The nature of folded states of globular proteins

Cited by (357)

Items 101–200 of 357

1. 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
2. Hydrodynamic effects in proteins
   Piotr Szymczak, Marek Cieplak · 2010 · Journal of Physics Condensed Matter
3. Exploring the Folding Free Energy Landscape of a β-Hairpin Miniprotein, Chignolin, Using Multiscale Free Energy Landscape Calculation Method
   Ryuhei Harada, Akio Kitao · 2011 · The Journal of Physical Chemistry B
4. 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
5. Molecular Shape Descriptors
   Gustavo A. Arteca · 1996 · Reviews in computational chemistry
6. 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
7. 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
8. Complex Systems: Equilibrium Configurations of N Equal Charges on a Sphere (2 ≤ N ≥ 112)
   THOMAS ERBER, G. Hockney · 1997 · Advances in chemical physics
9. Characterization of anharmonicities on complex potential energy surfaces: Perturbation theory and simulation
   F. Calvo, Jonathan P. K. Doye, David J. Wales · 2001 · The Journal of Chemical Physics
10. 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
11. Genotype networks in metabolic reaction spaces
    Areejit Samal, João F. Matias Rodrigues, Jürgen Jost, Olivier Martin, Andreas Wagner · 2010 · BMC Systems Biology
12. Principal coordinate analysis on a protein model
    Nuran Elmacı, R. Stephen Berry · 1999 · The Journal of Chemical Physics
13. Unidirectional Brownian motion observed in an in silico single molecule experiment of an actomyosin motor
    Mitsunori Takano, Tomoki P. Terada, Masaki Sasai · 2010 · Proceedings of the National Academy of Sciences
14. Bottom-Up Coarse-Graining of Peptide Ensembles and Helix–Coil Transitions
    Joseph F. Rudzinski, William G. Noid · 2015 · Journal of Chemical Theory and Computation
15. Charge fluctuation effects on the shape of flexible polyampholytes with applications to intrinsically disordered proteins
    Himadri S. Samanta, Debayan Chakraborty, Dave Thirumalai · 2018 · The Journal of Chemical Physics
16. The energy landscape for protein folding and possible connections to function
    Margaret S. Cheung, Leslie L. Chavez, José N. Onuchic · 2003 · Polymer
17. Watching solvent friction impede ultrafast barrier crossings: A direct test of Kramers theory
    Jessica M. Anna, Kevin J. Kubarych · 2010 · The Journal of Chemical Physics
18. A VDAC1-mediated NEET protein chain transfers [2Fe-2S] clusters between the mitochondria and the cytosol and impacts mitochondrial dynamics
    Ola Karmi, Henri‐Baptiste Marjault, Fang Bai, Susmita Roy, Yang‐Sung Sohn, Merav Darash‐Yahana, Faruck Morcos, Konstantinos Ioannidis, Yaakov Nahmias, Patricia Ann Jennings et al. · 2022 · Proceedings of the National Academy of Sciences
19. Entropic tempering: A method for overcoming quasiergodicity in simulation
    F. Calvo, Jonathan P. K. Doye · 2000 · Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics
20. Direct computation of long time processes in peptides and proteins: Reaction path study of the coil-to-helix transition in polyalanine
