Dynameomics: A Consensus View of the Protein Unfolding/Folding Transition State Ensemble across a Diverse Set of Protein Folds

Jonsson, Amanda L.; Scott, Kathryn A.; Daggett, Valerie

doi:10.1016/j.bpj.2009.09.012

Title: Dynameomics: A Consensus View of the Protein Unfolding/Folding Transition State Ensemble across a Diverse Set of Protein Folds

Authors:: Jonsson, Amanda L.; Scott, Kathryn A.; Daggett, Valerie

Publication Date:: Tue Dec 01 00:00:00 EST 2009

Sponsoring Org.:: USDOE

OSTI Identifier:: 1198103

Grant/Contract Number:: AC02-05CH11231

Resource Type:: Published Article

Journal Name:: Biophysical Journal

Additional Journal Information:: Journal Name: Biophysical Journal Journal Volume: 97 Journal Issue: 11; Journal ID: ISSN 0006-3495

Publisher:: Elsevier

Country of Publication:: United States

Language:: English

Citation Formats


                    Jonsson, Amanda L., Scott, Kathryn A., and Daggett, Valerie. Dynameomics: A Consensus View of the Protein Unfolding/Folding Transition State Ensemble across a Diverse Set of Protein Folds.  United States: N. p., 2009. 
Web.  doi:10.1016/j.bpj.2009.09.012.

Copy to clipboard


                    Jonsson, Amanda L., Scott, Kathryn A., & Daggett, Valerie. Dynameomics: A Consensus View of the Protein Unfolding/Folding Transition State Ensemble across a Diverse Set of Protein Folds.  United States.  https://doi.org/10.1016/j.bpj.2009.09.012

Copy to clipboard


                    Jonsson, Amanda L., Scott, Kathryn A., and Daggett, Valerie. Tue .  
"Dynameomics: A Consensus View of the Protein Unfolding/Folding Transition State Ensemble across a Diverse Set of Protein Folds".  United States.  https://doi.org/10.1016/j.bpj.2009.09.012.

Copy to clipboard


                    
@article{osti_1198103,

  title        = {Dynameomics: A Consensus View of the Protein Unfolding/Folding Transition State Ensemble across a Diverse Set of Protein Folds},

  author       = {Jonsson, Amanda L. and Scott, Kathryn A. and Daggett, Valerie},

  abstractNote = {},

  doi          = {10.1016/j.bpj.2009.09.012},

  journal      = {Biophysical Journal},

  number       = 11,

  volume       = 97,

  place        = {United States},

  year         = {Tue Dec 01 00:00:00 EST 2009},

  month        = {Tue Dec 01 00:00:00 EST 2009}

}

Copy to clipboard

Journal Article:

Free Publicly Available Full Text

Publisher's Version of Record
https://doi.org/10.1016/j.bpj.2009.09.012

Other availability

Search WorldCat to find libraries that may hold this journal

Citation Metrics:

Cited by: 24 works

Citation information provided by
Web of Science

Save / Share:

Export Metadata

Save to My Library

Works referenced in this record:

Folding Dynamics of the src SH3 Domain
journal, December 1997

Grantcharova, Viara P.; Baker, David
Biochemistry, Vol. 36, Issue 50
DOI: 10.1021/bi971786p

Microscopic Reversibility of Protein Folding in Molecular Dynamics Simulations of the Engrailed Homeodomain ^†
journal, July 2008

McCully, Michelle E.; Beck, David A. C.; Daggett, Valerie
Biochemistry, Vol. 47, Issue 27
DOI: 10.1021/bi800118b

Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution
journal, September 1995

Levitt, Michael; Hirshberg, Miriam; Sharon, Ruth
Computer Physics Communications, Vol. 91, Issue 1-3
DOI: 10.1016/0010-4655(95)00049-L

The Structure of the Major Transition State for Folding of an FF Domain from Experiment and Simulation
journal, July 2005

