Garcia Research Group

Recent Publications

Google Scholar (Angel Garcia [1] )

"Mechanism of enhanced mechanical stability of a minimal RNA kissing complex elucidated by nonequilibrium molecular dynamics simulations".

Chen AA, García AE. Proc Natl Acad Sci U S A. 2012 Jun 12;109(24):E1530-9. PubMed PMID: 22623526

"Cavities determine the pressure unfolding of proteins".

Roche J, Caro JA, Norberto DR, Barthe P, Roumestand C, Schlessman JL, Garcia AE, Garcia-Moreno B, and Royer CA. Proc Natl Acad Sci U S A. 2012 109(18):6945-6950. PubMed PMID:22496593

"Mirror Images as Naturally Competing Conformations in Protein Folding"

Noel JK, Schug A, Verma A, Wenzel W, Garcia AE, Onuchic JN, J Phys. Chem. 116 : 6880-6888 (2012)

“Influence of water-protein hydrogen bonding on the stability of Trp-Cage miniprotein: A comparison between the TIP3P and TIP4P-Ew water models”.

D. Paschek, R. Day and A. E. Garcia, Phys Chem Chem Phys. 13: 19840-19847 (2011)

“Protonation/Deprotonation effects on the stability of the Trp-Cage Miniprotein”

Camilo Jimenez-Cruz, G. I. Makhatadze and Angel E. Garcia, ChemPhysChem, 13: 17056- 17063 (2011) Special Issue on Physical Models of Protein Folding. DOI: 10.1039/c1cp21193e

"Concentration Dependence of NaCl ion distributions around DPPC lipid bilayers"

Jorge A Rodriguez and Angel E. Garcia, Interdisciplinary Sciences-- Computational Life Sciences, Special Issue on "ionic fluids and their biological application". Interdiscip Sci Comput Life Sci 3: 1-11 (2011). DOI: 10.1007/s12539-011-0107-4. Issue in Honor of Lesser Blum.

“Simulations of The Confinement Of Ubiquitin In Self -Assembled Reverse Micelles”

Jianhui Tian and Angel E Garcia, J.Chem. Phys. 134: 225101 (2011) (Issue Cover)

“Size and Sequence and the Volume Change of Protein Folding”

Jean-Baptiste Rouget, Tural Aksel, Julien Roche, Jean-Louis Saldana, Angel E. Garcia, Doug Barrick, and Catherine A. Royer., J Amer. Chem. Soc. 133: 6020-6027 (2011) dx.doi.org/10.1021/ja200228w

“Protein Stability at a Carbon Nanotube Interface”

S. Vaitheesewaran and A.E. Garcia, J. Chem. Phys. 134 :125101 (2011)

“Structure‐based Design of a Heptavalent Anthrax Toxin Inhibitor”

A. Joshi, S. Kate, V. Poon, D. Mondal, M. Boggara, A. Saraph, J. Martin, R. McAlpine, R. Day, A.E. Garcia, J. Mogridge, and R.S. Kane, Biomacromolecules, 12: 791-796 (2011)

"Backbone and Sidechain contributions in Protein Denaturation by Urea”,

D.R. Canchi and A.E. Garcia, Biophysical Journal 100: 1526-1533 (2011)

“Atomic-Level Characterization of the Ensemble of theAb(1–42) Monomer in Water Using Unbiased Molecular Dynamics Simulations and Spectral Algorithms”,

N.G. Sgourakis, M. Merced-Serrano, C. Boutsidis, P. Drineas, Z. Du, C. Wang and A. E. Garcia, J Mol. Biol. 405: 570-583 (2011)

Microsecond simulations of the folding/unfolding thermodynamics of the Trp-cage mini protein

Ryan Day, Dietmar Paschek and Angel E. Garcia, Proteins: Structure, Function and Bioinformatics, 78:1889-1899 (2010)

Studying pressure denaturation of a protein by molecular dynamics simulations

Sapna Sarupria, Tuhin Ghosh, Angel E. García, Shekhar Garde, Proteins: Structure, Function and Bioinformatics,78: 1641-1651 (2010)

