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José Onuchic

Research Profile

Physiology

Protein Folding

Concepts & Ideas

Occupations

Thermodynamics

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Chemicals & Drugs

Phenomena

Genes & Molecular Sequences

Amino Acid Sequences

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Publications

TOP 3
Joanna I Sułkowska; Kenneth C Millett; Jeffrey K Noel; César A Ramírez-Sarmiento; Eric J Rawdon; José N Onuchic
Knotting pathways in proteins.
Fang Bai; Jing Chen; Junfeng Gu; Honglin Li; Qiufeng Liu; Jianpeng Ma; José N Onuchic; Xicheng Wang; Yechun Xu; Hualiang Jiang
Free energy landscape for the binding process of Huperzine A to acetylcholinesterase.
José N Onuchic; Patricia A Jennings; Eshel Ben-Jacob
Learning from cancer how to defeat bacteria.

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All Publications

2013: Joanna I Sułkowska; Kenneth C Millett; Jeffrey K Noel; César A Ramírez-Sarmiento; Eric J Rawdon; José N Onuchic
Knotting pathways in proteins.
Biochemical Society transactions 2013;41(2):523-7.
2013: Fang Bai; Jing Chen; Junfeng Gu; Honglin Li; Qiufeng Liu; Jianpeng Ma; José N Onuchic; Xicheng Wang; Yechun Xu; Hualiang Jiang
Free energy landscape for the binding process of Huperzine A to acetylcholinesterase.
Proceedings of the National Academy of Sciences of the United States of America 2013;110(11):4273-8.
2013: José N Onuchic; Patricia A Jennings; Eshel Ben-Jacob
Learning from cancer how to defeat bacteria.
Proceedings of the National Academy of Sciences of the United States of America 2013;110(9):3212-3.
2013: Elizabeth Leigh Baxter; Aina E Cohen; Herbert L Axelrod; Rachel Nechushtai; José N Onuchic; Mark L Paddock; Phu Luong T Vo; Charles Wang; John A Zuris; Patricia A Jennings
Allosteric control in a metalloprotein dramatically alters function.
Proceedings of the National Academy of Sciences of the United States of America 2013;110(3):948-53.
2012: Daniel Schultz; José N Onuchic; Eshel Ben-Jacob
Turning death into creative force during biofilm engineering.
Proceedings of the National Academy of Sciences of the United States of America 2012;109(46):18633-4.
2012: David N Beratan; José N Onuchic
Redox redux.
Physical chemistry chemical physics : PCCP 2012;14(40):13728.
2012: Jin Wang; Paul C Whitford; Ronaldo J Oliveira; José N Onuchic; Erkang Wang; Jorge Chahine; Xiakun Chu; Wei Han; Vitor B P Leite
Topography of funneled landscapes determines the thermodynamics and kinetics of protein folding.
Proceedings of the National Academy of Sciences of the United States of America 2012;109(39):15763-8.
2012: Jeffrey K Noel; Paul C Whitford; José N Onuchic
The shadow map: a general contact definition for capturing the dynamics of biomolecular folding and function.
The journal of physical chemistry. B 2012;116(29):8692-702.
2012: Ryan L Hayes; Scott P Hennelly; Udayan Mohanty; Jeffrey K Noel; José N Onuchic; Paul C Whitford; Kevin Y Sanbonmatsu
Magnesium fluctuations modulate RNA dynamics in the SAM-I riboswitch.
Journal of the American Chemical Society 2012;134(29):12043-53.
2012: Paul C Whitford; Karissa Y Sanbonmatsu; José N Onuchic
Biomolecular dynamics: order-disorder transitions and energy landscapes.
Reports on progress in physics. Physical Society (Great Britain) 2012;75(7):076601.
2012: Joanna I Sułkowska; Martin Weigt; Terence Hwa; Faruck Morcos; José N Onuchic
Genomics-aided structure prediction.
Proceedings of the National Academy of Sciences of the United States of America 2012;109(26):10340-5.
2012: Jeffrey K Noel; Alexander Schug; Abhinav Verma; Wolfgang Wenzel; Angel E Garcia; José N Onuchic
Mirror images as naturally competing conformations in protein folding.
