Angel E. Garcia - Publications

Affiliations: 
Physics Rensselaer Polytechnic Institute, Troy, NY, United States 

89 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 Rosenman DJ, Clemente N, Ali M, García AE, Wang C. High pressure NMR reveals conformational perturbations by disease-causing mutations in amyloid β-peptide. Chemical Communications (Cambridge, England). PMID 29670961 DOI: 10.1039/c8cc01674g  0.32
2017 Zwarycz AS, Fossat MJ, Akanyeti O, Lin Z, Rosenman DJ, Garcia AE, Royer CA, Mills KV, Wang C. V67L Mutation Fills Internal Cavity to Stabilize RecA Mtu Intein. Biochemistry. PMID 28488863 DOI: 10.1021/acs.biochem.6b01264  0.32
2017 Kitazawa S, Fossat MJ, McCallum SA, Garcia AE, Royer CA. NMR and Computation Reveal a Pressure-Sensitive Folded Conformation of Trp-Cage. The Journal of Physical Chemistry. B. PMID 28107009 DOI: 10.1021/acs.jpcb.6b11810  0.32
2016 Fossat MJ, Dao TP, Jenkins K, Dellarole M, Yang Y, McCallum SA, Garcia AE, Barrick D, Roumestand C, Royer CA. High-Resolution Mapping of a Repeat Protein Folding Free Energy Landscape. Biophysical Journal. 111: 2368-2376. PMID 27926838 DOI: 10.1016/j.bpj.2016.08.027  0.32
2016 Miner JC, Chen AA, García AE. Free-energy landscape of a hyperstable RNA tetraloop. Proceedings of the National Academy of Sciences of the United States of America. PMID 27233937 DOI: 10.1073/pnas.1603154113  1
2015 Rosenman DJ, Wang C, Garcia AE. Characterization of Aβ Monomers Through the Convergence of Ensemble Properties Among Simulations with Multiple Force Fields. The Journal of Physical Chemistry. B. PMID 26562747 DOI: 10.1021/acs.jpcb.5b09379  0.32
2015 Neale C, Herce HD, Pomès R, García AE. Can Specific Protein-Lipid Interactions Stabilize an Active State of the Beta 2 Adrenergic Receptor? Biophysical Journal. 109: 1652-62. PMID 26488656 DOI: 10.1016/j.bpj.2015.08.028  1
2015 Tripathi S, Garcìa AE, Makhatadze GI. Alterations of Nonconserved Residues Affect Protein Stability and Folding Dynamics through Charge-Charge Interactions. The Journal of Physical Chemistry. B. 119: 13103-12. PMID 26413861 DOI: 10.1021/acs.jpcb.5b08527  1
2015 English CA, García AE. Charged Termini on the Trp-Cage Roughen the Folding Energy Landscape. The Journal of Physical Chemistry. B. 119: 7874-81. PMID 26018669 DOI: 10.1021/acs.jpcb.5b02040  1
2015 Saxena A, García AE. Multisite ion model in concentrated solutions of divalent cations (MgCl2 and CaCl2): osmotic pressure calculations. The Journal of Physical Chemistry. B. 119: 219-27. PMID 25482831 DOI: 10.1021/jp507008x  1
2014 Herce HD, Garcia AE, Cardoso MC. Fundamental molecular mechanism for the cellular uptake of guanidinium-rich molecules. Journal of the American Chemical Society. 136: 17459-67. PMID 25405895 DOI: 10.1021/ja507790z  1
2014 Akabori K, Huang K, Treece BW, Jablin MS, Maranville B, Woll A, Nagle JF, Garcia AE, Tristram-Nagle S. HIV-1 Tat membrane interactions probed using X-ray and neutron scattering, CD spectroscopy and MD simulations. Biochimica Et Biophysica Acta. 1838: 3078-87. PMID 25148702 DOI: 10.1016/j.bbamem.2014.08.014  1
2014 Jimenez-Cruz CA, Garcia AE. Equilibrium thermodynamics and folding kinetics of a short, fast-folding, beta-hairpin. Physical Chemistry Chemical Physics : Pccp. 16: 6422-9. PMID 24472872 DOI: 10.1039/c3cp54336f  1
2014 English CA, García AE. Folding and unfolding thermodynamics of the TC10b Trp-cage miniprotein. Physical Chemistry Chemical Physics : Pccp. 16: 2748-57. PMID 24448113 DOI: 10.1039/c3cp54339k  1
