Mixed-solvent molecular dynamics (MixMD) is a hotspot mapping technique that relies on molecular dynamics simulations of binary solvent mixtures. Previous work in the group on MixMD has established the technique's effectiveness in capturing binding sites of small organic compounds.1,2 The MixMD approach embraces full protein flexibility while allowing competition between probes and water. Sites preferentially mapped by probe molecules are more likely to be hotspots. First, we established a rigorous protocol for the identification of hotspots on the binding surface. There are two important requirements; 1) the high ranking hotspots must be mapped at very high signal to noise ratio and 2) the hotspots must be mapped by multiple probes. We have focused our probe molecule repertoire to include acetonitrile, isopropanol, and pyrimidine as these probes allowed us to capture a range of interaction types that include hydrophilic, hydrophobic, hydrogen bonding and aromatic interactions. Second, we used MixMD to identify both competitive and allosteric sites on proteins. The speed of GPU processors were necessary to use many probe types and many protein targets to demonstrate the robust nature and wide applicability of the technique. The proteins test cases were composed of Abl Kinase, Androgen Receptor, Chk1 Kinase, Glucokinase, Pdk1 Kinase, Protein-Tyrosine Phosphatase 1B, and Farnesyl Pyrophosphate Synthase. The success of the technique is demonstrated by the fact that the top four sites solely map the competitive and allosteric sites. While the lower ranked sites consistently map the multimerization interfaces, biologically relevant sites, and crystal packing interfaces. The influence of different starting structures and the limits of conformational sampling are discussed.References :(1)          Lexa, K. W.; Carlson, H. A. J. Am. Chem. Soc. 2011 , 133, 200�202.(2)          Lexa, K. W.; Carlson, H. A. J. Chem. Inf. Model. 2013 , 53, 391�402.

Moving beyond active-site detection: An application of MixMD to allosteric proteins

247th National Meeting (2014)

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