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

Cited by (1,005)

Items 601–700 of 1,005

  1. Quantitative criteria for native energetic heterogeneity influences in the prediction of protein folding kinetics
    Samuel S. Cho, Yaakov Levy, Peter Guy Wolynes · 2008 · Proceedings of the National Academy of Sciences
  2. Monodisperse self-assembly in a model with protein-like interactions
    Alex W. Wilber, Jonathan P. K. Doye, Ard A. Louis, Anna C. F. Lewis · 2009 · The Journal of Chemical Physics
  3. Protein folding simulations: From coarse‐grained model to all‐atom model
    Jian Zhang, Wenfei Li, Jun Wang, Meng Qin, Lei Wu, Zhiqiang Yan, Weixin Xu, Guanghong Zuo, Wei Wang · 2009 · IUBMB Life
  4. Water and molecular chaperones act as weak links of protein folding networks: Energy landscape and punctuated equilibrium changes point towards a game theory of proteins
    István A. Kovács, Máté Szalay, Péter Csermely · 2005 · FEBS Letters
  5. Multiple subsets of side-chain packing in partially folded states of α-lactalbumins
    K. Hun Mok, Toshio Nagashima, Iain J. Day, Peter J. Hore, Christopher Martin Dobson · 2005 · Proceedings of the National Academy of Sciences
  6. Learning To Fold Proteins Using Energy Landscape Theory
    Nicholas P. Schafer, Bobby L. Kim, Weihua Zheng, Peter Guy Wolynes · 2014 · Israel Journal of Chemistry
  7. The folding energy landscape of apoflavodoxin is rugged: Hydrogen exchange reveals nonproductive misfolded intermediates
    Yves J. M. Bollen, Monique B. Kamphuis, Carlo P. M. van Mierlo · 2006 · Proceedings of the National Academy of Sciences
  8. Deconstructing the Native State: Energy Landscapes, Function, and Dynamics of Globular Proteins
    Pavel I. Zhuravlev, Christopher K. Materese, Garegin A. Papoian · 2009 · The Journal of Physical Chemistry B
  9. NMR mapping of protein conformational landscapes using coordinated behavior of chemical shifts upon ligand binding
    Alessandro Cembran, Jonggul Kim, Jiali Gao, Gianluigi Veglia · 2014 · Physical Chemistry Chemical Physics
  10. What is the role of thermodynamics on protein stability?
    Sathyanarayana Naidu Gummadi · 2003 · Biotechnology and Bioprocess Engineering
  11. Protein Folding Pathways Studied by Pulsed- and Native-State Hydrogen Exchange
    Yawen Bai · 2006 · Chemical Reviews
  12. The Many Faces of Structure-Based Potentials: From Protein Folding Landscapes to Structural Characterization of Complex Biomolecules
    Jeffrey K. Noel, José N. Onuchic · 2012 · Biological and medical physics series
  13. Kinetics of lysozyme refolding: structural characterization of a non-specifically collapsed state using time-resolved X-ray scattering
    Lingling Chen, Gudrun Wildegger, Thomas Kiefhaber, Keith O. Hodgson, Sebastian Doniach · 1998 · Journal of Molecular Biology
