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A chirality index for investigating protein secondary structures and their time evolution
Author(s) -
Pietropaolo Adriana,
Muccioli Luca,
Berardi Roberto,
Zani Claudio
Publication year - 2008
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.21578
Subject(s) - protein secondary structure , chirality (physics) , protein structure , molecular dynamics , sequence (biology) , chemistry , biological system , crystallography , physics , computational chemistry , biology , biochemistry , quantum mechanics , nambu–jona lasinio model , quark , chiral symmetry breaking
We propose a methodology for the description of the secondary structure of proteins, based on assigning a chirality parameter to short aminoacid sequences according to their arrangement in space at a certain time. We validated the method on ideal and crystalline structures, showing that it can assign secondary structures and that this assignment is robust with respect to random conformational perturbations. From the values of the index and its pattern along a sequence it is possible to recognize many structural motifs of a protein, and in particular poly‐ L ‐proline II left‐handed helices, often not detected by secondary structure assignment algorithms. Assigning an instantaneous chirality index to the fragments also allows the dynamics to be studied. With this purpose, molecular dynamics simulations were carried out in water for selected hemoglobin (110 ns) and immunoglobulin antigen fragments (50 ns), showing the capability of the chiral index in identifying the stable secondary structure elements, as well as in following their time evolution and conformational changes during the trajectory. Proteins 2008. © 2007 Wiley‐Liss, Inc.