Nils-Alexander Lakomek and Korvin F A Walter and Christophe Farès and Oliver F Lange and Bert L de Groot and Helmut Grubmüller and Rafael Brüschweiler and Axel Munk and Stefan Becker and Jens Meiler and Christian Griesinger},
doi = {10.1007/s10858-008-9244-4},
issn = {0925-2738},
year = {2008},
date = {2008-07-01},
journal = {J Biomol NMR},
volume = {41},
number = {3},
pages = {139--155},
abstract = {Residual dipolar couplings (RDCs) provide information about the dynamic average orientation of inter-nuclear vectors and amplitudes of motion up to milliseconds. They complement relaxation methods, especially on a time-scale window that we have called supra-tau(c) (tau(c) < supra-tau(c) < 50 micros). Here we present a robust approach called Self-Consistent RDC-based Model-free analysis (SCRM) that delivers RDC-based order parameters-independent of the details of the structure used for alignment tensor calculation-as well as the dynamic average orientation of the inter-nuclear vectors in the protein structure in a self-consistent manner. For ubiquitin, the SCRM analysis yields an average RDC-derived order parameter of the NH vectors 0.72 +/- 0.02 compared to = 0.778 +/- 0.003 for the Lipari-Szabo order parameters, indicating that the inclusion of the supra-tau(c) window increases the averaged amplitude of mobility observed in the sub-supra-tau(c) window by about 34%. For the beta-strand spanned by residues Lys48 to Leu50, an alternating pattern of backbone NH RDC order parameter S2(rdc)(NH) = (0.59, 0.72, 0.59) was extracted. The backbone of Lys48, whose side chain is known to be involved in the poly-ubiquitylation process that leads to protein degradation, is very mobile on the supra-tau(c) time scale (S2(rdc)(NH) = 0.59 +/- 0.03), while it is inconspicuous (S2(LS)(NH)= 0.82) on the sub-tau(c) as well as on micros-ms relaxation dispersion time scales. The results of this work differ from previous RDC dynamics studies of ubiquitin in the sense that the results are essentially independent of structural noise providing a much more robust assessment of dynamic effects that underlie the RDC data.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Residual dipolar couplings (RDCs) provide information about the dynamic average orientation of inter-nuclear vectors and amplitudes of motion up to milliseconds. They complement relaxation methods, especially on a time-scale window that we have called supra-tau(c) (tau(c) < supra-tau(c) < 50 micros). Here we present a robust approach called Self-Consistent RDC-based Model-free analysis (SCRM) that delivers RDC-based order parameters-independent of the details of the structure used for alignment tensor calculation-as well as the dynamic average orientation of the inter-nuclear vectors in the protein structure in a self-consistent manner. For ubiquitin, the SCRM analysis yields an average RDC-derived order parameter of the NH vectors 0.72 +/- 0.02 compared to = 0.778 +/- 0.003 for the Lipari-Szabo order parameters, indicating that the inclusion of the supra-tau(c) window increases the averaged amplitude of mobility observed in the sub-supra-tau(c) window by about 34%. For the beta-strand spanned by residues Lys48 to Leu50, an alternating pattern of backbone NH RDC order parameter S2(rdc)(NH) = (0.59, 0.72, 0.59) was extracted. The backbone of Lys48, whose side chain is known to be involved in the poly-ubiquitylation process that leads to protein degradation, is very mobile on the supra-tau(c) time scale (S2(rdc)(NH) = 0.59 +/- 0.03), while it is inconspicuous (S2(LS)(NH)= 0.82) on the sub-tau(c) as well as on micros-ms relaxation dispersion time scales. The results of this work differ from previous RDC dynamics studies of ubiquitin in the sense that the results are essentially independent of structural noise providing a much more robust assessment of dynamic effects that underlie the RDC data.
Hanson, Susan M; Dawson, Eric S; Francis, Derek J; Eps, Ned Van; Klug, Candice S; Hubbell, Wayne L; Meiler, Jens; Gurevich, Vsevolod V
A model for the solution structure of the rod arrestin tetramer Journal Article
In: Structure, vol. 16, no. 6, pp. 924–934, 2008, ISSN: 0969-2126.
Abstract | Links | BibTeX | Tags:
@article{pmid18547524,
title = {A model for the solution structure of the rod arrestin tetramer},
author = {Susan M Hanson and Eric S Dawson and Derek J Francis and Ned Van Eps and Candice S Klug and Wayne L Hubbell and Jens Meiler and Vsevolod V Gurevich},
doi = {10.1016/j.str.2008.03.006},
issn = {0969-2126},
year = {2008},
date = {2008-06-01},
journal = {Structure},
volume = {16},
number = {6},
pages = {924--934},
abstract = {Visual rod arrestin has the ability to self-associate at physiological concentrations. We previously demonstrated that only monomeric arrestin can bind the receptor and that the arrestin tetramer in solution differs from that in the crystal. We employed the Rosetta docking software to generate molecular models of the physiologically relevant solution tetramer based on the monomeric arrestin crystal structure. The resulting models were filtered using the Rosetta energy function, experimental intersubunit distances measured with DEER spectroscopy, and intersubunit contact sites identified by mutagenesis and site-directed spin labeling. This resulted in a unique model for subsequent evaluation. The validity of the model is strongly supported by model-directed crosslinking and targeted mutagenesis that yields arrestin variants deficient in self-association. The structure of the solution tetramer explains its inability to bind rhodopsin and paves the way for experimental studies of the physiological role of rod arrestin self-association.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Visual rod arrestin has the ability to self-associate at physiological concentrations. We previously demonstrated that only monomeric arrestin can bind the receptor and that the arrestin tetramer in solution differs from that in the crystal. We employed the Rosetta docking software to generate molecular models of the physiologically relevant solution tetramer based on the monomeric arrestin crystal structure. The resulting models were filtered using the Rosetta energy function, experimental intersubunit distances measured with DEER spectroscopy, and intersubunit contact sites identified by mutagenesis and site-directed spin labeling. This resulted in a unique model for subsequent evaluation. The validity of the model is strongly supported by model-directed crosslinking and targeted mutagenesis that yields arrestin variants deficient in self-association. The structure of the solution tetramer explains its inability to bind rhodopsin and paves the way for experimental studies of the physiological role of rod arrestin self-association.
Lange, Oliver F; Lakomek, Nils-Alexander; Farès, Christophe; Schröder, Gunnar F; Walter, Korvin F A; Becker, Stefan; Meiler, Jens; Grubmüller, Helmut; Griesinger, Christian; de Groot, Bert L
Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution Journal Article
In: Science, vol. 320, no. 5882, pp. 1471–1475, 2008, ISSN: 1095-9203.
Abstract | Links | BibTeX | Tags:
@article{pmid18556554,
title = {Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution},
author = {Oliver F Lange and Nils-Alexander Lakomek and Christophe Farès and Gunnar F Schröder and Korvin F A Walter and Stefan Becker and Jens Meiler and Helmut Grubmüller and Christian Griesinger and Bert L de Groot},
doi = {10.1126/science.1157092},
issn = {1095-9203},
year = {2008},
date = {2008-06-01},
journal = {Science},
volume = {320},
number = {5882},
pages = {1471--1475},
abstract = {Protein dynamics are essential for protein function, and yet it has been challenging to access the underlying atomic motions in solution on nanosecond-to-microsecond time scales. We present a structural ensemble of ubiquitin, refined against residual dipolar couplings (RDCs), comprising solution dynamics up to microseconds. The ensemble covers the complete structural heterogeneity observed in 46 ubiquitin crystal structures, most of which are complexes with other proteins. Conformational selection, rather than induced-fit motion, thus suffices to explain the molecular recognition dynamics of ubiquitin. Marked correlations are seen between the flexibility of the ensemble and contacts formed in ubiquitin complexes. A large part of the solution dynamics is concentrated in one concerted mode, which accounts for most of ubiquitin's molecular recognition heterogeneity and ensures a low entropic complex formation cost.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Protein dynamics are essential for protein function, and yet it has been challenging to access the underlying atomic motions in solution on nanosecond-to-microsecond time scales. We present a structural ensemble of ubiquitin, refined against residual dipolar couplings (RDCs), comprising solution dynamics up to microseconds. The ensemble covers the complete structural heterogeneity observed in 46 ubiquitin crystal structures, most of which are complexes with other proteins. Conformational selection, rather than induced-fit motion, thus suffices to explain the molecular recognition dynamics of ubiquitin. Marked correlations are seen between the flexibility of the ensemble and contacts formed in ubiquitin complexes. A large part of the solution dynamics is concentrated in one concerted mode, which accounts for most of ubiquitin's molecular recognition heterogeneity and ensures a low entropic complex formation cost.
Alexander, Nathan; Bortolus, Marco; Al-Mestarihi, Ahmad; Mchaourab, Hassane; Meiler, Jens
De novo high-resolution protein structure determination from sparse spin-labeling EPR data Journal Article
In: Structure, vol. 16, no. 2, pp. 181–195, 2008, ISSN: 0969-2126.
