Theoretical Studies of Protein Folding

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, Cellmer et al., PNAS 2011). 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, consisting of measurements of transition paths in single molecule FRET experiments (see annual report on single molecule experiments), we are carrying out stochastic kinetic to make closer connections to molecular dynamics simulations.