  14. Are proteins made from a limited parts list?
    Nicholas C. Fitzkee, Patrick J. Fleming, Haipeng Gong, Nicholas Panasik, Timothy O. Street, George D. Rose · 2005 · Trends in Biochemical Sciences
  15. Surface-induced conformational changes in lattice model proteins by Monte Carlo simulation
    Victoria Castells, Shaoxiong Yang, Paul R. Van Tassel · 2002 · Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics
  16. Acidic conditions stabilise intermediates populated during the folding of Im7 and Im9 1 1Edited by C. R. Matthews
    Stanislaw A. Gorski, Andrew P. Capaldi, Colin Kleanthous, Sheena E. Radford · 2001 · Journal of Molecular Biology
  17. Analysis methods for comparison of multiple molecular dynamics trajectories: applications to protein unfolding pathways and denatured ensembles 1 1Edited by A. R. Fersht
    Steven L. Kazmirski, Aijun Li, Valerie Daggett · 1999 · Journal of Molecular Biology
  18. Non-Gaussian dynamics from a simulation of a short peptide: Loop closure rates and effective diffusion coefficients
    John J. Portman · 2003 · The Journal of Chemical Physics
  19. Modeling the structure of clusters of C60 molecules
    Jonathan P. K. Doye, David J. Wales, W. Branz, F. Calvo · 2001 · Physical review. B, Condensed matter
  20. Methods for exploring early events in protein folding
    Heinrich Röder, M.C.R. Shastry · 1999 · Current Opinion in Structural Biology
  21. Exploring structures in protein folding funnels with free energy functionals: the denatured ensemble
    Benjamin A. Shoemaker, Peter Guy Wolynes · 1999 · Journal of Molecular Biology
  22. Quantifying the topography of the intrinsic energy landscape of flexible biomolecular recognition
    Chu, Xiakun, Gan, Linfeng, Wang, Erkang, Wang, Jin · 2013 · Proceedings of the National Academy of Sciences
  23. Integrated prediction of protein folding and unfolding rates from only size and structural class
    David De Sancho, Víctor Muñoz · 2011 · Physical Chemistry Chemical Physics
  24. Ultrafast and downhill protein folding
    R. Brian Dyer · 2007 · Current Opinion in Structural Biology
  25. Mutations as trapdoors to two competing native conformations of the Rop-dimer
    Alexander H. Schug, Paul C. Whitford, Yaakov Levy, José N. Onuchic · 2007 · Proceedings of the National Academy of Sciences
  26. Stabilizing IκBα by “Consensus” Design
    Diego Ulises Ferreiro, Carla F. Cervantes, Stephanie M.E. Truhlar, Samuel S. Cho, Peter Guy Wolynes, Elizabeth A. Komives · 2006 · Journal of Molecular Biology
  27. Limited cooperativity in protein folding
    Víctor Muñoz, Luis Alberto Campos, Mourad Sadqi · 2016 · Current Opinion in Structural Biology
  28. Understanding protein domain-swapping using structure-based models of protein folding
    Nahren Manuel Mascarenhas, Shachi Gosavi · 2016 · Progress in Biophysics and Molecular Biology
  29. Thermodynamic and Kinetic Exploration of the Energy Landscape of Borrelia burgdorferi OspA by Native-state Hydrogen Exchange
    Shude Yan, Scott D. Kennedy, Shohei Koide · 2002 · Journal of Molecular Biology
  30. Sterically confined rearrangements of SARS-CoV-2 Spike protein control cell invasion
    Esteban Dodero‐Rojas, José N. Onuchic, Paul C. Whitford · 2021 · eLife
  31. Predicting protein conformational motions using energetic frustration analysis and AlphaFold2
    Xingyue Guan, Qian-Yuan Tang, Weitong Ren, Mingchen Chen, Wei Wang, Peter Guy Wolynes, Wenfei Li · 2024 · Proceedings of the National Academy of Sciences
  32. Engineering a β-Sheet Protein toward the Folding Speed Limit
    Houbi Nguyen, Marcus Jäger, Jeffery W. Kelly, Martin Gruebele · 2005 · The Journal of Physical Chemistry B
  33. Targeted Adversarial Learning Optimized Sampling
    Jun Zhang, Yi Yang, Frank Noé · 2019 · The Journal of Physical Chemistry Letters
  34. Folding kinetics of Che Y mutants with enhanced native α-helix propensities 1 1Edited by A. R. Fersht
    Eva López‐Hernández, Philippe Cronet, Luís Serrano, Víctor Muñoz · 1997 · Journal of Molecular Biology
  35. Disordered proteins follow diverse transition paths as they fold and bind to a partner
    Jae-Yeol Kim, Hoi Sung Chung · 2020 · Science
  36. Self-assembly of monodisperse clusters: Dependence on target geometry
    Alex W. Wilber, Jonathan P. K. Doye, Ard A. Louis · 2009 · The Journal of Chemical Physics
  37. SWARM-MD: Searching Conformational Space by Cooperative Molecular Dynamics
    Thomas Huber, Wilfred F. Van Gunsteren A · 1998 · The Journal of Physical Chemistry A
  38. An early transition state for folding of the P4-P6 RNA domain
    Scott K. Silverman, Thomas R. Cech · 2001 · RNA
  39. Topological Information Embodied in Local Juxtaposition Geometry Provides a Statistical Mechanical Basis for Unknotting by Type-2 DNA Topoisomerases
    Zhirong Liu, Jennifer K. Mann, Lynn Zechiedrich, Hue Sun Chan · 2006 · Journal of Molecular Biology
  40. Folding of a pressure-denatured model protein
    Ronaldo Mohana‐Borges, Jerson Lima Silva, Javier Ruiz‐Sanz, Gonzalo de Prat Gay · 1999 · Proceedings of the National Academy of Sciences
  41. Properties of AB copolymers with a special adsorption-tuned primary structure
    Ekaterina A. Zheligovskaya, Pavel G. Khalatur, Alexei R. Khokhlov · 1999 · Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics
  42. Backbone dynamics, fast folding, and secondary structure formation in helical proteins and peptides
    Corey Hardin, Zaida Ann Luthey-Schulten, Peter Guy Wolynes · 1999 · Proteins Structure Function and Bioinformatics
