Protein conformational changes: What can geometric nonlinear analysis tell us?

Abstract

Protein functioning is usually associated to conformational changes. In the last decades, several researchers have made use of elastic network models to investigate such shape changes, showing that these depend on the protein intrinsic flexibility. Moreover, it has been indicated that low-frequency modes, arising from the application of modal analysis, are strictly related to the conformational transition. Several efforts have also been made in order to generate feasible pathways as well as to investigate the active forces applied at specific locations driving the conformational change. The problem has usually been addressed by means of linear theories, under the assumption of small displacements. In this contribution, we question whether such assumption is reliable from a mechanical viewpoint. In particular, we investigate the influence of geometric nonlinearities, by applying both linear and (geometric) nonlinear analysis to the protein elastic network model and comparing the outcomes in terms of force profiles. Eventually, from the results regarding the conformational change of HIV-1 protease subunit, we show that the displacements should not be considered small a priori.