Alfredo Freites, PhD

Assistant Project Scientist

Department of Chemistry

Ph. D., Physics, 2004

University of California, Irvine

M. S., Physics, 2002

University of California, Irvine

Contact me: jfreites(at)uci.edu

I am interested on the application of computational and theoretical methods to the study of structure, dynamics and function of biomolecules. My current focus is on molecular simulations of membranes and membrane proteins, with an emphasis on the quantitative comparison of MD simulations with a variety of experimental data (e.g., neutron diffraction, NMR spectroscopy, and electrophysiological measurements), and the elucidation of the function of transporters, ion channels, and membrane associated peptide toxins. The goal of this work is to provide physicochemical insights into biological processes. We work closely with experimentalists to both validate our simulation results and suggest new avenues of inquiry.

P. J. Fleming, J. A. Freites, C. P. Moon, D. J. Tobias, and K. G. Fleming, Outer membrane phospholipase A in phospholipid bilayers: A model system for concerted computational and experimental investigations of amino acid side chain partitioning into lipid bilayers, Biochim. Biophys. Acta - Biomembranes 1818, 126-134 (2012).

M. L. Wood, E. V. Schow, J. A. Freites, S. H. White, F. Tombola, and D. J. Tobias, Water wires in atomistic models of the Hv1 proton channel, Biochim. Biophys. Acta - Biomembranes 1818, 286-293 (2012).

M. Andersson, J. A. Freites, D. J. Tobias, and S. H. White, Structural dynamics of the S4 voltage sensor helix in bilayers lacking lipid phosphates, J. Phys. Chem. B 115, 8732-8738 (2011).

M. Mihailescu, R. G. Vaswani, E. Jardón-Valadez, F. Castro-Román, J. A. Freites, D. L. Worcester, A. R. Chamberlin, D. J. Tobias, and S. H. White, Acyl-chain methyl distributions of liquid-ordered and -disordered membranes, Biophys. J. 100, 1455-1462 (2011).

W. D. Brubaker, J. A. Freites, K. J. Golchert, R. A. Shapiro, V. Morikis, D. J. Tobias, and R. W. Martin, Separating instability from aggregation propensity in gS-crystallin variants, Biophys. J. 100, 498-506 (2011).

E. V. Schow, J. A. Freites, P. Cheng, A. Bernsel, G. von Heijne, S. H. White, and D. J. Tobias, Arginine insertion in membranes: on the connection between molecular dynamics simulations and translocon-mediated insertion experiments, J. Membrane Biol. 239, 35-48 (2011).

A.-N. Bondar, C. Munoz del Val, J. A. Freites, D. J. Tobias, and S. H. White, Dynamics of SecY translocons with translocation-defective mutations, Structure 18, 847-857 (2010). [Featured Article]

J. B. Klauda, R. M. Venable, J. A. Freites, J. W. O’Conner, D. J. Tobias, C. Mondragon-Ramirez, I. Vorobyov, A. D. MacKerell Jr., and R. W. Pastor, Update of the CHARMM all-atom additive force fields for lipids: validation on six lipid types, J. Phys. Chem. B 114, 7830-7843 (2010).

E. V. Schow, J. A. Freites, K. Gogna, S. H. White, and D. J. Tobias, Down-state model of the voltage-sensing domain of a potassium channel, Biophys. J. 98, 2857-2866 (2010).

D. Krepkiy, M. Mihailescu, J. A. Freites, E. V. Schow, D. L. Worcester, K. Gawrisch, D. J. Tobias, S. H. White, and K. J. Swartz, Structure and hydration of membranes embedded with voltage-sensing domains, Nature 462, 473-479 (2009).

Y. Zhou, L. Guan, J. A. Freites, and H. R. Kaback H.R., Opening and closing of the periplasmic gate in lactose permease, Proc. Natl. Acad. Sci. USA 105, 3774-3778 (2008).

J. A. Freites, D. J. Tobias, and S. H. White, A voltage sensor water pore. Biophys. J. 91, L90-L92 (2006).

J. A. Freites, D. J. Tobias, G. von Heijne, and S. H. White, Interface connections of a transmembrane voltage sensor, Proc. Natl. Acad. Sci. USA 102, 15059-15064 (2005).

J. A. Freites, S. Ali, A. Rosengarth A., H. Luecke, and M. B. Dennin, Annexin A1 interaction with a zwitterionic phospholipid monolayer: a fluorescence microscopy study, Langmuir 20, 11674-11683 (2004).

J. A. Freites, Y. Choi, and D. J. Tobias, Molecular dynamics simulations of a pulmonary surfactant protein B peptide in a lipid monolayer, Biophys. J. 84, 2169-2180 (2003).

G. Gonzalez, J. A. Freites, and C. E. Rojas, Synthesis and characterization of nano-phase particles obtained by D.C. sputtering, Scripta Mater. 4, 1883-1887 (2001).

G. Gonzalez, C. Urbina de Navarro, J. A. Freites, and C. E. Rojas, Applications of ultramicrotomy in materials science, Acta Microscopica 3, 65-78 (1994).