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The STUDIA UNIVERSITATIS BABEŞ-BOLYAI issue article summary
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Abstract: The cytoplasmic proteins of some halophilic organisms – those with high cytoplasmic KCl concentration – have an unusually large number of acidic amino acids at their surface. This feature is thought to enable the proteins to function under those conditions, but how is yet unclear. One possible explanation is that acidic amino acids are necessary to maintain the hydration levels of the protein surface in the presence of high concentrations of K+ and Cl- ions. We investigate this hypothesis using molecular dynamics simulations and models we optimized to capture the balance of interactions between acidic amino acids, water and K+. We simulate multiple halophilic proteins at both high (2 mol/kg) and low (0.15 mol/kg) KCl molality. For comparison, we simulate also proteins from mesophilic organisms and without unusually high fraction of acidic amino acids. We quantify the composition of the solvent as a function of the distance to the protein surface, and the dynamics of the first solvation layer via the mean square displacement of its components. Results for an initial subset of proteins suggest that the first solvation layer has the same water concentration as the bulk solution under all conditions tested, and that K+ ions form preferentially solvent-shared ion pairs with the carboxylate groups in the acidic side chains. Water and ion dynamics are similar between halophiles and non-halophiles, and between high and low KCl concentrations, with diffusion coefficients differing by less than a factor of 3. Our preliminary results thus suggest that halophiles and mesophiles are similarly solvated, i.e., large numbers of acidic amino acids appear not to be necessary to maintain protein hydration at high KCl concentration. Simulations for a larger set of proteins are on-going. Conclusions based on the full set of proteins will be discussed at this meeting.
Keywords: acidic amino acids, composition of hydration layer, free energy perturbation, halophilic proteins, molecular dynamics simulations. |
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