Leslie L. Chavez, Shachi Gosavi, Patricia A. Jennings, and Jose' N. Onuchic.
Multiple routes lead to the native state in the energy landscape of the Beta-
trefoil family.
PNAS
103(27) 10254 - 10258 (2006).
[PDF] Publication
lists from Onuchic's group More to
come... Last update: 9-22-04
Shachi Gosavi, Leslie L. Chavez, Patricia A. Jennings, and Jose' N. Onuchic.
Topological Frustration and the Folding of Interleukin-1beta.
Journal of Molecular Biology
357(3) 986 - 996 (2006).
[PDF]
Sichun Yang, H. Levine, Jose' N. Onuchic, and Daniel L. Cox
Structure of infectious prions: stabilization by domain swapping.
FASEB J.
19 1178-1182 (2005).
[PDF]
Sichun Yang, H. Levine, and Jose' N. Onuchic
Protein oligomerization through domain swapping: Role of inter-molecular
interactions and protein concentration.
J Mol Biol.
352 (1) 202-211 (2005).
[PDF]
Wong L, Lieser SA, Miyashita O, Miller M, Tasken K, Onuchic JN, Adams JA,
Woods VL Jr, Jennings PA.
Coupled Motions in the SH2 and Kinase Domains of Csk Control Src Phosphorylation.
J Mol Biol.
351 (1) 131-143 (2005).
Finke JM, Onuchic JN.
Equilibrium and Kinetic Folding Pathways of a TIM Barrel with a Funneled Energy Landscape.
Biophys J.
89(1) 488-505 (2005).
Melinda Roy, Leslie L. Chavez, John M. Finke, David K. Heidary, Jose' N. Onuchic and Patricia A. Jennings.
The Native Energy Landscape for Interleukin-1beta. Modulation of the Population
Ensemble through Native-state Topology.
J. Mol. Biol. 348 (2) 335 - 347 (2005).
[html]
[PDF]
Miyashita O, Wolynes PG, Onuchic JN
Simple energy landscape model for the kinetics of functional transitions in proteins.
JOURNAL OF PHYSICAL CHEMISTRY B
109 (5) 1959-1969 (2005).
Sichun Yang, Samuel S. Cho, Yaakov Levy, Margaret S. Cheung, Herbert
Levine, Peter G. Wolynes, and Jose' N. Onuchic.
Domain swapping is a consequence of minimal frustration.
Proc. Natl. Acad. Sci.
101 (38) 13786-13791 (2004).
[PDF]
Leslie L. Chavez, Jose' N. Onuchic, and Cecilia Clementi.
Quantifying the roughness on the Free Energy Landscape: Entropic bottlenecks and
protein folding rates.
J. Am. Chem. Soc.
126 (27) 8426 - 8432 (2004).
Electronic Edition
[PDF]
Wong L, Lieser S, Chie-Leon B, Miyashita O, Aubol B, Shaffer J,
Onuchic JN, Jennings PA, Woods VL, Adams JA.
Dynamic coupling between the SH2 domain and active site of the COOH
terminal Src kinase, Csk.
J. of Mol. Bio.
341 (1) 93-106 (2004).
Stoycheva AD. Brooks CL. Onuchic JN.
Gatekeepers in the ribosomal protein S6: Thermodynamics, kinetics, and folding pathways revealed by a minimalist protein model.
J. of Mol. Bio.
340 (3) 571-585 (2004).
Levy Y. Caflisch A. Onuchic JN. Wolynes PG.
The folding and dimerization of HIV-1 protease: Evidence for a stable monomer from simulations.
Journal of Molecular Biology.
340(1) 67-79 (2004).
Levy Y. Onuchic JN.
Water and proteins: A love-hate relationship.
[Editorial Material] Proc. Natl. Acad. Sci.
101(10) 3325-3326 (2004).
Onuchic JN. Wolynes PG.
Theory of protein folding. Current Opinion in Structural Biology. 14(1):70-75, 2004 Feb.
A. M. Fernndez-Escamilla, M. S. Cheung, M. C. Vega, M. Wilmanns, J. N. Onuchic, and L. Serrano.
Solvation in protein folding analysis: Combination of theoretical and
experimental approaches
Proc. Natl. Acad. Sci.
101 2834-2839 (2004).
Y. Levy, P. G. Wolynes, and J. N. Onuchic.
Protein topology determines binding mechanism
Proc. Natl. Acad. Sci.
101 (2) 511-516 (2004).
Miyashita O, Onuchic JN, Wolynes PG.
Nonlinear elasticity, proteinquakes, and the energy landscapes of
functional transitions in proteins.
Proc. Natl. Acad. Sci.
100 (22) 12570-12575 (2003).
Jose N. Onuchic and Angel E. Garcia.
Folding a protein in a computer: An atomic description of the folding/unfolding of protein A.