Jemth, Per; Day, Ryan; Gianni, Stefano
Journal of Molecular Biology, Vol. 350, Issue 2
DOI: 10.1016/j.jmb.2005.04.067

The Folding Kinetics and Thermodynamics of the Fyn-SH3 Domain
journal, February 1998

Plaxco, Kevin W.; Guijarro, J. Iñaki; Morton, Craig J.
Biochemistry, Vol. 37, Issue 8
DOI: 10.1021/bi972075u

Simulation and Experiment at High Temperatures: Ultrafast Folding of a Thermophilic Protein by Nucleation-condensation
journal, April 2005

Ferguson, Neil; Day, Ryan; Johnson, Christopher M.
Journal of Molecular Biology, Vol. 347, Issue 4
DOI: 10.1016/j.jmb.2004.12.061

Structure of the Transition State for Folding of a Protein Derived from Experiment and Simulation
journal, March 1996

Daggett, Valerie; Li, Aijun; Itzhaki, Laura S.
Journal of Molecular Biology, Vol. 257, Issue 2
DOI: 10.1006/jmbi.1996.0173

How do small single-domain proteins fold?
journal, August 1998

Jackson, Sophie E.
Folding and Design, Vol. 3, Issue 4
DOI: 10.1016/S1359-0278(98)00033-9

The molecular basis for the chemical denaturation of proteins by urea
journal, April 2003

Bennion, B. J.; Daggett, V.
Proceedings of the National Academy of Sciences, Vol. 100, Issue 9
DOI: 10.1073/pnas.0930122100

Is there a unifying mechanism for protein folding?
journal, January 2003

Daggett, Valerie; Fersht, Alan R.
Trends in Biochemical Sciences, Vol. 28, Issue 1
DOI: 10.1016/S0968-0004(02)00012-9

Cutoff Size Need Not Strongly Influence Molecular Dynamics Results for Solvated Polypeptides ^†
journal, January 2005

Beck, David A. C.; Armen, Roger S.; Daggett, Valerie
Biochemistry, Vol. 44, Issue 2
DOI: 10.1021/bi0486381

Increasing Temperature Accelerates Protein Unfolding Without Changing the Pathway of Unfolding
journal, September 2002

Day, Ryan; Bennion, Brian J.; Ham, Sihyun
Journal of Molecular Biology, Vol. 322, Issue 1
DOI: 10.1016/S0022-2836(02)00672-1

Folding studies of immunoglobulin-like β-sandwich proteins suggest that they share a common folding pathway
journal, September 1999

Clarke, Jane; Cota, Ernesto; Fowler, Susan B.
Structure, Vol. 7, Issue 9
DOI: 10.1016/S0969-2126(99)80181-6

Calibration and Testing of a Water Model for Simulation of the Molecular Dynamics of Proteins and Nucleic Acids in Solution
journal, June 1997

Levitt, Michael; Hirshberg, Miriam; Sharon, Ruth
The Journal of Physical Chemistry B, Vol. 101, Issue 25
DOI: 10.1021/jp964020s

Identification and Characterization of the Unfolding Transition State of Chymotrypsin Inhibitor 2 by Molecular Dynamics Simulations
journal, March 1996

Li, Aijun; Daggett, Valerie
Journal of Molecular Biology, Vol. 257, Issue 2
DOI: 10.1006/jmbi.1996.0172

The Structure of the Transition State for Folding of Chymotrypsin Inhibitor 2 Analysed by Protein Engineering Methods: Evidence for a Nucleation-condensation Mechanism for Protein Folding
journal, November 1995

Itzhaki, Laura S.; Otzen, Daniel E.; Fersht, Alan R.
Journal of Molecular Biology, Vol. 254, Issue 2
DOI: 10.1006/jmbi.1995.0616

Using flexible loop mimetics to extend Φ-value analysis to secondary structure interactions
journal, October 2001

Ferguson, Neil; Pires, José Ricardo; Toepert, Florian
Proceedings of the National Academy of Sciences, Vol. 98, Issue 23
DOI: 10.1073/pnas.221467398

