Preferential interactions between small solutes and the protein backbone: a computational analysis.

Biochemistry
Liang MaQiang Cui

Abstract

To improve our understanding of the effects of small solutes on protein stability, we conducted atomistic simulations to quantitatively characterize the interactions between two broadly used small solutes, urea and glycine betaine (GB), and a triglycine peptide, which is a good model for a protein backbone. Multiple solute concentrations were analyzed, and each solute-peptide-water ternary system was studied with approximately 200-300 ns of molecular dynamics simulations with the CHARMM force field. The comparison between calculated preferential interaction coefficients (Gamma(23)) and experimentally measured values suggests that semiquantitative agreement with experiments can be obtained if care is exercised to balance interactions among the solute, protein, and water. On the other hand, qualitatively incorrect (i.e., wrong sign in Gamma(23)) results can be obtained if a solute model is constructed by directly taking parameters for chemically similar groups from an existing force field. Such sensitivity suggests that small solute thermodynamic data can be valuable in the development of accurate force field models of biomolecules. Further decomposition of Gamma(23) into group contributions leads to additional insights regarding...Continue Reading

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