Importance of solvent accessibility and contact surfaces in modeling side‐chain conformations in proteins

Eyal, Eran; Najmanovich, Rafaël; McConkey, Brendan J.; Edelman, Marvin; Sobolev, V. M.

doi:10.1002/jcc.10420

Cited by 127 publications

(130 citation statements)

References 51 publications

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“…An analysis carried out according to accessibility, shows that hidden residues are slightly better in concord (64%) with SC 4 than those exposed (49%). This result corroborates well the data of the literature on the quality of the side chain predictions [84,93]. All methods find between 55% and 65% of the contacts observed in the protein databank, but at most they For SCWRL (see Table 6 Table 4).…”

Section: Side-chain Replacementssupporting

confidence: 90%

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Protein contacts, inter-residue interactions and side-chain modelling

Faure¹,

Bornot²,

Brevern³

2008

Biochimie

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To cite this version:Guilhem Faure, Aurélie Bornot, Alexandre De Brevern. Protein contacts, inter-residue interactions and side-chain modelling.: protein contacts. Biochimie, Elsevier, 2008, 90 (4) AbstractThree-dimensional structures of proteins are the support of their biological functions.Their folds are stabilized by contacts between residues. Inner protein contacts are generally described through direct atomic contacts, i.e. interactions between side-chain atoms, while contact prediction methods mainly used inter-C distances. In this paper, we have analyzed the protein contacts on a recent high quality non-redundant databank using different criteria.First, we have studied the average number of contacts depending on the distance threshold to define a contact. Preferential contacts between types of amino acids have been highlighted.Detailed analyses have been done concerning the proximity of contacts in the sequence, the size of the proteins and fold classes. The strongest differences have been extracted, highlighting important residues.Then, we studied the influence of five different side-chain conformation prediction methods (SCWRL, IRECS, SCAP, SCATD and SSCOMP) on the distribution of contacts.The prediction rates of these different methods are quite similar. However, using a distance criterion between side-chains, the results are quite different, e.g. SCAP predicts 50% more contacts than observed, unlike other methods that predict fewer contacts than observed.Contacts deduced are quite distinct from one method to another with at most 75% contacts in common. Moreover, distributions of amino acid preferential contacts present unexpected behaviors distinct from previously observed in the X-ray structures, especially at the surface of proteins. For instance, the interactions involving Tryptophan greatly decrease.

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Section: Side-chain Replacementssupporting

confidence: 90%

“…SCCOMP makes a scoring function based on terms for complementarities (geometric and chemical compatibility), excluded volume, internal energy based on probability of rotamers, and solvent accessible surface [93]. SCAP specificities lead to a four coordinate rotamer libraries [94].…”

Section: Introductionmentioning

confidence: 99%

Protein contacts, inter-residue interactions and side-chain modelling

Faure¹,

Bornot²,

Brevern³

2008

Biochimie

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“…Side chains were added in the unfolded domain by using the SCCOMP program (43), and SAXS intensity curves were predicted by using the program CRYSOL (44). Individual intensities from each of the conformers were averaged and treated in an equivalent way to experimental data.…”

Section: Nmrmentioning

confidence: 99%

A structural model for unfolded proteins from residual dipolar couplings and small-angle x-ray scattering

Bernadó

Blanchard

Timmins

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

420

545

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Natively unfolded proteins play key roles in normal and pathological biochemical processes. Despite their importance for function, this category of proteins remains beyond the reach of classical structural biology because of their inherent conformational heterogeneity. We present a description of the intrinsic conformational sampling of unfolded proteins based on residue-specific ͞ propensities from loop regions of a folded protein database and simple volume exclusion. This approach is used to propose a structural model of the 57-aa, natively disordered region of the nucleocapsid-binding domain of Sendai virus phosphoprotein. Structural ensembles obeying these simple rules of conformational sampling are used to simulate averaged residual dipolar couplings (RDCs) and small-angle x-ray scattering data. This protein is particularly informative because RDC data from the equally sized folded and unfolded domains both report on the unstructured region, allowing a quantitative analysis of the degree of order present in this part of the protein. Close agreement between experimental and simulated RDC and small-angle x-ray scattering data validates this simple model of conformational sampling, providing a precise description of local structure and dynamics and average dimensions of the ensemble of sampled structures. RDC data from two urea-unfolded systems are also closely reproduced. The demonstration that conformational behavior of unfolded proteins can be accurately predicted from the primary sequence by using a simple set of rules has important consequences for our understanding of the structure and dynamics of the unstructured state.

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“…Specificities were found according to the distance in the sequence between residues in contact and some differences were observed compared to the literature [65]. Moreover, we highlighted biases of the side-chain replacement methods [66][67][68][69][70][71][72].…”

Section: Introductionmentioning

confidence: 78%

Analysis of protein contacts into Protein Units

2009

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Three-dimensional structures of proteins are the support of their biological functions.Their folds are maintained by inter-residue interactions which are one of the main focuses to understand the mechanisms of protein folding and stability. Furthermore, protein structures can be composed of single or multiple functional domains that can fold and function independently. Hence, dividing a protein into domains is useful for obtaining an accurate structure and function determination.In previous studies, we enlightened protein contact properties according to different

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Importance of solvent accessibility and contact surfaces in modeling side‐chain conformations in proteins

Cited by 127 publications

References 51 publications

Protein contacts, inter-residue interactions and side-chain modelling

Protein contacts, inter-residue interactions and side-chain modelling

A structural model for unfolded proteins from residual dipolar couplings and small-angle x-ray scattering

Analysis of protein contacts into Protein Units

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