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Zusammenfassung:
Solvent-damped, thermally activated motions of high molecular weight proteins and nucleic acid assemblies are key to understanding and controlling their functions and activities. The finite element method is a well-established approach to analyzing protein conformational fluctuations that are not accessible to all-atom representations. However, like conventional all-atom normal mode analysis, the finite element method has previously been used only to model protein dynamics in vacuum. Here, we extend the finite element based modeling approach to incorporate solvent damping for proteins and nucleic acid assemblies to compute non-equilibrium conformational properties. The proposed model is computationally effective for calculating translational and rotational diffusion coefficients in addition to dynamical motions in solvent, as demonstrated for Taq polymerase and several nanometer-scale DNA assemblies. A distinct advantage of the finite element-based approach is that computational cost does not increase with increasing molecular weight, rendering the procedure applicable to long time-scale structure-based simulations of high molecular weight assemblies including chaperones, molecular motors, and nucleic acid nanostructures.
