Journal de Physique I

Removal of kinetic traps and enhanced protein folding by strategic substitution of amino acids in a model α‐helical hairpin peptide

Prem P. Chapagain and Bernard S. Gerstman
Biopolymers 81 (3) 167 (2006)
https://doi.org/10.1002/bip.20388

Folding of small proteins: a matter of geometry?

P. F. N. Faísca * and M. M. Telo da Gama
Molecular Physics 103 (21-23) 2903 (2005)
https://doi.org/10.1080/00268970500221891

Self-organization in protein folding and the hydrophobic interaction

Bernard S. Gerstman and Prem P. Chapagain
The Journal of Chemical Physics 123 (5) (2005)
https://doi.org/10.1063/1.1990110

Mechanical unfolding of RNA hairpins

Changbong Hyeon and D. Thirumalai
Proceedings of the National Academy of Sciences 102 (19) 6789 (2005)
https://doi.org/10.1073/pnas.0408314102

Effect of Multiple Prolyl Isomerization Reactions on the Stability and Folding Kinetics of the Notch Ankyrin Domain: Experiment and Theory

Christina Marchetti Bradley and Doug Barrick
Journal of Molecular Biology 352 (2) 253 (2005)
https://doi.org/10.1016/j.jmb.2005.06.041

Temperature dependence and counter effect of the correlations of folding rate with chain length and with native topology

Hironori K. Nakamura and Mitsunori Takano
Physical Review E 71 (6) 061913 (2005)
https://doi.org/10.1103/PhysRevE.71.061913

Folding λ-Repressor at Its Speed Limit

Wei Yuan Yang and Martin Gruebele
Biophysical Journal 87 (1) 596 (2004)
https://doi.org/10.1529/biophysj.103.039040

The protein folding ‘speed limit’

Jan Kubelka, James Hofrichter and William A Eaton
Current Opinion in Structural Biology 14 (1) 76 (2004)
https://doi.org/10.1016/j.sbi.2004.01.013

Cooperativity and contact order in protein folding

Marek Cieplak
Physical Review E 69 (3) 031907 (2004)
https://doi.org/10.1103/PhysRevE.69.031907

Finite Size Effects on Thermal Denaturation of Globular Proteins

Mai Suan Li, Dmitri K. Klimov and D. Thirumalai
Physical Review Letters 93 (26) 268107 (2004)
https://doi.org/10.1103/PhysRevLett.93.268107

Thermal denaturation and folding rates of single domain proteins: size matters

Mai Suan Li, D.K Klimov and D Thirumalai
Polymer 45 (2) 573 (2004)
https://doi.org/10.1016/j.polymer.2003.10.066

Unification of the Folding Mechanisms of Non-two-state and Two-state Proteins

Kiyoto Kamagata, Munehito Arai and Kunihiro Kuwajima
Journal of Molecular Biology 339 (4) 951 (2004)
https://doi.org/10.1016/j.jmb.2004.04.015

Blake Gillespie and Kevin W. Plaxco
160 93 (2004)
https://doi.org/10.1007/1-4020-2340-5_5

Buffed energy landscapes: Another solution to the kinetic paradoxes of protein folding

Steven S. Plotkin and Peter G. Wolynes
Proceedings of the National Academy of Sciences 100 (8) 4417 (2003)
https://doi.org/10.1073/pnas.0330720100

Folding of proteins in Go models with angular interactions

Marek Cieplak and Trinh Xuan Hoang
Physica A: Statistical Mechanics and its Applications 330 (1-2) 195 (2003)
https://doi.org/10.1016/j.physa.2003.08.034

Finite size scaling of structural transitions in a simulated protein with secondary and tertiary structure

Prem P. Chapagain and Bernard S. Gerstman
The Journal of Chemical Physics 119 (2) 1174 (2003)
https://doi.org/10.1063/1.1579673

Fast Chain Contraction during Protein Folding: “Foldability” and Collapse Dynamics

Linlin Qiu, Cherian Zachariah and Stephen J. Hagen
Physical Review Letters 90 (16) 168103 (2003)
https://doi.org/10.1103/PhysRevLett.90.168103

