Environmental polarity induces conformational transitions in a helical peptide sequence from bacteriophage T4 lysozyme and its tandem duplicate: a molecular dynamics simulation study

Journal of Molecular Modeling
Harpreet Kaur, Yellamraju U Sasidhar

Abstract

Our recent molecular dynamics (MD) simulation of an insertion/duplication mutant 'L20' of bacteriophage T4 lysozyme demonstrated a solvent induced α→β transition in a loosely held duplicate helical region, while α-helical conformation in the parent region was relatively stabilized by its tertiary interactions with the neighboring residues. The solution NMR of the parent helical sequence, sans its protein context, showed no inherent tendency to adopt a particular secondary structure in pure water but showed α-helical propensity in TFE/water and SDS micelles. In this study we investigate the conformational preference of the 'parent' and 'duplicate' sequences, sans the protein context, in pure water and an apolar TFE/water solution. Apolar TFE/water solution is a model for non-polar protein context. We performed MD simulations of the two peptides, in explicit water and 80% (v/v) TFE/water, using GROMOS 53a6 force field, at 300 K and 1 bar (under NPT conditions). We show that in TFE/water mixture, salt bridges are stabilized by apolar TFE molecules and main chain-main chain hydrogen bonds promote the α-helical conformation, particularly in the duplicate peptide. Solvent exposure, in pure water, resulted in an α→β transition to form...Continue Reading

References

Jan 1, 1990·Proteins·E G Hutchinson, J M Thornton
Jul 20, 1973·Science·C B Anfinsen
Apr 20, 1973·Biochimica Et Biophysica Acta·P N LewisH A Scheraga
Oct 14, 1972·Journal of Molecular Biology·P M ColmanB W Matthews
Aug 25, 1983·Journal of Molecular Biology·D J Barlow, J M Thornton
Feb 1, 1996·Journal of Molecular Graphics·W HumphreyK Schulten
Oct 1, 1996·International Journal of Peptide and Protein Research·R Rajan, P Balaram
May 26, 1999·Proceedings of the National Academy of Sciences of the United States of America·M SagermannB W Matthews
Aug 28, 2002·Proceedings of the National Academy of Sciences of the United States of America·Danilo RoccatanoAlan E Mark
Jul 21, 2004·Journal of Computational Chemistry·Chris OostenbrinkWilfred F van Gunsteren
Jan 3, 2006·Journal of Molecular Graphics & Modelling·Sunita PatelYellamraju U Sasidhar
Feb 14, 2006·The Journal of Physical Chemistry. B·Alessandra VillaMario Salmona
Jun 13, 2006·Biophysical Journal·Guanghong Wei, Joan-Emma Shea
Sep 6, 2007·Journal of Peptide Science : an Official Publication of the European Peptide Society·Sunita Patel, Yellamraju U Sasidhar
Aug 12, 2008·Current Protein & Peptide Science·Danilo Roccatano
Mar 23, 2010·The Journal of Physical Chemistry. B·Takako Takeda, Dmitri K Klimov
Sep 21, 2010·Protein Science : a Publication of the Protein Society·Jane R AllisonWilfred F van Gunsteren
Sep 27, 2013·Biochemistry·Ricky B NellasTongye Shen
Mar 1, 2008·Journal of Chemical Theory and Computation·Berk HessErik Lindahl

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