2013 Jimenez-Cruz CA, Garcia AE. Reconstructing the Most Probable Folding Transition Path from Replica Exchange Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. 9: 3750-5. PMID 26584126 DOI: 10.1021/ct400170x  1
2013 Chen AA, García AE. High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations. Proceedings of the National Academy of Sciences of the United States of America. 110: 16820-5. PMID 24043821 DOI: 10.1073/pnas.1309392110  1
2013 Roche J, Dellarole M, Caro JA, Norberto DR, Garcia AE, Garcia-Moreno B, Roumestand C, Royer CA. Effect of internal cavities on folding rates and routes revealed by real-time pressure-jump NMR spectroscopy. Journal of the American Chemical Society. 135: 14610-8. PMID 23987660 DOI: 10.1021/ja406682e  1
2013 Rosenman DJ, Connors CR, Chen W, Wang C, García AE. Aβ monomers transiently sample oligomer and fibril-like configurations: ensemble characterization using a combined MD/NMR approach. Journal of Molecular Biology. 425: 3338-59. PMID 23811057 DOI: 10.1016/j.jmb.2013.06.021  1
2013 Stephenson W, Asare-Okai PN, Chen AA, Keller S, Santiago R, Tenenbaum SA, Garcia AE, Fabris D, Li PT. The essential role of stacking adenines in a two-base-pair RNA kissing complex. Journal of the American Chemical Society. 135: 5602-11. PMID 23517345 DOI: 10.1021/ja310820h  1
2013 Canchi DR, García AE. Cosolvent effects on protein stability. Annual Review of Physical Chemistry. 64: 273-93. PMID 23298246 DOI: 10.1146/annurev-physchem-040412-110156  1
2013 Tripathi S, Makhatadze GI, Garcia AE. Backtracking due to residual structure in the unfolded state changes the folding of the third fibronectin type III domain from tenascin-C. The Journal of Physical Chemistry. B. 117: 800-10. PMID 23268597 DOI: 10.1021/jp310046k  1
2012 Canchi DR, Jayasimha P, Rau DC, Makhatadze GI, Garcia AE. Molecular mechanism for the preferential exclusion of TMAO from protein surfaces. The Journal of Physical Chemistry. B. 116: 12095-104. PMID 22970901 DOI: 10.1021/jp304298c  1
2012 Chen AA, García AE. Mechanism of enhanced mechanical stability of a minimal RNA kissing complex elucidated by nonequilibrium molecular dynamics simulations. Proceedings of the National Academy of Sciences of the United States of America. 109: E1530-9. PMID 22623526 DOI: 10.1073/pnas.1119552109  1
2012 Noel JK, Schug A, Verma A, Wenzel W, Garcia AE, Onuchic JN. Mirror images as naturally competing conformations in protein folding. The Journal of Physical Chemistry. B. 116: 6880-8. PMID 22497217 DOI: 10.1021/jp212623d  1
2011 Tian J, Garcia AE. Simulation studies of protein folding/unfolding equilibrium under polar and nonpolar confinement. Journal of the American Chemical Society. 133: 15157-64. PMID 21854029 DOI: 10.1021/ja2054572  1
2011 Jimenez-Cruz CA, Makhatadze GI, Garcia AE. Protonation/deprotonation effects on the stability of the Trp-cage miniprotein. Physical Chemistry Chemical Physics : Pccp. 13: 17056-63. PMID 21773639 DOI: 10.1039/c1cp21193e  1
2011 Tian J, García AE. Simulations of the confinement of ubiquitin in self-assembled reverse micelles. The Journal of Chemical Physics. 134: 225101. PMID 21682536 DOI: 10.1063/1.3592712  0.56
2011 Vaitheeswaran S, Garcia AE. Protein stability at a carbon nanotube interface. The Journal of Chemical Physics. 134: 125101. PMID 21456701 DOI: 10.1063/1.3558776  1
