Randomness of the process of protein folding

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Abstract
How specific or definite are pathways of folding and unfolding in globular proteins? In order to study this question, computer simulation of the folding-unfolding transition was carried out in a 2-dimensional lattice model of proteins in which it is assumed that strongly specific intramolecular interactions contribute to the stability of the native conformation. This specificity of the interactions should tend to make the pathways of folding and unfolding more definite than reality. Yet, the analysis of the record of simulation indicates the process of transition to be stochastic rather than definite. This poses a fundamental problem of how to describe the pathways of folding and unfolding transition. It is argued that the description should consist of a definition of intermediate states in terms of characteristic conformational features and stochastic rules of transitions between these intermediate states. The simplest would be the case in which the transitions occur as a markoffian process.