Diffusing and Colliding: The Atomic Level Folding/Unfolding Pathway of a Small Helical Protein
journal, August 2004

DeMarco, Mari L.; Alonso, Darwin O. V.; Daggett, Valerie
Journal of Molecular Biology, Vol. 341, Issue 4
DOI: 10.1016/j.jmb.2004.06.074

CATH – a hierarchic classification of protein domain structures
journal, August 1997

Orengo, Ca; Michie, Ad; Jones, S.
Structure, Vol. 5, Issue 8
DOI: 10.1016/S0969-2126(97)00260-8

Families and the structural relatedness among globular proteins
journal, June 1993

Yee, David P.; Dill, Ken A.
Protein Science, Vol. 2, Issue 6
DOI: 10.1002/pro.5560020603

Stability and folding properties of a model β-sheet protein, Escherichia coli CspA
journal, February 1998

Reid, Katherine L.; Rodriguez, Hector M.; Hillier, Brian J.
Protein Science, Vol. 7, Issue 2
DOI: 10.1002/pro.5560070228

Hierarchy of structure loss in MD simulations of src SH3 domain unfolding
journal, September 1999

Tsai, Jerry; Levitt, Michael; Baker, David
Journal of Molecular Biology, Vol. 291, Issue 1
DOI: 10.1006/jmbi.1999.2949

Mapping the Interactions Present in the Transition State for Unfolding/Folding of FKBP12
journal, August 1999

Fulton, Kate F.; Main, Ewan R. G.; Daggett, Valerie
Journal of Molecular Biology, Vol. 291, Issue 2
DOI: 10.1006/jmbi.1999.2942

Φ-Analysis at the Experimental Limits: Mechanism of β-Hairpin Formation
journal, July 2006

Petrovich, Miriana; Jonsson, Amanda L.; Ferguson, Neil
Journal of Molecular Biology, Vol. 360, Issue 4
DOI: 10.1016/j.jmb.2006.05.050

The Folding Pathway of Spectrin R17 from Experiment and Simulation: Using Experimentally Validated MD Simulations to Characterize States Hinted at by Experiment
journal, May 2006

Scott, Kathryn A.; Randles, Lucy G.; Moran, Stephen J.
Journal of Molecular Biology, Vol. 359, Issue 1
DOI: 10.1016/j.jmb.2006.03.011

The role of the turn in β-hairpin formation during WW domain folding
journal, October 2007

Sharpe, Tim; Jonsson, Amanda L.; Rutherford, Trevor J.
Protein Science, Vol. 16, Issue 10
DOI: 10.1110/ps.073004907

Direct Observation of Microscopic Reversibility in Single-molecule Protein Folding
journal, February 2007

Day, Ryan; Daggett, Valerie
Journal of Molecular Biology, Vol. 366, Issue 2
DOI: 10.1016/j.jmb.2006.11.043

Characterization of the transition state of protein unfolding by use of molecular dynamics: chymotrypsin inhibitor 2.
journal, October 1994

Li, A.; Daggett, V.
Proceedings of the National Academy of Sciences, Vol. 91, Issue 22
DOI: 10.1073/pnas.91.22.10430

Synergy between simulation and experiment in describing the energy landscape of protein folding
journal, July 1998

Ladurner, Andreas G.; Itzhaki, Laura S.; Daggett, Valerie
Proceedings of the National Academy of Sciences, Vol. 95, Issue 15
DOI: 10.1073/pnas.95.15.8473

Role of native topology investigated by multiple unfolding simulations of four SH3 domains
journal, May 2001

Gsponer, Jörg; Caflisch, Amedeo
Journal of Molecular Biology, Vol. 309, Issue 1
DOI: 10.1006/jmbi.2001.4552

The intrinsic conformational propensities of the 20 naturally occurring amino acids and reflection of these propensities in proteins
journal, August 2008

Beck, D. A. C.; Alonso, D. O. V.; Inoyama, D.
Proceedings of the National Academy of Sciences, Vol. 105, Issue 34
DOI: 10.1073/pnas.0706527105

