José Onuchic

Harry C. and Olga K. Wiess Chair of Physics

JOSÉ ONUCHIC is a Professor of Physics and Astronomy, Chemistry and Biochemistry and Cell Biology at Rice University and is the co-Director of the NSF-sponsored Center for Theoretical Biological Physics. He did his undergraduate work at the University of São Paulo, Brazil, and received his PhD from Caltech at 1987 under the supervision of John J. Hopfield.  His thesis work was on new aspects of the theory of electron transfer reactions in biology. He then spent six month at the Institute for Theoretical Physics in Santa Barbara and after that went back to Brazil at the University of São Paulo as an Assistant Professor for two and half years. During this period he continued his work on electron transfer theory as well as on the theory of chemical reactions in condensed matter and molecular electronics. He came to the University of California at San Diego in 1990. In 1989 he was awarded the International Centre for Theoretical Physics Prize in honor of Werner Heisenberg in Trieste, Italy, in 1992 he received the Beckman Young Investigator Award, and he is a fellow of the American Physical Society. In 2006 he was elected a member of the National Academy of Sciences, USA, and in 2009 he was elected a fellow of the American Academy of Arts and Sciences and of the Brazilian Academy of Sciences. In 2011 he was awarded the Einstein Professorship by the Chinese Academy of Sciences (CAS) and recently he has been elected Fellow of the Biophysical Society. 

Publications

D.T. Capraro, M. Roy, J.N. Onuchic, S. Gosavi, and P.A. Jennings Beta-Bulge triggers route-switching on the functional landscape of interleukin-1 beta.  Proc. Natl. Acad. Sci. USA, 109 2012: 1490-1493

P.C. Whitford, K.Y. Sanbonmatsu, and J.N. Onuchic Biomolecular dynamics: order-disorder transitions and energy landscapes.  Rep. Prog. Phys., 75 2012: 076601

J.I. Sulkowska , E.J. Rawdon , K.C. Millett , J.N. Onuchic, and A. Stasiak Conservation of complex knotting and slipknotting patterns in proteins.  Proc. Natl. Acad. Sci. USA, 109 2012: E1715-E1723

J.I. Sulkowska, J.K. Noel, and J.N. Onuchic Energy landscape of knotted protein folding.  Proc. Natl. Acad. Sci. USA, 109 2012: 17783-17788

D. T. Capraro, S. Gosavi, M. Roy, J.N. Onuchic, and P.A. Jennings Folding Circular Permutants of IL-1 beta: Route Selection Driven by Functional Frustration.  PLoS ONE, 7(6) 2012: e38512

J.I. Sulkowska, F. Morcos, M. Weigt, T. Hwa and J.N. Onuchic Genomics-aided structure prediction.  Proc. Natl. Acad. Sci. USA, 109 2012: 10340-10345

J. Singh, P. Whitford, N. Hayre, J.N. Onuchic, and D. Cox Large-Scale Conformational Change in the Mammalian Prion Protein.  Prot.: Struct. Func. Bioinf., 80 2012: 1299-1307

R. Hayes, J. Noel, U. Mohanty, P. Whitford, S. Hennelly, J. Onuchic and K. Sanbonmatsu Magnesium Fluctuations Modulate RNA Dynamics in the SAM-I Riboswitch.  J. Am. Chem. Soc., 134 2012: 12043-12053

J.K. Noel, A. Schug, A. Verma, W. Wenzel, A.E. Garcia, and J.N. Onuchic Mirror Images as Naturally Competing Conformations in Protein Folding.  J. Phys. Chem. B, 116 2012: 6880-6888

D.N. Beratan and J.N. Onuchic Redox redux.  PHYSICAL CHEMISTRY CHEMICAL PHYSICS , 40 2012: 13728-13728

E.L. Baxter, P.A. Jennings and J.N. Onuchic Strand swapping regulates the iron-sulfur cluster in the diabetes drug target mitoNEET.  Proc. Natl. Acad. Sci. USA, 109 2012: 1955-1960

M.A. Jamros, L.C. Oliveira, P.C. Whitford, J.N. Onuchic, J.A. Adams, P. Jennings Substrate-Specific Reorganization of the Conformational Ensemble of CSK Implicates Novel Modes of Kinase Function.  PLoS Comp. Biol., 8(9) 2012: e1002695