Abstract | Links | BibTeX | Tags:
@article{pmid18275810,
title = {De novo high-resolution protein structure determination from sparse spin-labeling EPR data},
author = {Nathan Alexander and Marco Bortolus and Ahmad Al-Mestarihi and Hassane Mchaourab and Jens Meiler},
doi = {10.1016/j.str.2007.11.015},
issn = {0969-2126},
year = {2008},
date = {2008-02-01},
journal = {Structure},
volume = {16},
number = {2},
pages = {181--195},
abstract = {As many key proteins evade crystallization and remain too large for nuclear magnetic resonance spectroscopy, electron paramagnetic resonance (EPR) spectroscopy combined with site-directed spin labeling offers an alternative approach for obtaining structural information. Such information must be translated into geometric restraints to be used in computer simulations. Here, distances between spin labels are converted into distance ranges between beta carbons by using a "motion-on-a-cone" model, and a linear-correlation model links spin-label accessibility to the number of neighboring residues. This approach was tested on T4-lysozyme and alphaA-crystallin with the de novo structure prediction algorithm Rosetta. The results demonstrate the feasibility of obtaining highly accurate, atomic-detail models from EPR data by yielding 1.0 A and 2.6 A full-atom models, respectively. Distance restraints between amino acids far apart in sequence but close in space are most valuable for structure determination. The approach can be extended to other experimental techniques such as fluorescence spectroscopy, substituted cysteine accessibility method, or mutational studies.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
As many key proteins evade crystallization and remain too large for nuclear magnetic resonance spectroscopy, electron paramagnetic resonance (EPR) spectroscopy combined with site-directed spin labeling offers an alternative approach for obtaining structural information. Such information must be translated into geometric restraints to be used in computer simulations. Here, distances between spin labels are converted into distance ranges between beta carbons by using a "motion-on-a-cone" model, and a linear-correlation model links spin-label accessibility to the number of neighboring residues. This approach was tested on T4-lysozyme and alphaA-crystallin with the de novo structure prediction algorithm Rosetta. The results demonstrate the feasibility of obtaining highly accurate, atomic-detail models from EPR data by yielding 1.0 A and 2.6 A full-atom models, respectively. Distance restraints between amino acids far apart in sequence but close in space are most valuable for structure determination. The approach can be extended to other experimental techniques such as fluorescence spectroscopy, substituted cysteine accessibility method, or mutational studies.
2007
Smith, Jarrod A; Vanoye, Carlos G; George, Alfred L; Meiler, Jens; Sanders, Charles R
Structural models for the KCNQ1 voltage-gated potassium channel Journal Article
In: Biochemistry, vol. 46, no. 49, pp. 14141–14152, 2007, ISSN: 0006-2960.
Abstract | Links | BibTeX | Tags:
@article{pmid17999538,
title = {Structural models for the KCNQ1 voltage-gated potassium channel},
author = {Jarrod A Smith and Carlos G Vanoye and Alfred L George and Jens Meiler and Charles R Sanders},
doi = {10.1021/bi701597s},
issn = {0006-2960},
year = {2007},
date = {2007-12-01},
journal = {Biochemistry},
volume = {46},
number = {49},
pages = {14141--14152},
abstract = {Mutations in the human voltage-gated potassium channel KCNQ1 are associated with predisposition to deafness and various cardiac arrhythmia syndromes including congenital long QT syndrome, familial atrial fibrillation, and sudden infant death syndrome. In this work 3-D structural models were developed for both the open and closed states of human KCNQ1 to facilitate structurally based hypotheses regarding mutation-phenotype relationships. The KCNQ1 open state was modeled using Rosetta in conjunction with Molecular Operating Environment software, and is based primarily on the recently determined open state structure of rat Kv1.2 (Long, S. B., et al. (2005) Science 309, 897-903). The closed state model for KCNQ1 was developed based on the crystal structures of bacterial potassium channels and the closed state model for Kv1.2 of Yarov-Yarovoy et al. ((2006) Proc. Natl. Acad. Sci. U.S.A. 103, 7292-7207). Using the new models for KCNQ1, we generated a database for the location and predicted residue-residue interactions for more than 85 disease-linked sites in both open and closed states. These data can be used to generate structure-based hypotheses for disease phenotypes associated with each mutation. The potential utility of these models and the database is exemplified by the surprising observation that four of the five known mutations in KCNQ1 that are associated with gain-of-function KCNQ1 defects are predicted to share a common interface in the open state structure between the S1 segment of the voltage sensor in one subunit and both the S5 segment and top of the pore helix from another subunit. This interface evidently plays an important role in channel gating.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Mutations in the human voltage-gated potassium channel KCNQ1 are associated with predisposition to deafness and various cardiac arrhythmia syndromes including congenital long QT syndrome, familial atrial fibrillation, and sudden infant death syndrome. In this work 3-D structural models were developed for both the open and closed states of human KCNQ1 to facilitate structurally based hypotheses regarding mutation-phenotype relationships. The KCNQ1 open state was modeled using Rosetta in conjunction with Molecular Operating Environment software, and is based primarily on the recently determined open state structure of rat Kv1.2 (Long, S. B., et al. (2005) Science 309, 897-903). The closed state model for KCNQ1 was developed based on the crystal structures of bacterial potassium channels and the closed state model for Kv1.2 of Yarov-Yarovoy et al. ((2006) Proc. Natl. Acad. Sci. U.S.A. 103, 7292-7207). Using the new models for KCNQ1, we generated a database for the location and predicted residue-residue interactions for more than 85 disease-linked sites in both open and closed states. These data can be used to generate structure-based hypotheses for disease phenotypes associated with each mutation. The potential utility of these models and the database is exemplified by the surprising observation that four of the five known mutations in KCNQ1 that are associated with gain-of-function KCNQ1 defects are predicted to share a common interface in the open state structure between the S1 segment of the voltage sensor in one subunit and both the S5 segment and top of the pore helix from another subunit. This interface evidently plays an important role in channel gating.
Henry, L Keith; Meiler, Jens; Blakely, Randy D
Bound to be different: neurotransmitter transporters meet their bacterial cousins Journal Article
In: Mol Interv, vol. 7, no. 6, pp. 306–309, 2007, ISSN: 1534-0384.
Abstract | Links | BibTeX | Tags:
@article{pmid18199851,
title = {Bound to be different: neurotransmitter transporters meet their bacterial cousins},
author = {L Keith Henry and Jens Meiler and Randy D Blakely},
doi = {10.1124/mi.7.6.4},
issn = {1534-0384},
year = {2007},
date = {2007-12-01},
journal = {Mol Interv},
volume = {7},
number = {6},
pages = {306--309},
abstract = {The neurotransmitter transporters belonging to the solute carrier 6 (SLC6) family, including the gamma-aminobutyric acid (GAT), norepinephrine (NET), serotonin (SERT) and dopamine (DAT) transporters are extremely important drug targets of great clinical relevance. These Na+, Cl(-)-dependent transporters primarily function following neurotransmission to reset neuronal signaling by transporting neurotransmitter out of the synapse and back into the pre-synaptic neuron. Recent studies have tracked down an elusive binding site for Cl(-) that facilitates neurotransmitter transport using structural differences evident with bacterial family members (e.g., the Aquifex aeolicus leucine transporter LeuT Aa) that lack Cl(-) dependence. Additionally, the crystal structures of antidepressant-bound LeuT Aa reveals a surprising mode of drug interaction that may have relevance for medication development. The study of sequence and structural divergence between LeuT Aa and human SLC6 family transporters can thus inform us as to how and why neurotransmitter transporters evolved a reliance on extracellular Cl(-) to propel the transport cycle; what residue changes and helical rearrangements give rise to recognition of different substrates; and how drugs such as antidepressants, cocaine, and amphetamines halt (or reverse) the transport process.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The neurotransmitter transporters belonging to the solute carrier 6 (SLC6) family, including the gamma-aminobutyric acid (GAT), norepinephrine (NET), serotonin (SERT) and dopamine (DAT) transporters are extremely important drug targets of great clinical relevance. These Na+, Cl(-)-dependent transporters primarily function following neurotransmission to reset neuronal signaling by transporting neurotransmitter out of the synapse and back into the pre-synaptic neuron. Recent studies have tracked down an elusive binding site for Cl(-) that facilitates neurotransmitter transport using structural differences evident with bacterial family members (e.g., the Aquifex aeolicus leucine transporter LeuT Aa) that lack Cl(-) dependence. Additionally, the crystal structures of antidepressant-bound LeuT Aa reveals a surprising mode of drug interaction that may have relevance for medication development. The study of sequence and structural divergence between LeuT Aa and human SLC6 family transporters can thus inform us as to how and why neurotransmitter transporters evolved a reliance on extracellular Cl(-) to propel the transport cycle; what residue changes and helical rearrangements give rise to recognition of different substrates; and how drugs such as antidepressants, cocaine, and amphetamines halt (or reverse) the transport process.
McKinney, Brett A; Kallewaard, Nicole L; Crowe, James E; Meiler, Jens
Using the natural evolution of a rotavirus-specific human monoclonal antibody to predict the complex topography of a viral antigenic site Journal Article
In: Immunome Res, vol. 3, pp. 8, 2007, ISSN: 1745-7580.