2011 Rouget JB, Aksel T, Roche J, Saldana JL, Garcia AE, Barrick D, Royer CA. Size and sequence and the volume change of protein folding. Journal of the American Chemical Society. 133: 6020-7. PMID 21446709 DOI: 10.1021/ja200228w  1
2011 Canchi DR, García AE. Backbone and side-chain contributions in protein denaturation by urea. Biophysical Journal. 100: 1526-33. PMID 21402035 DOI: 10.1016/j.bpj.2011.01.028  1
2011 Joshi A, Kate S, Poon V, Mondal D, Boggara MB, Saraph A, Martin JT, McAlpine R, Day R, Garcia AE, Mogridge J, Kane RS. Structure-based design of a heptavalent anthrax toxin inhibitor. Biomacromolecules. 12: 791-6. PMID 21302959 DOI: 10.1021/bm101396u  1
2011 Sgourakis NG, Merced-Serrano M, Boutsidis C, Drineas P, Du Z, Wang C, Garcia AE. Atomic-level characterization of the ensemble of the Aβ(1-42) monomer in water using unbiased molecular dynamics simulations and spectral algorithms. Journal of Molecular Biology. 405: 570-83. PMID 21056574 DOI: 10.1016/j.jmb.2010.10.015  1
2010 Patel MM, Sgourakis NG, Garcia AE, Makhatadze GI. Experimental test of the thermodynamic model of protein cooperativity using temperature-induced unfolding of a Ubq-UIM fusion protein. Biochemistry. 49: 8455-67. PMID 20836541 DOI: 10.1021/bi101163u  1
2010 Zhuang W, Sgourakis NG, Li Z, Garcia AE, Mukamel S. Discriminating early stage A{beta}42 monomer structures using chirality-induced 2DIR spectroscopy in a simulation study. Proceedings of the National Academy of Sciences of the United States of America. 107: 15687-92. PMID 20798063 DOI: 10.1073/pnas.1002131107  1
2010 Day R, Paschek D, Garcia AE. Microsecond simulations of the folding/unfolding thermodynamics of the Trp-cage miniprotein. Proteins. 78: 1889-99. PMID 20408169 DOI: 10.1002/prot.22702  0.36
2010 Sgourakis NG, Garcia AE. The membrane complex between transducin and dark-state rhodopsin exhibits large-amplitude interface dynamics on the sub-microsecond timescale: insights from all-atom MD simulations. Journal of Molecular Biology. 398: 161-73. PMID 20184892 DOI: 10.1016/j.jmb.2010.02.032  0.84
2010 Sarupria S, Ghosh T, García AE, Garde S. Studying pressure denaturation of a protein by molecular dynamics simulations. Proteins. 78: 1641-51. PMID 20146357 DOI: 10.1002/prot.22680  1
2010 Canchi DR, Paschek D, García AE. Equilibrium study of protein denaturation by urea. Journal of the American Chemical Society. 132: 2338-44. PMID 20121105 DOI: 10.1021/ja909348c  1
2010 Sgourakis NG, Patel MM, Garcia AE, Makhatadze GI, McCallum SA. Conformational dynamics and structural plasticity play critical roles in the ubiquitin recognition of a UIM domain. Journal of Molecular Biology. 396: 1128-44. PMID 20053359 DOI: 10.1016/j.jmb.2009.12.052  1
2009 Herce HD, Garcia AE, Litt J, Kane RS, Martin P, Enrique N, Rebolledo A, Milesi V. Arginine-rich peptides destabilize the plasma membrane, consistent with a pore formation translocation mechanism of cell-penetrating peptides. Biophysical Journal. 97: 1917-25. PMID 19804722 DOI: 10.1016/j.bpj.2009.05.066  1
2009 Tian J, Garcia AE. An alpha-helical peptide in AOT micelles prefers to be localized at the water/headgroup interface. Biophysical Journal. 96: L57-9. PMID 19450460 DOI: 10.1016/j.bpj.2009.03.014  1
2008 Sgourakis NG, Day R, McCallum SA, Garcia AE. Pressure effects on the ensemble dynamics of ubiquitin inspected with molecular dynamics simulations and isotropic reorientational eigenmode dynamics. Biophysical Journal. 95: 3943-55. PMID 18621814 DOI: 10.1529/biophysj.108.133702  1