Proc. Natl. Acad. Sci.
100 (24) 13898-13903 (2003).
[PDF]
Margaret S. Cheung, John M. Finke, Ben Callahan, and Jose N. Onuchic.
Exploring the interplay of topology and secondary structural formation in the protein folding problem.
J Phys Chem B
107 (40) 11193-11200 (2003).
Antitsa D. Stoycheva, Jose N. Onuchic, and Charles L. Brooks.
Effect of Gatekeepers on the early folding kinetics of a model beta-barrel protein.
J Chem Phys
119 (11) 5722-5729 (2003).
Clementi, C; Garcia, AE; Onuchic, JN.
Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism all-atom representation study of protein L.
J Mol Bio
326 (3) 879-890 (2003).
Margaret S. Cheung, Angel E. Garcia, and Jose N. Onuchic.
Protein folding mediated by solvation: Water expulsion and formation of the
hydrophobic core occur after the structural collapse.
Proc Natl Acad Sci
99 (2) 685-690 (2002).
Shea, JE; Onuchic;
Brooks, CL.
Probing the folding free energy landscape of the Src-SH3 protein Domain.
Proc Natl Acad Sci
99 (25) 16064-68 (2002).
Chahine, J; Nymeyer, H; Leite, V; Socci, N; Onuchic, J.
Specific and nonspecific collapse in protein folding funnels.
Phys Rev Lett
88 (16) p. 168101 (2002).
Clementi, C; Jennings, PA; Onuchic, JN.
Prediction of folding mechanism for circluar-permuted proteins.
J Mol Bio
311 (4) 879-890 (2001).
Shea, JE; Onuchic;
Brooks, CL.
Energetic frustration and the nature of the transition state in protein
folding.
J Chem Phys
113(17) 7663-7671 (2000).
Clementi, C; Nymeyer, H; Onuchic, JN.
Topological and energetic factors: What determines the structural details
of the transition state ensemble and "en-route" intermediates for protein
folding? An investigation for small globular proteins.
J Mol Bio
298(5) 937-953 (2000).
Plotkin S.S. and
Onuchic, J.N. Investigation of routes and
funnels in protein folding by free energy functional methods.
Proc Natl Acad Sci
97 (12) 6509-6514 (2000).
postscript version
Clementi, C; Jennings, PA; Onuchic, JN.
How native-state topology affects the folding of dihydrofolate reductase
and interleukin-1 beta.
Proc Natl Acad Sci
97 (11) 5871-5876 (2000).
Garcia, AE; Hillson, N; Onuchic, JN.
Solvent effects on protein folding/unfolding.
Progress Of Theoretical Physics Suppliment
138 282-291.(2000).
Nymeyer, H; Socci, ND; Onuchic, JN.
Landscape approaches for determining the ensemble of folding transition
states: Success and failure hinge on the degree of frustration.
Proc Natl Acad Sci
97(2)634-639(2000).
Hillson, N; Onuchic, JN; Garcia, AE.
Pressure-induced protein-folding/unfolding kinetics.
Proc Natl Acad Sci
96(26)14848-14853.(1999).
Shea, JE; Onuchic, JN; Brooks, CL.
Exploring the origins of topological frustration: Design of a minimally
frustrated model of fragment B of protein A.
Proc Natl Acad Sci
96(22)12512-12517(1999).
Onuchic, JN; Wang, J; Wolynes, PG.
Analyzing single molecule trajectories on complex energy landscapes using
replica correlation functions.
Chemical Physics
271(1)175-184(1999). postscript
version
Socci, N,D.,
Onuchic, J.N., and Wolynes, P.G. Stretching
Lattice Models of Protein Folding.
Proc Natl Acad Sci USA
96(5)2031-2035.(1999).
postscript version Onuchic, J.N.,
Nymeyer, H., Garcia, A.E., Chahine, J., and Socci, N.D. The Energy Landscape Theory of Protein Folding: Insights into
Folding Mechanisms and Scenarios.
Advances in Protein Chemistry
53 87-152 (2000)
postscript version Socci, N. D.,
Onuchic, J.N., and Wolynes, P. G. Diffusive
Dynamics of the Reaction Coordinate for Protein Folding Funnels.
In Press: J. Chem. Phys. April 15, 1996. HTML version, postscript version Socci, N. D., and
Onuchic, J. N. Kinetic and thermodynamic
analysis of proteinlike heteropolymers: Monte Carlo histogram method.
J Chem Phys, 103(11) 4732-4744 (1995). postscript version Socci, N. D., and
Onuchic, J. N. Folding kinetics of proteinlike
heteropolymers.
J Chem Phys, 101(2) 1519-1528
(1994). HTML version,
postscript version Socci, N. D.,
Bialek, W., and Onuchic, J. N. Properties and
origins of protein secondary structure.
Phys Rev E
49(4b) 3440-3443 (1994). postscript version