MOLECULAR-DYNAMICS SIMULATION OF A RHINOVIRUS CAPSID UNDER ROTATIONALSYMMETRY BOUNDARY-CONDITIONS

The rotational symmetry boundary condition proposed by Cagin et al. [J . Comp. Chem., 12, 627 (1991)] is implemented in the molecular dynamic s simulation program, APRICOT, to make simulations of icosahedrally sy mmetrical capsids practical. The principle of the rotational symmetry boundary condition is strictly formulated with a new algorithm to trac k each atom by protomer and cell number. Further, the 60 cells and the 60 protomers of a capsid are treated as elements of the point group I . This treatment is necessary to determine the protomer numbers of ato ms and to define indicators of atom pairs named relative protomer numb ers. A method designated border residue flags is also introduced to fu rther accelerate neighbor atom pair list generation. The method as we have implemented it is so fast that it was possible, using inexpensive workstations, to perform a 60-ps molecular dynamics simulation on an entire structure of a rhinoviral capsid including a 71-Angstrom-thick shell of water molecules. This work is the first molecular dynamics si mulation of an entire capsid under rotational symmetry boundary condit ions. The structure of the capsid is well conserved during the simulat ion. Because conventional periodic boundary conditions are not applica ble to rotational symmetries, it has been difficult, until this study, to perform calculations on macromolecules in crystallographic or nonc rystallographic symmetries that are composed of rotational symmetries and linear translation. Therefore, our development is expected to prov ide a powerful tool for studies of macromolecules in such symmetries. The merits, limitations, and possibilities for further elaboration of this development are discussed. (C) 1996 by John Wiley & Sons, Inc.