Funnels, pathways, and the energy landscape of protein folding: A synthesis

Bryngelson, Joseph D., Onuchic, José Nelson, Socci, Nicholas D., Wolynes, Peter G.·1995·Proteins: Structure, Function, and Bioinformatics

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  1. Protein folding: The stepwise assembly of foldon units
    Haripada Maity, Mita Maity, Krishna M.G. Mallela, Leland C. Mayne, S. Walter Englander · 2005 · Proceedings of the National Academy of Sciences
  2. Clustering of low-energy conformations near the native structures of small proteins
    David Shortle, Kim T. Simons, David A. Baker · 1998 · Proceedings of the National Academy of Sciences
  3. Progress in Modeling of Protein Structures and Interactions.
    Schueler-Furman, Ora, Wang, Chu, Bradley, Phil, Misura, Kira, Baker, David · 2005 · Science
  4. Conformational changes associated with protein–protein interactions
    Chern-Sing Goh, Duncan Milburn, Mark Gerstein · 2004 · Current Opinion in Structural Biology
  5. Chaperonin Function: Folding by Forced Unfolding
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  6. Heteropolymer freezing and design: Towards physical models of protein folding
    Pande, Vijay S., Grosberg, Alexander Yu., Tanaka, Toyoichi · 2000 · Reviews of Modern Physics
  7. Metal-Directed Protein Self-Assembly
    Eric N. Salgado, Robert J. Radford, F. Akif Tezcan · 2010 · Accounts of Chemical Research
  8. Experimental determination of upper bound for transition path times in protein folding from single-molecule photon-by-photon trajectories
    Hoi Sung Chung, John M. Louis, William A. Eaton · 2009 · Proceedings of the National Academy of Sciences
  9. Principles of Protein Stability and Their Application in Computational Design
    Adi Goldenzweig, Sarel Jacob Fleishman · 2018 · Annual Review of Biochemistry
  10. Protein unfolding: Rigidity lost
    Andrew J. Rader, Brandon M. Hespenheide, Leslie A. Kuhn, Michael F. Thorpe · 2002 · Proceedings of the National Academy of Sciences
  11. Structure-derived potentials and protein simulations
    Robert L. Jernigan, İvet Bahar · 1996 · Current Opinion in Structural Biology
  12. The experimental survey of protein-folding energy landscapes
    Mikael Oliveberg, Peter Guy Wolynes · 2005 · Quarterly Reviews of Biophysics
  13. Functional aspects of protein flexibility
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  14. RNA and Protein Folding: Common Themes and Variations
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  15. The Levinthal paradox: yesterday and today
    Martin Karplus · 1997 · Folding and Design
  16. Kinetics of Folding of Proteins and RNA
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  18. Evidence for barrier-limited protein folding kinetics on the microsecond time scale
    M.C.Ramachandra Shastry, Heinrich Röder · 1998 · Nature Structural Biology
  19. Landscapes and their correlation functions
    Peter Florian Stadler · 1996 · Journal of Mathematical Chemistry
  20. An expanding arsenal of experimental methods yields an explosion of insights into protein folding mechanisms
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  21. Modeling evolutionary landscapes: Mutational stability, topology, and superfunnels in sequence space
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  22. Sub-microsecond Protein Folding
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  23. Non-native α-helical intermediate in the refolding of β-lactoglobulin, a predominantly β-sheet protein
    Daizo Hamada, Shin-ichi Segawa, Yuji Goto · 1996 · Nature Structural & Molecular Biology
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    Shuji Akiyama, Satoshi Takahashi, Tetsunari Kimura, Koichiro Ishimori, Isao Morishima, Yukihiro Nishikawa, Tetsuro Fujisawa · 2002 · Proceedings of the National Academy of Sciences
  26. Pathways for protein folding: is a new view needed?
    Vijay S. Pande, Alexander Y. Grosberg, Toyoichi Tanaka, Daniel S. Rokhsar · 1998 · Current Opinion in Structural Biology
