Theoretical Studies of Protein Folding and Function

National Institute Of Diabetes And Digestive And Kidney Diseases

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Abstract

A major challenge to advancing our understanding of how proteins fold is the development of an analytical theoretical model capable of calculating the quantities directly measured in both equilibrium and kinetic experiments. That is, we require a partition function to predict thermodynamic properties and a master equation to predict kinetic properties. To this end we have been developing an Ising-like model, with the major input being the contact map of the native structure. This model has been remarkably successful in quantitatively accounting for a wide range of data for the 35-residue subdomain from the villin headpiece, the smallest naturally occurring protein that autonomously folds into a globular structure (see Kubelka et al., PNAS 2008;Cellmer et al., PNAS 2008). These data include, heat capacity, tryptophan fluorescence quantum yield (QY), and natural circular dichroism spectrum (CD) as a function of temperature in both denaturants and viscogens, while the kinetic data consist of time courses of the QY from nanosecond laser temperature jump experiments as a function of temperature, denaturant concentration, and viscosity. Anticipating the next generation of folding experiments measurement of transition paths in single molecule FRET experiments - the rate matrix for the 100,000 microstates of the model is being analyzed using theoretical methods developed by Szabo and Hummer to predict the complete distribution of folding pathways and the relative contribution of each pathway to the folding flux.