H. Lammert, P.G. Wolynes, and J.N. Onuchic. The Role of Atomic Level Steric Effects and Attractive Forces in Protein Folding.  Prot.: Struct. Func. Bioinf., 80 2012: 362-373

J.K. Noel, P.C. Whitford and J.N. Onuchic. The Shadow Map: A General Contact Definition for Capturing the Dynamics of Biomolecular Folding and Function.  J. Phys. Chem. B, 116 2012: 8692-8702

E. Haglund, J.I. Sulkowska , Z. He, G.-S. Feng, J.N. Onuchic and P. Jennings The Unique Cysteine Knot Regulates the Pleotropic Hormone Leptin.  PLoS ONE, 7(9) 2012: e45654

H. Lammert, J.K. Noel and J.N. Onuchic The dominant folding route minimizes backbone distortion in SH3.  PLoS Comp. Biol., 8(11) 2012: e1002776

J.K. Noel and J.N. Onuchic The many faces of structure-based potentials: from protein folding landscapes to structural characterization of complex biomolecules.  Computational Modeling of Biological Systems: From Molecules to Pathways 2012: 31-54

B. Jana, C. Hyeon and J.N. Onuchic The origin of minus-end directionality and mechanochemistry of Ncd motors.  PLoS Comp. Biol., 8(11) 2012: e1002783

J. Wang, R.J. Oliveira, X. Chua, P.C. Whitford, J. Chahine, W. Han, E. Wang, J.N. Onuchic and V.B.P. Leite Topography of funneled landscapes determines the thermodynamics and kinetics of protein folding.  Proc. Natl. Acad. Sci. USA, 109 2012: 15763-15768

D. Schultz, J.N. Onuchic, and E. Ben-Jacob Turning death into creative force during biofilm engineering.  Proc. Natl. Acad. Sci. USA, 109 2012: 18633-18634

C. Hyeon and J.N.Onuchic A Structural Perspective on the Dynamics of Kinesin Motors.  Biophys. J., 101 2011: 2749-2759

Y. Suzuki, J.K. Noel, and J.N. Onuchic A semi-analytical description of protein folding that incorporates detailed geometrical information.  J. Chem. Phys., 134 2011: 245101

R. Nechushtai , H. Lammert , D. Michaeli , Y. Eisenberg-Domovich , J. Zuris , M. Luca , D. Capraro , A. Fish , O. Shimshon , M. Roy , A. Schug , P. Whitford , O. Livnah , J.N. Onuchic, and P.A. Jennings Allostery in the ferredoxin protein motif does not involve a conformational switch.  Proc. Natl. Acad. Sci., 108 2011: 2240-2245

F. Morcos , A. Pagnani , Br. Lunt , A. Bertolino , D. Marks , C. Sander, R. Zecchina , J.N. Onuchic, T. Hwa and Ma. Weigt Direct-coupling analysis of residue co-evolution captures native contacts across many protein families.  Proc. Natl. Acad. Sci., 108 2011: E1293-E1301

P. C. Whitford, Y. Yu, S. Hennely, A. Ahmed, F. Tama, C. Spahn, J. N. Onuchic, and K. Y. Sanbonmatsu Excited states of ribosome translocation revealed through integrative molecular modeling.  Proc. Natl. Acad. Sci., 108 2011: 18943-18948

J.A. Zuris, Y. Harir, A.R. Conlan, M. Shvartsman, S. Tamir, M.L. Paddock, J.N. Onuchic, R. Mittler, Z.I. Cabantchik, P.A. Jennings, and R. Nechushtai Facile transfer of [2Fe-2S] clusters from the diabetes drug target, MitoNEET, to an apoacceptor protein.  Proc. Natl. Acad. Sci., 108 2011: 13047-13052

E.B. Baxter, P.A. Jennings, and J.N. Onuchic Interdomain communication revealed in the diabetes drug target mitoNEET.  Proc. Natl. Acad. Sci., 108 2011: 5266-5271

F.M. Ferreira, L.C. Oliveira, G.G. Germino, J.N. Onuchic, and L.F.Onuchic The Macromolecular Assembly of Polycystin-2 Intracytosolic C-Terminal Domain.  Proc. Natl. Acad. Sci., 108 2011: 9833-9828