The journal of physical chemistry. B 2012;116(23):6880-8.
2012: Elizabeth Leigh Baxter; Patricia A Jennings; José N Onuchic
Strand swapping regulates the iron-sulfur cluster in the diabetes drug target mitoNEET.
Proceedings of the National Academy of Sciences of the United States of America 2012;109(6):1955-60.
2012: Dominique T Capraro; Shachi Gosavi; José N Onuchic; Melinda Roy; Patricia A Jennings
β-Bulge triggers route-switching on the functional landscape of interleukin-1β.
Proceedings of the National Academy of Sciences of the United States of America 2012;109(5):1490-3.
2012: Biman Jana; Changbong Hyeon; José N Onuchic
The origin of minus-end directionality and mechanochemistry of Ncd motors.
PLoS computational biology 2012;8(11):e1002783.
2012: Heiko Lammert; Jeffrey K Noel; José N Onuchic
The dominant folding route minimizes backbone distortion in SH3.
PLoS computational biology 2012;8(11):e1002776.
2012: Ellinor Haglund; Zhao He; Patricia A Jennings; Gen-Sheng Feng; Joanna I Sułkowska; José N Onuchic
The unique cysteine knot regulates the pleotropic hormone leptin.
PloS one 2012;7(9):e45654.
2012: Michael A Jamros; Leandro C Oliveira; José N Onuchic; Paul C Whitford; Joseph A Adams; Patricia A Jennings
Substrate-specific reorganization of the conformational ensemble of CSK implicates novel modes of kinase function.
PLoS computational biology 2012;8(9):e1002695.
2012: Dominique T Capraro; Shachi Gosavi; José N Onuchic; Melinda Roy; Patricia A Jennings
Folding circular permutants of IL-1β: route selection driven by functional frustration.
PloS one 2012;7(6):e38512.
2011: Changbong Hyeon; José N Onuchic
A structural perspective on the dynamics of kinesin motors.
Biophysical journal 2011;101(11):2749-59.
2011: Faruck Morcos; José N Onuchic; Andrea Pagnani; Chris Sander; Arianna Bertolino; Terence Hwa; Bryan Lunt; Debora S Marks; Riccardo Zecchina; Martin Weigt
Direct-coupling analysis of residue coevolution captures native contacts across many protein families.
Proceedings of the National Academy of Sciences of the United States of America 2011;108(49):E1293-301.
2011: Paul C Whitford; Yanan Yu; Christian M T Spahn; Florence Tama; Aqeel Ahmed; Scott P Hennelly; José N Onuchic; Kevin Y Sanbonmatsu
Excited states of ribosome translocation revealed through integrative molecular modeling.
Proceedings of the National Academy of Sciences of the United States of America 2011;108(47):18943-8.
2011: John A Zuris; Zvi Ioav Cabantchik; Andrea R Conlan; Yael Harir; Patricia A Jennings; Dorit Michaeli; Ron Mittler; José N Onuchic; Mark L Paddock; Maya Shvartsman; Sagi Tamir; Rachel Nechushtai
Facile transfer of [2Fe-2S] clusters from the diabetes drug target mitoNEET to an apo-acceptor protein.
Proceedings of the National Academy of Sciences of the United States of America 2011;108(32):13047-52.
2011: Yoko Suzuki; Jeffrey K Noel; José N Onuchic
A semi-analytical description of protein folding that incorporates detailed geometrical information.
The Journal of chemical physics 2011;134(24):245101.
2011: Frederico M Ferreira; Gregory G Germino; Leandro C Oliveira; José N Onuchic; Luiz F Onuchic
Macromolecular assembly of polycystin-2 intracytosolic C-terminal domain.
Proceedings of the National Academy of Sciences of the United States of America 2011;108(24):9833-8.
2011: Elizabeth L Baxter; Patricia A Jennings; José N Onuchic
Interdomain communication revealed in the diabetes drug target mitoNEET.
Proceedings of the National Academy of Sciences of the United States of America 2011;108(13):5266-71.
2011: Rachel Nechushtai; Heiko Lammert; Dorit Michaeli; Yael Eisenberg-Domovich; John A Zuris; Maria A Luca; Dominique T Capraro; Alexander Fish; Odelia Shimshon; Melinda Roy; Alexander Schug; Paul C Whitford; Oded Livnah; José N Onuchic; Patricia A Jennings
Allostery in the ferredoxin protein motif does not involve a conformational switch.
