Water molecules play a crucial role in mediating the interaction between a ligand and a macromolecular receptor. An understanding of the nature and role of each water molecule in the active site of a protein could greatly increase the efficiency of rational drug design approaches: if the propensity of a water molecule for displacement can be determined, then synthetic effort may be most profitably applied to the design of specific ligands with the displacement of this water molecule in mind. In this paper, a thermodynamic analysis of water molecules in the binding sites of six proteins, each complexed with a number of inhibitors, is presented. Two classes of water molecules were identified: those conserved and not displaced by any of the ligands, and those that are displaced by some ligands. The absolute binding free energies of 54 water molecules were calculated using the double decoupling method, with replica exchange thermodynamic integration in Monte Carlo simulations. It was found that conserved water molecules are on average more tightly bound than displaced water molecules. In addition, Bayesian statistics is used to calculate the probability that a particular water molecule may be displaced by an appropriately designed ligand, given the calculated binding free energy of the water molecule. This approach therefore allows the numerical assessment of whether or not a given water molecule should be targeted for displacement as part of a rational drug design strategy.

A recently defined charge set, to be used in conjunction with the all-atom CHARMM27r force field, has been validated for a series of phosphatidylcholine lipids. The work of Sonne et al. successfully replicated experimental bulk membrane behaviour for dipalmitoylphosphatidylcholine (DPPC) under the isothermal-isobaric (NPT) ensemble. Previous studies using the defined CHARMM27r charge set have resulted in lateral membrane contraction when used in the tensionless NPT ensemble, forcing the lipids to adopt a more ordered conformation than predicted experimentally. The current study has extended the newly defined charge set to 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC) and 1-palmitoyl-2-docosahexaenoyl-sn-glycero-3-phosphatidylcholine (PDPC). Molecular dynamics simulations were run for each of the lipids (including DPPC) using both the CHARMM27r charge set and the newly defined modified charge set. In all three cases a significant improvement was seen in both bulk membrane properties and individual atomistic effects. Membrane width, area per lipid and the depth of water penetration were all seen to converge to experimental values. Deuterium order parameters generated with the new charge set showed increased disorder across the width of the bilayer and reflected both results from experiment and similar simulations run with united atom models. These newly validated models can now find use in mixed biological simulations under the tensionless ensemble without concern for lateral contraction.

Guanine quadruplexes have received a lot of attention due to their possible role as therapeutic agents. Specifically, it is the ability of these quadruplex structures to inhibit telomerase, an enzyme found to be highly active in a large percentage of tumor cells and thought to confer immortality upon these cells. However, although a great deal of research has focused on enhancing the formation of these structures and their anticancer activity, many questions remain about the quadruplex structures themselves. The current study probes the nature of these quadruplex structures at the atomic level. Individual atomic energies have been computed for the quadruplex structure and compared to the atomic energies of the unfolded telomere to determine the energetic consequences of quadruplex formation. The results suggest several interesting trends, most notably that the guanine quartets exhibit an alternating pattern of stabilization and destabilization and these regions actually overlap in the intact quadruplex. In addition, the TTA loop segments are largely stabilized, whereas the atoms in the sugar-phosphate backbone exhibit mostly minor changes going from the unfolded to folded state. Inclusion of additional sodium cations in the central core of the quadruplex has a minimal effect on the atomic energies except for the atoms that are closest to the cations, which are largely stabilized in the presence of these ions.