Abstract | Links | BibTeX | Tags:
@article{pmid17877819,
title = {Using the natural evolution of a rotavirus-specific human monoclonal antibody to predict the complex topography of a viral antigenic site},
author = {Brett A McKinney and Nicole L Kallewaard and James E Crowe and Jens Meiler},
doi = {10.1186/1745-7580-3-8},
issn = {1745-7580},
year = {2007},
date = {2007-09-01},
journal = {Immunome Res},
volume = {3},
pages = {8},
abstract = {BACKGROUND: Understanding the interaction between viral proteins and neutralizing antibodies at atomic resolution is hindered by a lack of experimentally solved complexes. Progress in computational docking has led to the prediction of increasingly high-quality model antibody-antigen complexes. The accuracy of atomic-level docking predictions is improved when integrated with experimental information and expert knowledge.nnMETHODS: Binding affinity data associated with somatic mutations of a rotavirus-specific human adult antibody (RV6-26) are used to filter potential docking orientations of an antibody homology model with respect to the rotavirus VP6 crystal structure. The antibody structure is used to probe the VP6 trimer for candidate interface residues.nnRESULTS: Three conformational epitopes are proposed. These epitopes are candidate antigenic regions for site-directed mutagenesis of VP6, which will help further elucidate antigenic function. A pseudo-atomic resolution RV6-26 antibody-VP6 complex is proposed consistent with current experimental information.nnCONCLUSION: The use of mutagenesis constraints in docking calculations allows for the identification of a small number of alternative arrangements of the antigen-antibody interface. The mutagenesis information from the natural evolution of a neutralizing antibody can be used to discriminate between residue-scale models and create distance constraints for atomic-resolution docking. The integration of binding affinity data or other information with computation may be an advantageous approach to assist peptide engineering or therapeutic antibody design.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
BACKGROUND: Understanding the interaction between viral proteins and neutralizing antibodies at atomic resolution is hindered by a lack of experimentally solved complexes. Progress in computational docking has led to the prediction of increasingly high-quality model antibody-antigen complexes. The accuracy of atomic-level docking predictions is improved when integrated with experimental information and expert knowledge.nnMETHODS: Binding affinity data associated with somatic mutations of a rotavirus-specific human adult antibody (RV6-26) are used to filter potential docking orientations of an antibody homology model with respect to the rotavirus VP6 crystal structure. The antibody structure is used to probe the VP6 trimer for candidate interface residues.nnRESULTS: Three conformational epitopes are proposed. These epitopes are candidate antigenic regions for site-directed mutagenesis of VP6, which will help further elucidate antigenic function. A pseudo-atomic resolution RV6-26 antibody-VP6 complex is proposed consistent with current experimental information.nnCONCLUSION: The use of mutagenesis constraints in docking calculations allows for the identification of a small number of alternative arrangements of the antigen-antibody interface. The mutagenesis information from the natural evolution of a neutralizing antibody can be used to discriminate between residue-scale models and create distance constraints for atomic-resolution docking. The integration of binding affinity data or other information with computation may be an advantageous approach to assist peptide engineering or therapeutic antibody design.
Reese, Marcel; Sánchez-Pedregal, Víctor M; Kubicek, Karel; Meiler, Jens; Blommers, Marcel J J; Griesinger, Christian; Carlomagno, Teresa
Structural basis of the activity of the microtubule-stabilizing agent epothilone a studied by NMR spectroscopy in solution Journal Article
In: Angew Chem Int Ed Engl, vol. 46, no. 11, pp. 1864–1868, 2007, ISSN: 1433-7851.
@article{pmid17274084,
title = {Structural basis of the activity of the microtubule-stabilizing agent epothilone a studied by NMR spectroscopy in solution},
author = {Marcel Reese and Víctor M Sánchez-Pedregal and Karel Kubicek and Jens Meiler and Marcel J J Blommers and Christian Griesinger and Teresa Carlomagno},
doi = {10.1002/anie.200604505},
issn = {1433-7851},
year = {2007},
date = {2007-01-01},
journal = {Angew Chem Int Ed Engl},
volume = {46},
number = {11},
pages = {1864--1868},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2006
Zanghellini, Alexandre; Jiang, Lin; Wollacott, Andrew M; Cheng, Gong; Meiler, Jens; Althoff, Eric A; Röthlisberger, Daniela; Baker, David
New algorithms and an in silico benchmark for computational enzyme design Journal Article
In: Protein Sci, vol. 15, no. 12, pp. 2785–2794, 2006, ISSN: 0961-8368.
Abstract | Links | BibTeX | Tags:
@article{pmid17132862,
title = {New algorithms and an in silico benchmark for computational enzyme design},
author = {Alexandre Zanghellini and Lin Jiang and Andrew M Wollacott and Gong Cheng and Jens Meiler and Eric A Althoff and Daniela Röthlisberger and David Baker},
doi = {10.1110/ps.062353106},
issn = {0961-8368},
year = {2006},
date = {2006-12-01},
journal = {Protein Sci},
volume = {15},
number = {12},
pages = {2785--2794},
abstract = {The creation of novel enzymes capable of catalyzing any desired chemical reaction is a grand challenge for computational protein design. Here we describe two new algorithms for enzyme design that employ hashing techniques to allow searching through large numbers of protein scaffolds for optimal catalytic site placement. We also describe an in silico benchmark, based on the recapitulation of the active sites of native enzymes, that allows rapid evaluation and testing of enzyme design methodologies. In the benchmark test, which consists of designing sites for each of 10 different chemical reactions in backbone scaffolds derived from 10 enzymes catalyzing the reactions, the new methods succeed in identifying the native site in the native scaffold and ranking it within the top five designs for six of the 10 reactions. The new methods can be directly applied to the design of new enzymes, and the benchmark provides a powerful in silico test for guiding improvements in computational enzyme design.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The creation of novel enzymes capable of catalyzing any desired chemical reaction is a grand challenge for computational protein design. Here we describe two new algorithms for enzyme design that employ hashing techniques to allow searching through large numbers of protein scaffolds for optimal catalytic site placement. We also describe an in silico benchmark, based on the recapitulation of the active sites of native enzymes, that allows rapid evaluation and testing of enzyme design methodologies. In the benchmark test, which consists of designing sites for each of 10 different chemical reactions in backbone scaffolds derived from 10 enzymes catalyzing the reactions, the new methods succeed in identifying the native site in the native scaffold and ranking it within the top five designs for six of the 10 reactions. The new methods can be directly applied to the design of new enzymes, and the benchmark provides a powerful in silico test for guiding improvements in computational enzyme design.
Meiler, Jens; Baker, David
ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility Journal Article
In: Proteins, vol. 65, no. 3, pp. 538–548, 2006, ISSN: 1097-0134.
Abstract | Links | BibTeX | Tags:
@article{pmid16972285,
title = {ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility},
author = {Jens Meiler and David Baker},
doi = {10.1002/prot.21086},
issn = {1097-0134},
year = {2006},
date = {2006-11-01},
journal = {Proteins},
volume = {65},
number = {3},
pages = {538--548},
abstract = {Protein-small molecule docking algorithms provide a means to model the structure of protein-small molecule complexes in structural detail and play an important role in drug development. In recent years the necessity of simulating protein side-chain flexibility for an accurate prediction of the protein-small molecule interfaces has become apparent, and an increasing number of docking algorithms probe different approaches to include protein flexibility. Here we describe a new method for docking small molecules into protein binding sites employing a Monte Carlo minimization procedure in which the rigid body position and orientation of the small molecule and the protein side-chain conformations are optimized simultaneously. The energy function comprises van der Waals (VDW) interactions, an implicit solvation model, an explicit orientation hydrogen bonding potential, and an electrostatics model. In an evaluation of the scoring function the computed energy correlated with experimental small molecule binding energy with a correlation coefficient of 0.63 across a diverse set of 229 protein- small molecule complexes. The docking method produced lowest energy models with a root mean square deviation (RMSD) smaller than 2 A in 71 out of 100 protein-small molecule crystal structure complexes (self-docking). In cross-docking calculations in which both protein side-chain and small molecule internal degrees of freedom were varied the lowest energy predictions had RMSDs less than 2 A in 14 of 20 test cases.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Protein-small molecule docking algorithms provide a means to model the structure of protein-small molecule complexes in structural detail and play an important role in drug development. In recent years the necessity of simulating protein side-chain flexibility for an accurate prediction of the protein-small molecule interfaces has become apparent, and an increasing number of docking algorithms probe different approaches to include protein flexibility. Here we describe a new method for docking small molecules into protein binding sites employing a Monte Carlo minimization procedure in which the rigid body position and orientation of the small molecule and the protein side-chain conformations are optimized simultaneously. The energy function comprises van der Waals (VDW) interactions, an implicit solvation model, an explicit orientation hydrogen bonding potential, and an electrostatics model. In an evaluation of the scoring function the computed energy correlated with experimental small molecule binding energy with a correlation coefficient of 0.63 across a diverse set of 229 protein- small molecule complexes. The docking method produced lowest energy models with a root mean square deviation (RMSD) smaller than 2 A in 71 out of 100 protein-small molecule crystal structure complexes (self-docking). In cross-docking calculations in which both protein side-chain and small molecule internal degrees of freedom were varied the lowest energy predictions had RMSDs less than 2 A in 14 of 20 test cases.
Sánchez-Pedregal, Víctor M; Kubicek, Karel; Meiler, Jens; Lyothier, Isabelle; Paterson, Ian; Carlomagno, Teresa
In: Angew Chem Int Ed Engl, vol. 45, no. 44, pp. 7388–7394, 2006, ISSN: 1433-7851.
