Model, water molecule

FATO molecular mechanics of oxygen atom. Model water molecule.4... 

Donor-acceptor interactions of the model water molecule... 

The inclusion of modelled water molecules in more recent, higher resolution structures for the Rb sphaeroides and Rps. viridis reaction centres has revealed ehains of connected water molecules and polar residues linking the Qg binding poeket with the cytoplasmic surface of the protein (Lancaster and Michel, 1999 Abresch et al, 1998 Fritzsch et al., 1998 Lancaster and Michel, 1997 Stowell et al., 1997 Lancaster and Michel, 1996 Deisenhofer et al, 1995 Ermler et al., 1994a,b). It has been proposed that these chains deliver protons to acidic amino acids that have been implicated in protonation of the reduced Qg UQjq (Abresch et al., 1998 Lancaster and Michel, 1997 Stowell et al., 1997 Lancaster and Miehel, 1996 Ermler et al., 1994a Beroza et al., 1992 Okamura and Feher, 1992). 

Figure 9. Boundary potential (kcal/mol) versus ro (A) for the oxygen atom of an ST2 model water molecule. The calculation is for an 11-A reaction zone and only the van der Waals forces are included (see Eq. 12).

Verdonk, M.L., Chessari, G Cole, JC., Hartshorn, M.J., Murray, C.W, Nissink, J.W.M., Taylor, R.D., and Taylor, R. (2005) Modeling water molecules in protein-ligand docking using GOLD. 

The molecular dynamics approach allows for the simulation of the system components individually with atomic resolution. Broadly speaking, an appropriately constrained Newtonian dynamics is used to capture the evolution of particles representing individual ions, atoms, or groups of atoms in the force field generated by electrostatic and van der Waals interactions together with boundary conditions. One difference between molecular dynamics and Brownian dynamics is the way the solvent is modeled Water molecules are typically treated explicitly within the molecular dynamics framework. 

Let us assume we perform a standard 20 ns MD simulation of a protein having a reasonable initial structure. We will add a box of model water molecules at least 6 (or 9) Angstrom thick at each protein border region. 

A number of early studies correlated the surface area of a molecule with solubility and with the free eneigy of transfer from either the pure hydrocarbon or a hydrocarbon solution to water. Here the surface area is defined by the locus of points traced out by the center of a (solvent) sphere, rolling over the surface of the molecule. This is the accessible surface (see Figure 3 of Molecular Surface and Volume). The accessible surface is a natural generalization of the collision diameter idea as it relates to spherical molecules. The packing of spherical molecular models around CPK models was first tried, and while the number of model water molecules packed around hydrocarbon molecules correlated with solubility, a natural step was to consider a continuous surface through the centers of the waters, which is the accessible surface. For the sake of simplicity, waters are taken to be spherical otherwise, the accessible surface would be unnecessarily complicated. This was more reproducible and could be more easily computerized than the packing of molecules. 

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