Characterization of the conformational space of a triple-stranded beta-sheet forming peptide with molecular dynamics simulations

Proteins
Patricia Soto, Giorgio Colombo

Abstract

Molecular dynamics (MD) simulations have been performed on a series of mutants of the 20 amino acid peptide Betanova in order to critically assess the ability of MD simulations to reproduce the folding and stability of small beta-sheet-forming peptides on currently accessible timescales. Simulations were performed in both water and in 40% methanol solution, using an explicit solvent model. The simulations suggest that all mutants adopt a wide range of conformations in solution, that the structures are highly flexible, and that stabilization of compact structures is due to a delicate balance of hydrophobic and polar side-chain interactions. Simulations longer than 100 ns, although not sufficient for a complete thermodynamic and kinetic description of the system, sample an ensemble of compact conformations characterized by the loss of ordered beta-sheet secondary structure. This suggests that no significant free energy barrier separates the different conformations available.

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Citations

Jan 19, 2007·The Journal of Chemical Physics·Philippe Derreumaux, Normand Mousseau
Sep 21, 2010·Biochimica Et Biophysica Acta·Konstantin KleninWolfgang Wenzel
Jun 30, 2007·Proteins·Julien MaupetitPhilippe Derreumaux
Jun 22, 2010·Biopolymers·Danny P Chagolla, John T Gerig

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