@article{pmid17036370,
title = {The tubulin-bound conformation of discodermolide derived by NMR studies in solution supports a common pharmacophore model for epothilone and discodermolide},
author = {Víctor M Sánchez-Pedregal and Karel Kubicek and Jens Meiler and Isabelle Lyothier and Ian Paterson and Teresa Carlomagno},
doi = {10.1002/anie.200602793},
issn = {1433-7851},
year = {2006},
date = {2006-11-01},
journal = {Angew Chem Int Ed Engl},
volume = {45},
number = {44},
pages = {7388--7394},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Lakomek, Nils A; Carlomagno, Teresa; Becker, Stefan; Griesinger, Christian; Meiler, Jens
A thorough dynamic interpretation of residual dipolar couplings in ubiquitin Journal Article
In: J Biomol NMR, vol. 34, no. 2, pp. 101–115, 2006, ISSN: 0925-2738.
Abstract | Links | BibTeX | Tags:
@article{pmid16518697,
title = {A thorough dynamic interpretation of residual dipolar couplings in ubiquitin},
author = {Nils A Lakomek and Teresa Carlomagno and Stefan Becker and Christian Griesinger and Jens Meiler},
doi = {10.1007/s10858-005-5686-0},
issn = {0925-2738},
year = {2006},
date = {2006-02-01},
journal = {J Biomol NMR},
volume = {34},
number = {2},
pages = {101--115},
abstract = {The presence of slow motions with large amplitudes, as detected by measurements based on residual dipolar couplings [Peti, W., Meiler, J., Brueschweiler, R. and Griesinger, C. (2002) J. Am. Chem. Soc., 124, 5822-5833], has stirred up much discussion in recent years. Based on ubiquitin NH residual dipolar couplings (rdcs) measured in 31 different alignment conditions, a model-free analysis of structure and dynamics [Meiler, J., Peti, W., Prompers, J., Griesinger, C. and Brueschweiler, R. (2001) J. Am. Chem. Soc., 123, 6098-6107] is presented. Starting from this broad experimental basis, rdc-based order parameters with so far unattained accuracy were determined. These rdc-based order parameters underpin the presence of new modes of motion slower than the inverse overall tumbling correlation time. Amplitudes and anisotropies of the motion were derived. The effect of structural noise on the results was proven to be negligible.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The presence of slow motions with large amplitudes, as detected by measurements based on residual dipolar couplings [Peti, W., Meiler, J., Brueschweiler, R. and Griesinger, C. (2002) J. Am. Chem. Soc., 124, 5822-5833], has stirred up much discussion in recent years. Based on ubiquitin NH residual dipolar couplings (rdcs) measured in 31 different alignment conditions, a model-free analysis of structure and dynamics [Meiler, J., Peti, W., Prompers, J., Griesinger, C. and Brueschweiler, R. (2001) J. Am. Chem. Soc., 123, 6098-6107] is presented. Starting from this broad experimental basis, rdc-based order parameters with so far unattained accuracy were determined. These rdc-based order parameters underpin the presence of new modes of motion slower than the inverse overall tumbling correlation time. Amplitudes and anisotropies of the motion were derived. The effect of structural noise on the results was proven to be negligible.
2005
Lakomek, Nils A; Farès, Christophe; Becker, Stefan; Carlomagno, Teresa; Meiler, Jens; Griesinger, Christian
Side-chain orientation and hydrogen-bonding imprint supra-Tau(c) motion on the protein backbone of ubiquitin Journal Article
In: Angew Chem Int Ed Engl, vol. 44, no. 47, pp. 7776–7778, 2005, ISSN: 1433-7851.
@article{pmid16276548,
title = {Side-chain orientation and hydrogen-bonding imprint supra-Tau(c) motion on the protein backbone of ubiquitin},
author = {Nils A Lakomek and Christophe Farès and Stefan Becker and Teresa Carlomagno and Jens Meiler and Christian Griesinger},
doi = {10.1002/anie.200502573},
issn = {1433-7851},
year = {2005},
date = {2005-12-01},
journal = {Angew Chem Int Ed Engl},
volume = {44},
number = {47},
pages = {7776--7778},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Sánchez-Pedregal, Víctor M; Reese, Marcel; Meiler, Jens; Blommers, Marcel J J; Griesinger, Christian; Carlomagno, Teresa
The INPHARMA method: protein-mediated interligand NOEs for pharmacophore mapping Journal Article
In: Angew Chem Int Ed Engl, vol. 44, no. 27, pp. 4172–4175, 2005, ISSN: 1433-7851.
@article{pmid15929149,
title = {The INPHARMA method: protein-mediated interligand NOEs for pharmacophore mapping},
author = {Víctor M Sánchez-Pedregal and Marcel Reese and Jens Meiler and Marcel J J Blommers and Christian Griesinger and Teresa Carlomagno},
doi = {10.1002/anie.200500503},
issn = {1433-7851},
year = {2005},
date = {2005-07-01},
journal = {Angew Chem Int Ed Engl},
volume = {44},
number = {27},
pages = {4172--4175},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Meiler, Jens; Baker, David
The fumarate sensor DcuS: progress in rapid protein fold elucidation by combining protein structure prediction methods with NMR spectroscopy Journal Article
In: J Magn Reson, vol. 173, no. 2, pp. 310–316, 2005, ISSN: 1090-7807.
Abstract | Links | BibTeX | Tags:
@article{pmid15780923,
title = {The fumarate sensor DcuS: progress in rapid protein fold elucidation by combining protein structure prediction methods with NMR spectroscopy},
author = {Jens Meiler and David Baker},
doi = {10.1016/j.jmr.2004.11.031},
issn = {1090-7807},
year = {2005},
date = {2005-04-01},
journal = {J Magn Reson},
volume = {173},
number = {2},
pages = {310--316},
abstract = {We illustrate how moderate resolution protein structures can be rapidly obtained by interlinking computational prediction methodologies with un- or partially assigned NMR data. To facilitate the application of our recently described method of ranking and subsequent refining alternative structural models using unassigned NMR data [Proc. Natl. Acad. Sci. USA 100 (2003) 15404] for such "structural genomics"-type experiments it is combined with protein models from several prediction techniques, enhanced to utilize partial assignments, and applied on a protein with an unknown structure and fold. From the original NMR spectra obtained for the 140 residue fumarate sensor DcuS, 1100 1H, 13C, and 15N chemical shift signals, 3000 1H-1H NOESY cross peak intensities, and 209 backbone residual dipolar couplings were extracted and used to rank models produced by de novo structure prediction and comparative modeling methods. The ranking proceeds in two steps: first, an optimal assignment of the NMR peaks to atoms is found for each model independently, and second, the models are ranked based on the consistency between the NMR data and the model assuming these optimal assignments. The low-resolution model selected using this ranking procedure had the correct overall fold and a global backbone RMSD of 6.0 angstrom, and was subsequently refined to 3.7 angstrom RMSD. With the incorporation of a small number of NOE and residual dipolar coupling constraints available very early in the traditional spectral assignment process, a model with an RMSD of 2.8 angstrom could rapidly be built. The ability to generate moderate resolution models within days of NMR data collection should facilitate large scale NMR structure determination efforts.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
We illustrate how moderate resolution protein structures can be rapidly obtained by interlinking computational prediction methodologies with un- or partially assigned NMR data. To facilitate the application of our recently described method of ranking and subsequent refining alternative structural models using unassigned NMR data [Proc. Natl. Acad. Sci. USA 100 (2003) 15404] for such "structural genomics"-type experiments it is combined with protein models from several prediction techniques, enhanced to utilize partial assignments, and applied on a protein with an unknown structure and fold. From the original NMR spectra obtained for the 140 residue fumarate sensor DcuS, 1100 1H, 13C, and 15N chemical shift signals, 3000 1H-1H NOESY cross peak intensities, and 209 backbone residual dipolar couplings were extracted and used to rank models produced by de novo structure prediction and comparative modeling methods. The ranking proceeds in two steps: first, an optimal assignment of the NMR peaks to atoms is found for each model independently, and second, the models are ranked based on the consistency between the NMR data and the model assuming these optimal assignments. The low-resolution model selected using this ranking procedure had the correct overall fold and a global backbone RMSD of 6.0 angstrom, and was subsequently refined to 3.7 angstrom RMSD. With the incorporation of a small number of NOE and residual dipolar coupling constraints available very early in the traditional spectral assignment process, a model with an RMSD of 2.8 angstrom could rapidly be built. The ability to generate moderate resolution models within days of NMR data collection should facilitate large scale NMR structure determination efforts.
Bradley, Philip; Malmström, Lars; Qian, Bin; Schonbrun, Jack; Chivian, Dylan; Kim, David E; Meiler, Jens; Misura, Kira M S; Baker, David
Free modeling with Rosetta in CASP6 Journal Article
In: Proteins, vol. 61 Suppl 7, pp. 128–134, 2005, ISSN: 1097-0134.
