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Conformational dynamics of a short antigenic peptide in its free and antibody bound forms gives insight into the role of beta-turns in peptide immunogenicity

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Title Conformational dynamics of a short antigenic peptide in its free and antibody bound forms gives insight into the role of beta-turns in peptide immunogenicity
 
Creator SHUKLA, RT
SASIDHAR, YU
 
Subject PARTICLE MESH EWALD
MOLECULAR-DYNAMICS
STRUCTURAL BASIS
NEUTRALIZING ANTIBODY
CRYSTAL-STRUCTURE
LOCAL SEQUENCE
INDUCED FIT
V3 LOOP
SIMULATIONS
PROTEINS
antigen
antibody
beta-turn
peptide immunogenicity
molecular dynamics simulations
 
Description Earlier immunological experiments with a synthetic 36-residue peptide (75-110) from Influenza hemagglutinin have been shown to elicit anti-peptide antibodies (Ab) which could cross-react with the parent protein. In this article, we have studied the conformational features of a short antigenic (Ag) peptide ((98)YPYDVPDYASLRS(110)) from Influenza hemagglutinin in its free and antibody (Ab) bound forms with molecular dynamics simulations using GROMACS package and OPLS-AA/L all-atom force field at two different temperatures (293 K and 310 K). Multiple simulations for the free Ag peptide show sampling of ordered conformations and suggest different conformational preferences of the peptide at the two temperatures. The free Ag samples a conformation crucial for Ab binding (-turn formed by DYAS sequence) with greater preference at 310 K while, it samples a native-like conformation with relatively greater propensity at 293 K. The sequence DYAS samples -turn conformation with greater propensity at 310 K as part of the hemagglutinin protein also. The bound Ag too samples the -turn involving DYAS sequence and in addition it also samples a -turn formed by the sequence YPYD at its N-terminus, which seems to be induced upon binding to the Ab. Further, the bound Ag displays conformational flexibility at both 293 K and 310 K, particularly at terminal residues. The implications of these results for peptide immunogenicity and Ag-Ab recognition are discussed. Proteins 2015; 83:1352-1367. (c) 2015 Wiley Periodicals, Inc.
 
Publisher WILEY-BLACKWELL
 
Date 2016-01-14T10:47:16Z
2016-01-14T10:47:16Z
2015
 
Type Article
 
Identifier PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 83(7)1352-1367
0887-3585
1097-0134
http://dx.doi.org/10.1002/prot.24831
http://dspace.library.iitb.ac.in/jspui/handle/100/17396
 
Language en