José Antonio Gárate

Young Research Scientist

Research area: Molecular dynamics, Biomolecular simulations, free-energy calculations and small-molecules confinement within narrow nanotubes.

Computational Biology Laboratory, Fundación Ciencia & Vida
Principal Investigator: Dr. Tomás Perez-Acle (tomas@dlab.cl)

B.S Biotechnology, University of Chile (2005)
Molecular Biotechnology Engineer, University of Chile (2007)
PhD in Chemical and Bioprocess Engineering , University College Dublin (2010)

Curriculum Vitae

 

Contact Information:
E-mail: jgarate at dlab.cl
Telephone: +56 2 23672023
Address: Laboratorio de Biología Computacional, Av. Zañartu 1482, Ñuñoa, Santiago, Chile.

Research Statement:

During the last 20 years, computational techniques have become an indispensable tool for the understanding of chemical processes at the nanoscale level, which, even though the huge advancements in the manipulation of matter at the molecular level (e.g. single-molecule techniques), in general remains hardly accessible by traditional experimental means. The popularity and acceptance of Molecular Simulation as a well established fi eld, is thanks to its contributions in physics, chemistry, biology between others, expanding the knowledge on the aforementioned fields and, in practice, bridging the gap between “pure theory” and the empirical world. Its rapid development, thanks to the interdisciplinary combined efforts of chemists, physicists and computational scientists has triggered the generation of novel algorithms, new software and faster computational resources, rendering molecular simulation a widespread technique easy accessible to wider audiences. Among the great many methodologies belonging to this field, Molecular Dynamics is widely used for the study and characterization of molecules at an atomic resolution. MD deals with the numerical solution of the N -body problem for atomic and molecular systems, elegantly combining statical mechanics and classical physics through the time-dependent integration of Newtons equations of motion. These equations, even in the simplest systems, are of such complexity that the integration must be done with numerical methods over a huge quantity of discrete time-steps, instead of being performed in an analytical, continuous fashion. For atomistic simulations, the magnitude of these time steps is in the range of femtoseconds (fs ). At each time-step, the coordinates are used to calculate the potential energy of the system (V ) and the negative rst derivative (with respect to the position of each atom), the force, using a molecular mechanics force field (FF). A long series of these calculations allows for the generation of a trajectory through phase space, 6N dimensional space (where N is the total number of atoms of the system), defined by the three atomic spatial position and velocity arrays, as representative of a statistical mechanical ensemble of microstates.

MD is very versatile technique, thus as a group focused on MD we are interested in broad and interdisciplinary range of topic; among such are:

– Method development.
– Free-energy calculations.
– Small molecules confined within narrow pores and nanotubes.
– Biomolecular channels such as Aquaporins.
– Carbon-based nanoparticles nanotoxicity.
– Mechanical unfolding of knotted proteins.

Selected Peer-reviewed Publications (last 5 years):

