Abstract

During this fiscal year we devoted considerable efforts towards efficient highly parallel implementations of classical molecular dynamics. The highly efficient PMEMD molecular dynamics code developed and maintained by our group (in particular Robert Duke) was further developed to achieve parallel scaling out to hundreds of processors, allowing us to thoroughly simulate the large protein complexes involved in blood coagulation and related processes. We also explored and modified two recent accelerated sampling methodologies, allowing thorough exploration of conformational free energy surfaces. Importantly, these new methods open new possibilities beyond the reach of conventional molecular simulations.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Institute of Environmental Health Sciences (NIEHS)
Type
Investigator-Initiated Intramural Research Projects (ZIA)
Project #
1ZIAES043010-24
Application #
7967987
Study Section
Project Start
Project End
Budget Start
Budget End
Support Year
24
Fiscal Year
2009
Total Cost
$716,729
Indirect Cost

  Institution

Name
National Institute of Environmental Health Sciences
Department
Type
DUNS #
City
State
Country
Zip Code

  Publications

Zheng, Xunhai; Mueller, Geoffrey A; Kim, Kyungmin et al. (2017) Identification of drivers for the metamorphic transition of HIV-1 reverse transcriptase. Biochem J 474:3321-3338
Lee, Chang Jun; Wu, Sangwook; Eun, Changsun et al. (2010) A revisit to the one form kinetic model of prothrombinase. Biophys Chem 149:28-33
Elking, Dennis M; Perera, Lalith; Duke, Robert et al. (2010) Atomic forces for geometry-dependent point multipole and gaussian multipole models. J Comput Chem 31:2702-13
de Courcy, B; Pedersen, L G; Parisel, O et al. (2010) Understanding selectivity of hard and soft metal cations within biological systems using the subvalence concept. I. Application to blood coagulation: direct cation-protein electronic effects vs. indirect interactions through water networks. J Chem Theory Comput 6:1048-1063
Elking, Dennis M; Cisneros, G Andres; Piquemal, Jean-Philip et al. (2010) Gaussian Multipole Model (GMM). J Chem Theory Comput 6:190-202
Zurita, Adolfo; Zhang, Yinghao; Pedersen, Lee et al. (2010) Obligatory role in GTP hydrolysis for the amide carbonyl oxygen of the Mg(2+)-coordinating Thr of regulatory GTPases. Proc Natl Acad Sci U S A 107:9596-601
Lee, Chang Jun; Chandrasekaran, Vasu; Wu, Sangwook et al. (2010) Recent estimates of the structure of the factor VIIa (FVIIa)/tissue factor (TF) and factor Xa (FXa) ternary complex. Thromb Res 125 Suppl 1:S7-S10
Liu, Shubin; Hu, Hao; Pedersen, Lee G (2010) Steric, quantum, and electrostatic effects on S(N)2 reaction barriers in gas phase. J Phys Chem A 114:5913-8
Cisneros, G Andrés; Perera, Lalith; Schaaper, Roel M et al. (2009) Reaction mechanism of the epsilon subunit of E. coli DNA polymerase III: insights into active site metal coordination and catalytically significant residues. J Am Chem Soc 131:1550-6
Mutoh, Shingo; Osabe, Makoto; Inoue, Kaoru et al. (2009) Dephosphorylation of threonine 38 is required for nuclear translocation and activation of human xenobiotic receptor CAR (NR1I3). J Biol Chem 284:34785-92

Showing the most recent 10 out of 23 publications