Abstract | Links | BibTeX | Tags:
@article{pmid16187354,
title = {Free modeling with Rosetta in CASP6},
author = {Philip Bradley and Lars Malmström and Bin Qian and Jack Schonbrun and Dylan Chivian and David E Kim and Jens Meiler and Kira M S Misura and David Baker},
doi = {10.1002/prot.20729},
issn = {1097-0134},
year = {2005},
date = {2005-01-01},
journal = {Proteins},
volume = {61 Suppl 7},
pages = {128--134},
abstract = {We describe Rosetta predictions in the Sixth Community-Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP), focusing on the free modeling category. Methods developed since CASP5 are described, and their application to selected targets is discussed. Highlights include improved performance on larger proteins (100-200 residues) and the prediction of a 70-residue alpha-beta protein to near-atomic resolution.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
We describe Rosetta predictions in the Sixth Community-Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP), focusing on the free modeling category. Methods developed since CASP5 are described, and their application to selected targets is discussed. Highlights include improved performance on larger proteins (100-200 residues) and the prediction of a 70-residue alpha-beta protein to near-atomic resolution.
Graña, Osvaldo; Baker, David; MacCallum, Robert M; Meiler, Jens; Punta, Marco; Rost, Burkhard; Tress, Michael L; Valencia, Alfonso
CASP6 assessment of contact prediction Journal Article
In: Proteins, vol. 61 Suppl 7, pp. 214–224, 2005, ISSN: 1097-0134.
Abstract | Links | BibTeX | Tags:
@article{pmid16187364,
title = {CASP6 assessment of contact prediction},
author = {Osvaldo Graña and David Baker and Robert M MacCallum and Jens Meiler and Marco Punta and Burkhard Rost and Michael L Tress and Alfonso Valencia},
doi = {10.1002/prot.20739},
issn = {1097-0134},
year = {2005},
date = {2005-01-01},
journal = {Proteins},
volume = {61 Suppl 7},
pages = {214--224},
abstract = {Here we present the evaluation results of the Critical Assessment of Protein Structure Prediction (CASP6) contact prediction category. Contact prediction was assessed with standard measures well known in the field and the performance of specialist groups was evaluated alongside groups that submitted models with 3D coordinates. The evaluation was mainly focused on long range contact predictions for the set of new fold targets, although we analyzed predictions for all targets. Three groups with similar levels of accuracy and coverage performed a little better than the others. Comparisons of the predictions of the three best methods with those of CASP5/CAFASP3 suggested some improvement, although there were not enough targets in the comparisons to make this statistically significant.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Here we present the evaluation results of the Critical Assessment of Protein Structure Prediction (CASP6) contact prediction category. Contact prediction was assessed with standard measures well known in the field and the performance of specialist groups was evaluated alongside groups that submitted models with 3D coordinates. The evaluation was mainly focused on long range contact predictions for the set of new fold targets, although we analyzed predictions for all targets. Three groups with similar levels of accuracy and coverage performed a little better than the others. Comparisons of the predictions of the three best methods with those of CASP5/CAFASP3 suggested some improvement, although there were not enough targets in the comparisons to make this statistically significant.
2004
Meiler, Jens; Köck, Matthias
Novel methods of automated structure elucidation based on 13C NMR spectroscopy Journal Article
In: Magn Reson Chem, vol. 42, no. 12, pp. 1042–1045, 2004, ISSN: 0749-1581.
Abstract | Links | BibTeX | Tags:
@article{pmid15470690,
title = {Novel methods of automated structure elucidation based on 13C NMR spectroscopy},
author = {Jens Meiler and Matthias Köck},
doi = {10.1002/mrc.1424},
issn = {0749-1581},
year = {2004},
date = {2004-12-01},
journal = {Magn Reson Chem},
volume = {42},
number = {12},
pages = {1042--1045},
abstract = {Three new approaches for automated structure elucidations of organic molecules using NMR spectroscopic data were introduced recently. These approaches apply a neural network 13C NMR chemical shift prediction method to rank the results of structure generators by their agreement of the predicted and experimental chemical shifts. These three existing implementations are compared using realistic example molecules. The applicability and reliability of such approaches is addressed.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Three new approaches for automated structure elucidations of organic molecules using NMR spectroscopic data were introduced recently. These approaches apply a neural network 13C NMR chemical shift prediction method to rank the results of structure generators by their agreement of the predicted and experimental chemical shifts. These three existing implementations are compared using realistic example molecules. The applicability and reliability of such approaches is addressed.
Kuhn, Michael; Meiler, Jens; Baker, David
Strand-loop-strand motifs: prediction of hairpins and diverging turns in proteins Journal Article
In: Proteins, vol. 54, no. 2, pp. 282–288, 2004, ISSN: 1097-0134.
Abstract | Links | BibTeX | Tags:
@article{pmid14696190,
title = {Strand-loop-strand motifs: prediction of hairpins and diverging turns in proteins},
author = {Michael Kuhn and Jens Meiler and David Baker},
doi = {10.1002/prot.10589},
issn = {1097-0134},
year = {2004},
date = {2004-02-01},
journal = {Proteins},
volume = {54},
number = {2},
pages = {282--288},
abstract = {Beta-sheet proteins have been particularly challenging for de novo structure prediction methods, which tend to pair adjacent beta-strands into beta-hairpins and produce overly local topologies. To remedy this problem and facilitate de novo prediction of beta-sheet protein structures, we have developed a neural network that classifies strand-loop-strand motifs by local hairpins and nonlocal diverging turns by using the amino acid sequence as input. The neural network is trained with a representative subset of the Protein Data Bank and achieves a prediction accuracy of 75.9 +/- 4.4% compared to a baseline prediction rate of 59.1%. Hairpins are predicted with an accuracy of 77.3 +/- 6.1%, diverging turns with an accuracy of 73.9 +/- 6.0%. Incorporation of the beta-hairpin/diverging turn classification into the ROSETTA de novo structure prediction method led to higher contact order models and somewhat improved tertiary structure predictions for a test set of 11 all-beta-proteins and 3 alphabeta-proteins. The beta-hairpin/diverging turn classification from amino acid sequences is available online for academic use (Meiler and Kuhn, 2003; www.jens-meiler.de/turnpred.html).},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Beta-sheet proteins have been particularly challenging for de novo structure prediction methods, which tend to pair adjacent beta-strands into beta-hairpins and produce overly local topologies. To remedy this problem and facilitate de novo prediction of beta-sheet protein structures, we have developed a neural network that classifies strand-loop-strand motifs by local hairpins and nonlocal diverging turns by using the amino acid sequence as input. The neural network is trained with a representative subset of the Protein Data Bank and achieves a prediction accuracy of 75.9 +/- 4.4% compared to a baseline prediction rate of 59.1%. Hairpins are predicted with an accuracy of 77.3 +/- 6.1%, diverging turns with an accuracy of 73.9 +/- 6.0%. Incorporation of the beta-hairpin/diverging turn classification into the ROSETTA de novo structure prediction method led to higher contact order models and somewhat improved tertiary structure predictions for a test set of 11 all-beta-proteins and 3 alphabeta-proteins. The beta-hairpin/diverging turn classification from amino acid sequences is available online for academic use (Meiler and Kuhn, 2003; www.jens-meiler.de/turnpred.html).
Griesinger, Christian; Peti, Wolfgang; Meiler, Jens; Brüschweiler, Rafael
Projection angle restraints for studying structure and dynamics of biomolecules Journal Article
In: Methods Mol Biol, vol. 278, pp. 107–121, 2004, ISSN: 1064-3745.
Abstract | Links | BibTeX | Tags:
@article{pmid15317994,
title = {Projection angle restraints for studying structure and dynamics of biomolecules},
author = {Christian Griesinger and Wolfgang Peti and Jens Meiler and Rafael Brüschweiler},
doi = {10.1385/1-59259-809-9:107},
issn = {1064-3745},
year = {2004},
date = {2004-01-01},
journal = {Methods Mol Biol},
volume = {278},
pages = {107--121},
abstract = {This chapter presents a methodology that allows for the structural and dynamic characterization of biomolecules by means of projection restraints obtained from residual magnetic dipolar couplings. Dipolar couplings reflect the projection of individual internuclear vectors onto the alignment tensor. This technique allows determination of the dynamics of the protein backbone on time-scales, namely, between the rotational tumbling correlation time and approx 50 micros. This range of time-scales has been previously inaccessible by other nuclear magnetic resonance (NMR) techniques. In addition, information about the anisotropy of the motion is obtained.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
This chapter presents a methodology that allows for the structural and dynamic characterization of biomolecules by means of projection restraints obtained from residual magnetic dipolar couplings. Dipolar couplings reflect the projection of individual internuclear vectors onto the alignment tensor. This technique allows determination of the dynamics of the protein backbone on time-scales, namely, between the rotational tumbling correlation time and approx 50 micros. This range of time-scales has been previously inaccessible by other nuclear magnetic resonance (NMR) techniques. In addition, information about the anisotropy of the motion is obtained.
2003
Meiler, Jens; Baker, David
Rapid protein fold determination using unassigned NMR data Journal Article
In: Proc Natl Acad Sci U S A, vol. 100, no. 26, pp. 15404–15409, 2003, ISSN: 0027-8424.
