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Chapter 3

Simulations of the Tomato Bushy Stunt Virus Capsid


The spherical protein capsid of the tomato bushy stunt virus expands by 10%when calcium ions are removed from the system and the pH is raised above 7[50]. We have attempted to simulate this effect using molecular dynamics. Although we calculate velocities for only the three proteins of the asymmetric unit plus associated ions, we include the nonbonded interactions of all 180 proteins (nearly 500,000 atoms) in the virus coat. The Cell-Multipole Method (CMM)[51] enables us to calculate the nonbond interactions in this gigantic system. Also, in order to increase the timelength of the simulation, we employ internal coordinate dynamics, using Newton-Euler Inverse Mass Operator (NEIMO) Dynamics[53], which enable us to use timesteps of 2 femtoseconds for proteins of this size.
Sat Jun 18 14:06:11 PDT 1994