Solvent Simulations of Biomolecules in Cellular Environments

Michael Feig, Seiichiro Tanizaki, and Maryann Sayadi  

Annual Reports in Computational Chemistry, Vol. 4 ISSN 1574-1400, DOI 10.1016/S1574-1400(08)00006-6 

Numerous simulations with implicit solvent have been reported over the last decades with increasing levels of realism [5]. Many of these simulations involve peptides and small proteins over time scales that could not be reached easily with explicit solvent representations [6-8]. There are many fewer cases where implicit solvent simulations were used to study larger biomolecules and biomolecular complexes [9,10]. Such simulations have remained rare for the following reasons  

As a consequence, the structural integrity of larger biomolecules may not be maintained as well with implicit solvent [14]. 

The mean-field effect of the environment can be included in biomolecular simulations simply by adding an expression for the solvation free energy of an instantaneous solute conformation to a given molecular mechanics force field [1]. Such an implicit solvent potential addresses the thermodynamic component of solute-solvent interactions. Kinetic and hydrodynamic properties may be reintroduced through the use of Langevin dynamics where coupling with a temperature bath is implemented through stochastic collisions and solvent friction [2,3,18]. 

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Implicit Solvent Simulations of Biomolecules in Cellular Environments... 

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