Abstract | Links | BibTeX | Tags:
@article{pmid14668443,
title = {Rapid protein fold determination using unassigned NMR data},
author = {Jens Meiler and David Baker},
doi = {10.1073/pnas.2434121100},
issn = {0027-8424},
year = {2003},
date = {2003-12-01},
journal = {Proc Natl Acad Sci U S A},
volume = {100},
number = {26},
pages = {15404--15409},
abstract = {Experimental structure determination by x-ray crystallography and NMR spectroscopy is slow and time-consuming compared with the rate at which new protein sequences are being identified. NMR spectroscopy has the advantage of rapidly providing the structurally relevant information in the form of unassigned chemical shifts (CSs), intensities of NOESY crosspeaks [nuclear Overhauser effects (NOEs)], and residual dipolar couplings (RDCs), but use of these data are limited by the time and effort needed to assign individual resonances to specific atoms. Here, we develop a method for generating low-resolution protein structures by using unassigned NMR data that relies on the de novo protein structure prediction algorithm, rosetta [Simons, K. T., Kooperberg, C., Huang, E. & Baker, D. (1997) J. Mol. Biol. 268, 209-225] and a Monte Carlo procedure that searches for the assignment of resonances to atoms that produces the best fit of the experimental NMR data to a candidate 3D structure. A large ensemble of models is generated from sequence information alone by using rosetta, an optimal assignment is identified for each model, and the models are then ranked based on their fit with the NMR data assuming the identified assignments. The method was tested on nine protein sequences between 56 and 140 amino acids and published CS, NOE, and RDC data. The procedure yielded models with rms deviations between 3 and 6 A, and, in four of the nine cases, the partial assignments obtained by the method could be used to refine the structures to high resolution (0.6-1.8 A) by repeated cycles of structure generation guided by the partial assignments, followed by reassignment using the newly generated models.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Experimental structure determination by x-ray crystallography and NMR spectroscopy is slow and time-consuming compared with the rate at which new protein sequences are being identified. NMR spectroscopy has the advantage of rapidly providing the structurally relevant information in the form of unassigned chemical shifts (CSs), intensities of NOESY crosspeaks [nuclear Overhauser effects (NOEs)], and residual dipolar couplings (RDCs), but use of these data are limited by the time and effort needed to assign individual resonances to specific atoms. Here, we develop a method for generating low-resolution protein structures by using unassigned NMR data that relies on the de novo protein structure prediction algorithm, rosetta [Simons, K. T., Kooperberg, C., Huang, E. & Baker, D. (1997) J. Mol. Biol. 268, 209-225] and a Monte Carlo procedure that searches for the assignment of resonances to atoms that produces the best fit of the experimental NMR data to a candidate 3D structure. A large ensemble of models is generated from sequence information alone by using rosetta, an optimal assignment is identified for each model, and the models are then ranked based on their fit with the NMR data assuming the identified assignments. The method was tested on nine protein sequences between 56 and 140 amino acids and published CS, NOE, and RDC data. The procedure yielded models with rms deviations between 3 and 6 A, and, in four of the nine cases, the partial assignments obtained by the method could be used to refine the structures to high resolution (0.6-1.8 A) by repeated cycles of structure generation guided by the partial assignments, followed by reassignment using the newly generated models.
Meiler, Jens; Baker, David
Coupled prediction of protein secondary and tertiary structure Journal Article
In: Proc Natl Acad Sci U S A, vol. 100, no. 21, pp. 12105–12110, 2003, ISSN: 0027-8424.
Abstract | Links | BibTeX | Tags:
@article{pmid14528006,
title = {Coupled prediction of protein secondary and tertiary structure},
author = {Jens Meiler and David Baker},
doi = {10.1073/pnas.1831973100},
issn = {0027-8424},
year = {2003},
date = {2003-10-01},
journal = {Proc Natl Acad Sci U S A},
volume = {100},
number = {21},
pages = {12105--12110},
abstract = {The strong coupling between secondary and tertiary structure formation in protein folding is neglected in most structure prediction methods. In this work we investigate the extent to which nonlocal interactions in predicted tertiary structures can be used to improve secondary structure prediction. The architecture of a neural network for secondary structure prediction that utilizes multiple sequence alignments was extended to accept low-resolution nonlocal tertiary structure information as an additional input. By using this modified network, together with tertiary structure information from native structures, the Q3-prediction accuracy is increased by 7-10% on average and by up to 35% in individual cases for independent test data. By using tertiary structure information from models generated with the ROSETTA de novo tertiary structure prediction method, the Q3-prediction accuracy is improved by 4-5% on average for small and medium-sized single-domain proteins. Analysis of proteins with particularly large improvements in secondary structure prediction using tertiary structure information provides insight into the feedback from tertiary to secondary structure.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The strong coupling between secondary and tertiary structure formation in protein folding is neglected in most structure prediction methods. In this work we investigate the extent to which nonlocal interactions in predicted tertiary structures can be used to improve secondary structure prediction. The architecture of a neural network for secondary structure prediction that utilizes multiple sequence alignments was extended to accept low-resolution nonlocal tertiary structure information as an additional input. By using this modified network, together with tertiary structure information from native structures, the Q3-prediction accuracy is increased by 7-10% on average and by up to 35% in individual cases for independent test data. By using tertiary structure information from models generated with the ROSETTA de novo tertiary structure prediction method, the Q3-prediction accuracy is improved by 4-5% on average for small and medium-sized single-domain proteins. Analysis of proteins with particularly large improvements in secondary structure prediction using tertiary structure information provides insight into the feedback from tertiary to secondary structure.
Meiler, Jens; Peti, Wolfgang; Griesinger, Christian
Dipolar couplings in multiple alignments suggest alpha helical motion in ubiquitin Journal Article
In: J Am Chem Soc, vol. 125, no. 27, pp. 8072–8073, 2003, ISSN: 0002-7863.
Abstract | Links | BibTeX | Tags:
@article{pmid12837055,
title = {Dipolar couplings in multiple alignments suggest alpha helical motion in ubiquitin},
author = {Jens Meiler and Wolfgang Peti and Christian Griesinger},
doi = {10.1021/ja029816l},
issn = {0002-7863},
year = {2003},
date = {2003-07-01},
journal = {J Am Chem Soc},
volume = {125},
number = {27},
pages = {8072--8073},
abstract = {Recently, residual dipolar couplings (RDCs) of backbone N-HN vectors measured in 11 different alignment media were analyzed with respect to structure and dynamics in a model-free way in terms of generalized order parameters and motional anisotropies. The anisotropies in the central alpha-helix were found to be strikingly uniformly distributed. In this communication, these parameters are further interpreted in terms of physically feasible cooperative reorientational motion of the helix with respect to the core of the protein. The RDCs are compatible with a model in which all N-HN vectors of the alpha-helix of ubiquitin exhibit correlated anisotropic excursions with amplitudes of 21 degrees and 12 degrees along two orthogonal directions x' ' and y' ' of a coordinate system C' ', if z' ' represents the helix axis. Such motion contradicts neither NOE data nor molecular force-field calculations.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Recently, residual dipolar couplings (RDCs) of backbone N-HN vectors measured in 11 different alignment media were analyzed with respect to structure and dynamics in a model-free way in terms of generalized order parameters and motional anisotropies. The anisotropies in the central alpha-helix were found to be strikingly uniformly distributed. In this communication, these parameters are further interpreted in terms of physically feasible cooperative reorientational motion of the helix with respect to the core of the protein. The RDCs are compatible with a model in which all N-HN vectors of the alpha-helix of ubiquitin exhibit correlated anisotropic excursions with amplitudes of 21 degrees and 12 degrees along two orthogonal directions x' ' and y' ' of a coordinate system C' ', if z' ' represents the helix axis. Such motion contradicts neither NOE data nor molecular force-field calculations.
Carlomagno, Teresa; Blommers, Marcel J J; Meiler, Jens; Jahnke, Wolfgang; Schupp, Thomas; Petersen, Frank; Schinzer, Dieter; Altmann, Karl-Heinz; Griesinger, Christian
In: Angew Chem Int Ed Engl, vol. 42, no. 22, pp. 2511–2515, 2003, ISSN: 1433-7851.
@article{pmid12800173,
title = {The high-resolution solution structure of epothilone A bound to tubulin: an understanding of the structure-activity relationships for a powerful class of antitumor agents},
author = {Teresa Carlomagno and Marcel J J Blommers and Jens Meiler and Wolfgang Jahnke and Thomas Schupp and Frank Petersen and Dieter Schinzer and Karl-Heinz Altmann and Christian Griesinger},
doi = {10.1002/anie.200351276},
issn = {1433-7851},
year = {2003},
date = {2003-06-01},
journal = {Angew Chem Int Ed Engl},
volume = {42},
number = {22},
pages = {2511--2515},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Meiler, Jens
PROSHIFT: protein chemical shift prediction using artificial neural networks Journal Article
In: J Biomol NMR, vol. 26, no. 1, pp. 25–37, 2003, ISSN: 0925-2738.
