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Local structural differences in homologous proteins: specificities in different SCOP classes.
Joseph A. P., Valadié H., Srinivasan N., De Brevern A. G.
PLoS ONE 7, 6 (2012) e38805 - http://www.hal.inserm.fr/inserm-00750286
 (22745680) 
Local structural differences in homologous proteins: specificities in different SCOP classes.
Agnel Praveen Joseph1, Hélène Valadié2, Narayanaswamy Srinivasan3, Alexandre De Brevern () 1
1 :  DSIMB - Dynamique des Structures et Interactions des Macromolécules Biologiques
http://www.dsimb.inserm.fr
Université Paris VII - Paris Diderot – INTS – INSERM : U665
Faculté des Sciences et techniques - Université de La Réunion 15 avenue René Cassin CS92003 97744 SAINT DENIS CEDEX 9
France
2 :  Bioinformatique génomique et moléculaire
INSERM : U726 – Université Paris VII - Paris Diderot
2, Place Jussieu 75251 PARIS CEDEX 05
France
3 :  Molecular Biophysics Unit
http://pauling.mbu.iisc.ernet.in/
Indian Institute of Science
Bangalore 560 012
Inde
DSIMB
Local Structure Variations
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.
Sciences du Vivant/Biochimie, Biologie Moléculaire
Sciences du Vivant/Bio-Informatique, Biostatistique
Informatique/Bio-informatique
Anglais
1932-6203

Articles dans des revues avec comité de lecture
10.1371/journal.pone.0038805
PLoS ONE
Publisher Public Library of Science
ISSN 1932-6203 
internationale
2012
22/06/2012
7
6
e38805

amino acid – local structures – backbone conformation – structural alphabet – Protein Blocks – protein folds – indel – structure comparison – Protein Data Bank.
French Ministry of Research, University of Paris Diderot - Paris 7, French National Institute for Blood Transfusion (INTS), French Institute for Health and Medical Research (INSERM), Indian Department of Biotechnology, CEFIPRA/IFCPAR for collaborative grant (number 3903-E).
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Joseph_Valadie_Srinivasan_de_Brevern_PlosOne_2012-preprint.pdf(2.1 MB)
ANNEX
Supplementary_data_PlosOne.doc(1002.5 KB)