Probabilistic structural dynamics of protein folding

We consider stochastic modeling of protein folding. The protein folding pro blem requires understanding the characteristics of the folded shape and of the folding process. Recent advances in experimental study of protein foldi ng lead to measurements of mean-square displacements Of atoms in proteins, via X-ray diffraction and elastic incoherent neutron scattering. We propose to use techniques from probabilistic structural dynamics in the understand ing of statistical characteristics such as mean-square displacements for pr otein folding. Stationary mean-square displacements of atoms in a protein i s expressed in terms of potential energy. Non-stationary mean-square displa cements can be obtained by numerically solving stochastic differential equa tions for the motion of atoms or the associated Fokker-Planck equations. (C ) 2000 Elsevier Science Inc. All rights reserved.