Abstract | Links | BibTeX | Tags:
@article{pmid12766400,
title = {PROSHIFT: protein chemical shift prediction using artificial neural networks},
author = {Jens Meiler},
doi = {10.1023/a:1023060720156},
issn = {0925-2738},
year = {2003},
date = {2003-05-01},
journal = {J Biomol NMR},
volume = {26},
number = {1},
pages = {25--37},
abstract = {The importance of protein chemical shift values for the determination of three-dimensional protein structure has increased in recent years because of the large databases of protein structures with assigned chemical shift data. These databases have allowed the investigation of the quantitative relationship between chemical shift values obtained by liquid state NMR spectroscopy and the three-dimensional structure of proteins. A neural network was trained to predict the (1)H, (13)C, and (15)N of proteins using their three-dimensional structure as well as experimental conditions as input parameters. It achieves root mean square deviations of 0.3 ppm for hydrogen, 1.3 ppm for carbon, and 2.6 ppm for nitrogen chemical shifts. The model reflects important influences of the covalent structure as well as of the conformation not only for backbone atoms (as, e.g., the chemical shift index) but also for side-chain nuclei. For protein models with a RMSD smaller than 5 A a correlation of the RMSD and the r.m.s. deviation between the predicted and the experimental chemical shift is obtained. Thus the method has the potential to not only support the assignment process of proteins but also help with the validation and the refinement of three-dimensional structural proposals. It is freely available for academic users at the PROSHIFT server: www.jens-meiler.de/proshift.html},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The importance of protein chemical shift values for the determination of three-dimensional protein structure has increased in recent years because of the large databases of protein structures with assigned chemical shift data. These databases have allowed the investigation of the quantitative relationship between chemical shift values obtained by liquid state NMR spectroscopy and the three-dimensional structure of proteins. A neural network was trained to predict the (1)H, (13)C, and (15)N of proteins using their three-dimensional structure as well as experimental conditions as input parameters. It achieves root mean square deviations of 0.3 ppm for hydrogen, 1.3 ppm for carbon, and 2.6 ppm for nitrogen chemical shifts. The model reflects important influences of the covalent structure as well as of the conformation not only for backbone atoms (as, e.g., the chemical shift index) but also for side-chain nuclei. For protein models with a RMSD smaller than 5 A a correlation of the RMSD and the r.m.s. deviation between the predicted and the experimental chemical shift is obtained. Thus the method has the potential to not only support the assignment process of proteins but also help with the validation and the refinement of three-dimensional structural proposals. It is freely available for academic users at the PROSHIFT server: www.jens-meiler.de/proshift.html
Bradley, Philip; Chivian, Dylan; Meiler, Jens; Misura, Kira M S; Rohl, Carol A; Schief, William R; Wedemeyer, William J; Schueler-Furman, Ora; Murphy, Paul; Schonbrun, Jack; Strauss, Charles E M; Baker, David
Rosetta predictions in CASP5: successes, failures, and prospects for complete automation Journal Article
In: Proteins, vol. 53 Suppl 6, pp. 457–468, 2003, ISSN: 1097-0134.
Abstract | Links | BibTeX | Tags:
@article{pmid14579334,
title = {Rosetta predictions in CASP5: successes, failures, and prospects for complete automation},
author = {Philip Bradley and Dylan Chivian and Jens Meiler and Kira M S Misura and Carol A Rohl and William R Schief and William J Wedemeyer and Ora Schueler-Furman and Paul Murphy and Jack Schonbrun and Charles E M Strauss and David Baker},
doi = {10.1002/prot.10552},
issn = {1097-0134},
year = {2003},
date = {2003-01-01},
journal = {Proteins},
volume = {53 Suppl 6},
pages = {457--468},
abstract = {We describe predictions of the structures of CASP5 targets using Rosetta. The Rosetta fragment insertion protocol was used to generate models for entire target domains without detectable sequence similarity to a protein of known structure and to build long loop insertions (and N-and C-terminal extensions) in cases where a structural template was available. Encouraging results were obtained both for the de novo predictions and for the long loop insertions; we describe here the successes as well as the failures in the context of current efforts to improve the Rosetta method. In particular, de novo predictions failed for large proteins that were incorrectly parsed into domains and for topologically complex (high contact order) proteins with swapping of segments between domains. However, for the remaining targets, at least one of the five submitted models had a long fragment with significant similarity to the native structure. A fully automated version of the CASP5 protocol produced results that were comparable to the human-assisted predictions for most of the targets, suggesting that automated genomic-scale, de novo protein structure prediction may soon be worthwhile. For the three targets where the human-assisted predictions were significantly closer to the native structure, we identify the steps that remain to be automated.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
We describe predictions of the structures of CASP5 targets using Rosetta. The Rosetta fragment insertion protocol was used to generate models for entire target domains without detectable sequence similarity to a protein of known structure and to build long loop insertions (and N-and C-terminal extensions) in cases where a structural template was available. Encouraging results were obtained both for the de novo predictions and for the long loop insertions; we describe here the successes as well as the failures in the context of current efforts to improve the Rosetta method. In particular, de novo predictions failed for large proteins that were incorrectly parsed into domains and for topologically complex (high contact order) proteins with swapping of segments between domains. However, for the remaining targets, at least one of the five submitted models had a long fragment with significant similarity to the native structure. A fully automated version of the CASP5 protocol produced results that were comparable to the human-assisted predictions for most of the targets, suggesting that automated genomic-scale, de novo protein structure prediction may soon be worthwhile. For the three targets where the human-assisted predictions were significantly closer to the native structure, we identify the steps that remain to be automated.
2002
Hutter, Michael C; Krebs, Joachim; Meiler, Jens; Griesinger, Christian; Carafoli, Ernesto; Helms, Volkhard
A structural model of the complex formed by phospholamban and the calcium pump of sarcoplasmic reticulum obtained by molecular mechanics Journal Article
In: Chembiochem, vol. 3, no. 12, pp. 1200–1208, 2002, ISSN: 1439-4227.
Abstract | Links | BibTeX | Tags:
@article{pmid12465028,
title = {A structural model of the complex formed by phospholamban and the calcium pump of sarcoplasmic reticulum obtained by molecular mechanics},
author = {Michael C Hutter and Joachim Krebs and Jens Meiler and Christian Griesinger and Ernesto Carafoli and Volkhard Helms},
doi = {10.1002/1439-7633(20021202)3:12<1200::AID-CBIC1200>3.0.CO;2-H},
issn = {1439-4227},
year = {2002},
date = {2002-12-01},
journal = {Chembiochem},
volume = {3},
number = {12},
pages = {1200--1208},
abstract = {Phospholamban (PLN) is an intrinsic membrane protein of 52 amino acids that modulates the activity of the reticular Ca(2+) ion pump. We recently solved the three-dimensional structure of chemically synthesized, unphosphorylated, monomeric PLN (C41F) by high-resolution nuclear magnetic resonance spectroscopy in chloroform/methanol. The structure is composed of two alpha-helical regions connected by a beta turn (Type III). We used this structure and the crystallographic structure of the sarcoplasmic reticulum calcium pump (SERCA) recently determined by Toyoshima and co-workers and modeled into its E(2) form by Stokes (1KJU) or by Toyoshima (1FQU). We applied restrained and unrestrained energy optimizations and used the AMBER molecular mechanics force field to model the complex formed between PLN and the pump. The results indicate that transmembrane helix 6 (M6) of the SERCA pump is energetically favored, with respect to the other transmembrane helices, as the PLN binding partner within the membrane and is the only one of these helices that also permits contact between the N-terminal residues of PLN and the critical cytosolic binding loop region of the pump. This result is in agreement with published biochemical data and with the predictions of previous mutagenesis work on the membrane sector of the pump. The model reveals that PLN does not span the entire width of the membrane, that is, its hydrophobic C-terminal end is located near the center of the transmembrane region of the SERCA pump. The model also shows that interaction with M6 is stabilized by additional contacts made by PLN to M4. The contact between the N-terminal portion of PLN and the pump is stabilized by a number of salt and hydrogen-bond bridges, which may be abolished by phosphorylation of PLN. The contacts between the cytosolic portions of PLN and the pump are only observed in the E(2) conformation of the pump. Our model of the complex also offers a plausible structural explanation for the preference of protein kinase A for phosphorylation of Ser16 of PLN.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Phospholamban (PLN) is an intrinsic membrane protein of 52 amino acids that modulates the activity of the reticular Ca(2+) ion pump. We recently solved the three-dimensional structure of chemically synthesized, unphosphorylated, monomeric PLN (C41F) by high-resolution nuclear magnetic resonance spectroscopy in chloroform/methanol. The structure is composed of two alpha-helical regions connected by a beta turn (Type III). We used this structure and the crystallographic structure of the sarcoplasmic reticulum calcium pump (SERCA) recently determined by Toyoshima and co-workers and modeled into its E(2) form by Stokes (1KJU) or by Toyoshima (1FQU). We applied restrained and unrestrained energy optimizations and used the AMBER molecular mechanics force field to model the complex formed between PLN and the pump. The results indicate that transmembrane helix 6 (M6) of the SERCA pump is energetically favored, with respect to the other transmembrane helices, as the PLN binding partner within the membrane and is the only one of these helices that also permits contact between the N-terminal residues of PLN and the critical cytosolic binding loop region of the pump. This result is in agreement with published biochemical data and with the predictions of previous mutagenesis work on the membrane sector of the pump. The model reveals that PLN does not span the entire width of the membrane, that is, its hydrophobic C-terminal end is located near the center of the transmembrane region of the SERCA pump. The model also shows that interaction with M6 is stabilized by additional contacts made by PLN to M4. The contact between the N-terminal portion of PLN and the pump is stabilized by a number of salt and hydrogen-bond bridges, which may be abolished by phosphorylation of PLN. The contacts between the cytosolic portions of PLN and the pump are only observed in the E(2) conformation of the pump. Our model of the complex also offers a plausible structural explanation for the preference of protein kinase A for phosphorylation of Ser16 of PLN.
