Pozvánka na seminář ÚFCH

Abstrakt (anglicky):

We combine ab initio and classical molecular dynamics simulations with analytic modeling to provide a molecular description of how a solute perturbs the structure and dynamics of water and, conversely, of the role of water in biological function, more specifically in the chemical step of enzyme catalysis.

In the first part we investigate why some salts accelerate water dynamics. While most salts retard the dynamics of water and increase the viscosity of the solution, some salts have an opposite effect. A complete molecular picture of acceleration is still missing and using simulations to resolve it is not straightforward. None of the non-polarizable force-fields can reproduce the increase in translational diffusion in some electrolyte solutions, including e.g. CsI. In contrast, recent simulations have shown that both ab initio molecular dynamics and classical description with an electronic continuum correction treatment of polarization yield a qualitatively correct behavior. Using both approaches we provide a molecular description of the factors causing this acceleration.

In the second part we examine the role of water in the chemical step of enzyme catalysis. Interestingly, enzymes can exhibit catalytic activity not only in their natural aqueous environment, but also in organic solvents. This is advantageous for their use in technological applications. However, in such an environment the reaction rates are substantially slower. Several reasons have been suggested including, e.g., the loss of enzyme conformational flexibility in absence of water or decrease of the polarity in the active site. We examined different hypotheses. Instead of the traditional explanations we observe the presence of a nonproductive substrate conformation, which is stabilized in the dehydrated environment and explains the measured decrease in activity.