Analysis of protein contacts into Protein Units

Faure, Guilhem; Bornot, Aurélie; Brevern, Alexandre G. de

doi:10.1016/j.biochi.2009.04.008

Cited by 15 publications

(13 citation statements)

References 123 publications

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“…This SA gives a reasonable approximation of local protein 3D structures with a root mean square deviation ( rmsd ) of about 0.42 Å [54]. PB description has been used in several bioinformatics approaches including modeling and structure prediction [44], [55], [56], [57], [58], [59], [60], [61], [62], [63], [64], [65], [66], [67], [68], [69], [70], [71]. Figure 2 shows practical examples on the association of different PBs with regular secondary structures and Table 1 summarizes this relationship using PROMOTIF [42] based secondary structure assignment.…”

Section: Introductionmentioning

confidence: 99%

Local Structural Differences in Homologous Proteins: Specificities in Different SCOP Classes

et al. 2012

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The constant increase in the number of solved protein structures is of great help in understanding the basic principles behind protein folding and evolution. 3-D structural knowledge is valuable in designing and developing methods for comparison, modelling and prediction of protein structures. These approaches for structure analysis can be directly implicated in studying protein function and for drug design. The backbone of a protein structure favours certain local conformations which include α-helices, β-strands and turns. Libraries of limited number of local conformations (Structural Alphabets) were developed in the past to obtain a useful categorization of backbone conformation. Protein Block (PB) is one such Structural Alphabet that gave a reasonable structure approximation of 0.42 Å. In this study, we use PB description of local structures to analyse conformations that are preferred sites for structural variations and insertions, among group of related folds. This knowledge can be utilized in improving tools for structure comparison that work by analysing local structure similarities. Conformational differences between homologous proteins are known to occur often in the regions comprising turns and loops. Interestingly, these differences are found to have specific preferences depending upon the structural classes of proteins. Such class-specific preferences are mainly seen in the all-β class with changes involving short helical conformations and hairpin turns. A test carried out on a benchmark dataset also indicates that the use of knowledge on the class specific variations can improve the performance of a PB based structure comparison approach. The preference for the indel sites also seem to be confined to a few backbone conformations involving β-turns and helix C-caps. These are mainly associated with short loops joining the regular secondary structures that mediate a reversal in the chain direction. Rare β-turns of type I’ and II’ are also identified as preferred sites for insertions.

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Section: Introductionmentioning

confidence: 99%

Local Structural Differences in Homologous Proteins: Specificities in Different SCOP Classes

et al. 2012

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“…PBs have proven their efficiency in the description and the prediction of long fragments ( ;Hansmann, 2008Benros et al, 2009;;;), to compare protein al., 2006de Brevern and Hazout, 2003de Brevern et al, 2002;), to build globular ( ) and transmembrane protein Tyagi et al, 2008Tyagi et al, 2006aTyagi et al, 2006bDong et al, 2007;), to define a reduced amino acid alphabet dedicated to de Brevern et al, 2005 mutation design ( ), to design peptides ( ), to define binding site signatures ( Etchebest et al, 2007Thomas et al, 2006Dudev and Lim, 2007 or to analyze protein contacts ( ). The features of this alphabet have been compared with those of 8 other structural Faure et al, 2009 alphabets showing clearly that our PB alphabet is highly informative, with the best predictive ability of those tested ( ). Karchin et al, 2003 In this paper, we focus on the prediction of short loops from sequence.…”

Section: Introductionmentioning

confidence: 99%

Protein short loop prediction in terms of a structural alphabet

Tyagi

Bornot

Offmann

et al. 2009

Computational Biology and Chemistry

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In the present study, we used our structural alphabet to predict the loops connecting two repetitive structures. Thus, we showed the interest to take into account the flanking regions, leading to prediction rate improvement up to 19.8 , but we also underline the % sensitivity of such an approach. This research can be used to propose different structures for the loops and to probe and sample their flexibility. It is a useful tool for loop prediction and leads to insights to flexible docking approach. ab initio

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“…, a contact is defined if a distance between atoms is less than 8.0 Å [76], [77], [78]. Unlike the accessibility, PPII DSSP is similar to β-strand in terms of the average number of contacts.…”

Section: Resultsmentioning

confidence: 99%

Assignment of PolyProline II Conformation and Analysis of Sequence – Structure Relationship

et al. 2011

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BackgroundSecondary structures are elements of great importance in structural biology, biochemistry and bioinformatics. They are broadly composed of two repetitive structures namely α-helices and β-sheets, apart from turns, and the rest is associated to coil. These repetitive secondary structures have specific and conserved biophysical and geometric properties. PolyProline II (PPII) helix is yet another interesting repetitive structure which is less frequent and not usually associated with stabilizing interactions. Recent studies have shown that PPII frequency is higher than expected, and they could have an important role in protein – protein interactions.Methodology/Principal FindingsA major factor that limits the study of PPII is that its assignment cannot be carried out with the most commonly used secondary structure assignment methods (SSAMs). The purpose of this work is to propose a PPII assignment methodology that can be defined in the frame of DSSP secondary structure assignment. Considering the ambiguity in PPII assignments by different methods, a consensus assignment strategy was utilized. To define the most consensual rule of PPII assignment, three SSAMs that can assign PPII, were compared and analyzed. The assignment rule was defined to have a maximum coverage of all assignments made by these SSAMs. Not many constraints were added to the assignment and only PPII helices of at least 2 residues length are defined.Conclusions/SignificanceThe simple rules designed in this study for characterizing PPII conformation, lead to the assignment of 5% of all amino as PPII. Sequence – structure relationships associated with PPII, defined by the different SSAMs, underline few striking differences. A specific study of amino acid preferences in their N and C-cap regions was carried out as their solvent accessibility and contact patterns. Thus the assignment of PPII can be coupled with DSSP and thus opens a simple way for further analysis in this field.

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Analysis of protein contacts into Protein Units

Cited by 15 publications

References 123 publications

Local Structural Differences in Homologous Proteins: Specificities in Different SCOP Classes

Local Structural Differences in Homologous Proteins: Specificities in Different SCOP Classes

Protein short loop prediction in terms of a structural alphabet

Assignment of PolyProline II Conformation and Analysis of Sequence – Structure Relationship

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