Proceedings of the National Academy of Sciences of the United States of America 2011;108(6):2240-5.
2010: Andreas H Ratje; Justus Loerke; Aleksandra Mikolajka; Matthias Brünner; Peter W Hildebrand; Agata L Starosta; Alexandra Dönhöfer; Sean connell; Paola Fucini; Thorsten Mielke; Paul C Whitford; José N Onuchic; Yanan Yu; Karissa Y Sanbonmatsu; Roland K Hartmann; Pawel A Penczek; Daniel N Wilson; Christian M T Spahn
Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites.
Nature 2010;468(7324):713-6.
2010: Alexander Schug; José N Onuchic
From protein folding to protein function and biomolecular binding by energy landscape theory.
Current opinion in pharmacology 2010;10(6):709-14.
2010: Michael A Jamros; Leandro C Oliveira; Paul C Whitford; José N Onuchic; Joseph A Adams; Donald K Blumenthal; Patricia A Jennings
Proteins at work: a combined small angle X-RAY scattering and theoretical determination of the multiple structures involved on the protein kinase functional landscape.
The Journal of biological chemistry 2010;285(46):36121-8.
2010: Paul C Whitford; José N Onuchic; Karissa Y Sanbonmatsu
Connecting energy landscapes with experimental rates for aminoacyl-tRNA accommodation in the ribosome.
Journal of the American Chemical Society 2010;132(38):13170-1.
2010: Jeffrey K Noel; Joanna I Sułkowska; José N Onuchic
Slipknotting upon native-like loop formation in a trefoil knot protein.
Proceedings of the National Academy of Sciences of the United States of America 2010;107(35):15403-8.
2010: Ronaldo J Oliveira; Paul C Whitford; Jorge Chahine; Jin Wang; José N Onuchic; Vitor B P Leite
The origin of nonmonotonic complex behavior and the effects of nonnative interactions on the diffusive properties of protein folding.
Biophysical journal 2010;99(2):600-8.
2010: Jeffrey K Noel; Paul C Whitford; Kevin Y Sanbonmatsu; José N Onuchic
SMOG@ctbp: simplified deployment of structure-based models in GROMACS.
Nucleic acids research 2010;38(Web Server issue):W657-61.
2010: Paul C Whitford; Peter Geggier; Roger B Altman; Scott C Blanchard; José N Onuchic; Karissa Y Sanbonmatsu
Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways.
RNA (New York, N.Y.) 2010;16(6):1196-204.
2010: Daniel Bölinger; Joanna I Sułkowska; Hsiao-Ping Hsu; Leonid A Mirny; Mehran Kardar; José N Onuchic; Peter Virnau
A Stevedore's protein knot.
PLoS computational biology 2010;6(4):e1000731.
2010: Alexander Schug; Martin Weigt; James A Hoch; José N Onuchic; Terence Hwa; Hendrik Szurmant
Computational modeling of phosphotransfer complexes in two-component signaling.
Methods in enzymology 2010;471():43-58.
2009: Joanna I Sułkowska; Piotr Sułkowski; José N Onuchic
Jamming proteins with slipknots and their free energy landscape.
Physical review letters 2009;103(26):268103.
2009: Alexander Schug; Martin Weigt; José N Onuchic; Terence Hwa; Hendrik Szurmant
High-resolution protein complexes from integrating genomic information with molecular simulation.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(52):22124-9.
2009: Daniel Schultz; Peter G Wolynes; Eshel Ben-Jacob; José N Onuchic
Deciding fate in adverse times: sporulation and competence in Bacillus subtilis.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(50):21027-34.
2009: Heiko Lammert; Alexander Schug; José N Onuchic
Robustness and generalization of structure-based models for protein folding and function.
Proteins 2009;77(4):881-91.
2009: Antonio F Pereira de Araujo; José N Onuchic
A sequence-compatible amount of native burial information is sufficient for determining the structure of small globular proteins.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(45):19001-4.
2009: Changbong Hyeon; Stefan Klumpp; José N Onuchic
Kinesin's backsteps under mechanical load.
