个人简介

B.Sc., Universidad Nacional Aut髇oma de M閤ico (Mexico City) 1999 Ph.D., Duke University (Durham, NC) 2004 Postdoctoral Fellow, National Institute of Environmental Health Sciences, 2004-2009

研究领域

Physical (Theoretical/Computational)

The use of computers to study a wide range of chemical and biological phenomena has increased with increasing computational power. Simulation of biological systems using classical and combined quantum/classical methods has provided insights into a variety of biological processes. Classical simulations rely on the use of parametric functions called force fields for the calculation of molecular properties. Our lab is interested in developing and applying new methods for simulations of chemical and biochemical systems. We are developing the Gaussian Electrostatic Model (GEM) force field. GEM is based on the reproduction of molecular densities using Gaussian functions. The use of Gaussians for the representation of the charge density results in a very accurate description of the molecular fragment. These densities are employed to calculate each term of the quantum mechanical intermolecular interaction, i.e., Coulomb, exchange-repulsion, polarization and charge transfer. GEM has been shown to have errors below thermal noise at room temperature for each of these terms. DNA replication and repair are extremely important processes in living organisms. These transactions play a crucial role in the cell cycle. Errors in DNA replication can produce mutations that can lead to disease or even death. We are interested in molecular mechanisms involved in DNA replication fidelity and repair. Examples of areas of research in this field include: Investigating the relation between metals and DNA polymerase fidelity. We are also collaborating with Profs. D. Rueda and L. Romano to investigate a putative novel fidelity checking mechanism in Klenow fragment. Additionally we are using computational methods to study the AlkB family of enzymes, in charge of DNA de-alkylation.

近期论文

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Cisneros G.A., Babin V., Sagui C., "Electrostatics Interactions in Classical Simulations", in "Biomolecular Simulations: Methods and Protocols" for the Book Series: Methods in Molecular Biology, L. Monticelli and E. Salonen, Eds., Springer Science+Business Media New York, Vol. 924, pp. 243-270, DOI:10.1007/978-1-62703-017-5, 2013. Cisneros G.A., "Application of Gaussian Electrostatic Model (GEM) distributed multipoles in the AMOEBA force field", J. Chem. Theo. Comp., 12, 5072-5080 2012. Moore J.D., Lord R.L. Cisneros G.A., Allen M.J., "Concentration-independent pH detection with a luminescent dimetallic Eu(III)-based probe", J. Am. Chem. Soc., 134, 17372-17375, 2012. Swett R., Cisneros G.A., Feig A., "Conformational Analysis of Clostridium difficile Toxin B and its Implications for Substrate Recognition", PLoS ONE, 7 (7) , e41518, 2012. Graham S.E., Syeda FS. Cisneros G.A., "Computational prediction of residues involved in fidelity checking for DNA synthesis in DNA polymerase I", Biochemistry, 51, 2569-2578, 2012. Zhao L., Dewage S.W., Bell M.J., Chang K.-M., Fatma S., Joshi N.V., Silva G.N., Cisneros G.A., Hendrickson T.L., "The kinase activity of the Helicobacter pylori Asp-tRNAAsn/Glu-tRNAGln amidotransferase is sensitive to distal mutations in its putative ammonia chanel", Biochemistry, 51, 273, 285, 2012. Chaudret R., Piquemal J.P., Cisneros G.A., "Correlation between electron localization and metal ion mutagenicity in DNA synthesis from QM/MM calculations", Phys. Chem. Chem. Phys, 13, 11239-11247, 2011. Chaudret R., Cisneros G.A., Parisel O. Piquemal J.P., "Unraveling Low Barrier Hydrogen Bonds in complex systems using a simple quantum topological criterion", Chem. Eur. J., 17, 2833-2837, 2011.