    Shuanghong Huo, John E. Straub · 1999 · Proteins Structure Function and Bioinformatics
21. A coarse‐grained potential for fold recognition and molecular dynamics simulations of proteins
    Peter Májek, Ron Elber · 2009 · Proteins Structure Function and Bioinformatics
22. Recovering physical potentials from a model protein databank
    J. Wayne Mullinax, William G. Noid · 2010 · Proceedings of the National Academy of Sciences
23. Correlation between rate of folding, energy landscape, and topology in the folding of a model protein HP-36
    Arnab Mukherjee, Biman Bagchi · 2003 · The Journal of Chemical Physics
24. Complementary Matching in Domain Formation within Lipid Bilayers
    Mark J. Stevens · 2005 · Journal of the American Chemical Society
25. The role of sidechain packing and native contact interactions in folding: Discontinuous molecular dynamics folding simulations of an all-atom Gō model of fragment B of Staphylococcal protein A
    Apichart Linhananta, Yaoqi Zhou · 2002 · The Journal of Chemical Physics
26. Conformational heterogeneity in human interphase chromosome organization reconciles the FISH and Hi-C paradox
    Guang Shi, Dave Thirumalai · 2019 · Nature Communications
27. Dynamic Asymmetry Exposes 2019-nCoV Prefusion Spike
    Susmita Roy, Akhilesh Jaiswar, Raju Sarkar · 2020 · The Journal of Physical Chemistry Letters
28. Translocation of a β-hairpin-forming peptide through a cylindrical tunnel
    Serdal Kırmızıaltın, Venkat Ganesan, Dmitrii E. Makarov · 2004 · The Journal of Chemical Physics
29. Conformation-dependent environments in folding proteins
    Ariel Fernández · 2001 · The Journal of Chemical Physics
30. Folding of Human Telomerase RNA Pseudoknot Using Ion-Jump and Temperature-Quench Simulations
    Shi Biyun, Samuel S. Cho, Dave Thirumalai · 2011 · Journal of the American Chemical Society
31. A generalized-Yvon-Born-Green method for coarse-grained modeling
    Joseph F. Rudzinski, William G. Noid · 2015 · The European Physical Journal Special Topics
32. Stability of a protein tethered to a surface
    Miriam Friedel, Andrij Baumketner, Joan‐Emma Shea · 2007 · The Journal of Chemical Physics
33. Proposed mechanism for stability of proteins to evolutionary mutations
    Erik D. Nelson, José N. Onuchic · 1998 · Proceedings of the National Academy of Sciences
34. Molecular dynamics of conformational substates for a simplified protein model
    Helmut Grubmüller, Paul Tavan · 1994 · The Journal of Chemical Physics
35. Minimal Models for Proteins and RNA: From Folding to Function
    David L. Pincus, Samuel S. Cho, Changbong Hyeon, Dave Thirumalai · 2008 · Progress in molecular biology and translational science
36. When is a potential accurate enough for structure prediction? Theory and application to a random heteropolymer model of protein folding
    Joseph D. Bryngelson · 1994 · The Journal of Chemical Physics
37. An Efficient Monte Carlo Model of Protein Chains. Modeling the Short-Range Correlations between Side Group Centers of Mass
    Andrzej Koliński, Lukasz Jaroszewski, Piotr Rotkiewicz, Jeffrey Skolnick · 1998 · The Journal of Physical Chemistry B