Coil‐Globule Collapse in Flexible Macromolecules

Bahattin M. Baysal and Frank E. Karasz
Macromolecular Theory and Simulations 12 (9) 627 (2003)
https://doi.org/10.1002/mats.200350028

Universality Classes in Folding Times of Proteins

Marek Cieplak and Trinh Xuan Hoang
Biophysical Journal 84 (1) 475 (2003)
https://doi.org/10.1016/S0006-3495(03)74867-X

A simple lattice model that exhibits a protein‐like cooperative all‐or‐none folding transition

Andrzej Kolinski, Dominik Gront, Piotr Pokarowski and Jeffrey Skolnick
Biopolymers 69 (3) 399 (2003)
https://doi.org/10.1002/bip.10385

Experimental Tests of Villin Subdomain Folding Simulations

Jan Kubelka, William A. Eaton and James Hofrichter
Journal of Molecular Biology 329 (4) 625 (2003)
https://doi.org/10.1016/S0022-2836(03)00519-9

The topomer search model: A simple, quantitative theory of two‐state protein folding kinetics

Dmitrii E. Makarov and Kevin W. Plaxco
Protein Science 12 (1) 17 (2003)
https://doi.org/10.1110/ps.0220003

Effect of secondary structure on protein aggregation: A replica exchange simulation study

D. Bratko and H. W. Blanch
The Journal of Chemical Physics 118 (11) 5185 (2003)
https://doi.org/10.1063/1.1546429

Free Volume Concept in Application to Folding Kinetics of Random Heteropolymers

Yaroslav E. Ryabov
The Journal of Physical Chemistry B 107 (43) 12009 (2003)
https://doi.org/10.1021/jp035216c

How fast is protein hydrophobic collapse?

Mourad Sadqi, Lisa J. Lapidus and Victor Muñoz
Proceedings of the National Academy of Sciences 100 (21) 12117 (2003)
https://doi.org/10.1073/pnas.2033863100

Chain length is the main determinant of the folding rate for proteins with three-state folding kinetics

Oxana V. Galzitskaya, Sergiy O. Garbuzynskiy, Dmitry N. Ivankov and Alexei V. Finkelstein
Proteins: Structure, Function, and Genetics 51 (2) 162 (2003)
https://doi.org/10.1002/prot.10343

Dependence of Folding Rates on Protein Length

Mai Suan Li, D. K. Klimov and D. Thirumalai
The Journal of Physical Chemistry B 106 (33) 8302 (2002)
https://doi.org/10.1021/jp025837q

Conformational landscape of cytochrome c folding studied by microsecond-resolved small-angle x-ray scattering

Shuji Akiyama, Satoshi Takahashi, Tetsunari Kimura, Koichiro Ishimori, Isao Morishima, Yukihiro Nishikawa and Tetsuro Fujisawa
Proceedings of the National Academy of Sciences 99 (3) 1329 (2002)
https://doi.org/10.1073/pnas.012458999

Folding in lattice models with side chains

Mai Suan Li, D.K. Klimov and D. Thirumalai
Computer Physics Communications 147 (1-2) 625 (2002)
https://doi.org/10.1016/S0010-4655(02)00349-1

Kinetic nonoptimality and vibrational stability of proteins

Marek Cieplak and Trinh Xuan Hoang
Proteins: Structure, Function, and Bioinformatics 44 (1) 20 (2001)
https://doi.org/10.1002/prot.1067

EARLY EVENTS IN RNA FOLDING

D Thirumalai, Namkyung Lee, Sarah A Woodson and DK Klimov
Annual Review of Physical Chemistry 52 (1) 751 (2001)
https://doi.org/10.1146/annurev.physchem.52.1.751

Population analyses of kinetic partitioning in protein folding

Hironori K. Nakamura and Masaki Sasai
Proteins: Structure, Function, and Bioinformatics 43 (3) 280 (2001)
https://doi.org/10.1002/prot.1039

Competition between protein folding and aggregation: A three-dimensional lattice-model simulation

D. Bratko and H. W. Blanch
The Journal of Chemical Physics 114 (1) 561 (2001)
https://doi.org/10.1063/1.1330212

Role of counterion condensation in folding of the Tetrahymena ribozyme II. Counterion-dependence of folding kinetics

