On the contribution of normal modes of elastic network models in prediction of conformational changes

摘要

Conformational changes of proteins during binding to other biomolecules play a vital role in many biological processes in a living body. There have been a lot of efforts to predict the conformational changes using normal modes of various elastic network models. In all the studies, usually a single or a few lowest modes are considered. In this study, we consider the contribution of all normal modes on the unbound structure of protein to predict the bound form. The results show that low frequency normal modes are not sufficient for describing these motions and there are contributing normal modes even in the high frequency range. The results also indicate that high decaying and low cutoff radii network models show similar behavior in their prediction of the conformational changes.