Biological macromolecules constantly sample different conformation states accessible at non-zero temperature and typical biochemical experiments measure ensemble-averaged quantitates. In order to deliver the same quantity, the numerical protocol should also model the relevant processes using ensemble of structures, not just the averaged or representative one. However, generating ensemble of structures representing particular reaction or process is not trivial because of the reaction time-scale and associated sampling errors. Here we ask the following questions: Can single frame structure be used to deliver ensemble-averaged polar solvation energy and can it be used to assess the strength of ensemble-averaged electrostatic pair-wise interactions? For this purpose we carry molecular dynamics (MD) simulations on a set of 91 proteins and calculate their ensemble-averaged electrostatic properties mentioned above. Further we use the corresponding X-ray structures, without being subjected to MD simulations and apply the recently reported smooth Gaussian-based dielectric function in DelPhi to calculate the same quantities. We demonstrate that computationally costly MD simulations can be avoided and the ensemble-averaged polar solvation energy and electrostatic pair wise interactions can be obtained with a single frame non-minimized structure.

Modeling ensemble-averaged electrostatics with smooth Gaussian-based dielectric function

248th National Meeting (2014)

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