Susan L. Heilman-Miller, Jie Pan, D. Thirumalai and Sarah A. Woodson
Journal of Molecular Biology 309 (1) 57 (2001)
https://doi.org/10.1006/jmbi.2001.4660

Chaperonin-Mediated Protein Folding

D. Thirumalai and George H. Lorimer
Annual Review of Biophysics and Biomolecular Structure 30 (1) 245 (2001)
https://doi.org/10.1146/annurev.biophys.30.1.245

Roles of native topology and chain-length scaling in protein folding: A simulation study with a Gō-like model

Nobuyasu Koga and Shoji Takada
Journal of Molecular Biology 313 (1) 171 (2001)
https://doi.org/10.1006/jmbi.2001.5037

Early stages of homopolymer collapse

A. Halperin and Paul Goldbart
Physical Review E 61 (1) 565 (2000)
https://doi.org/10.1103/PhysRevE.61.565

Lattice model of transmembrane polypeptide folding

C.-M. Chen
Physical Review E 63 (1) 010901 (2000)
https://doi.org/10.1103/PhysRevE.63.010901

Scaling of Folding Properties in Go Models of Proteins

Marek Cieplak and Trinh Xuan Hoang
Journal of Biological Physics 26 (4) 273 (2000)
https://doi.org/10.1023/A:1010359024559

Mechanisms and kinetics of β-hairpin formation

D. K. Klimov and D. Thirumalai
Proceedings of the National Academy of Sciences 97 (6) 2544 (2000)
https://doi.org/10.1073/pnas.97.6.2544

Probing the role of local propensity in peptide turn formation

D. Mohanty, R. Elber and D. Thirumalai
International Journal of Quantum Chemistry 80 (4-5) 1125 (2000)
https://doi.org/10.1002/1097-461X(2000)80:4/5<1125::AID-QUA62>3.0.CO;2-J

Native topology determines force-induced unfolding pathways in globular proteins

D. K. Klimov and D. Thirumalai
Proceedings of the National Academy of Sciences 97 (13) 7254 (2000)
https://doi.org/10.1073/pnas.97.13.7254

Spin analogues of proteins: scaling of `folding' properties

Trinh Xuan Hoang, Nazar Sushko, Mai Suan Li and Marek Cieplak
Journal of Physics A: Mathematical and General 33 (22) 3977 (2000)
https://doi.org/10.1088/0305-4470/33/22/302

Molecular dynamics of folding of secondary structures in Go-type models of proteins

Trinh Xuan Hoang and Marek Cieplak
The Journal of Chemical Physics 112 (15) 6851 (2000)
https://doi.org/10.1063/1.481261

Fast folding of a ribozyme by stabilizing core interactions: evidence for multiple folding pathways in RNA 1 1Edited by I. Tinoco

Jie Pan, Michael L. Deras and Sarah A. Woodson
Journal of Molecular Biology 296 (1) 133 (2000)
https://doi.org/10.1006/jmbi.1999.3439

Simulation of heteropolymer collapse with an explicit solvent in two dimensions

James M. Polson and Martin J. Zuckermann
The Journal of Chemical Physics 113 (3) 1283 (2000)
https://doi.org/10.1063/1.481906

Fast folding of Escherichia coli cyclophilin A: a hypothesis of a unique hydrophobic core with a phenylalanine cluster

Teikichi Ikura, Toshiya Hayano, Nobuhiro Takahashi and Kunihiro Kuwajima
Journal of Molecular Biology 297 (3) 791 (2000)
https://doi.org/10.1006/jmbi.2000.3580

Magnesium-dependent folding of self-splicing RNA: Exploring the link between cooperativity, thermodynamics, and kinetics

Jie Pan, D. Thirumalai and Sarah A. Woodson
Proceedings of the National Academy of Sciences 96 (11) 6149 (1999)
https://doi.org/10.1073/pnas.96.11.6149

Folding in two-dimensional off-lattice models of proteins

Mai Li and Marek Cieplak
Physical Review E 59 (1) 970 (1999)
https://doi.org/10.1103/PhysRevE.59.970

Scaling behavior of stochastic minimization algorithms in a perfect funnel landscape

