Further Development of Rotational Symmetry Boundary Conditions: Pentamer Computational Cell

Abstract

The rotational symmetry boundary condition (RSBC) is a method to accelerate simulation of rotationally symmetric protein assembly. The RSBC has been applied to calculation of icosahedral virus capsids to investigate virus infection. Because an icosahedral capsid is composed of 60 identical asymmetric units, the unit has been adopted for computational cell of RSBC and the simulations have been accelerated by at least 60 times. However, it is not possible to include motion of ions or asymmetric deformation of protein around the 5fold axis in the present RSBC program. Therefore, use of a pentamer composed of 5 asymmetric units for compuational cell is expected to allow analysis on asymmetric properties around the 5fold axis. We reports further development of program of RSBC and details of related mathematical basis for use of pentamer computational cells.