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

Nikolaos G. Sgourakis and Angel E. Garcia, Journal of Molecular Biology, J Mol. Biol. 398: 161-173 (2010)

Conformational Dynamics and Structural Plasticity Play Critical Roles in the Ubiquitin Recognition of a UIM Domain

Nikolaos G. Sgourakis, Mayank M. Patel, Angel E. Garcia, George I. Makhatadze and Scott A. McCallum, Journal of Molecular Biology, Volume 396, Issue 4, 5 March 2010, Pages 1128-1144, ISSN 0022-2836, DOI: 10.1016/j.jmb.2009.12.052.

Equilibrium Study of Protein Denaturation by Urea

Deepak R. Canchi, Dietmar Paschek and Angel E. Garcia, J. Am. Chem. Soc., 2010, 132 (7), pp 2338–2344

An Alpha-Helical Peptide in AOT Micelles Prefers to be Localized at the Water/Headgroup Interface

Jianhui Tian, Angel E. Garcia, Biophysical Journal, Volume 96, Issue 10, 20 May 2009, Pages L57-L59, ISSN 0006-3495, DOI: 10.1016/j.bpj.2009.03.014.

Pressure Effects on the Ensemble Dynamics of Ubiquitin Inspected with Molecular Dynamics Simulations and Isotropic Reorientational Eigenmode Dynamics

Nikolaos G. Sgourakis, Ryan Day, Scott A. McCallum and Angel E. Garcia,

Biophysical Journal, Volume 95, Issue 8, 3943-3955, 15 October 2008,,

Arginine-Rich Peptides Destabilize the Plasma Membrane, Consistent with a Pore Formation Translocation Mechanism of Cell-Penetrating Peptides

H.D. Herce, A.E. Garcia, J. Litt, R.S. Kane, P. Martin, N. Enrique, A. Rebolledo, V. Milesi, Biophysical Journal, Volume 97, Issue 7, 7 October 2009, Pages 1917-1925, ISSN 0006-3495, DOI: 10.1016/j.bpj.2009.05.066.

Global versus local features of an unfolded peptide system – Aβ42 modeled by Dynamics simulations and NMR experiments

Nikolaos G. Sgourakis, and Angel E. Garcia, In book "From Denatured States to Intrinsically Disordered". Vladimir Uversky and T. Creamer, Editors. (2008)

The Alzheimer's peptides adopt distinct conformations in water: A Combined MD/NMR study

Nikolaos G. Sgourakis, Yilin Yan, Scott A. McCallum, Chunyu Wang and Angel E. Garcia,

Journal of Molecular Biology, Volume 368, Issue 5, 18 May 2007, Pages 1448-1457

Publications by topic

Pressure


Jean-Baptiste Rouget, Tural Aksel, Julien Roche, Jean-Louis Saldana, Angel E. Garcia, Doug Barrick, and Catherine A. Royer., J Amer. Chem. Soc. 133: 6020-6027 (2011) dx.doi.org/10.1021/ja200228w
Ryan Day, Dietmar Paschek and Angel E. Garcia, Proteins: Structure, Function and Bioinformatics, 78:1889-1899 (2010)
Sapna Sarupria, Tuhin Ghosh, Angel E. García, Shekhar Garde, Proteins: Structure, Function and Bioinformatics,78: 1641-1651 (2010)

Protein Folding

D.R. Canchi and A.E. Garcia, Biophysical Journal 100: 1526-1533 (2011)

Amyloids

Membrane Protein/Peptides

Nikolaos G. Sgourakis and Angel E. Garcia, Journal of Molecular Biology, J Mol. Biol. 398: 161-173 (2010)
H.D. Herce, A.E. Garcia, J. Litt, R.S. Kane, P. Martin, N. Enrique, A. Rebolledo, V. Milesi, Biophysical Journal, Volume 97, Issue 7, 7 October 2009, Pages 1917-1925, ISSN 0006-3495, DOI: 10.1016/j.bpj.2009.05.066


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