Abstract:

This chapter presents an overview of computational techniques for reconstructing the folding mechanisms of proteins from their crystal structures. The chapter describes analytical and computational tools for determining and characterizing protein-folding kinetics from crystal structures. It also discusses new protein model and shows that the thermodynamics of Src SH3 from molecular dynamics simulations is consistent with that observed experimentally. The revolution in protein crystallography has resulted in the identification of a large number of protein structures. The chapter discusses several studies that are based on the Go model. In one such study, it identifies the most evasive protein-folding transition state ensemble for Src SH3 protein and finds that it is consistent with experimental observations. These studies suggest that protein-folding kinetics can be determined to a reasonably detailed level from the knowledge of crystal structure. The chapter also dissects the transition state ensemble by studying the wiring properties of protein graphs. The structural properties of protein graphs are related to protein topology and thus may explain the kinetics of the folding process. These studies unveil the expanding possibilities for studying protein-folding kinetics from their crystal structures.

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