Meiler, Jens; Maier, Walter; Will, Martin; Meusinger, Reinhard
Using neural networks for (13)c NMR chemical shift prediction-comparison with traditional methods Journal Article
In: J Magn Reson, vol. 157, no. 2, pp. 242–252, 2002, ISSN: 1090-7807.
Abstract | Links | BibTeX | Tags:
@article{pmid12323143,
title = {Using neural networks for (13)c NMR chemical shift prediction-comparison with traditional methods},
author = {Jens Meiler and Walter Maier and Martin Will and Reinhard Meusinger},
doi = {10.1006/jmre.2002.2599},
issn = {1090-7807},
year = {2002},
date = {2002-08-01},
journal = {J Magn Reson},
volume = {157},
number = {2},
pages = {242--252},
abstract = {Interpretation of (13)C chemical shifts is essential for structure elucidation of organic molecules by NMR. In this article, we present an improved neural network approach and compare its performance to that of commonly used approaches. Specifically, our recently proposed neural network (J. Chem. Inf. Comput. Sci. 2000, 40, 1169-1176) is improved by introducing an extended hybrid numerical description of the carbon atom environment, resulting in a standard deviation (std. dev.) of 2.4 ppm for an independent test data set of approximately 42,500 carbons. Thus, this neural network allows fast and accurate (13)C NMR chemical shift prediction without the necessity of access to molecule or fragment databases. For an unbiased test dataset containing 100 organic structures the accuracy of the improved neural network was compared to that of a prediction method based on the HOSE code (hierarchically ordered spherical description of environment) using SPECINFO. The results show the neural network predictions to be of quality (std. dev. = 2.7 ppm) comparable to that of the HOSE code prediction (std. dev. = 2.6 ppm). Further we compare the neural network predictions to those of a wide variety of other (13)C chemical shift prediction tools including incremental methods (CHEMDRAW, SPECTOOL), quantum chemical calculation (GAUSSIAN, COSMOS), and HOSE code fragment-based prediction (SPECINFO, ACD/CNMR, PREDICTIT NMR) for the 47 (13)C-NMR shifts of Taxol, a natural product including many structural features of organic substances. The smallest standard deviations were achieved here with the neural network (1.3 ppm) and SPECINFO (1.0 ppm).},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Interpretation of (13)C chemical shifts is essential for structure elucidation of organic molecules by NMR. In this article, we present an improved neural network approach and compare its performance to that of commonly used approaches. Specifically, our recently proposed neural network (J. Chem. Inf. Comput. Sci. 2000, 40, 1169-1176) is improved by introducing an extended hybrid numerical description of the carbon atom environment, resulting in a standard deviation (std. dev.) of 2.4 ppm for an independent test data set of approximately 42,500 carbons. Thus, this neural network allows fast and accurate (13)C NMR chemical shift prediction without the necessity of access to molecule or fragment databases. For an unbiased test dataset containing 100 organic structures the accuracy of the improved neural network was compared to that of a prediction method based on the HOSE code (hierarchically ordered spherical description of environment) using SPECINFO. The results show the neural network predictions to be of quality (std. dev. = 2.7 ppm) comparable to that of the HOSE code prediction (std. dev. = 2.6 ppm). Further we compare the neural network predictions to those of a wide variety of other (13)C chemical shift prediction tools including incremental methods (CHEMDRAW, SPECTOOL), quantum chemical calculation (GAUSSIAN, COSMOS), and HOSE code fragment-based prediction (SPECINFO, ACD/CNMR, PREDICTIT NMR) for the 47 (13)C-NMR shifts of Taxol, a natural product including many structural features of organic substances. The smallest standard deviations were achieved here with the neural network (1.3 ppm) and SPECINFO (1.0 ppm).
Peti, Wolfgang; Meiler, Jens; Brüschweiler, Rafael; Griesinger, Christian
Model-free analysis of protein backbone motion from residual dipolar couplings Journal Article
In: J Am Chem Soc, vol. 124, no. 20, pp. 5822–5833, 2002, ISSN: 0002-7863.
Abstract | Links | BibTeX | Tags:
@article{pmid12010057,
title = {Model-free analysis of protein backbone motion from residual dipolar couplings},
author = {Wolfgang Peti and Jens Meiler and Rafael Brüschweiler and Christian Griesinger},
doi = {10.1021/ja011883c},
issn = {0002-7863},
year = {2002},
date = {2002-05-01},
journal = {J Am Chem Soc},
volume = {124},
number = {20},
pages = {5822--5833},
abstract = {On the basis of the measurement of NH residual dipolar couplings (RDCs) in 11 different alignment media, an RDC-based order parameter is derived for each residue in the protein ubiquitin. Dipolar couplings are motionally averaged in the picosecond to millisecond time range and, therefore, reflect motion slower than the inverse overall tumbling correlation time of the protein. It is found that there is considerable motion that is slower than the correlation time and could not be detected with previous NMR methodology. Amplitudes and anisotropies of the motion can be derived from the model-free analysis. The method can be applied provided that at least five sufficiently different alignment media can be found for the biomolecule under investigation.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
On the basis of the measurement of NH residual dipolar couplings (RDCs) in 11 different alignment media, an RDC-based order parameter is derived for each residue in the protein ubiquitin. Dipolar couplings are motionally averaged in the picosecond to millisecond time range and, therefore, reflect motion slower than the inverse overall tumbling correlation time of the protein. It is found that there is considerable motion that is slower than the correlation time and could not be detected with previous NMR methodology. Amplitudes and anisotropies of the motion can be derived from the model-free analysis. The method can be applied provided that at least five sufficiently different alignment media can be found for the biomolecule under investigation.
Meiler, Jens; Will, Martin
Genius: a genetic algorithm for automated structure elucidation from 13C NMR spectra Journal Article
In: J Am Chem Soc, vol. 124, no. 9, pp. 1868–1870, 2002, ISSN: 0002-7863.
Abstract | Links | BibTeX | Tags:
@article{pmid11866596,
title = {Genius: a genetic algorithm for automated structure elucidation from 13C NMR spectra},
author = {Jens Meiler and Martin Will},
doi = {10.1021/ja0109388},
issn = {0002-7863},
year = {2002},
date = {2002-03-01},
journal = {J Am Chem Soc},
volume = {124},
number = {9},
pages = {1868--1870},
abstract = {The automated structure elucidation of organic molecules from experimentally obtained properties is extended by an entirely new approach. A genetic algorithm is implemented that uses molecular constitution structures as individuals. With this approach, the structure of organic molecules can be optimized to meet experimental criteria, if in addition a fast and accurate method for the prediction of the used physical or chemical features is available. This is demonstrated using 13C NMR spectrum as readily obtainable information. By means of artificial neural networks a fast and accurate method for calculating the 13C NMR spectrum of the generated structures exists. The method is implemented and tested successfully for organic molecules with up to 18 non-hydrogen atoms.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The automated structure elucidation of organic molecules from experimentally obtained properties is extended by an entirely new approach. A genetic algorithm is implemented that uses molecular constitution structures as individuals. With this approach, the structure of organic molecules can be optimized to meet experimental criteria, if in addition a fast and accurate method for the prediction of the used physical or chemical features is available. This is demonstrated using 13C NMR spectrum as readily obtainable information. By means of artificial neural networks a fast and accurate method for calculating the 13C NMR spectrum of the generated structures exists. The method is implemented and tested successfully for organic molecules with up to 18 non-hydrogen atoms.
Meiler, Jens; Sanli, Erdogan; Junker, Jochen; Meusinger, Reinhard; Lindel, Thomas; Will, Martin; Maier, Walter; Köck, Matthias
Validation of structural proposals by substructure analysis and 13C NMR chemical shift prediction Journal Article
In: J Chem Inf Comput Sci, vol. 42, no. 2, pp. 241–248, 2002, ISSN: 0095-2338.
Abstract | Links | BibTeX | Tags:
@article{pmid11911693,
title = {Validation of structural proposals by substructure analysis and 13C NMR chemical shift prediction},
author = {Jens Meiler and Erdogan Sanli and Jochen Junker and Reinhard Meusinger and Thomas Lindel and Martin Will and Walter Maier and Matthias Köck},
doi = {10.1021/ci010294n},
issn = {0095-2338},
year = {2002},
date = {2002-01-01},
journal = {J Chem Inf Comput Sci},
volume = {42},
number = {2},
pages = {241--248},
abstract = {The 2D NMR-guided computer program COCON can be extremely valuable for the constitutional analysis of unknown compounds, if its results are evaluated by neural network-assisted 13C NMR chemical shift and substructure analyses. As instructive examples, data sets of four differently complex marine natural products were thoroughly investigated. As a significant step towards a true automated structure elucidation, it is shown that the primary COCON output can be safely diminished to less than 1% of its original size without losing the correct structural proposal.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The 2D NMR-guided computer program COCON can be extremely valuable for the constitutional analysis of unknown compounds, if its results are evaluated by neural network-assisted 13C NMR chemical shift and substructure analyses. As instructive examples, data sets of four differently complex marine natural products were thoroughly investigated. As a significant step towards a true automated structure elucidation, it is shown that the primary COCON output can be safely diminished to less than 1% of its original size without losing the correct structural proposal.