2008 Garcia AE, Paschek D. Simulation of the pressure and temperature folding/unfolding equilibrium of a small RNA hairpin. Journal of the American Chemical Society. 130: 815-7. PMID 18154332 DOI: 10.1021/ja074191i  0.36
2008 Garcia AE. Molecular dynamics simulations of protein folding. Methods in Molecular Biology (Clifton, N.J.). 413: 315-30. PMID 18075171  1
2007 Herce HD, Garcia AE. Cell penetrating peptides: how do they do it? Journal of Biological Physics. 33: 345-56. PMID 19669523 DOI: 10.1007/s10867-008-9074-3  1
2007 Herce HD, Garcia AE. Molecular dynamics simulations suggest a mechanism for translocation of the HIV-1 TAT peptide across lipid membranes. Proceedings of the National Academy of Sciences of the United States of America. 104: 20805-10. PMID 18093956 DOI: 10.1073/pnas.0706574105  1
2007 Yang S, Onuchic JN, García AE, Levine H. Folding time predictions from all-atom replica exchange simulations. Journal of Molecular Biology. 372: 756-63. PMID 17681536 DOI: 10.1016/j.jmb.2007.07.010  1
2007 Damjanović A, Schlessman JL, Fitch CA, García AE, García-Moreno E B. Role of flexibility and polarity as determinants of the hydration of internal cavities and pockets in proteins. Biophysical Journal. 93: 2791-804. PMID 17604315 DOI: 10.1529/biophysj.107.104182  1
2007 Herce HD, Garcia AE, Darden T. The electrostatic surface term: (I) periodic systems. The Journal of Chemical Physics. 126: 124106. PMID 17411107 DOI: 10.1063/1.2714527  1
2007 Sgourakis NG, Yan Y, McCallum SA, Wang C, Garcia AE. The Alzheimer's peptides Abeta40 and 42 adopt distinct conformations in water: a combined MD / NMR study. Journal of Molecular Biology. 368: 1448-57. PMID 17397862 DOI: 10.1016/j.jmb.2007.02.093  1
2007 Paschek D, Nymeyer H, García AE. Replica exchange simulation of reversible folding/unfolding of the Trp-cage miniprotein in explicit solvent: on the structure and possible role of internal water. Journal of Structural Biology. 157: 524-33. PMID 17293125 DOI: 10.1016/j.jsb.2006.10.031  1
2007 Jayachandran G, Vishal V, García AE, Pande VS. Local structure formation in simulations of two small proteins. Journal of Structural Biology. 157: 491-9. PMID 17098444 DOI: 10.1016/j.jsb.2006.10.001  1
2006 Herce HD, Garcia AE. Correction of apparent finite size effects in the area per lipid of lipid membranes simulations. The Journal of Chemical Physics. 125: 224711. PMID 17176158 DOI: 10.1063/1.2378893  1
2005 Damjanović A, García-Moreno B, Lattman EE, García AE. Molecular dynamics study of water penetration in staphylococcal nuclease. Proteins. 60: 433-49. PMID 15971206 DOI: 10.1002/prot.20486  1
2005 Garcia AE, Onuchic JN. Folding a protein in the computer: reality or hope? Structure (London, England : 1993). 13: 497-8. PMID 15837185 DOI: 10.1016/j.str.2005.03.005  1
2005 Nymeyer H, Woolf TB, Garcia AE. Folding is not required for bilayer insertion: replica exchange simulations of an alpha-helical peptide with an explicit lipid bilayer. Proteins. 59: 783-90. PMID 15828005 DOI: 10.1002/prot.20460  1
2005 Paschek D, Gnanakaran S, Garcia AE. Simulations of the pressure and temperature unfolding of an alpha-helical peptide. Proceedings of the National Academy of Sciences of the United States of America. 102: 6765-70. PMID 15800045 DOI: 10.1073/pnas.0408527102  0.36
2004 Nymeyer H, Gnanakaran S, García AE. Atomic simulations of protein folding, using the replica exchange algorithm. Methods in Enzymology. 383: 119-49. PMID 15063649 DOI: 10.1016/S0076-6879(04)83006-4  1
