Direct observation of microscopic reversibility in single-molecule protein folding.

[1]  David A C Beck,et al.  Exploring the energy landscape of protein folding using replica-exchange and conventional molecular dynamics simulations. , 2007, Journal of structural biology.

[2]  Ryan Day,et al.  Ensemble versus single-molecule protein unfolding. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[3]  Valerie Daggett,et al.  Simulation and experiment conspire to reveal cryptic intermediates and a slide from the nucleation-condensation to framework mechanism of folding. , 2005, Journal of molecular biology.

[4]  V. Daggett,et al.  Sensitivity of the folding/unfolding transition state ensemble of chymotrypsin inhibitor 2 to changes in temperature and solvent , 2005, Protein science : a publication of the Protein Society.

[5]  A. Fersht,et al.  Simulation and experiment at high temperatures: ultrafast folding of a thermophilic protein by nucleation-condensation. , 2005, Journal of molecular biology.

[6]  David A. C. Beck,et al.  Cutoff size need not strongly influence molecular dynamics results for solvated polypeptides. , 2005, Biochemistry.

[7]  Valerie Daggett,et al.  Ultrafast folding of α3D: A de novo designed three-helix bundle protein , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[8]  J. Onuchic,et al.  Folding a protein in a computer: An atomic description of the folding/unfolding of protein A , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[9]  Valerie Daggett,et al.  Unifying features in protein-folding mechanisms , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[10]  R. Zhou.  Trp-cage: Folding free energy landscape in explicit water , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[11]  William Swope,et al.  Understanding folding and design: Replica-exchange simulations of ``Trp-cage'' miniproteins , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[12]  Valerie Daggett,et al.  The present view of the mechanism of protein folding , 2003, Nature Reviews Molecular Cell Biology.

[13]  E. Rhoades,et al.  Watching proteins fold one molecule at a time , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[14]  Valerie Daggett,et al.  The complete folding pathway of a protein from nanoseconds to microseconds , 2003, Nature.

[15]  A. Fersht,et al.  Is there a unifying mechanism for protein folding? , 2003, Trends in biochemical sciences.

[16]  V. Daggett,et al.  Increasing temperature accelerates protein unfolding without changing the pathway of unfolding. , 2002, Journal of molecular biology.

[17]  V. Daggett,et al.  Probing the energy landscape of protein folding/unfolding transition states. , 2002, Journal of molecular biology.

[18]  A. Fersht,et al.  Protein Folding and Unfolding at Atomic Resolution , 2002, Cell.

[19]  W. Delano.  The PyMOL Molecular Graphics System , 2002 .

[20]  A. Fersht,et al.  Using flexible loop mimetics to extend Φ-value analysis to secondary structure interactions , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[21]  J. Espenson,et al.  Issues of microscopic reversibility and an isomeric intermediate in ligand substitution reactions of five-coordinate oxorhenium(V) dithiolate complexes. , 2001, Journal of the American Chemical Society.

[22]  Valerie Daggett,et al.  Protein folding from a highly disordered denatured state: The folding pathway of chymotrypsin inhibitor 2 at atomic resolution , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[23]  V Daggett,et al.  Direct comparison of experimental and calculated folding free energies for hydrophobic deletion mutants of chymotrypsin inhibitor 2: free energy perturbation calculations using transition and denatured states from molecular dynamics simulations of unfolding. , 2001, Biochemistry.

[24]  A. Fersht,et al.  Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[25]  D. Leeson,et al.  Protein folding and unfolding on a complex energy landscape. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[26]  Vladimir I. Minkin,et al.  International Union of Pure and Applied Chemistry Organic Chemistry Division Commission on Physical Organic Chemistry Glossary of Terms Used in Theoretical Organic Chemistry , 2022 .

[27]  P. Kollman,et al.  Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. , 1998, Science.

[28]  A. Fersht.  Structure and mechanism in protein science , 1998 .

[29]  A. Fersht,et al.  Synergy between simulation and experiment in describing the energy landscape of protein folding. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[30]  Valerie Daggett,et al.  Molecular dynamics simulations of hydrophobic collapse of ubiquitin , 1998, Protein science : a publication of the Protein Society.

[31]  Michael Levitt,et al.  Calibration and Testing of a Water Model for Simulation of the Molecular Dynamics of Proteins and Nucleic Acids in Solution , 1997 .

[32]  A. Li,et al.  Identification and characterization of the unfolding transition state of chymotrypsin inhibitor 2 by molecular dynamics simulations. , 1996, Journal of molecular biology.

[33]  A. Fersht,et al.  Structure of the transition state for folding of a protein derived from experiment and simulation. , 1996, Journal of molecular biology.

[34]  A. Li,et al.  Investigation of the solution structure of chymotrypsin inhibitor 2 using molecular dynamics: comparison to x-ray crystallographic and NMR data. , 1995, Protein engineering.

[35]  M. Levitt,et al.  Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution , 1995 .

[36]  V. Daggett,et al.  Molecular dynamics simulations of protein unfolding and limited refolding: characterization of partially unfolded states of ubiquitin in 60% methanol and in water. , 1995, Journal of molecular biology.

[37]  A. Fersht,et al.  Backbone dynamics of chymotrypsin inhibitor 2: effect of breaking the active site bond and its implications for the mechanism of inhibition of serine proteases. , 1995, Biochemistry.

[38]  A. Fersht,et al.  The structure of the transition state for the association of two fragments of the barley chymotrypsin inhibitor 2 to generate native-like protein: implications for mechanisms of protein folding. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[39]  A. Li,et al.  Characterization of the transition state of protein unfolding by use of molecular dynamics: chymotrypsin inhibitor 2. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[40]  A. Fersht,et al.  Direct observation of better hydration at the N terminus of an alpha-helix with glycine rather than alanine as the N-cap residue. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[41]  G. Petsko,et al.  Effects of temperature on protein structure and dynamics: X-ray crystallographic studies of the protein ribonuclease-A at nine different temperatures from 98 to 320 K. , 1993, Biochemistry.

[42]  F M Poulsen,et al.  Refinement of the three-dimensional solution structure of barley serine proteinase inhibitor 2 and comparison with the structures in crystals. , 1991, Journal of molecular biology.

[43]  A. Fersht,et al.  Folding of chymotrypsin inhibitor 2. 1. Evidence for a two-state transition. , 1991, Biochemistry.

[44]  I. Kuntz,et al.  Thermal expansion of a protein. , 1987, Biochemistry.

[45]  J. Gallagher,et al.  NBS/NRC Steam Tables: Thermodynamic and Transport Properties and Computer Programs for Vapor and Liquid States of Water in SI Units, , 1984 .

[46]  F. Westheimer.  Pseudo-rotation in the hydrolysis of phosphate esters , 1968 .