6 research outputs found
Low-energy unphysical saddle in polynomial molecular potentials
Vibrational spectra of polyatomic molecules are often obtained from a
polynomial expansion of the adiabatic potential around a minimum. For several
molecules, we show that such an approximation displays an unphysical saddle
point of comparatively small energy, leading to a region where the potential is
negative and unbounded. This poses an upper limit for a reliable evaluation of
vibrational levels. We argue that the presence of such saddle points is
general.Comment: The preprint version of the published Mol. Phys. paper, 19 pages, 3
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Dowser++, a new method of hydrating protein structures
A new method of hydrating protein structures, which we call Dowser++, is presented. The method is based on a semi-empirical modification of a popular program for protein hydration Dowser, and the usage of protocols AutoDock Vina, and WaterDock. The positions of water molecules predicted by Dowser++ were compared with experimental data for a set of 14 high-resolution crystal structures of oligopeptide-binding protein (OppA) containing a large number of resolved internal water molecules, as well as for the D- and K-channels of cytochrome c oxidase, and the recent data on PSII. Comparison is also made with the predictions of the original Dowser, and its improved version, Dowser+, described in our previous publication. We also present a model for quantitative estimation of the quality of water molecules placement made by a program, which includes an assumption of possible false negative data from the crystallographic analysis. The comparison of predictions made by Dowser++, Dowser and Dowser+ demonstrates significant improvement of predictive power of the new method. Proteins 2016; 84:1347-1357. © 2016 Wiley Periodicals, Inc
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Dipole Moment and Binding Energy of Water in Proteins from Crystallographic Analysis
The energetics of water molecules in proteins is studied using the water placement software Dowser. We compared the water position predictions for 14 high-resolution crystal structures of oligopeptide-binding protein (OppA) containing a large number of resolved internal water molecules. From the analysis of the outputs of Dowser with variable parameters and comparison with experimental X-ray data, we derived an estimate of the average dipole moment of water molecules located in the internal cavities of the protein and their binding energies. The water parameters thus obtained from the experimental data are then analyzed within the framework of charge-scaling theory developed recently by this group; the parameters are shown to be in good agreement with the predictions that the theory makes for the dipole moment in a protein environment. The water dipole in the protein environment is found to be much different from that in the bulk and in such models as SPC or TIPnP. The role of charge scaling due to electronic polarizability of the protein is discussed