Distribution of cooperative interactions in barnase at different time windows by coarse-grained simulations

The backbone dynamics of barnase has been studied by a recently developed off lattice Monte Carlo (MC)/Metropolis simulation technique, where a low-resolution model (virtual-bond model) is used together with knowledge-based potentials, with the main emphasis on its cooperative motions at different time windows. The conformations generated around the native state are analysed by time-dependent auto- and cross-conformational correlation functions of the virtual bonds. There exists a correlation between the long time auto-correlated behaviour of the bond rotations and the potential stability of the respective regions. The analysis at different time windows reveals that there are cooperative motions between the bond rotations, which are only near neighbours and basically local motions at all time windows. However, as the time window widens, a progressive increase in the number of correlated pairs, which are separated far along the sequence and are not necessarily close in space, is observed. The structural distribution of these motions shows that the cooperative interactions are not bi-directional and that different residues have a different role within the network of interactions. Thus, the conditions yielding global motion coherence can be accounted for by the existence of anisotropic cooperative long-range interactions among the units in cooperation with the short-range interactions. (C) 2001 Elsevier Science Ltd. All rights reserved.