2003 García AE, Onuchic JN. Folding a protein in a computer: an atomic description of the folding/unfolding of protein A. Proceedings of the National Academy of Sciences of the United States of America. 100: 13898-903. PMID 14623983 DOI: 10.1073/pnas.2335541100  1
2003 Nymeyer H, García AE. Simulation of the folding equilibrium of alpha-helical peptides: a comparison of the generalized Born approximation with explicit solvent. Proceedings of the National Academy of Sciences of the United States of America. 100: 13934-9. PMID 14617775 DOI: 10.1073/pnas.2232868100  1
2003 Ghosh T, Garde S, García AE. Role of backbone hydration and salt-bridge formation in stability of alpha-helix in solution. Biophysical Journal. 85: 3187-93. PMID 14581218 DOI: 10.1016/S0006-3495(03)74736-5  1
2003 Clementi C, García AE, Onuchic JN. Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism: all-atom representation study of protein L. Journal of Molecular Biology. 326: 933-54. PMID 12581651 DOI: 10.1016/S0022-2836(02)01379-7  1
2002 Cheung MS, García AE, Onuchic JN. Protein folding mediated by solvation: water expulsion and formation of the hydrophobic core occur after the structural collapse. Proceedings of the National Academy of Sciences of the United States of America. 99: 685-90. PMID 11805324 DOI: 10.1073/pnas.022387699  1
2002 Ghosh T, García AE, Garde S. Enthalpy and entropy contributions to the pressure dependence of hydrophobic interactions Journal of Chemical Physics. 116: 2480-2486. DOI: 10.1063/1.1431582  1
2001 Ghosh T, García AE, Garde S. Molecular dynamics simulations of pressure effects on hydrophobic interactions. Journal of the American Chemical Society. 123: 10997-1003. PMID 11686704 DOI: 10.1021/ja010446v  1
2001 Baker CH, Tomlinson SR, García AE, Harman JG. Amino acid substitution at position 99 affects the rate of CRP subunit exchange. Biochemistry. 40: 12329-38. PMID 11591152 DOI: 10.1021/bi010834  1
2001 Vigil D, Gallagher SC, Trewhella J, García AE. Functional dynamics of the hydrophobic cleft in the N-domain of calmodulin. Biophysical Journal. 80: 2082-92. PMID 11325712 DOI: 10.1016/S0006-3495(01)76182-6  1
2001 Hummer G, García AE, Garde S. Helix nucleation kinetics from molecular simulations in explicit solvent Proteins: Structure, Function and Genetics. 42: 77-84. PMID 11093262 DOI: 10.1002/1097-0134(20010101)42:1<77::AID-PROT80>3.0.CO;2-#  1
2000 Hummer G, García AE, Garde S. Conformational diffusion and helix formation kinetics Physical Review Letters. 85: 2637-2640. PMID 10978126 DOI: 10.1103/PhysRevLett.85.2637  1
2000 Onuchic JN, Nymeyer H, García AE, Chahine J, Socci ND. The energy landscape theory of protein folding: insights into folding mechanisms and scenarios. Advances in Protein Chemistry. 53: 87-152. PMID 10751944 DOI: 10.1016/S0065-3233(00)53003-4  1
1999 Garde S, García AE, Pratt LR, Hummer G. Temperature dependence of the solubility of non-polar gases in water. Biophysical Chemistry. 78: 21-32. PMID 17030303 DOI: 10.1016/S0301-4622(99)00018-6  1
1999 Hillson N, Onuchic JN, Garcia AE. Pressure-induced protein-folding/unfolding kinetics Proceedings of the National Academy of Sciences of the United States of America. 96: 14848-14853. PMID 10611301 DOI: 10.1073/pnas.96.26.14848  1
1998 Mariappan SV, Silks LA, Chen X, Springer PA, Wu R, Moyzis RK, Bradbury EM, Garcia AE, Gupta G. Solution structures of the Huntington's disease DNA triplets, (CAG)n. Journal of Biomolecular Structure & Dynamics. 15: 723-44. PMID 9514249 DOI: 10.1080/07391102.1998.10508988  1