Structural Analysis of the Rate-limiting Transition States in the Folding of Im7 and Im9: Similarities and Differences in the Folding of Homologous Proteins
journal, February 2003

Friel, Claire T.; Capaldi, Andrew P.; Radford, Sheena E.
Journal of Molecular Biology, Vol. 326, Issue 1
DOI: 10.1016/S0022-2836(02)01249-4

Simulation and Experiment Conspire to Reveal Cryptic Intermediates and a Slide from the Nucleation-condensation to Framework Mechanism of Folding
journal, July 2005

White, George W. N.; Gianni, Stefano; Grossmann, J. Gunter
Journal of Molecular Biology, Vol. 350, Issue 4
DOI: 10.1016/j.jmb.2005.05.005

SCOP: A structural classification of proteins database for the investigation of sequences and structures
journal, April 1995

Murzin, Alexey G.; Brenner, Steven E.; Hubbard, Tim
Journal of Molecular Biology, Vol. 247, Issue 4
DOI: 10.1016/S0022-2836(05)80134-2

A consensus view of fold space: Combining SCOP, CATH, and the Dali Domain Dictionary
journal, October 2003

Day, Ryan; Beck, David A. C.; Armen, Roger S.
Protein Science, Vol. 12, Issue 10
DOI: 10.1110/ps.0306803

Methods for molecular dynamics simulations of protein folding/unfolding in solution
journal, September 2004

Beck, D.
Methods, Vol. 34, Issue 1
DOI: 10.1016/j.ymeth.2004.03.008

Testing protein-folding simulations by experiment: B domain of protein A
journal, April 2004

Sato, Satoshi; Religa, Tomasz L.; Daggett, Valerie
Proceedings of the National Academy of Sciences, Vol. 101, Issue 18
DOI: 10.1073/pnas.0401396101

Dynameomics: Large‐scale assessment of native protein flexibility
journal, December 2008

Benson, Noah C.; Daggett, Valerie
Protein Science, Vol. 17, Issue 12
DOI: 10.1110/ps.037473.108

Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
journal, December 1983

Kabsch, Wolfgang; Sander, Christian
Biopolymers, Vol. 22, Issue 12
DOI: 10.1002/bip.360221211

Structure of the transition state for the folding/unfolding of the barley chymotrypsin inhibitor 2 and its implications for mechanisms of protein folding.
journal, October 1994

Otzen, D. E.; Itzhaki, L. S.; elMasry, N. F.
Proceedings of the National Academy of Sciences, Vol. 91, Issue 22
DOI: 10.1073/pnas.91.22.10422

Demonstration of a low-energy on-pathway intermediate in a fast-folding protein by kinetics, protein engineering, and simulation
journal, April 2004

Jemth, P.; Gianni, S.; Day, R.
Proceedings of the National Academy of Sciences, Vol. 101, Issue 17
DOI: 10.1073/pnas.0401732101

Dynameomics: mass annotation of protein dynamics and unfolding in water by high-throughput atomistic molecular dynamics simulations
journal, April 2008

Beck, D. A. C.; Jonsson, A. L.; Schaeffer, R. D.
Protein Engineering Design and Selection, Vol. 21, Issue 6
DOI: 10.1093/protein/gzn011

Sensitivity of the folding/unfolding transition state ensemble of chymotrypsin inhibitor 2 to changes in temperature and solvent
journal, May 2005

Day, Ryan; Daggett, Valerie
Protein Science, Vol. 14, Issue 5
DOI: 10.1110/ps.041226005

Dynameomics: design of a computational lab workflow and scientific data repository for protein simulations
journal, April 2008

Simms, A. M.; Toofanny, R. D.; Kehl, C.
Protein Engineering Design and Selection, Vol. 21, Issue 6
DOI: 10.1093/protein/gzn012

Dynameomics: a multi-dimensional analysis-optimized database for dynamic protein data
journal, April 2008