  27. Chaperonin-facilitated protein folding: optimization of rate and yield by an iterative annealing mechanism.
    Matthew J. Todd, G. Lorimer, D. Thirumalai · 1996 · Proceedings of the National Academy of Sciences of the United States of America
  28. The energy landscape theory of protein folding: Insights into folding mechanisms and scenarios
    José N. Onuchic, Hugh Nymeyer, Angel E. Garcı́a, Jorge Chahine, Nicholas D. Socci · 2000 · Advances in protein chemistry
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    Chi-Kin Chan, Yi Hu, Satoshi Takahashi, Denis L. Rousseau, William A. Eaton, James Hofrichter · 1997 · Proceedings of the National Academy of Sciences
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    Simona Cocco, Christoph Feinauer, Matteo Figliuzzi, Rémi Monasson, Martin Weigt · 2017 · Reports on Progress in Physics
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    Nicholas J. Anthis, G. Marius Clore · 2015 · Quarterly Reviews of Biophysics
  38. Potential Energy and Free Energy Landscapes
    David J. Wales, Tetyana V. Bogdan · 2006 · The Journal of Physical Chemistry B
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    Gupta, Rajat, Kasturi, Prasad, Bracher, Andreas, Loew, Christian, Zheng, Min, Villella, Adriana, Garza, Dan, Hartl, F Ulrich, Raychaudhuri, Swasti · 2011 · Nature Methods
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    Rick Russell, Xiaowei Zhuang, Hazen P. Babcock, Ian S. Millett, Sebastian Doniach, Steven Chu, Daniel Herschlag · 2001 · Proceedings of the National Academy of Sciences
  42. Simplified amino acid alphabets for protein fold recognition and implications for folding
    Lynne Reed Murphy, Anders Wallqvist, Ronald M. Levy · 2000 · Protein Engineering Design and Selection
  43. Viscosity Dependence of the Folding Rates of Proteins
    Dmitri K. Klimov, Dave Thirumalai · 1997 · Physical Review Letters
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    Tobias Sikosek, Hue Sun Chan · 2014 · Journal of The Royal Society Interface
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    Robert H. Leary · 2000 · Journal of Global Optimization
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    Shoji Takada · 2012 · Current Opinion in Structural Biology
  57. How protein thermodynamics and folding mechanisms are altered by the chaperonin cage: Molecular simulations
    Fumiko Takagi, Nobuyasu Koga, Shoji Takada · 2003 · Proceedings of the National Academy of Sciences
  58. Folding funnels and energy landscapes of larger proteins within the capillarity approximation
    Wolynes, Peter G. · 1997 · Proceedings of the National Academy of Sciences
  59. RNA folding energy landscapes
    Shi‐Jie Chen, Ken A. Dill · 2000 · Proceedings of the National Academy of Sciences
  60. Quantifying the Roughness on the Free Energy Landscape: Entropic Bottlenecks and Protein Folding Rates
    Leslie L. Chavez, José N. Onuchic, Cecilia Clementi · 2004 · Journal of the American Chemical Society
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    Gregory R. Bowman, Vijay S. Pande · 2010 · Proceedings of the National Academy of Sciences
  64. Peptoid nanosheets exhibit a new secondary-structure motif
    Ranjan V. Mannige, Thomas K. Haxton, Caroline Proulx, Ellen Jean Robertson, Alessia Battigelli, Glenn L. Butterfoss, Ronald N. Zuckermann, Stephen Whitelam · 2015 · Nature
  65. Chain Length Scaling of Protein Folding Time
    A. M. Gutin, Victor Abkevich, Eugene I. Shakhnovich · 1996 · Physical Review Letters
  66. Protein folding and misfolding: mechanism and principles
    S. Walter Englander, Leland C. Mayne, Krishna M.G. Mallela · 2007 · Quarterly Reviews of Biophysics
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    Hoi Sung Chung, Stefano Piana, David Elliot Shaw, William A. Eaton · 2015 · Science
  69. Submillisecond kinetics of protein folding
    William A. Eaton, Víctor Muñoz, Peggy A. Thompson, Chi-Kin Chan, James Hofrichter · 1997 · Current Opinion in Structural Biology
  70. Energy Landscapes: From Clusters to Biomolecules
    David J. Wales, Jonathan P. K. Doye, Mark A. Miller, Paul N. Mortenson, Tiffany R. Walsh · 2000 · Advances in chemical physics
  71. On the role of frustration in the energy landscapes of allosteric proteins
    Diego Ulises Ferreiro, Joseph A. Hegler, Elizabeth A. Komives, Peter Guy Wolynes · 2011 · Proceedings of the National Academy of Sciences
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    Eszter Herczenik, Martijn F.B.G. Gebbink · 2008 · The FASEB Journal
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    Cheng‐Yen Huang, Zelleka Getahun, Yongjin Zhu, Jason W. Klemke, William F. DeGrado, Feng Gai · 2002 · Proceedings of the National Academy of Sciences
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    Martin Gruebele · 1999 · Annual Review of Physical Chemistry
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    Jonathan P. K. Doye · 2002 · Physical Review Letters
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    Hue Sun Chan, Zhuqing Zhang, Stefan Wallin, Zhirong Liu · 2011 · Annual Review of Physical Chemistry
  80. Simple model of protein folding kinetics.
    Robert W. Zwanzig · 1995 · Proceedings of the National Academy of Sciences
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    Sergey V. Solomatin, Max Greenfeld, Steven Chu, Daniel Herschlag · 2010 · Nature
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  87. Modeling the formation and growth of atmospheric molecular clusters: A review
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    Paul C. Whitford, Peter Geggier, Roger B. Altman, Scott C. Blanchard, José N. Onuchic, Karissa Y. Sanbonmatsu · 2010 · RNA
  90. Symmetry and the energy landscapes of biomolecules
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  95. Rate of protein folding near the point of thermodynamic equilibrium between the coil and the most stable chain fold
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