Physical chemistry chemical physics : PCCP 2009;11(24):4899-910.
2009: Yann Gambin; Alexander Schug; Edward A Lemke; Jason J Lavinder; Allan Chris M Ferreon; Thomas J Magliery; José N Onuchic; Ashok A Deniz
Direct single-molecule observation of a protein living in two opposed native structures.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(25):10153-8.
2009: Paul C Whitford; Jeffrey K Noel; Shachi Gosavi; Alexander Schug; Kevin Y Sanbonmatsu; José N Onuchic
An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields.
Proteins 2009;75(2):430-41.
2009: Joanna I Sułkowska; Piotr Sułkowski; José N Onuchic
Dodging the crisis of folding proteins with knots.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(9):3119-24.
2009: Changbong Hyeon; Patricia A Jennings; Joseph A Adams; José N Onuchic
Ligand-induced global transitions in the catalytic domain of protein kinase A.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(9):3023-8.
2009: Paul C Whitford; Alexander Schug; John Saunders; Scott P Hennelly; José N Onuchic; Kevin Y Sanbonmatsu
Nonlocal helix formation is key to understanding S-adenosylmethionine-1 riboswitch function.
Biophysical journal 2009;96(2):L7-9.
2008: Daniel Schultz; Aleksandra M Walczak; José N Onuchic; Peter G Wolynes
Extinction and resurrection in gene networks.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(49):19165-70.
2008: Dominique T Capraro; Melinda Roy; José N Onuchic; Patricia Jennings
Backtracking on the folding landscape of the beta-trefoil protein interleukin-1beta?
Proceedings of the National Academy of Sciences of the United States of America 2008;105(39):14844-8.
2008: Jian Liu; Arshad Desai; José N Onuchic; Terence Hwa
An integrated mechanobiochemical feedback mechanism describes chromosome motility from prometaphase to anaphase in mitosis.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(37):13752-7.
2008: Benjamin T Andrews; Shachi Gosavi; John M Finke; José N Onuchic; Patricia Jennings
The dual-basin landscape in GFP folding.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(34):12283-8.
2008: Shachi Gosavi; Paul C Whitford; Patricia Jennings; José N Onuchic
Extracting function from a beta-trefoil folding motif.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(30):10384-9.
2008: Leandro C Oliveira; Alexander Schug; José N Onuchic
Geometrical features of the protein folding mechanism are a robust property of the energy landscape: a detailed investigation of several reduced models.
The journal of physical chemistry. B 2008;112(19):6131-6.
2008: Paul C Whitford; Shachi Gosavi; José N Onuchic
Conformational transitions in adenylate kinase. Allosteric communication reduces misligation.
The Journal of biological chemistry 2008;283(4):2042-8.
2008: Yoko Suzuki; Jeff K Noel; José N Onuchic
An analytical study of the interplay between geometrical and energetic effects in protein folding.
The Journal of chemical physics 2008;128(2):025101.
2007: Alexander Schug; Paul C Whitford; Yaakov Levy; José N Onuchic
Mutations as trapdoors to two competing native conformations of the Rop-dimer.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(45):17674-9.
2007: Daniel Schultz; Eshel Ben-Jacob; José N Onuchic; Peter G Wolynes
Molecular level stochastic model for competence cycles in Bacillus subtilis.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(45):17582-7.
2007: Changbong Hyeon; José N Onuchic
Mechanical control of the directional stepping dynamics of the kinesin motor.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(44):17382-7.
2007: Jian Liu; Arshad Desai; José N Onuchic; Terence Hwa
A mechanobiochemical mechanism for monooriented chromosome oscillation in mitosis.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(41):16104-9.
2007: Sichun Yang; José N Onuchic; Angel E García; Herbert Levine
Folding time predictions from all-atom replica exchange simulations.
Journal of molecular biology 2007;372(3):756-63.
2007: Daniel Schultz; José N Onuchic; Peter G Wolynes
Understanding stochastic simulations of the smallest genetic networks.
The Journal of chemical physics 2007;126(24):245102.
2007: John M Finke; Patricia Jennings; Jennifer C Lee; José N Onuchic; Jay R Winkler
Equilibrium unfolding of the poly(glutamic acid)20 helix.
