Theory and simulation of macromolecular crowding effects on protein folding stability and kinetics

Details Theory and simulation of macromolecular crowding effects on protein folding stability and kinetics Theory and simulation of macromolecular crowding effects on protein folding stability and kinetics

2009-02-26

arxiv.org/abs/0902.4648v1

Physics

Condensed Matter

Soft Condensed Matter

Scientific paper

We investigate the effect of macromolecular crowding on protein folding, using purely repulsive crowding particles and a self-organizing polymer model of protein folding. We find that the thermodynamics of folding for typical alpha-, beta- and alpha/beta-proteins are well described by an adaptation of the scaled particle theory (SPT). In this approach, the native state, transition state, and the unfolded protein are treated as effective hard spheres with radii approximately independent of the size and concentration of the crowders. The same model predicts the effect of crowding on the folding barrier and therefore refolding rates with no adjustable parameters. A simple extension of the SPT model, assuming additivity, can also describe the behavior of mixtures of crowding particles.

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