Model for the simultaneous evolution of protein sequences and conformations

摘要: Protein molecule folds because its sequence is quenched while its conformation dynamically evolves governed by the quenched sequence. Sequence design procedures known in the literature usually operate by computationally annealing the sequence on the background of properly quenched conformation. There are suggestions in the literature to invigorate both the sequence design and the computational folding algorithms by considering the simultaneous evolution of both sequence and conformation, assuming that these two sets of degrees of freedom interact with thermostats of two different temperatures. To examine this procedure, we study the model of random walks on the graph in which each vertex represents the state of a protein, including both sequence and conformation. The graph has bonds of two sorts, some represent change of conformation (physical motion), while others represent change of …