Biopolymers 2007;86(3):193-211.
2007: Paul C Whitford; Osamu Miyashita; Yaakov Levy; José N Onuchic
Conformational transitions of adenylate kinase: switching by cracking.
Journal of molecular biology 2007;366(5):1661-71.
2007: Changbong Hyeon; José N Onuchic
Internal strain regulates the nucleotide binding site of the kinesin leading head.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(7):2175-80.
2007: Jamie E Mills; Paul C Whitford; Jennifer Shaffer; José N Onuchic; Joseph A Adams; Patricia Jennings
A novel disulfide bond in the SH2 Domain of the C-terminal Src kinase controls catalytic activity.
Journal of molecular biology 2007;365(5):1460-8.
2007: Yaakov Levy; José N Onuchic; Peter G Wolynes
Fly-casting in protein-DNA binding: frustration between protein folding and electrostatics facilitates target recognition.
Journal of the American Chemical Society 2007;129(4):738-9.
2006: Jian Liu; José N Onuchic
A driving and coupling "Pac-Man" mechanism for chromosome poleward translocation in anaphase A.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(49):18432-7.
2006: B Robert Simler; Yaakov Levy; José N Onuchic; C Robert Matthews
The folding energy landscape of the dimerization domain of Escherichia coli Trp repressor: a joint experimental and theoretical investigation.
Journal of molecular biology 2006;363(1):262-78.
2006: José N Onuchic; Chigusa Kobayashi; Osamu Miyashita; Patricia Jennings; Kim K Baldridge
Exploring biomolecular machines: energy landscape control of biological reactions.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2006;361(1472):1439-43.
2006: Kei-ichi Okazaki; Nobuyasu Koga; Shoji Takada; José N Onuchic; Peter G Wolynes
Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(32):11844-9.
2006: Sichun Yang; José N Onuchic; Herbert Levine
Effective stochastic dynamics on a protein folding energy landscape.
The Journal of chemical physics 2006;125(5):054910.
2006: Leslie L Chavez; Shachi Gosavi; Patricia Jennings; José N Onuchic
Multiple routes lead to the native state in the energy landscape of the beta-trefoil family.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(27):10254-8.
2006: Shachi Gosavi; Leslie L Chavez; Patricia Jennings; José N Onuchic
Topological frustration and the folding of interleukin-1 beta.
Journal of molecular biology 2006;357(3):986-96.
2006: Yaakov Levy; José N Onuchic
Mechanisms of protein assembly: lessons from minimalist models.
Accounts of chemical research 2006;39(2):135-42.
2006: Yaakov Levy; José N Onuchic
Water mediation in protein folding and molecular recognition.
Annual review of biophysics and biomolecular structure 2006;35():389-415.
2005: Aleksandra M Walczak; José N Onuchic; Peter G Wolynes
Absolute rate theories of epigenetic stability.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(52):18926-31.
2005: J E M Hornos; D Schultz; G C P Innocentini; J Wang; Aleksandra M Walczak; José N Onuchic; Peter G Wolynes
Self-regulating gene: an exact solution.
Physical review. E, Statistical, nonlinear, and soft matter physics 2005;72(5 Pt 1):051907.
2005: Sichun Yang; Herbert Levine; José N Onuchic; Daniel Cox
Structure of infectious prions: stabilization by domain swapping.
FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2005;19(13):1778-82.
2005: Sichun Yang; Herbert Levine; José N Onuchic
Protein oligomerization through domain swapping: role of inter-molecular interactions and protein concentration.
Journal of molecular biology 2005;352(1):202-11.
2005: Yoko Suzuki; José N Onuchic
Modeling the interplay between geometrical and energetic effects in protein folding.
The journal of physical chemistry. B 2005;109(34):16503-10.
2005: Lilly Wong; Scot A Lieser; Osamu Miyashita; Meghan Miller; Kjetil Tasken; José N Onuchic; Joseph A Adams; Virgil L Woods; Patricia Jennings
Coupled motions in the SH2 and kinase domains of Csk control Src phosphorylation.
Journal of molecular biology 2005;351(1):131-43.
2005: John M Finke; José N Onuchic
Equilibrium and kinetic folding pathways of a TIM barrel with a funneled energy landscape.
