Effects of urea, tetramethyl urea, and trimethylamine N-oxide on aqueous solution structure and solvation of protein backbones: a molecular dynamics simulation study

The Journal of Physical Chemistry. B
Haiyan WeiYi Qin Gao

Abstract

The effects of urea, tetramethyl urea (TMU), and trimethylamine N-oxide (TMAO) on the structure and dynamics of aqueous solutions are studied using molecular dynamics simulations. It was found that urea has little effects on the water-water hydrogen-bond length and angle distributions except that it induces a slight collapse of the second shell in the hydrogen-bonding network. TMU and TMAO both strengthen the individual hydrogen bonds and significantly slow the orientational relaxation of water, but have opposite effects on the second shell structure of the hydrogen-bonding network: TMU distorts while TMAO enhances the tetrahedral water structure. Furthermore, TMAO significantly weakens the interactions between the amide carbonyl group and the water molecules, while TMU and urea both strengthen these interactions, with the effect of urea being much less significant than that of TMU. These conclusions are supported by molecular dynamics simulations of three different systems: a model amide compound CH(3)-NH-CO-CH(3) (NMA), and two polypeptides, GB1 and ELP. Consistent with earlier studies, we also found that urea interacts strongly with the carbonyl group through direct hydrogen bonding. The simulations for the denaturation of t...Continue Reading

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