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Energetics of beta-turn formation in a mutant peptide YPGDV from influenza hemagglutinin: an MD simulation study

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Title Energetics of beta-turn formation in a mutant peptide YPGDV from influenza hemagglutinin: an MD simulation study
 
Creator SHUKLA, RT
SASIDHAR, YU
 
Subject MOLECULAR-DYNAMICS SIMULATIONS
PARTICLE MESH EWALD
STAPHYLOCOCCAL NUCLEASE
NEUTRALIZING ANTIBODY
VIRUS HEMAGGLUTININ
SECONDARY STRUCTURE
CRYSTAL-STRUCTURE
AQUEOUS-SOLUTION
LINEAR PEPTIDE
V3 LOOP
 
Description Reverse turns play an important role in protein folding, molecular recognition and in eliciting immune response. While sequence determinants of reverse turns are known, not much is known about their energetics. In this paper we have investigated the thermodynamics of a reverse turn sequence YPGDV, an experimentally well characterized turn sequence, using molecular dynamics simulations performed over a range of temperatures from 280-360 K using GROMACS 4.0.4 software and all atom OPLS-AA/L force field. The change in folding free energy (Delta A(folding)) for the beta-turn formation in YPGDV peptide shows a linear relationship with temperature. We find that the entropy change (Delta S-folding) for the beta-turn formation is close to zero and the internal energy change (Delta U-folding) is a modest -3.8 kJ mol(-1). These thermodynamic quantities are interpreted in terms of intra-molecular (intra-peptide) and inter-molecular (peptide-solvent) hydrogen bonding interactions. Implications for protein folding and peptide immunogenicity are discussed.
 
Publisher ROYAL SOC CHEMISTRY
 
Date 2014-10-15T08:17:03Z
2014-10-15T08:17:03Z
2013
 
Type Article
 
Identifier PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 15(42)18571-18583
1463-9076
1463-9084
http://dx.doi.org/10.1039/c3cp52166d
http://dspace.library.iitb.ac.in/jspui/handle/100/14661
 
Language en