  43. How does a small molecule bind at a cryptic binding site?
    Yibing Shan, Venkatesh P. Mysore, Abba E. Leffler, Eric T. Kim, Shiori Sagawa, David Elliot Shaw · 2022 · PLoS Computational Biology
  44. Characterizing the Rate-Limiting Step of Trp-Cage Folding by All-Atom Molecular Dynamics Simulations
    Shibasish Chowdhury, Mathew C. Lee, Yong Duan · 2004 · The Journal of Physical Chemistry B
  45. Importance Sampling for Multiscale Diffusions
    Paul G. Dupuis, Konstantinos Spiliopoulos, Hui Wang · 2012 · Multiscale Modeling and Simulation
  46. Emerging computational approaches for the study of protein allostery
    Galen Collier, Vanessa Ortiz · 2013 · Archives of Biochemistry and Biophysics
  47. Structural characterization of a misfolded intermediate populated during the folding process of a PDZ domain
    Stefano Gianni, Ylva Ivarsson, Alfonso De Simone, Carlo Travaglini‐Allocatelli, Maurizio Brunori, Michele Vendruscolo · 2010 · Nature Structural & Molecular Biology
  48. Maximum-Likelihood Phylogenetic Inference with Selection on Protein Folding Stability
    Miguel Arenas, Agustín Sánchez-Cobos, Ugo Bastolla · 2015 · Molecular Biology and Evolution
  49. Genomic Energy Landscapes
    Bin Zhang, Peter Guy Wolynes · 2016 · Biophysical Journal
  50. Aqueous ionic liquids in comparison with standard co-solutes
    Ewa Anna Oprzeska‐Zingrebe, Jens Smiatek · 2018 · Biophysical Reviews
  51. Connecting the Sequence-Space of Bacterial Signaling Proteins to Phenotypes Using Coevolutionary Landscapes
    Ryan R. Cheng, Olle Nordesjö, Ryan L. Hayes, Herbert Levine, Samuel Coulbourn Flores, José N. Onuchic, Faruck Morcos · 2016 · Molecular Biology and Evolution
  52. Folding Free Energy Landscape of Ordered and Intrinsically Disordered Proteins
    Song‐Ho Chong, Sihyun Ham · 2019 · Scientific Reports
  53. Fluctuation-dissipation ratios in the dynamics of self-assembly
    Robert L. Jack, Michael F. Hagan, David Chandler · 2007 · Physical Review E
  54. Insights into thermal resistance of proteins from the intrinsic stability of their α-helices
    Michael Petukhov, Yury Kil, Seiki Kuramitsu, V. A. Lanzov · 1997 · Proteins Structure Function and Bioinformatics
  55. Folding of the disulfide-bonded β-sheet protein tendamistat: rapid two-state folding without hydrophobic collapse 1 1Edited by A. R. Fersht
    Nancy Schönbrunner, Klaus‐Peter Koller, Thomas Kiefhaber · 1997 · Journal of Molecular Biology
  56. Theory, simulations, and experiments show that proteins fold by multiple pathways
    William A. Eaton, Peter Guy Wolynes · 2017 · Proceedings of the National Academy of Sciences
  57. Structural characterization of MG and pre-MG states of proteins by MD simulations, NMR, and other techniques
    Abdullah Naiyer, Md. Imtaiyaz Hassan, Asimul Islam, Monica Sundd, Faizan Ahmad · 2015 · Journal of Biomolecular Structure and Dynamics
  58. The Native Ensemble and Folding of a Protein Molten-Globule: Functional Consequence of Downhill Folding