Biophysical journal 2005;89(1):488-505.
2005: Samuel S Cho; Yaakov Levy; José N Onuchic; Peter G Wolynes
Overcoming residual frustration in domain-swapping: the roles of disulfide bonds in dimerization and aggregation.
Physical biology 2005;2(2):S44-55.
2005: Melinda Roy; Leslie L Chavez; John M Finke; David K Heidary; José N Onuchic; Patricia Jennings
The native energy landscape for interleukin-1beta. Modulation of the population ensemble through native-state topology.
Journal of molecular biology 2005;348(2):335-47.
2005: Angel E Garcia; José N Onuchic
Folding a protein in the computer: reality or hope?
Structure (London, England : 1993) 2005;13(4):497-8.
2005: Osamu Miyashita; Melvin Y Okamura; José N Onuchic
Interprotein electron transfer from cytochrome c2 to photosynthetic reaction center: tunneling across an aqueous interface.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(10):3558-63.
2005: Yaakov Levy; Samuel S Cho; José N Onuchic; Peter G Wolynes
A survey of flexible protein binding mechanisms and their transition states using native topology based energy landscapes.
Journal of molecular biology 2005;346(4):1121-45.
2005: Yaakov Levy; Samuel S Cho; Tongye Shen; José N Onuchic; Peter G Wolynes
Symmetry and frustration in protein energy landscapes: a near degeneracy resolves the Rop dimer-folding mystery.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(7):2373-8.
2005: Osamu Miyashita; Peter G Wolynes; José N Onuchic
Simple energy landscape model for the kinetics of functional transitions in proteins.
The journal of physical chemistry. B 2005;109(5):1959-69.
2004: Vitor B P Leite; José N Onuchic; George Stell; Jin Wang
Probing the kinetics of single molecule protein folding.
Biophysical journal 2004;87(6):3633-41.
2004: Osamu Miyashita; José N Onuchic; Melvin Y Okamura
Transition state and encounter complex for fast association of cytochrome c2 with bacterial reaction center.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(46):16174-9.
2004: Sichun Yang; Samuel S Cho; Yaakov Levy; Margaret S Cheung; Herbert Levine; Peter G Wolynes; José N Onuchic
Domain swapping is a consequence of minimal frustration.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(38):13786-91.
2004: John M Finke; Margaret S Cheung; José N Onuchic
A structural model of polyglutamine determined from a host-guest method combining experiments and landscape theory.
Biophysical journal 2004;87(3):1900-18.
2004: Lilly Wong; Scot A Lieser; Barbara Chie-Leon; Osamu Miyashita; Brandon E Aubol; Jennifer Shaffer; José N Onuchic; Patricia Jennings; Virgil L Woods; Joseph A Adams
Dynamic coupling between the SH2 domain and active site of the COOH terminal Src kinase, Csk.
Journal of molecular biology 2004;341(1):93-106.
2004: Leslie L Chavez; José N Onuchic; Cecilia Clementi
Quantifying the roughness on the free energy landscape: entropic bottlenecks and protein folding rates.
Journal of the American Chemical Society 2004;126(27):8426-32.
2004: Antitsa D Stoycheva; Charles L Brooks; José N Onuchic
Gatekeepers in the ribosomal protein s6: thermodynamics, kinetics, and folding pathways revealed by a minimalist protein model.
Journal of molecular biology 2004;340(3):571-85.
2004: Yaakov Levy; Amedeo Caflisch; José N Onuchic; Peter G Wolynes
The folding and dimerization of HIV-1 protease: evidence for a stable monomer from simulations.
Journal of molecular biology 2004;340(1):67-79.
2004: Yaakov Levy; José N Onuchic
Water and proteins: a love-hate relationship.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(10):3325-6.
2004: A M Fernández-Escamilla; Margaret S Cheung; M Cristina Vega; Matthias Wilmanns; José N Onuchic; Luis Serrano
Solvation in protein folding analysis: combination of theoretical and experimental approaches.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(9):2834-9.
2004: Ming-Liang Tan; Ilya A Balabin; José N Onuchic
Dynamics of electron transfer pathways in cytochrome C oxidase.
Biophysical journal 2004;86(3):1813-9.
