of Work: The objective of these studies is to apply state of the artmolecularsimulation methodology as an adjunct to experimentalstructure-functionstudies of the HIV-1 Reverse Transcriptase. In this year wecarried out a number of studies aimed at characterizingthe level of accuracy attainable with our simulation methodology.These studies revealed to us the critical importance of the DNAforce field used. Although the DNA simulations carried out inrecent years are of unprecedented accuracy, some shortcomings arestill apparent. We also began work to improve the form of theseforce fields. The hope is that next generation force fields willbe better able to reproducethe known sequence-dependent structural features which arethought to influence the processivity and fidelity of HIV-1 RTcatalyzed DNA replication. We began work on modeling the effect of active site residuesubstitutionsand local DNA sequence changes on processivity and fidelity.In particular we have begun study on the R72A mutation, whichexhibitsan anomolous anti-mutator phenotype in most sequence contexts buta profound mutator phenotype in a particular context

Agency
National Institute of Health (NIH)
Institute
National Institute of Environmental Health Sciences (NIEHS)
Type
Intramural Research (Z01)
Project #
1Z01ES090601-06
Application #
6432432
Study Section
(LSB)
Project Start
Project End
Budget Start
Budget End
Support Year
6
Fiscal Year
2000
Total Cost
Indirect Cost
Name
U.S. National Inst of Environ Hlth Scis
Department
Type
DUNS #
City
State
Country
United States
Zip Code
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
Jiao, Dian; Golubkov, Pavel A; Darden, Thomas A et al. (2008) Calculation of protein-ligand binding free energy by using a polarizable potential. Proc Natl Acad Sci U S A 105:6290-5
Cisneros, G Andres; Elking, Dennis; Piquemal, Jean-Philip et al. (2007) Numerical fitting of molecular properties to Hermite Gaussians. J Phys Chem A 111:12049-56
Gresh, Nohad; Cisneros, G Andres; Darden, Thomas A et al. (2007) Anisotropic, Polarizable Molecular Mechanics Studies of Inter- and Intramolecular Interactions and Ligand-Macromolecule Complexes. A Bottom-Up Strategy. J Chem Theory Comput 3:1960-1986
Elking, Dennis; Darden, Tom; Woods, Robert J (2007) Gaussian induced dipole polarization model. J Comput Chem 28:1261-74
Babin, Volodymyr; Baucom, Jason; Darden, Thomas A et al. (2006) Molecular dynamics simulations of DNA with polarizable force fields: convergence of an ideal B-DNA structure to the crystallographic structure. J Phys Chem B Condens Matter Mater Surf Interfaces Biophys 110:11571-81
Hamburgh, Monica E; Curr, Kenneth A; Monaghan, Melissa et al. (2006) Structural determinants of slippage-mediated mutations by human immunodeficiency virus type 1 reverse transcriptase. J Biol Chem 281:7421-8
Cisneros, G Andres; Piquemal, Jean-Philip; Darden, Thomas A (2006) Generalization of the Gaussian electrostatic model: extension to arbitrary angular momentum, distributed multipoles, and speedup with reciprocal space methods. J Chem Phys 125:184101
Fisher, Timothy S; Darden, Tom; Prasad, Vinayaka R (2003) Mutations proximal to the minor groove-binding track of human immunodeficiency virus type 1 reverse transcriptase differentially affect utilization of RNA versus DNA as template. J Virol 77:5837-45
Fisher, Timothy S; Darden, Tom; Prasad, Vinayaka R (2003) Substitutions at Phe61 in the beta3-beta4 hairpin of HIV-1 reverse transcriptase reveal a role for the Fingers subdomain in strand displacement DNA synthesis. J Mol Biol 325:443-59