个人简介

BS, University of Maryland, 1982 MA, Columbia University, 1984 MPhil, Columbia University, 1986 PhD, Columbia University, 1987 NIH Postdoctoral Fellow, Harvard University, 1987-1990

研究领域

Theoretical Chemistry/Physical Chemistry/Biological Chemistry

The Straub Group investigates fundamental aspects of protein dynamics and thermodynamics underlying the formation of protein structure, through folding and aggregation, and enabling protein function, through pathways of energy flow and signaling. Student and postdoctoral research scientists in the Straub Group work to develop and employ state-of-the-art computational methods while working in collaboration with leading experimental research groups. Kinetic and thermodynamic properties defining protein aggregation are elucidated through pioneering computational studies of the earliest stages of amyloid protein aggregation, including the formation of small oligomers (dimers through hexamers) from monomeric protein, and the production of monomeric protein from amyloid precursor proteins. Novel computational algorithms for enhanced sampling of conformational ensembles in complex biomolecular systems include effective approaches for global optimization and enhanced conformational sampling, in complex molecular systems, and novel coarse-grained models of proteins, for use in protein structure prediction. Novel computational approaches for the exploration of reaction dynamics allow for direct simulation of both ultrafast (quantum) and long-time (classical) dynamical events that translate how protein structure supports dynamical energy flow associated with protein function. Pathways and mechanism for energy and signal flow in proteins are explored using classical and quantum dynamical simulations. This includes fundamental aspects of energy transfer associated with ligand binding and redox events in a variety of heme protein systems, with the ultimate goal of relating protein dynamics to function. Professor Straub’s book, “Proteins: Energy, Heat and Signal Flow,” co-edited with David Leitner, captures the state-of-the-art in theoretical studies of protein dynamics and signaling.

近期论文

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"Investigating the solid-liquid phase transition of water nano films using the generalized replica exchange method," Q. Lu, J. Kim, J. D. Farrell, D. J. Wales, and J.E. Straub, J. Chem. Phys. 141, 18C525 (2014). "Empirical maps for the calculation of amide I vibrational spectra of proteins from classical molecular dynamics simulations," E. Malolepsza and J.E. Straub, J. Phys. Chem. B 118, 7848-7855 (2014). "Propensity to form amyloid fibrils is encoded as excitations in the free energy landscape of monomeric proteins," P.I. Zhuravlev, G. Reddy, J.E. Straub, and D. Thirumalai, J. Mol. Bio. 426, 2653-2666 (2014). L. Dominguez, L. Foster, S.C. Meredith, J.E. Straub, and D. Thirumalai, "Structural heterogeneity in transmembrane amyloid precursor protein homodimer is a consequence of environmental selection," J. Am. Chem. Soc. 136, 9619-9626 (2014). J. K. Agbo, Y. Xu, P. Zhang, J. E. Straub, and D. M. Leitner, "Vibrational energy flow across heme-cytochrome c and cytochrome c-water interfaces," Theor. Chem. Acc. 133, 1504 (2014). W.J. Cho, J. Kim, J. Lee, T. Keyes, J. E. Straub, and K.S. Kim, "Limit of metastability for liquid and vapor phases of water," Phys. Rev. Lett. 112, 157802 (2014). J.E. Straub and D. Thirumalai, "Membrane protein interactions are key to understanding amyloid formation," J. Phys. Chem. Lett. 5, 633-635 (2014). L. Dominguez, S.C. Meredith, J.E. Straub, and D. Thirumalai, "Transmembrane fragment structures of Amyloid Precursor Protein depend on membrane surface curvature [Communication]," J. Am. Chem. Soc. 136, 854-857 (2014). Y. Matsunaga, A. Baba, C.B. Li, J.E. Straub, M. Toda, T. Komatsuzaki, and R. S. Berry, "Spatio-temporal hierarchy in the dynamics of a minimalist protein model," J. Chem. Phys. 139, 215101 (2013). A.V. Martinez, L. Dominguez, E. Malolepsza, A. Moser, Z. Ziegler, and J.E. Straub, "Probing the structure and dynamics of confined water in AOT reverse micelles," J. Phys. Chem. B 117, 7345-7351 (2013). P. Zhang, S. W. Ahn, and J. E. Straub,"‘Strange Kinetics’ in the temperature dependence of methionine ligand rebinding dynamics in cytochrome c," J. Phys. Chem. B 117, 7190-7202 (2013). Q. Lu, J. Kim, and J. E. Straub, "Order parameter free enhanced sampling of the vapor-liquid transition using the generalized replica exchange method," J. Chem. Phys. 138, 104119 (2013). Q. Lu, J. Kim, and J.E. Straub, "Exploring the solid-liquid phase change of an adapted Dzugutov model using Generalized Replica Exchange Method," J. Phys. Chem. B 116, 8654-8661 (2012). J. Kim, J. E. Straub, and T. Keyes, "Replica Exchange Statistical Temperature Molecular Dynamics Algorithm," J. Phys. Chem. B 116, 8646-8653 (2012). P. Zhang, E. Malolepsza, and J. E. Straub, "Dynamics of methionine ligand rebinding in cytochrome c," J. Phys. Chem. B 116, 6980-6990 (2012). D. Thirumalai, G. Reddy, and J. E. Straub, "Role of water in protein aggregation and amyloid polymorphism," Acc. Chem. Res. 45, 83-92 (2012).