2004b) ‘Conformational subspace in simulation of early-stage protein folding

ABSTRACT A probability calculus was used to simulate the early stages of protein folding in ab initio structure prediction. The probabilities of par-ticular and angles for each of 20 amino acids as they occur in crystal forms of proteins were used to calculate the amount of information necessary for the occurrence of given and angles to be pre-dicted. It was found that the amount of information needed to predict and angles with 5 ° precision is much higher than the amount of information actu-ally carriedby individual aminoacids in thepolypep-tide chain. To handle this problem, a limited confor-mational space for the preliminary search for optimal polypeptide structure is proposed based on a simplified geometrical model of the polypeptide chain and on the probability calculus. These two models, geometric andprobabilistic, based ondiffer-ent sources, yield a common conclusion concerning how a limited conformational space can represent an early stage of polypeptide chain-folding simula-tion. The ribonuclease molecule was used to test the limited conformational space as a tool for modeling early-stage folding. Proteins 2004;55:115–127