    Athi N. Naganathan, Modesto Orozco · 2011 · Journal of the American Chemical Society
  59. Comparative Study of Protein Unfolding in Aqueous Urea and Dimethyl Sulfoxide Solutions: Surface Polarity, Solvent Specificity, and Sequence of Secondary Structure Melting
    Susmita Roy, Biman Bagchi · 2014 · The Journal of Physical Chemistry B
  60. Design and introduction of a disulfide bridge in firefly luciferase: increase of thermostability and decrease of pH sensitivity
    Mehdi Imani, Saman Hosseinkhani, Shahin Ahmadian, Mahboobeh Nazari · 2010 · Photochemical & Photobiological Sciences
  61. Particle dynamics in two-dimensional random-energy landscapes: Experiments and simulations
    Florian Platten, Christoph Zunke, Richard D. L. Hanes, Jörg Bewerunge, Imad Ladadwa, Andreas Heuer, Stefan U. Egelhaaf · 2013 · Physical Review E
  62. Characterizing the Protein Folding Transition State Using ψ Analysis
    Tobin R. Sosnick, Bryan A. Krantz, Robin S. Dothager, Michael C. Baxa · 2006 · Chemical Reviews
  63. Specificity quantification of biomolecular recognition and its implication for drug discovery
    Zhiqiang Yan, Jin Wang · 2012 · Scientific Reports
  64. Direct Observation of Protein Unfolded State Compaction in the Presence of Macromolecular Crowding
    Therese Mikaelsson, Jörgen Ådén, Lennart B.‐Å. Johansson, Pernilla E. Wittung-Stafshede · 2013 · Biophysical Journal
  65. Computational and Experimental Characterizations of Silver Nanoparticle–Apolipoprotein Biocorona
    Rongzhong Li, Ran Chen, Pengyu Chen, Yimei Wen, Pu Chun Ke, Samuel S. Cho · 2013 · The Journal of Physical Chemistry B
  66. Cytochrome c folding dynamics
    Jay R. Winkler · 2004 · Current Opinion in Chemical Biology
  67. Determination, prediction, and understanding of structures, using the energy landscapes of chemical systems – Part II
    Johann Christian Schön, Martin Jansen · 2001 · Zeitschrift für Kristallographie - Crystalline Materials
  68. Residues participating in the protein folding nucleus do not exhibit preferential evolutionary conservation
    Stefan M. Larson, Ingo Ruczinski, Alan R. Davidson, David A. Baker, Kevin W. Plaxco · 2002 · Journal of Molecular Biology
  69. Evidence of turn and salt bridge contributions to β-hairpin stability: MD simulations of C-terminal fragment from the B1 domain of protein G
    Jerry W. Tsai, Michael Levitt · 2002 · Biophysical Chemistry
  70. Non-native local interactions in protein folding and stability: introducing a helical tendency in the all β-sheet α-spectrin SH3 domain
    Jesús Prìeto, Matthias Wilmans, María Angeles Jiménez, Manuel Rico, Luís Serrano · 1997 · Journal of Molecular Biology
  71. Dynamics of protein folding: Probing the kinetic network of folding–unfolding transitions with experiment and theory
    Ginka S. Buchner, Ronan D. Murphy, Nicolae‐Viorel Buchete, Jan Kubelka · 2010 · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics
  72. Power-law distributions for the areas of the basins of attraction on a potential energy landscape
    Claire P. Massen, Jonathan P. K. Doye · 2007 · Physical Review E
  73. Energy landscapes of colloidal clusters: thermodynamics and rearrangement mechanisms
    F. Calvo, Jonathan P. K. Doye, David J. Wales · 2011 · Nanoscale
  74. How many dimensions are required to approximate the potential energy landscape of a model protein?
    Tamiki Komatsuzaki, Kyoko Hoshino, Yasuhiro Matsunaga, Gareth J. Rylance, Roy L. Johnston, David J. Wales · 2005 · The Journal of Chemical Physics
  75. The dual-basin landscape in GFP folding
    Benjamin T. Andrews, Shachi Gosavi, John M. Finke, José N. Onuchic, Patricia Ann Jennings · 2008 · Proceedings of the National Academy of Sciences
  76. Folding without charges
    Martin Kurnik, Linda Hedberg, Jens Danielsson, Mikael Oliveberg · 2012 · Proceedings of the National Academy of Sciences
  77. Solvation and desolvation effects in protein folding: native flexibility, kinetic cooperativity and enthalpic barriers under isostability conditions
    Zhirong Liu, Hue Sun Chan · 2005 · Physical Biology
  78. The Energy Landscape Analysis of Cancer Mutations in Protein Kinases
    Anshuman Dixit, Gennady M. Verkhivker · 2011 · PLoS ONE
  79. Force-dependent switch in protein unfolding pathways and transition-state movements
    Pavel I. Zhuravlev, Michael Hinczewski, Shaon Chakrabarti, Susan Marqusee, Dave Thirumalai · 2016 · Proceedings of the National Academy of Sciences
  80. Cooperative and Directional Folding of the preQ1 Riboswitch Aptamer Domain
    Jun Feng, Nils G. Walter, Charles L. Brooks · 2011 · Journal of the American Chemical Society
  81. Protein Misfolding Diseases and Therapeutic Approaches
    Kusum Yadav, Anurag Yadav, Priyanka Vashistha, Veda Prakash Pandey, Upendra Nath Dwivedi · 2019 · Current Protein and Peptide Science
  82. Searching the landscape of flux vacua with genetic algorithms
    Alex Cole, Andreas Schachner, Gary Shiu · 2019 · Journal of High Energy Physics
  83. Nanosecond Folding Dynamics of a Three-Stranded β-Sheet
    Yao Xu, Pradipta Purkayastha, Feng Gai · 2006 · Journal of the American Chemical Society
  84. Study of the Villin headpiece folding dynamics by combining coarse‐grained Monte Carlo evolution and all‐atom molecular dynamics
    Giacomo Mori, Giorgio Colombo, Cristian Micheletti · 2004 · Proteins Structure Function and Bioinformatics
  85. Virtual atom representation of hydrogen bonds in minimal off-lattice models of α helices: effect on stability, cooperativity and kinetics
    Dmitri K. Klimov, Marcos R. Betancourt, Dave Thirumalai · 1998 · Folding and Design
  86. Analysis of topological and nontopological structural similarities in the PDB: New examples with old structures
    Nickolai N. Alexandrov, Daniel Fischer · 1996 · Proteins Structure Function and Bioinformatics
  87. Reaching the protein folding speed limit with large, sub-microsecond pressure jumps
    Charles Dumont, T. Emilsson, Martin Gruebele · 2009 · Nature Methods
  88. The Davydov/Scott Model for Energy Storage and Transport in Proteins
    Leonor Cruzeiro-Hansson · 2009 · Journal of Biological Physics
  89. Folding energy landscape and network dynamics of small globular proteins
    Naoto Hori, George Chikenji, R. Stephen Berry, Shoji Takada · 2008 · Proceedings of the National Academy of Sciences
  90. Parallel G-triplexes and G-hairpins as potential transitory ensembles in the folding of parallel-stranded DNA G-Quadruplexes
    Petr Stadlbauer, Petra Kührová, Lukáš Vicherek, Pavel Banáš, Michal Otyepka, Lukáš Trantı́rek, Jiřı́ Šponer · 2019 · Nucleic Acids Research
  91. Proteinfaltung aus theoretischer und experimenteller Sicht
    Christopher Martin Dobson, Andrej Šali, Martin Karplus · 1998 · Angewandte Chemie
  92. Global aspects of the energy landscape of metastable crystal structures in ionic compounds
    Martine Wevers, Johann Christian Schön, Martin Jansen · 1999 · Journal of Physics Condensed Matter
  93. Elementary Steps in Protein Folding
    Oliver Bieri, Thomas Kiefhaber · 1999 · Biological Chemistry
  94. Lattice model for rapidly folding protein-like heteropolymers.
    Indira H. Shrivastava, Saraswathi Vishveshwara, Marek Cieplak, Amos Maritan, Jayanth R. Banavar · 1995 · Proceedings of the National Academy of Sciences
  95. Identification of amino acid sequences with good folding properties in an off-lattice model
    Anders Irbäck, Carsten Peterson, Frańk Potthast · 1997 · Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics
  96. Folding funnels: The key to robust protein structure prediction
    Corey Hardin, Michael P. Eastwood, Michael C. Prentiss, Zaida Ann Luthey-Schulten, Peter Guy Wolynes · 2001 · Journal of Computational Chemistry
  97. Programmed folding of DNA origami structures through single-molecule force control
    Wooli Bae, Kipom Kim, Duyoung Min, Je‐Kyung Ryu, Changbong Hyeon, Tae‐Young Yoon · 2014 · Nature Communications
  98. To Tie or Not to Tie? That Is the Question
    Paweł Dąbrowski-Tumański, Joanna Ida Sulkowska · 2017 · Polymers
  99. Contrasting Effects of Guanidinium Chloride and Urea on the Activity and Unfolding of Lysozyme
    Biswajit Biswas, Aswathy N. Muttathukattil, Govardhan Reddy, Prashant Chandra Singh · 2018 · ACS Omega
  100. A look back at the molten globule state of proteins: thermodynamic aspects
    Eva Judy, Nand Kishore · 2019 · Biophysical Reviews