assignment of polyproline ii conformation and analysis of sequence – structure relationship转让polyproline ii构象和序列-结构关系的分析.pdf

Assignment of PolyProline II Conformation and Analysis of Sequence – Structure Relationship Yohann Mansiaux1,2,3., Agnel Praveen Joseph1,2,3., Jean-Christophe Gelly1,2,3, Alexandre G. de Brevern1,2,3* ´ ´ 1 INSERM, UMR-S 665, Dynamique des Structures et Interactions des Macromolecules Biologiques (DSIMB), Paris, France, 2 Universite Paris Diderot - Paris 7, Paris, France, 3 Institut National de la Transfusion Sanguine (INTS), Paris, France Abstract Background: Secondary structures are elements of great importance in structural biology, biochemistry and bioinformatics. They are broadly composed of two repetitive structures namely a-helices and b-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 Findings: A 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 assignm