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Rensselaer Polytechnic Institute Department of Biological Sciences
Biology Faculty
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Department of Biological Sciences
1W14 Jonsson-Rowland Science Center
Rensselaer Polytechnic Institute
110 Eighth Street
Troy, NY 12180-3590

Phone: (518) 276-6446
Fax: (518) 276-2344

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Biology Home Undergraduate Graduate Faculty Research News and Events Contacts
Angel E. García

Professor of Physics
Senior Constellation Chaired Professor in Biocomputation and Bioinformatics

Education and Training

B.S., University of Puerto Rico, Rio Piedras, Puerto Rico
Physics

M.S., University of Puerto Rico, Rio Piedras, Puerto Rico
Physics

Ph.D., Cornell University, Ithaca, NY
Theoretical Physics

Dr. García is the Senior Constellation Professor of Biocomputation and Bioinformatics at Rensselaer. Before joining Rensselaer he was Group Leader at the Theoretical Biology and Biophysics Group at Los Alamos National Laboratory. Dr García is a Fellow of the American Physical Society. He received the Edward Bouchet Award from the American Physical Society in 2006. Dr. García is the Associate Editor of Proteins, Structure, Function and Bioinformatics and belongs to the editorial board of Biophysical Journal and Molecular Simulations. He is a member of the American Physical Society, Biophysical Society, American Chemical Society, Protein Society and the American Association for the Advancement of Science.

Contact

E-mail: angel@rpi.edu
Tel: (518) 276-4206
Fax: (518) 276-6680

Office: Center for Biotechnology and Interdisciplinary Studies Rm. 3244C

Rensselaer Polytechnic Institute
110 8th Street
Troy, NY 12180

Research Interests

Protein folding, Pressure effects in Protein and RNA Folding, Protein-membrane interactions and antimicrobial peptides, Protein aggregation, Biomolecular dynamics and statistical mechanics.

Angel García is interested in theoretical and computational aspects related to biomolecular dynamics and statistical mechanics. His main research objectives are to understand the folding, dynamics and stability of biomolecules from physical principles. He has developed a method for extracting dynamical coordinates that best describe biomolecular fluctuations. These modes are non-linear in the sense that multiple basins of attraction are sampled during a molecular dynamics trajectory. Another aspect of his research has been to develop Potentials of Mean Force that describe biomolecular hydration and ionic interactions. Currently he is performing highly parallel replica-exchange (also known as parallel tempering) simulations of the folding and thermodynamics of proteins and peptides in explicit aqueous solutions His group is applying these simulation methods to study protein folding, binding and aggregation (amyloid formation). Other research interests include the hydrophobic effect, and enzyme catalysis, nucleic acid structure and dynamics, and peptide interactions with membranes.

Selected Publications

A. Chen  and A. E.  Garcia, “Mechanism of enhanced mechanical stability of a minimal RNA kissing complex elucidated by nonequilibrium molecular dynamics simulations” Proc. Natl. Acad. Sci. (USA) 109:  E1530-E1539  (2012)

J. Tian and A. E. Garcia, “Simulations of the confinement of ubiquitin in self-assembled reverse micelles”, J. Chem. Phys. 134: 225101  (2011).

D. R. Canchi and  A.E. Garcia, “Backbone and Side-Chain Contributions in Protein Denaturation by Urea”, Biophys. J., 100: 1526-1533 (2011)

D. R. Canchi, D. Pascheck, and  A.E. Garcia, “Equilibrium Study of Protein Denaturation by Urea”, J. Amer. Chem. Soc. 132: 2338-2344 (2010).

H. D. Herce, A.E. Garcia, J.Litt et al., “Arginine-Rich Peptides Destabilize the Plasma Membrane, Consistent with a Pore Formation Translocation Mechanism of Cell-Penetrating Peptides”, Biophys. J. 97: 1917-1925 (2009).

D. Paschek, H. Sascha and A.E. Garcia, “Computing the stability diagram of the Trp-cage miniprotein”,  Proc. Natl. Acad. Sci. (USA) 105: 17454-17759 (2008).

H. Herce and A.E. Garcia, “Molecular dynamics simulations suggest a translocation mechanism of the HIV-1TAT peptide across lipid membranes”, Proc. Natl. Acad. Sci. (USA). 104: 20805-20810 (2007)

Yang, J.N. Onuchic, A.E. Garcia, and H. Levine, “Folding Time Predictions from All-Atom Replica Exchange Simulations”, J. Mol. Biol. 372: 756-763 (2007)

N. G. Sgourakis, Y. Yan, S.A. McCAllum, C. Wang, and A.E. Garcia, “The Alzheimer’s peptides Ab40 and Ab42 adopt distinct conformations in water: A combined MD/NMR study.” J. Mol. Biol. 368: 1448-1457 (2007).

D. Paschek, S. Gnanakaran, and A.E. Garcia, “Simulations of the Pressure and Temperature Unfolding of an Alpha Helical Peptide.” Proc. Natl. Acad. Sci. (USA) 102: 6765-6770 (2005).

D. Paschek and A.E. Garcia, “Reversible temperature and pressure denaturation of a protein fragment: Replica exchange molecular dynamics simulation study.” Phys. Rev. Let. 93: 238105 (2004)

A.E. Garcia and J.N. Onuchic, Folding a protein in a computer; an atomic description of the folding/unfolding of protein A. ", Proc. Natl. Acad. Sci. 100:13898-13903 (2003).

H. Nymeyer and A. E. Garcia How Good is the GB/SA Approximation: A Side-by-Side Comparison with Explicit Solvent Simulations. ", Proc. Natl. Acad. Sci. 100:13934-13939 (2003).

M. S. Cheung and A.E. Garcia and J. N. Onuchic, “Protein folding mediated by solvation: water expelling and formation of the hydrophobic core occur after the structural collapse'', Proc. Natl. Acad. Sci. (USA) 99:685-690 (2002)

A. E. Garcia and K. Y. Sanbonmatsu "Alpha helical stabilization by side chain shielding of backbone hydrogen bonds", Proc. Natl. Acad. Sci. (USA) 99:2782-2787 (2002)

A.E. Garcia and K. S. Sanbonmatsu, ''Exploring the Energy Landscape of a beta hairpin in explicit solvent", Proteins, Str. Funct. & Genet. 42:345-354 (2001)

A.E. Garcia and G. Hummer. “Water Penetration and Escape in Proteins", Proteins, Structure, Function and Genetics, 38:261-272 (2000).

H. Nymeyer, A. E. Garcia and J. N. Onuchic, “Folding Funnels and Frustration in Off-Lattice Minimalist Protein Landscapes", Proc. Natl.  Acad. Sci. (USA), 95:5921-5928 (1998).

G. Hummer, S. Garde, A. E. Garcia, M. Paulaitis and L.R. Pratt, “The Pressure Dependence of Hydrophobic Interactions is Consistent with the Observed Pressure Denaturation of Proteins", Proc. Natl. Acad. Sci. 95:1552—1555 (1998).

S. Garde, G. Hummer, A.E. Garcia, M.E. Paulaitis and L. R. Pratt, “Origin of Entropy Convergence in Hydrophobic Hydration and Protein Folding." Phys. Rev. Lett. 77: 4966-4968 (1996).

G. Hummer, Garde, S., Garcia, A.E., Pohorille, A., and Pratt, L. R., “An information theory model of hydrophobic interactions." Proc. Natl. Acad. Sci.  93: 8951-8955 (1996).

A. E. Garcia.  “Large-Amplitude Non-Linear Motions in Proteins."  Phys.  Rev. Lett., 68:2696-2700 (1992)

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