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Complexes of the antibiotics novobiocin and clorobiocin with DNA gyrase are illustrative of the importance of bound water to binding thermodynamics. Mutants resistant to novobiocin as well as those with a decreased affinity for novobiocin over clorobiocin both involve a less favorable entropy of binding, which more than compensates for a more favorable(More)
The five-site transferable interaction potential (TIP5P) for water is most accurate at reproducing experimental data when used with a simple spherical cutoff for the long-ranged electrostatic interactions. When used with other methods for treating long-ranged interactions, the model is considerably less accurate. With small modifications, a new TIP5P-like(More)
A new molecular dynamics model in which the point charges on atomic sites are allowed to fluctuate in response to the environment is developed and applied to water. The idea for treating charges as variables is based on the concept of electronegativity equalization according to which: (a) the electronegativity of an atomic site is dependent on the atom's(More)
Tannins act as antioxidants, anticarcinogens, cardio-protectants, anti-inflammatory and anti-microbial agents and bind to salivary peptides by hydrophilic and hydrophobic mechanisms. Electrospray Ionization Mass Spectrometry (ESI-MS) has been used to assess both hydrophilic and hydrophobic components of noncovalent binding in protein complexes. In the(More)
Free energy calculations for the transfer of a water molecule from the pure liquid to an interior cavity site in a protein are presented. Two different protein cavities, in bovine pancreatic trypsin inhibitor (BPTI) and in the I76A mutant of barnase, represent very different environments for the water molecule: one which is polar, forming four water-protein(More)
To examine the wide variety of cavities available to water molecules inside proteins, a model of the protein cavities is developed with the local environment treated at atomic detail and the nonlocal environment treated approximately. The cavities are then changed to vary in size and in the number of hydrogen bonds available to a water molecule inside the(More)
We established the charge and structure of the oil/water interface by combining ζ-potential measurements, sum frequency scattering (SFS) and molecular dynamics simulations. The SFS experiments show that the orientation of water molecules can be followed on the oil droplet/water interface. The average water orientation on a neat oil droplet/water interface(More)
Molecular dynamics simulations are used to calculate the free energy of methane association in water, using the polarizable fluctuating charge model that treats the charges on atomic sites as dynamical variables. Compared with previous studies using nonpolarizable potentials, the inclusion of polarizability leads only to small differences in the methane(More)
Free energy calculations from molecular simulations using thermodynamic integration or free energy perturbation require long simulation times to achieve sufficient precision. If entropic and enthalpic components of the free energy are desired, then the computational requirements are larger still. Here we present how parallel tempering (PT) Monte Carlo and(More)
Theories of solvation free energies often involve electrostatic potentials at the position of a solute charge. Simulation calculations that apply cutoffs and periodic boundary conditions based on molecular centers result in center-dependent contributions to electrostatic energies due to a systematic sorting of charges in radial shells. This sorting of(More)