KINETIC MODELING OF PROTEIN FOLDING AND ASSOCIATION

Cornell University Ithaca, Ithaca NY

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Abstract

We are using the SP to fit kinetic state models to our experimental data. Such kinetic models allow individual folding events, such as the isomerization of prolines or the collapse of a hydrophobic core, to be investigated; such information is very hard to obtain otherwise. The fitting is normally accomplished using simulated annealing Monte Carlo methods. This paper fit experimental data exhaustively to all possible models of proline isomerization in ribonuclease A. This modelling identified regions of the protein which are essential in its conformational folding, and analyzed the state of the protein's internal hydrogen bonds. We are actively pursuing this approach of making localized changes in ribonuclease A, and studying their effects on its conformational folding. Four additional papers citing the Theory Center are being prepared at present. We are developing a molecular model of its conformational folding, to serve as a quantitative benchmark against which computer simulations will be compared.