REACH Coarse-Grained Biomolecular Simulation: Transferability between Different Protein Structural Classes

¹ Oak Ridge National Laboratory

^* To whom correspondence should be addressed. E-mail: smithjc{at}ornl.gov.

Submitted on February 18, 2008
Revised on March 29, 2008
Accepted on 18 April 2008

	Abstract

Coarse graining of protein interactions provides a means of simulating large biological systems. The REACH coarse-graining method, in which the force constants of a residue-scale elastic network model are calculated from the variance-covariance matrix obtained from atomistic molecular dynamics (MD) simulation, involves direct mapping between scales without the need for iterative optimization. Here, the transferability of the REACH force field is examined between protein molecules of different structural classes. As test cases, myoglobin (all ), plastocyanin (all ) and dihydrofolate reductase (/) are taken. The force constants derived are found to be closely similar in all three proteins. A MD version of REACH is presented, and low-temperature coarse-grained REACH MD simulations of the three proteins compared with atomistic MD results. The mean-square fluctuations of the atomistic MD are well reproduced by the coarse-grained MD. Model functions for the coarse-grained interactions, derived by averaging over the three proteins, are also shown to produce fluctuations in good agreement with the atomistic MD. The results indicate that, similarly to the usage of atomistic force fields, it is now possible to use a single, generic REACH force field for all protein studies, without having first to derive parameters from atomistic MD simulation for each individual system studied. The REACH method is thus likely to be a reliable way of determining spatiotemporal motion of a variety of proteins without the need for expensive computation of long atomistic MD simulations.

Key Words: (coarse-grained) Molecular Dynamics (MD) simulation, REACH, coarse-grained force constants, secondary structure, transferability