2004: José N Onuchic; Peter G Wolynes
Theory of protein folding.
Current opinion in structural biology 2004;14(1):70-5.
2004: Yaakov Levy; Peter G Wolynes; José N Onuchic
Protein topology determines binding mechanism.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(2):511-6.
2003: Angel E García; José N Onuchic
Folding a protein in a computer: an atomic description of the folding/unfolding of protein A.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(24):13898-903.
2003: Osamu Miyashita; José N Onuchic; Peter G Wolynes
Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(22):12570-5.
2003: Osamu Miyashita; José N Onuchic; Melvin Y Okamura
Continuum electrostatic model for the binding of cytochrome c2 to the photosynthetic reaction center from Rhodobacter sphaeroides.
Biochemistry 2003;42(40):11651-60.
2003: Nancy Sung; Jeffrey I Gordon; George D Rose; Elizabeth D Getzoff; Stephen J Kron; David Mumford; José N Onuchic; Norbert F Scherer; DeWitt L Sumners; Nancy Kopell
Science education. Educating future scientists.
Science (New York, N.Y.) 2003;301(5639):1485.
2003: Cecilia Clementi; Angel E García; José N Onuchic
Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism: all-atom representation study of protein L.
Journal of molecular biology 2003;326(3):933-54.
2002: Joan-Emma Shea; José N Onuchic; Charles L Brooks
Probing the folding free energy landscape of the Src-SH3 protein domain.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(25):16064-8.
2002: Osamu Miyashita; H L Axelrod; José N Onuchic
Different scenarios for inter-protein electron tunneling: the effect of water-mediated pathways.
Journal of biological physics 2002;28(3):383-94.
2002: Steven S Plotkin; José N Onuchic
Understanding protein folding with energy landscape theory. Part II: Quantitative aspects.
Quarterly reviews of biophysics 2002;35(3):205-86.
2002: Steven S Plotkin; José N Onuchic
Understanding protein folding with energy landscape theory. Part I: Basic concepts.
Quarterly reviews of biophysics 2002;35(2):111-67.
2002: Jorge Chahine; Hugh Nymeyer; Vitor B P Leite; Nicholas D Socci; José N Onuchic
Specific and nonspecific collapse in protein folding funnels.
Physical review letters 2002;88(16):168101.
2002: Margaret S Cheung; Angel E García; José N Onuchic
Protein folding mediated by solvation: water expulsion and formation of the hydrophobic core occur after the structural collapse.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(2):685-90.
2001: Cecilia Clementi; Patricia Jennings; José N Onuchic
Prediction of folding mechanism for circular-permuted proteins.
Journal of molecular biology 2001;311(4):879-90.
2001: Charles L Brooks; José N Onuchic; D J Wales
Statistical thermodynamics. Taking a walk on a landscape.
Science (New York, N.Y.) 2001;293(5530):612-3.
2000: Ilya A Balabin; José N Onuchic
Dynamically controlled protein tunneling paths in photosynthetic reaction centers.
Science (New York, N.Y.) 2000;290(5489):114-7.
2000: Steven S Plotkin; José N Onuchic
Investigation of routes and funnels in protein folding by free energy functional methods.
Proceedings of the National Academy of Sciences of the United States of America 2000;97(12):6509-14.
2000: Cecilia Clementi; Patricia Jennings; José N Onuchic
How native-state topology affects the folding of dihydrofolate reductase and interleukin-1beta.
Proceedings of the National Academy of Sciences of the United States of America 2000;97(11):5871-6.
2000: Cecilia Clementi; Hugh Nymeyer; José N Onuchic
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.
Journal of molecular biology 2000;298(5):937-53.
2000: Hugh Nymeyer; Nicholas D Socci; José N Onuchic
Landscape approaches for determining the ensemble of folding transition states: success and failure hinge on the degree of frustration.
Proceedings of the National Academy of Sciences of the United States of America 2000;97(2):634-9.
2000: José N Onuchic; Hugh Nymeyer; Angel E García; Jorge Chahine; Nicholas D Socci
The energy landscape theory of protein folding: insights into folding mechanisms and scenarios.
Advances in protein chemistry 2000;53():87-152.
1999: N Hillson; José N Onuchic; Angel E García
Pressure-induced protein-folding/unfolding kinetics.
