The structure and dynamics of proteins and nucleic acids is well-understood at a single molecule level and under dilute or crystallographic conditions. However, much uncertainty remains about the effect of cellular environments on biological macromolecules. Early work has emphasized the volume exclusion effect due to crowding in the cellular milieu that is generally expected to favor compact, native configurations but more recent experimental and computational studies suggest that destabilization of native structures is also possible due to attractive interactions with surrounding proteins and altered solvation effects. Results from atomistic computer simulations of a number of different systems are presented to examine the detailed contributions of cellular environments on biomolecular structure and dynamics. Protein destabilization is discussed for villin in dense protein G/villin mixtures, and recent results from large-scale cytoplasmic simulations are presented that provide the most comprehensive view to date of physical interactions between biological macromolecules in realistic cellular environments.

Connecting structural biology to cellular scales: Atomistic simulations of cytoplasmic environments

251st National Meeting (2016)

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