  1. Sebastian E. Gutierrez-Maldonado, Jose Antonio Garate, Maria Jose Retamal, Marcelo Cisternas, Ulrich G. Volkmann, Tomas Perez-Acle “Accessing the structural and thermodynamic properties of ultra-thin layers of C32 adsorbed on a SiO2 surface” Chem. Phys. Lett, accepted (2017).
  2. F Villanelo, Y Escalona, C Pareja-Barrueto, JA Garate, IM Skerrett, T Perez-Acle “Accessing gap-junction channel structure-function relationships through molecular modelling and simulations” BMC Cell Biology, 18(Suppl 1):5 (2017).
  3. Niall J. English and Jose Antonio Garate “Near-microsecond human aquaporin 4 gating dynamics in static and alternating external electric fields: Nonequilibrium molecular dynamics” J. Chem. Phys, 145:085102 (2016).
  4. Marracino Paolo,Liberti Micaela, Trapani Erika, Burnham Christian J,Avena, Massimiliano, Garate, José-Antonio, Apollonio Francesca, English, Niall J”Human Aquaporin 4 Gating Dynamics under Perpendicularly-Oriented Electric-Field Impulses: A Molecular Dynamics Study.” IJMS, 1422-0067 (2016).
  5. Yerko Escalona, Jose A. Garate, Raul Araya-Secchi, Tien Huynh, Ruhong Zhou and Tomas Perez-Acle, “Exploring the membrane potential of simple dual-membrane systems as models for Gap-junction channels.” Biophys J. accepted (2016).
  6. Jose Antonio Garate and Tomas Perez-Acle “From dimers to collective dipoles: Structure and dynamics of methanol/ethanol partition by narrow carbon nanotubes” J. Chem. Phys, 144;6:064105 (2016).
  7. Yu Chong, Cuicui Ge1, Zaixing Yang1, Jose Antonio Garate, Zonglin Gu, Jeffrey K. Weber, Jiajia Liu, and Ruhong Zhou “Reduced cytotoxicity of graphene nanosheets mediated by blood-protein coating ” ACS Nano, 9;6;5713-5724 (2015).
  8. Guangxing Duan, Seung-gu Kang,Jose Antonio Garate, Xing Tian, Cuicui Ge, Ruhong Zhou “Protein Corona Mitigates the Cytotoxicity of Graphene Oxide by Reducing Cell Membrane Penetration ” Nanoscale 7;37: 19949-19957 (2015).
  9. Hua Yue, Wei Wei, Zonglin Gu, Dezhi Ni,Nana Luo,Zaixing Yang,Lin Zhao, Jose- Antonio Garate, Ruhong Zhou, Zhiguo Su and Guanghui Ma “Exploration of graphene oxide as an intelligent platform for cancer vaccines ” Nanoscale 7;47:19949-19957 (2015).
  10. Jiajia Liu, Zaixing Yang, Haotian Li, Zonglin Gu, Jose-Antonio Garate, and Ruhong Zhou “Dewetting transition assisted clearance of (NFGAILS) amyloid fibrils from cell membranes by graphene ” J. Chem. Phys. 14;141:22D520 (2014).
  11. JA Garate,J Stöckl,María del Carmen Fernández-Alonso,Daniel Artner, Mira Haegman, Chris Oostenbrink, Jesús Jiménez-Barbero, Rudi Beyaert, Holger Heine, Paul Kosma, and Alla Zamyatina “Anti-endotoxic Activity and Structural basis for human MD-2·TLR4 Antagonism of Tetraacylated Lipid A Mimetics based on GlcN(-)GlcN Scaffold” J. Innate. Immun. Doi: 10.1177/1753425914550426 (2014).
  12. Raul Araya-Secchi, Tomas Perez-Acle, Seung-gu Kang, Tien Huynh, Alejandro Bernardin, Yerko Escalona, Jose- Antonio Garate, Agustin D. Martinez, Isaac E. Garcıa, Juan C. Saez, Ruhong Zhou “Characterization of a Novel Water Pocket Inside the Human Cx26 Hemichannel Structure” Biophys J. 107 599-612 (2014).
  13. JA Garate, T Perez-Acle, C Oostenbrink , “On the thermodynamics of carbon nanotube single-file water loading:
    free energy, energy and entropy calculations” Phys. Chem. Chem.Phys. 16, 5119-5128 (2014).
  14. B Lai, G Nagy, JA Garate, C Oostenbrink , “Entropic and enthalpic contributions to stereospecific ligand binding from enhanced sampling methods” J. Chem. Inf. Model. 54 (1) 151-58, (2014).
  15. R Reale, NJ English, JA Garate, P Marracino, M Liberti, F Apollonio , “Human aquaporin 4 gating dynamics under and after nanosecond-scalestatic and alternating electric field impulses: A molecular dynamics study of field effects and relaxation” J. Chem. Phys 139, 205101 (2013).
  16. Artner D, Oblak A, Ittig S, Garate JA, Horvat S, Arrieumerlou C, Hofinger A, Oostenbrink C, Jerala R, Kosma P, Zamyatina A. , Conformationally Constrained Lipid A Mimetics for Exploration of Structural Basis of TLR4/MD-2 Activation by Lipopolysaccharide.” ACS Chem Biol 8 (11), 2423–32 (2013).
  17. Garate JA, Oostenbrink C. , “Free-energy differences between states with different conformational ensembles.” J Comput Chem 34(16),1398-408 (2013).
  18. Garate JA, Oostenbrink C. , “Lipid A from lipopolysaccharide recognition: structure, dynamics and cooperativity by molecular dynamics simulations.” Proteins 81(4),658-74 (2013).
  19. El-Hendawy MM, Garate JA, English NJ, O’Reilly S, Mooney DA, “Diffusion and interactions of carbon dioxide and oxygen in the vicinity of the active site of Rubisco: molecular dynamics and quantum chemical studies” J. Chem. Phys 137,145103 (2012).
  20. A Singh, R D Gunning, S Ahmed, C A Barrett, N J English, J-A Garate, K M Ryan “Controlled semiconductor nanorod assembly from solution: influence of concentration, charge and solvent nature” J. Mater. Chem., 22,
    1562-69 (2012).
  21. Garate JA, English NJ, Singh A, Ryan KM, Mooney DA, MacElroy JM, “Electrophoretic deposition of poly(3- decylthiophene) onto gold-mounted cadmium selenide nanorods.” Langmuir 27(22):13506-13 (2011).
  22. R Araya-Secchi, JA Garate, DS Holmes, T Perez-Acle, “Molecular Dynamics Study of the Archaeal Aquaporin
    AqpM Extends the Evidence for a New Family of Aquaporins” BMC Genomics, 12:S8 (2011).
  23. J.-A. Garate, N.J. English and J.M.D. MacElroy, “Human aquaporin 4 gating dynamics in dc and ac electric fields: a molecular dynamics study” J. Chem. Phys 134,055110 (2011).
  24. J.-A. Garate, N.J. English and J.M.D. MacElroy, “Static and alternating electric field and distance-dependent effects on carbon nanotube-assisted water self-diffusion across lipid membranes” J. Chem. Phys 131,114508 (2009).
  25. JA Garate, M de los Ángeles Valenzuela, MP Gárate, AF Olea”Aggregation of Alcohols Ethoxylates in n- Heptane” J Surfact Deterg 12:231–236 (2009).
  26. J.-A. Garate, N.J. English and J.M.D. MacElroy, “Carbon nanotube assisted water self-diffusion across lipid membranes in the absence and presence of electric fields” Molecular Simulation Vol. 35, Nos. 1–2, 3–12 (2009).
  27. A. Gonzalez,L. Sepulveda Duran ,R. Araya-Secchi, J. A. Garate ,C. D. Pessoa- Mahana,C. F. Lagos,and T. Perez-Acle “Computational modeling study of functional microdomains in cannabinoid receptor type 1” Bioorganic and Medicinal Chemistry 16 4378–4389 (2008).
  28. M Colombres, J.A. Garate ,CF Lagos, R. Araya-Secchi, P. Norambuena, S. Quiroz, L. Larrondo, T. Pérez-Acle, J. Eyzaguirre “An eleven amino acid residue deletion expands the substrate specificity of acetyl xylan esterase II (AXE II)from Penicillium purpurogenum”, J Comput Aided Mol Des 22:19–28 (2008).

Book Chapter:

N.J. English, J.-A. Garate and J.M.D. MacElroy “Electric-field and friction effects on Carbon nanotube assisted water self-diffusion across lipid membranes” Carbon Nanotubes – Growth and Applications, InTech, August,
2011.