Proceedings of the National Academy of Sciences of the United States of America 1999;96(26):14848-53.
1999: J E Shea; José N Onuchic; Charles L Brooks
Exploring the origins of topological frustration: design of a minimally frustrated model of fragment B of protein A.
Proceedings of the National Academy of Sciences of the United States of America 1999;96(22):12512-7.
1999: N D Socci; José N Onuchic; P G Wolynes
Stretching lattice models of protein folding.
Proceedings of the National Academy of Sciences of the United States of America 1999;96(5):2031-5.
1998: Charles L Brooks; Martin Gruebele; José N Onuchic; P G Wolynes
Chemical physics of protein folding.
Proceedings of the National Academy of Sciences of the United States of America 1998;95(19):11037-8.
1998: N D Socci; José N Onuchic; P G Wolynes
Protein folding mechanisms and the multidimensional folding funnel.
Proteins 1998;32(2):136-58.
1998: Hugh Nymeyer; Angel E García; José N Onuchic
Folding funnels and frustration in off-lattice minimalist protein landscapes.
Proceedings of the National Academy of Sciences of the United States of America 1998;95(11):5921-8.
1997: José N Onuchic
Contacting the protein folding funnel with NMR.
Proceedings of the National Academy of Sciences of the United States of America 1997;94(14):7129-31.
1996: Peter G Wolynes; Zaida Luthey-Schulten; José N Onuchic
Fast-folding experiments and the topography of protein folding energy landscapes.
Chemistry & biology 1996;3(6):425-32.
1996: José N Onuchic; N D Socci; Zaida Luthey-Schulten; Peter G Wolynes
Protein folding funnels: the nature of the transition state ensemble.
Folding & design 1996;1(6):441-50.
1995: J J Regan; Angel J Di Bilio; R Langen; L K Skov; Jay R Winkler; H B Gray; José N Onuchic
Electron tunneling in azurin: the coupling across a beta-sheet.
Chemistry & biology 1995;2(7):489-96.
1995: W B Curry; M D Grabe; I V Kurnikov; S S Skourtis; DN Beratan; J J Regan; A J Aquino; P Beroza; José N Onuchic
Pathways, pathway tubes, pathway docking, and propagators in electron transfer proteins.
Journal of bioenergetics and biomembranes 1995;27(3):285-93.
1995: José N Onuchic; Peter G Wolynes; Zaida Luthey-Schulten; N D Socci
Toward an outline of the topography of a realistic protein-folding funnel.
Proceedings of the National Academy of Sciences of the United States of America 1995;92(8):3626-30.
1995: Peter G Wolynes; José N Onuchic; Devarajan Thirumalai
Navigating the folding routes.
Science (New York, N.Y.) 1995;267(5204):1619-20.
1995: J D Bryngelson; José N Onuchic; N D Socci; Peter G Wolynes
Funnels, pathways, and the energy landscape of protein folding: a synthesis.
Proteins 1995;21(3):167-95.
1992: DN Beratan; José N Onuchic; Jay R Winkler; H B Gray
Electron-tunneling pathways in proteins.
Science (New York, N.Y.) 1992;258(5089):1740-1.
1992: P E Leopold; Mauricio Montal; José N Onuchic
Protein folding funnels: a kinetic approach to the sequence-structure relationship.
Proceedings of the National Academy of Sciences of the United States of America 1992;89(18):8721-5.
1992: José N Onuchic; DN Beratan; Jay R Winkler; H B Gray
Pathway analysis of protein electron-transfer reactions.
Annual review of biophysics and biomolecular structure 1992;21():349-77.
1991: DN Beratan; J N Betts; José N Onuchic
Protein electron transfer rates set by the bridging secondary and tertiary structure.
Science (New York, N.Y.) 1991;252(5010):1285-8.
1988: William Bialek; José N Onuchic
Protein dynamics and reaction rates: mode-specific chemistry in large molecules?
Proceedings of the National Academy of Sciences of the United States of America 1988;85(16):5908-12.
1988: James A Cowan; R K Upmacis; DN Beratan; José N Onuchic; H B Gray
Long-range electron transfer in myoglobin.
Annals of the New York Academy of Sciences 1988;550():68-84.