38. Sequence periodicity and secondary structure propensity in model proteins
    Giovanni Bellesia, Andrew I. Jewett, Joan‐Emma Shea · 2009 · Protein Science
39. Heterogeneous Morphology and Dynamics of Polyelectrolyte Brush Condensates in Trivalent Counterion Solution
    Liu, Lei, Pincus, Philip A., Hyeon, Changbong · 2017 · Macromolecules
40. Solvent Viscosity Dependence of the Protein Folding Dynamics
    Young Min Rhee, Vijay S. Pande · 2008 · The Journal of Physical Chemistry B
41. On the dynamics of molecular conformation
    Igor Mezić · 2006 · Proceedings of the National Academy of Sciences
42. Folding on the Chaperone: Yield Enhancement Through Loose Binding
    Andrew I. Jewett, Joan‐Emma Shea · 2006 · Journal of Molecular Biology
43. Gradual development of protein-like global structures through functional selection.
    Tetsuya Yomo, Masaki Sasai, Seiji Saito · 1999 · Nature Structural Biology
44. A reduced model of short range interactions in polypeptide chains
    Andrzej Koliński, Mariusz Milik, Jakub Rycombel, Jeffrey Skolnick · 1995 · The Journal of Chemical Physics
45. Unfolding and translocation pathway of substrate protein controlled by structure in repetitive allosteric cycles of the ClpY ATPase
    Andrea N. Kravats, Manori Jayasinghe, George Stan · 2011 · Proceedings of the National Academy of Sciences
46. First-order coil-globule transition driven by vibrational entropy
    Carlo Maffi, Marco Baiesi, Lapo Casetti, Francesco Piazza, Paolo De Los Rios · 2012 · Nature Communications
47. Conformational space annealing and an off-lattice frustrated model protein
    Seung‐Yeon Kim, Sung Jong Lee, Jooyoung Lee · 2003 · The Journal of Chemical Physics
48. Satisfying turns in folding transitions
    Martin Gruebele, Peter Guy Wolynes · 1998 · Nature Structural & Molecular Biology
49. Insights into Cotranslational Nascent Protein Behavior from Computer Simulations
    Fabio Trovato, Edward P. O’Brien · 2016 · Annual Review of Biophysics
50. Evolution of the Potential Energy Landscape with Static Pulling Force for Two Model Proteins
    David J. Wales, Teresa L. Head-Gordon · 2012 · The Journal of Physical Chemistry B
51. A metastable state in folding simulations of a protein model
    Aaron R. Dinner, Martin Karplus · 1998 · Nature Structural Biology
52. Unfolding and refolding of the native structure of bovine pancreatic trypsin inhibitor studied by computer simulations
    Mengqiuyue Hao, Matthew R. Pincus, Shalom R. Rackovsky, Harold A. Scheraga · 1993 · Biochemistry
53. Kinetics of a Gaussian random copolymer as a prototype for protein folding
    É. G. Timoshenko, Yu. A. Kuznetsov, Kenneth A. Dawson · 1996 · Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics
54. Theoretical and computational validation of the Kuhn barrier friction mechanism in unfolded proteins
    Stanislav M. Avdoshenko, Atanu Das, Rohit Satija, Garegin A. Papoian, Dmitrii E. Makarov · 2017 · Scientific Reports
55. Contacting the protein folding funnel with NMR
    José N. Onuchic · 1997 · Proceedings of the National Academy of Sciences
56. Effect of salt bridges on the energy landscape of a model protein
    David J. Wales, Peter E. J. Dewsbury · 2004 · The Journal of Chemical Physics
57. A Challenge for Peptide Coarse Graining: Transferability of Fragment‐Based Models
    Ozge Engin, Alessandra Villa, Christine Peter, Mehmet Sayar · 2011 · Macromolecular Theory and Simulations
58. Paddling mechanism for the substrate translocation by AAA+ motor revealed by multiscale molecular simulations
    Nobuyasu Koga, Tomoshi Kameda, Kei-ichi Okazaki, Shoji Takada · 2009 · Proceedings of the National Academy of Sciences
59. Energy Landscape Distortions and the Mechanical Unfolding of Proteins
    Daniel J. Lacks · 2005 · Biophysical Journal
