Solvent-protein interactions motions

The simulation results presented in this section illustrate two essential features of the solvent and of solvent-protein interactions which influence protein dynamics. One is concerned with the spatial coupling (i.e., the degree of coupling between solvent and protein, which is related to solvent accessibility or some other measure of direct relatively short-range solvent-protein interactions), and the second is concerned with the time-scale coupling (i.e., the degree to which the motions of the solvent are commensurate with the temporal... 

R. A. Marcus Even though solvents and solvent-solute interactions or interactions with a protein can be very complicated and the resulting motion can be highly anharmonic, under a particular condition there can be a great simplification because of the many coordinates (perhaps analogous to the central-limit theorem in probability theory). 

The first term represents the forces due to the electrostatic field, the second describes forces that occur at the boundary between solute and solvent regime due to the change of dielectric constant, and the third term describes ionic forces due to the tendency of the ions in solution to move into regions of lower dielectric. Applications of the so-called PBSD method on small model systems and for the interaction of a stretch of DNA with a protein model have been discussed recently ([Elcock et al. 1997]). This simulation technique guarantees equilibrated solvent at each state of the simulation and may therefore avoid some of the problems mentioned in the previous section. Due to the smaller number of particles, the method may also speed up simulations potentially. Still, to be able to simulate long time scale protein motion, the method might ideally be combined with non-equilibrium techniques to enforce conformational transitions. 

In the high temperature limit where all the nuclear motions coupled to the process can be described classically, the nuclear factor is expressed in terms of only two parameters the driving force of the reaction AG°, and the whole reorganization energy X (expressions (13) and (14)). Detailed calculations carried out in the case of cytochrome c have demonstrated that AG° is a complex quantity, which depends not only on the electronic properties of the redox centers but also on those of the protein and of the surrounding solvent [100]. Usually, AG can be evaluated from measurements of redox potentials and of eventual interaction energies between the different parts of the systems (Appendix). 

The motions of proteins are usually simulated in aqueous solvent. The water molecules can be represented either explicitly or implicitly. To include water molecules explicitly implies more time-consuming calculations, because the interactions of each protein atom with the water atoms and the water molecules with each other are computed at each integration time step. The most expensive part of the energy and force calculations is the nonbonded interactions because these scale as 77 where N is the number of atoms in the system. Therefore, it is common to neglect nonbonded interactions between atoms separated by more than a defined cut-off ( 10 A). This cut-off is questionable for electrostatic interactions because of their 1/r dependence. Therefore, in molecular dynamics simulations, a Particle Mesh Ewald method is usually used to approximate the long-range electrostatic interactions (71, 72). 

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