K. Hamacher and W. Wenzel
Physical Review E 59 (1) 938 (1999)
https://doi.org/10.1103/PhysRevE.59.938

Scaling of Folding Properties in Simple Models of Proteins

Marek Cieplak, Trinh Xuan Hoang and Mai Suan Li
Physical Review Letters 83 (8) 1684 (1999)
https://doi.org/10.1103/PhysRevLett.83.1684

Statistical Mechanics of Biocomplexity

Wolfgang Wenzel and Kay Hamacher
Lecture Notes in Physics, Statistical Mechanics of Biocomplexity 527 62 (1999)
https://doi.org/10.1007/BFb0105008

Submillisecond folding of the peripheral subunit-binding domain 1 1Edited by P. E. Wright

Shari Spector and Daniel P Raleigh
Journal of Molecular Biology 293 (4) 763 (1999)
https://doi.org/10.1006/jmbi.1999.3189

Deciphering the timescales and mechanisms of protein folding using minimal off-lattice models

D THIRUMALAI and D KLIMOV
Current Opinion in Structural Biology 9 (2) 197 (1999)
https://doi.org/10.1016/S0959-440X(99)80028-1

THE FAST PROTEIN FOLDING PROBLEM

M. Gruebele
Annual Review of Physical Chemistry 50 (1) 485 (1999)
https://doi.org/10.1146/annurev.physchem.50.1.485

Backbone dynamics, fast folding, and secondary structure formation in helical proteins and peptides

Corey Hardin, Zaida Luthey-Schulten and Peter G. Wolynes
Proteins: Structure, Function, and Genetics 34 (3) 281 (1999)
https://doi.org/10.1002/(SICI)1097-0134(19990215)34:3<281::AID-PROT2>3.0.CO;2-2

Searching for “downhill scenarios” in protein folding

William A. Eaton
Proceedings of the National Academy of Sciences 96 (11) 5897 (1999)
https://doi.org/10.1073/pnas.96.11.5897

Compactness of the denatured state of a fast-folding protein measured by submillisecond small-angle x-ray scattering

Lois Pollack, Mark W. Tate, Nicholas C. Darnton, James B. Knight, Sol M. Gruner, William A. Eaton and Robert H. Austin
Proceedings of the National Academy of Sciences 96 (18) 10115 (1999)
https://doi.org/10.1073/pnas.96.18.10115

Temperature dependence of the folding rate in a simple protein model: Search for a “glass” transition

A. Gutin, A. Sali, V. Abkevich, M. Karplus and E. I. Shakhnovich
The Journal of Chemical Physics 108 (15) 6466 (1998)
https://doi.org/10.1063/1.476053

On the transition coordinate for protein folding

Rose Du, Vijay S. Pande, Alexander Yu. Grosberg, Toyoichi Tanaka and Eugene S. Shakhnovich
The Journal of Chemical Physics 108 (1) 334 (1998)
https://doi.org/10.1063/1.475393

Self-consistently optimized energy functions for protein structure prediction by molecular dynamics

Kristin K. Koretke, Zaida Luthey-Schulten and Peter G. Wolynes
Proceedings of the National Academy of Sciences 95 (6) 2932 (1998)
https://doi.org/10.1073/pnas.95.6.2932

Rate of protein folding near the point of thermodynamic equilibrium between the coil and the most stable chain fold: Influence of chain knotting on the rate of folding

Alexei V Finkelstein and Azat Ya Badretdinov
Folding and Design 3 (1) 67 (1998)
https://doi.org/10.1016/S1359-0278(98)00009-1

Protein folding in the landscape perspective: Chevron plots and non-arrhenius kinetics

Hue Sun Chan and Ken A. Dill
Proteins: Structure, Function, and Genetics 30 (1) 2 (1998)
https://doi.org/10.1002/(SICI)1097-0134(19980101)30:1<2::AID-PROT2>3.0.CO;2-R

3D Protein Folds: Homologs Against Errors—a Simple Estimate Based on the Random Energy Model

Alexei V. Finkelstein
Physical Review Letters 80 (21) 4823 (1998)
https://doi.org/10.1103/PhysRevLett.80.4823