60. Hydrodynamic interactions in protein folding
    Marek Cieplak, Szymon Niewieczerzał · 2009 · The Journal of Chemical Physics
61. Self-assembly of peptides into a β-barrel motif
    Miriam Friedel, Joan‐Emma Shea · 2004 · The Journal of Chemical Physics
62. Computer design of idealized β-motifs
    Andrzej Koliński, Wojciech Galazka, Jeffrey Skolnick · 1995 · The Journal of Chemical Physics
63. Shape changes and cooperativity in the folding of the central domain of the 16S ribosomal RNA
    Hori, Naoto, Denesyuk, Natalia A., Thirumalai, D. · 2021 · Proceedings of the National Academy of Sciences
64. Energy Landscape and Global Optimization for a Frustrated Model Protein
    Mark T. Oakley, David J. Wales, Roy L. Johnston · 2011 · The Journal of Physical Chemistry B
65. Ion Condensation onto Ribozyme Is Site Specific and Fold Dependent
    Naoto Hori, Natalia A. Denesyuk, Dave Thirumalai · 2019 · Biophysical Journal
66. Spatiotemporal correlations in denatured proteins: The dependence of fluorescence resonance energy transfer (FRET)-derived protein reconfiguration times on the location of the FRET probes
    Dmitrii E. Makarov · 2010 · The Journal of Chemical Physics
67. Molecular simulation of protein aggregation
    D. Bratko, Troy Cellmer, John M. Prausnitz, Harvey W. Blanch · 2006 · Biotechnology and Bioengineering
68. The competition between protein folding and aggregation: Off‐lattice minimalist model studies
    Troy Cellmer, D. Bratko, John M. Prausnitz, Harvey W. Blanch · 2004 · Biotechnology and Bioengineering
69. The Origin of Minus-end Directionality and Mechanochemistry of Ncd Motors
    Biman Jana, Changbong Hyeon, José N. Onuchic · 2012 · PLoS Computational Biology
70. Multicanonical jump walk annealing: An efficient method for geometric optimization
    Huafeng Xu, B. J. Berne · 2000 · The Journal of Chemical Physics
71. Hydrophobicity at the surface of proteins
    Marco Scarsi, Nicolas Majeux, Amedeo Caflisch · 1999 · Proteins Structure Function and Bioinformatics
72. Monovalent ions modulate the flux through multiple folding pathways of an RNA pseudoknot
    Jorjethe Roca, Naoto Hori, Saroj Baral, Yogambigai Velmurugu, Ranjani Narayanan, Prasanth Narayanan, Dave Thirumalai, Anjum Ansari · 2018 · Proceedings of the National Academy of Sciences
73. Protein collapse is encoded in the folded state architecture
    Himadri S. Samanta, Pavel I. Zhuravlev, Michael Hinczewski, Naoto Hori, Shaon Chakrabarti, Dave Thirumalai · 2017 · Soft Matter
74. Charge Density of Cation Determines Inner versus Outer Shell Coordination to Phosphate in RNA
    Hung T. Nguyen, Dave Thirumalai · 2020 · The Journal of Physical Chemistry B
75. Chromatin dynamics controls epigenetic domain formation
    Marina Katava, Guang Shi, Dave Thirumalai · 2022 · Biophysical Journal
76. RNA G-quadruplex folding is a multi-pathway process driven by conformational entropy
    Marijana Ugrina, Ines Burkhart, Diana Müller, Harald Schwalbe, Nadine Schwierz · 2023 · Nucleic Acids Research
77. Measuring distances within unfolded biopolymers using fluorescence resonance energy transfer: The effect of polymer chain dynamics on the observed fluorescence resonance energy transfer efficiency
    Dmitrii E. Makarov, Kevin W. Plaxco · 2009 · The Journal of Chemical Physics
78. Contact pair dynamics during folding of two small proteins: Chicken villin head piece and the Alzheimer protein β-amyloid
    Arnab Mukherjee, Biman Bagchi · 2004 · The Journal of Chemical Physics
79. Effects of Disulfide Bonds on Folding Behavior and Mechanism of the β-Sheet Protein Tendamistat
    Meng Qin, Jian Zhang, Wei Wang · 2005 · Biophysical Journal
80. How Co-translational Folding of Multi-domain Protein Is Affected by Elongation Schedule: Molecular Simulations
    Tomohiro Tanaka, Naoto Hori, Shoji Takada · 2015 · PLoS Computational Biology
