During this fiscal year we devoted major effort to work aimed at introducing polarizability into molecular force fields. Much of the work involved examining multipole expansions as a way to build accuracy into force field calculations. In one of the published studies it was shown that both static and geometry-dependent multipole models are able to reproduce total molecular forces and torques with repect to ab initio, whereas geometry-dependent multipoles are necessary to reproduce ab initio atomic forces. In another published work, a finite field method for calculating spherical tensor molecular polarizability tensors by numerical derivatives of induced molecular multipole with respect to gradients of the electrostatic potential are developed for arbitrary l and l'. These developments should be useful for the development of newer force fields that can be used to more accurately describe bio-macromolecules. Finally, we have developed code for partitioning the electron density into atomic contributions within the Hirshfeld-Iterated scheme. The codes developed in these studies are freely available. In addition, most of the applications required by NIEHS scientists to perform molecular modeling and dynamics were carried out with some of the programs that we had contributed to create (for example: Amber). These applications involve (but not limited to) mutational studies of TTP, a protein involved in RNA degradation;Aprataxin, HIV reverse transcriptase, construction of human constitutively active receptor (hCAR), Pinobarbital binding to EGF receptor, modeling of DNA with the inclusion of some ribonucleotides in the sequence.

Project Start
Project End
Budget Start
Budget End
Support Year
27
Fiscal Year
2012
Total Cost
$336,096
Indirect Cost
City
State
Country
Zip Code
Mueller, G A; Randall, T A; Glesner, J et al. (2016) Serological, genomic and structural analyses of the major mite allergen Der p 23. Clin Exp Allergy 46:365-76
Schellenberg, Matthew J; Perera, Lalith; Strom, Christina N et al. (2016) Reversal of DNA damage induced Topoisomerase 2 DNA-protein crosslinks by Tdp2. Nucleic Acids Res 44:3829-44
Takaku, Motoki; Grimm, Sara A; Shimbo, Takashi et al. (2016) GATA3-dependent cellular reprogramming requires activation-domain dependent recruitment of a chromatin remodeler. Genome Biol 17:36
Perera, Lalith; Freudenthal, Bret D; Beard, William A et al. (2015) Requirement for transient metal ions revealed through computational analysis for DNA polymerase going in reverse. Proc Natl Acad Sci U S A 112:E5228-36
Freudenthal, Bret D; Beard, William A; Perera, Lalith et al. (2015) Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide. Nature 517:635-9
Wells, Melissa L; Hicks, Stephanie N; Perera, Lalith et al. (2015) Functional equivalence of an evolutionarily conserved RNA binding module. J Biol Chem :
Zheng, Xunhai; Perera, Lalith; Mueller, Geoffrey A et al. (2015) Asymmetric conformational maturation of HIV-1 reverse transcriptase. Elife 4:
Liu, Chunhui; Sheng, Juzheng; Krahn, Juno M et al. (2014) Molecular mechanism of substrate specificity for heparan sulfate 2-O-sulfotransferase. J Biol Chem 289:13407-18
Zhang, Jun; Tan, Dazhi; DeRose, Eugene F et al. (2014) Molecular mechanisms for the regulation of histone mRNA stem-loop-binding protein by phosphorylation. Proc Natl Acad Sci U S A 111:E2937-46
Choi, Youn-Jeong; Lai, Wi S; Fedic, Robert et al. (2014) The Drosophila Tis11 protein and its effects on mRNA expression in flies. J Biol Chem 289:35042-60

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