Comment on “Chain Length Scaling of Protein Folding Time”

Carlos J. Camacho
Physical Review Letters 80 (1) 207 (1998)
https://doi.org/10.1103/PhysRevLett.80.207

Native secondary structure formation in RNA may be a slave to tertiary folding

D. Thirumalai
Proceedings of the National Academy of Sciences 95 (20) 11506 (1998)
https://doi.org/10.1073/pnas.95.20.11506

Contact order, transition state placement and the refolding rates of single domain proteins 1 1Edited by P. E. Wright

Kevin W Plaxco, Kim T Simons and David Baker
Journal of Molecular Biology 277 (4) 985 (1998)
https://doi.org/10.1006/jmbi.1998.1645

Linking rates of folding in lattice models of proteins with underlying thermodynamic characteristics

D. K. Klimov and D. Thirumalai
The Journal of Chemical Physics 109 (10) 4119 (1998)
https://doi.org/10.1063/1.477012

Phase diagram of a Gaussian random copolymer

E. G. Timoshenko, Yu. A. Kuznetsov and K. A. Dawson
Physical Review E 55 (5) 5750 (1997)
https://doi.org/10.1103/PhysRevE.55.5750

THEORY OF PROTEIN FOLDING: The Energy Landscape Perspective

José Nelson Onuchic, Zaida Luthey-Schulten and Peter G. Wolynes
Annual Review of Physical Chemistry 48 (1) 545 (1997)
https://doi.org/10.1146/annurev.physchem.48.1.545

Statistical mechanics of a correlated energy landscape model for protein folding funnels

Steven S. Plotkin, Jin Wang and Peter G. Wolynes
The Journal of Chemical Physics 106 (7) 2932 (1997)
https://doi.org/10.1063/1.473355

A coarse-grained, “realistic” model for protein folding

Pierpaolo Bruscolini
The Journal of Chemical Physics 107 (18) 7512 (1997)
https://doi.org/10.1063/1.474991

Nucleation mechanisms in protein folding

Alan R Fersht
Current Opinion in Structural Biology 7 (1) 3 (1997)
https://doi.org/10.1016/S0959-440X(97)80002-4

From Levinthal to pathways to funnels

Ken A. Dill and Hue Sun Chan
Nature Structural & Molecular Biology 4 (1) 10 (1997)
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Folding of RNA involves parallel pathways

Jie Pan, D. Thirumalai and Sarah A. Woodson
Journal of Molecular Biology 273 (1) 7 (1997)
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Protein folding kinetics: timescales, pathways and energy landscapes in terms of sequence-dependent properties

Thomas Veitshans, Dmitri Klimov and Devarajan Thirumalai
Folding and Design 2 (1) 1 (1997)
https://doi.org/10.1016/S1359-0278(97)00002-3

Statics, metastable states, and barriers in protein folding: A replica variational approach

Shoji Takada and Peter G. Wolynes
Physical Review E 55 (4) 4562 (1997)
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Thermodynamics of protein folding: A statistical mechanical study of a small all-β protein

Zhuyan Guo and Charles L. Brooks
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Microscopic theory of critical folding nuclei and reconfiguration activation barriers in folding proteins

Shoji Takada and Peter G. Wolynes
The Journal of Chemical Physics 107 (22) 9585 (1997)
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Compaction and folding in model proteins

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Viscosity Dependence of the Folding Rates of Proteins

D. K. Klimov, and D. Thirumalai
Physical Review Letters 79 (2) 317 (1997)
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Entropic Barriers, Frustration, and Order: Basic Ingredients in Protein Folding

Carlos J. Camacho
Physical Review Letters 77 (11) 2324 (1996)
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On potential energy surfaces and relaxation to the global minimum

Jonathan P. K. Doye and David J. Wales
The Journal of Chemical Physics 105 (18) 8428 (1996)
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Chain Length Scaling of Protein Folding Time

A. M. Gutin, V. I. Abkevich and E. I. Shakhnovich
Physical Review Letters 77 (27) 5433 (1996)
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Optical Triggers of Protein Folding

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Criterion that Determines the Foldability of Proteins

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From Minimal Models to Real Proteins: Time Scales for Protein Folding Kinetics

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