1998 Hummer G, Garde S, García AE, Paulaitis ME, Pratt LR. The pressure dependence of hydrophobic interactions is consistent with the observed pressure denaturation of proteins. Proceedings of the National Academy of Sciences of the United States of America. 95: 1552-5. PMID 9465053 DOI: 10.1073/pnas.95.4.1552  1
1998 Hummer G, Pratt LR, García AE. Molecular theories and simulation of ions and polar molecules in water Journal of Physical Chemistry A. 102: 7885-7895.  1
1997 García AE, Krumhansl JA, Frauenfelder H. Variations on a theme by Debye and Waller: from simple crystals to proteins. Proteins. 29: 153-60. PMID 9329080 DOI: 10.1002/(SICI)1097-0134(199710)29:2<153::AID-PROT3>3.0.CO;2-E  1
1997 Hummer G, Pratt LR, García AE. Multistate Gaussian model for electrostatic solvation free energies Journal of the American Chemical Society. 119: 8523-8527. DOI: 10.1021/ja971148u  1
1997 Hummer G, Pratt LR, García AE. Ion sizes and finite-size corrections for ionic-solvation free energies Journal of Chemical Physics. 107: 9275-9277.  1
1997 Hummer G, Pratt LR, García AE, Berne BJ, Rick SW. Electrostatic potentials and free energies of solvation of polar and charged molecules Journal of Physical Chemistry B. 101: 3017-3020.  1
1996 Hummer G, Garde S, García AE, Pohorille A, Pratt LR. An information theory model of hydrophobic interactions. Proceedings of the National Academy of Sciences of the United States of America. 93: 8951-5. PMID 11607700 DOI: 10.1073/pnas.93.17.8951  1
1996 Tung CS, Oprea TI, Hummer G, García AE. Three-dimensional model of a selective theophylline-binding RNA molecule Journal of Molecular Recognition. 9: 275-286. PMID 9131469 DOI: 10.1002/(SICI)1099-1352(199607)9:4<275::AID-JMR337>3.0.CO;2-8  1
1996 García AE, Harman JG. Simulations of CRP:(cAMP)2 in noncrystalline environments show a subunit transition from the open to the closed conformation Protein Science. 5: 62-71. PMID 8771197  1
1996 Hummer G, Pratt LR, Garcia AE. Free energy of ionic hydration Journal of Physical Chemistry. 100: 1206-1215. DOI: 10.1021/jp951011v  1
1995 Hummer G, Pratt LR, García AE. Hydration free energy of water Journal of Physical Chemistry. 99: 14188-14194. DOI: 10.1021/j100038a062  1
1994 Pratt LR, Hummer G, Garciá AE. Ion pair potentials-of-mean-force in water Biophysical Chemistry. 51: 147-165. DOI: 10.1016/0301-4622(94)00057-3  1
1991 Soumpasis DM, Tung CS, Garcia AE. Rigorous description of GNA structures. II. on the computation of best axes, planes, and helices from atomic coordinates Journal of Biomolecular Structure and Dynamics. 8: 867-888. PMID 2059344 DOI: 10.1080/07391102.1991.10507850  1
1990 Garcia AE, Gupta G, Soumpasis DM, Tung CS. Energetics of the hairpin to mismatched duplex transition of d(Gccgcagc) on nacl solution Journal of Biomolecular Structure and Dynamics. 8: 173-186. PMID 2275792 DOI: 10.1080/07391102.1990.10507796  1
1990 Lumpkin AH, Trewhella J, Garcia AE. Potential biophysical application of the Los Alamos infrared free electron laser: DNA spectroscopy Nuclear Inst. and Methods in Physics Research, A. 296: 809-813. DOI: 10.1016/0168-9002(90)91311-X  1
1987 Garcia AE, Krumhansl JA. Agreement between single crystal x-ray and molecular mechanical sugar ring conformations Journal of Biomolecular Structure and Dynamics. 5: 513-537. PMID 3271484 DOI: 10.1080/07391102.1987.10506411  1
Show low-probability matches.