Conformational changes of trialanine in sodium halide solutions: An in silico study

Fedorov, Maxim V. and Goodman, Jonathan M. and Kolombet, Vladimir V. and Schumm, Stephan and Socorro, Ingrid M. (2009) Conformational changes of trialanine in sodium halide solutions: An in silico study. Journal of Molecular Liquids, 147 (1-2). pp. 117-123. ISSN 0167-7322

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Abstract

In this study we are trying to understand the effects of aqueous sodium halide solutions on conformational properties of trialanine. We performed long-scale MD simulations of a trialanine peptide in different sodium halide solutions with varying concentrations of the salt (0.20. 0.50, 1.0 and 2.0 M). By Clustering the conformational space of the tripeptide, we show that the molecular dynamics trajectories of this molecule form only a few major conformation clusters for each of the sixteen salt solutions under study. This gives its a way to compress the information contained in a terabyte of the simulation data to a small number of representative molecular geometries. These representative structures give insights into molecular mechanism of salt effects on peptide conformations. The results show that salts are able to make significant changes to the conformational landscape of trialanine. and that sodium chloride is particularly effective.