Analysis of loop boundaries using different local structure assignment methods |
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Authors: | Manoj Tyagi Aurélie Bornot Bernard Offmann Alexandre G. de Brevern |
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Affiliation: | 1. Laboratoire de Biochimie et Génétique Moléculaire, Université de La Réunion, BP 7151, 15 avenue René Cassin, 97715 Saint Denis Messag Cedex 09, La Réunion, France;2. INSERM UMR‐S 726, DSIMB, Equipe de Bioinformatique Génomique et Moléculaire (EBGM), Université Paris Diderot‐Paris 7, case 7113, 2, place Jussieu, 75251 PARIS Cedex 05, France;3. Manoj Tyagi and Aurélie Bornot contributed equally to this work.;4. INSERM UMR‐S 665, DSIMB, Université Paris Diderot‐Paris 7, Institut National de Transfusion Sanguine (INTS), 6, rue Alexandre Cabanel, 75739 Paris cedex 15, France;5. INSERM UMR‐S 665, DSIMB, Université de La Réunion, BP 7151, 15 avenue René Cassin, 97715 Saint Denis Messag Cedex 09, La Réunion, France;6. PEACCEL, 37, rue de Vienne, 97430 Le Tampon, France |
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Abstract: | Loops connect regular secondary structures. In many instances, they are known to play important biological roles. Analysis and prediction of loop conformations depend directly on the definition of repetitive structures. Nonetheless, the secondary structure assignment methods (SSAMs) often lead to divergent assignments. In this study, we analyzed, both structure and sequence point of views, how the divergence between different SSAMs affect boundary definitions of loops connecting regular secondary structures. The analysis of SSAMs underlines that no clear consensus between the different SSAMs can be easily found. Because these latter greatly influence the loop boundary definitions, important variations are indeed observed, that is, capping positions are shifted between different SSAMs. On the other hand, our results show that the sequence information in these capping regions are more stable than expected, and, classical and equivalent sequence patterns were found for most of the SSAMs. This is, to our knowledge, the most exhaustive survey in this field as (i) various databank have been used leading to similar results without implication of protein redundancy and (ii) the first time various SSAMs have been used. This work hence gives new insights into the difficult question of assignment of repetitive structures and addresses the issue of loop boundaries definition. Although SSAMs give very different local structure assignments capping sequence patterns remain efficiently stable. |
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Keywords: | protein structures biochemistry amino acids secondary structures propensities |
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