81. Influence of the Shape of Crowding Particles on the Structural Transitions in a Polymer
    Alexander N. Kudlay, Margaret S. Cheung, Dave Thirumalai · 2012 · The Journal of Physical Chemistry B
82. Archetypal energy landscapes: Dynamical diagnosis
    Florin Despa, David J. Wales, R. Stephen Berry · 2004 · The Journal of Chemical Physics
83. Solute excluded-volume effects on the stability of globular proteins: A statistical thermodynamic theory
    Yaoqi Zhou, Carol K. Hall · 1998 · Biopolymers
84. Structural Change and Nucleotide Dissociation of Myosin Motor Domain: Dual Gō Model Simulation
    Fumiko Takagi, Macoto Kikuchi · 2007 · Biophysical Journal
85. Gatekeepers in the Ribosomal Protein S6: Thermodynamics, Kinetics, and Folding Pathways Revealed by a Minimalist Protein Model
    Antitsa D. Stoycheva, Charles L. Brooks, José N. Onuchic · 2004 · Journal of Molecular Biology
86. Molecular dynamics simulations of a protein model in uniform and elongational flows
    Alexander S. Lemak, James R. Lepock, Jeff Z. Y. Chen · 2003 · Proteins Structure Function and Bioinformatics
87. Sizes, conformational fluctuations, and SAXS profiles for intrinsically disordered proteins
    Mauro L. Mugnai, Debayan Chakraborty, Hung T. Nguyen, Farkhad Maksudov, Abhinaw Kumar, Wade F. Zeno, Jeanne C. Stachowiak, John E. Straub, Dave Thirumalai · 2025 · Protein Science
88. Dependence of folding dynamics and structural stability on the location of a hydrophobic pair in β‐hairpins
    Hideo Imamura, Jeff Z. Y. Chen · 2006 · Proteins Structure Function and Bioinformatics
89. Intrinsic α‐helical and β‐sheet conformational preferences: A computational case study of alanine
    Diego Caballero, Jukka Määttä, Alice Qinhua Zhou, Maria Sammalkorpi, Corey S. O’Hern, Lynne Regan · 2014 · Protein Science
90. Computer simulations of protein translocation
    Serdal Kırmızıaltın, Lei Huang, Dmitrii E. Makarov · 2006 · physica status solidi (b)
91. Molecular Simulations of Ion Effects on the Thermodynamics of RNA Folding
    Natalia A. Denesyuk, Naoto Hori, Dave Thirumalai · 2018 · The Journal of Physical Chemistry B
92. Exploring the effects of hydrogen bonding and hydrophobic interactions on the foldability and cooperativity of helical proteins using a simplified atomic model
    Michael Knott, Hue Sun Chan · 2004 · Chemical Physics
93. Quantum Thermal Annealing with Renormalization: Application to a Frustrated Model Protein
    Yong-Han Lee, B. J. Berne · 2000 · The Journal of Physical Chemistry A
94. Foldability and the funnel of HP-36 protein sequence: Use of hydropathy scale in protein folding
    Goundla Srinivas, Biman Bagchi · 2002 · The Journal of Chemical Physics
95. Cooperativity and stability in a Langevin model of proteinlike folding
    Gabriel F. Berriz, A. M. Gutin, Eugene I. Shakhnovich · 1997 · The Journal of Chemical Physics
96. Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot under Tension
    Naoto Hori, Natalia A. Denesyuk, Dave Thirumalai · 2016 · Journal of Molecular Biology
97. Universal model for α-helix and β-sheet structures in protein
    Jeff Z. Y. Chen, Hideo Imamura · 2003 · Physica A Statistical Mechanics and its Applications
98. Assisted Peptide Folding by Surface Pattern Recognition
    Zhuoyun Zhuang, Andrew I. Jewett, Silvan Kuttimalai, Giovanni Bellesia, Sandrasegaram Gnanakaran, Joan‐Emma Shea · 2011 · Biophysical Journal
99. Effect of gatekeepers on the early folding kinetics of a model β-barrel protein
    Antitsa D. Stoycheva, José N. Onuchic, Charles L. Brooks · 2003 · The Journal of Chemical Physics
100. Unfolding proteins in an external field: Can we always observe the intermediate states?
     Alexander S. Lemak, James R. Lepock, Jeff Z. Y. Chen · 2003 · Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics