Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains

@article{Dunbrack1994ConformationalAO,
  title={Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains},
  author={Roland L. Dunbrack and Martin Karplus},
  journal={Nature Structural Biology},
  year={1994},
  volume={1},
  pages={334-340}
}
Amino acids have sidechain rotamer preferences dependent on the backbone dihedral angles φ and ψ. These preferences provide a method for rapid structure prediction which is a significant improvement over backbone-independent rotamer libraries. We demonstrate here that simple arguments based on conformational analysis can account for many of the features of the observed backbone dependence of the sidechain rotamers. Steric repulsions corresponding to the ‘butane’ and ‘syn-pentane’ effects make… Expand
Comparing theoretical and experimental backbone-dependent sidechain conformational preferences for linear, branched, aromatic and polar residues
Abstract An Ecepp-3 conformational study based on a φ-ψ grid search with sidechain minimization was carried out on the N-acetyl N′-methyl amides of four representative amino acids: Met, Phe, Ile, andExpand
Dependence of Sidechain Rotamer Preference on Backbone Conformation: Relative Free Energy Calculations for Valine and Leucine
Three dimensional relative free energy calculations are used to directly calculate the dependence of the preferred sidechain rotamers for valine and leucine on the conformation of the backbone.Expand
Modeling side-chain conformation.
  • M. Vásquez
  • Chemistry, Medicine
  • Current opinion in structural biology
  • 1996
TLDR
Although further work is needed to address the issue of backbone displacements, the recent progress solves the packing problem to a significant degree and opens the way for fruitful incorporation of these methods into general procedures for homology modeling and studies of ligand-protein interactions. Expand
Side-Chain Conformational Preferences Govern Protein-Protein Interactions.
TLDR
The analysis of side-chain conformational preferences in residues that contribute significantly to binding suggests that preferred rotamers contribute directly to specificity in protein complex formation and provides guidelines for peptidomimetic inhibitor design. Expand
Effects of side-chain orientation on the 13C chemical shifts of antiparallel β-sheet model peptides
TLDR
The results suggest that predicted 13Cα and 13Cβ chemical shifts, based only on backbone (φ,ψ) dihedral angles from high-resolution X-ray structure data or from NMR-derived models, may differ significantly from those observed in solution if the dihedral-angle preferences for the side chains are not taken into account. Expand
Conformational landscape of substituted prolines
TLDR
This review has explored the conformational landscape of several termini capped mono-(2-, 3-, 4-, and 5-) substituted proline derivatives in the Cambridge Structural Database, correlating observed conformations with the nature of substituents and deciphering the underlying interactions for the observed structural biases. Expand
Restricted sidechain plasticity in the structures of native proteins and complexes
TLDR
It is reported here that sidechains in native structures and interfaces are significantly more constrained than designed interfaces and structures with equal computed binding energy or stability, which may reflect selection against potentially deleterious non‐native interactions. Expand
The interrelationships of side-chain and main-chain conformations in proteins.
TLDR
Analyses of residues occurring with disallowed main-chain conformation or with multiple conformations shed some light on why some residues are less favoured in thermophiles. Expand
Steric interactions determine side-chain conformations in protein cores.
TLDR
This approach can identify the amino acids for which hard-sphere interactions alone are sufficient and those for which additional interactions are necessary to accurately predict side-chain conformations in protein cores, and can predict alternate side- chain conformations of core residues, which are supported by the observed electron density. Expand
Predicting the side‐chain dihedral angle distributions of nonpolar, aromatic, and polar amino acids using hard sphere models
TLDR
It is found that a hard‐sphere model for a dipeptide mimetic that includes only steric interactions plus stereochemical constraints is able to recapitulate the key features of the back‐bone dependent observed amino acid side‐chain dihedral angle distributions. Expand
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 31 REFERENCES
An analysis of side-chain conformation in proteins.
The crystal structures of a number of globular proteins are currently available. An analysis of the distribution of side-chains among different allowed conformations in these proteins has beenExpand
Backbone-dependent rotamer library for proteins. Application to side-chain prediction.
TLDR
A backbone-dependent rotamer library for amino acid side-chains is developed and used for constructing protein side-chain conformations from the main-chain co-ordinates and it is evident from the results that a single protein does not adequately test a prediction scheme. Expand
Rotamers: to be or not to be? An analysis of amino acid side-chain conformations in globular proteins.
TLDR
The "rotamericity" not only remains substantially below 100% (70 to 95% for various amino acids) with improving crystallographic resolution but actually decreases for 8 out of 17 amino acid types after a critical resolution limit is crossed. Expand
Conformation of amino acid side-chains in proteins.
TLDR
Configurations that are rare for exposed residues are even rarer for buried residues, suggesting that, while the folded structure puts little strain on side-chain conformations, the side- chain positions with the lowest energy in the unfolded structure are chosen preferentially during folding. Expand
A new approach to the rapid determination of protein side chain conformations.
TLDR
Successful applications of two efficient algorithms which allow amino acid side chain conformations to be optimized rapidly for a given peptide backbone conformation to the prediction of known protein conformations are presented. Expand
Side-chain torsional potentials: effect of dipeptide, protein, and solvent environment.
TLDR
The results are discussed in terms of the details of the interactions due to the surrounding, calculated solvent-accessibility figures and the temperature factors derived from the crystallographic refinement of the pancreatic trypsin inhibitor. Expand
Statistical and energetic analysis of side-chain conformations in oligopeptides.
TLDR
This study of the observed side-chain conformations has led to a refinement of one of the energy parameters used in empirical conformational energy computations. Expand
Analysis of the relationship between side-chain conformation and secondary structure in globular proteins.
TLDR
More accurate distributions for the side-chain dihedral angles which were obtained from the increased number of proteins determined to high resolution are presented. Expand
A method to configure protein side-chains from the main-chain trace in homology modelling.
TLDR
The prediction accuracy of the present homology modelling technique was assessed relative to other automated procedures and was found to yield improved predictions relative to the known side-chain conformations determined by X-ray crystallography. Expand
Conformational analysis of the 20 naturally occurring amino acid residues using ECEPP.
TLDR
Conformational energy calculations using ECEPP (Empirical Conformational Energy Program for Peptides) were carried out on the N-acetyl-N'-methylamides of the 20 naturally occurring amino acids, and the results are categorized most easily by use of a new conformational letter code. Expand
...
1
2
3
4
...