Kehl, C.; Simms, A. M.; Toofanny, R. D.
Protein Engineering Design and Selection, Vol. 21, Issue 6
DOI: 10.1093/protein/gzn015

Molecular dynamics simulations of protein folding from the transition state
journal, April 2002

Gsponer, J.; Caflisch, A.
Proceedings of the National Academy of Sciences, Vol. 99, Issue 10
DOI: 10.1073/pnas.092686399

Keeping it in the family: folding studies of related proteins
journal, February 2001

Gunasekaran, Kannan; Eyles, Stephen J.; Hagler, Arnold T.
Current Opinion in Structural Biology, Vol. 11, Issue 1
DOI: 10.1016/S0959-440X(00)00173-1

A normalized root-mean-spuare distance for comparing protein three-dimensional structures
journal, December 2008

Carugo, Oliviero; Pongor, Sándor
Protein Science, Vol. 10, Issue 7
DOI: 10.1110/ps.690101

Folding of chymotrypsin inhibitor 2. 1. Evidence for a two-state transition
journal, October 1991

Jackson, Sophie E.; Fersht, Alan R.
Biochemistry, Vol. 30, Issue 43
DOI: 10.1021/bi00107a010

Combined Molecular Dynamics and Φ-Value Analysis of Structure−Reactivity Relationships in the Transition State and Unfolding Pathway of Barnase: Structural Basis of Hammond and Anti-Hammond Effects
journal, December 1998

Daggett, Valerie; Li, Aijun; Fersht, Alan R.
Journal of the American Chemical Society, Vol. 120, Issue 49
DOI: 10.1021/ja981558y

Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain
journal, August 1998

Grantcharova, Viara P.; Riddle, David S.; Santiago, Jed V.
Nature Structural & Molecular Biology, Vol. 5, Issue 8
DOI: 10.1038/1412

Staphylococcal protein A: Unfolding pathways, unfolded states, and differences between the B and E domains
journal, January 2000

Alonso, Darwin O. V.; Daggett, Valerie
Proceedings of the National Academy of Sciences, Vol. 97, Issue 1
DOI: 10.1073/pnas.97.1.133

The Protein Data Bank
journal, January 2000

Berman, H. M.
Nucleic Acids Research, Vol. 28, Issue 1
DOI: 10.1093/nar/28.1.235

Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation
journal, November 2000

Mayor, U.; Johnson, C. M.; Daggett, V.
Proceedings of the National Academy of Sciences, Vol. 97, Issue 25
DOI: 10.1073/pnas.250473497

Hydrophobic core packing in the SH3 domain folding transition state
journal, January 2002

Northey, Julian G. B.; Di Nardo, Ariel A.; Davidson, Alan R.
Nature Structural Biology, Vol. 9, Issue 2
DOI: 10.1038/nsb748

The complete folding pathway of a protein from nanoseconds to microseconds
journal, February 2003

Mayor, Ugo; Guydosh, Nicholas R.; Johnson, Christopher M.
Nature, Vol. 421, Issue 6925
DOI: 10.1038/nature01428

Solution structure of a protein denatured state and folding intermediate
journal, October 2005

Religa, T. L.; Markson, J. S.; Mayor, U.
Nature, Vol. 437, Issue 7061
DOI: 10.1038/nature04054

Unifying features in protein-folding mechanisms
journal, October 2003

Gianni, S.; Guydosh, N. R.; Khan, F.
Proceedings of the National Academy of Sciences, Vol. 100, Issue 23
DOI: 10.1073/pnas.1835776100

Similar Records in DOE PAGES and OSTI.GOV collections:

The Dynameomics Entropy Dictionary: A Large-Scale Assessment of Conformational Entropy across Protein Fold Space

Journal Article Towse, Clare-Louise ; Akke, Mikael ; Daggett, Valerie - Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry

Molecular dynamics (MD) simulations contain considerable information with regard to the motions and fluctuations of a protein, the magnitude of which can be used to estimate conformational entropy. In this report we survey conformational entropy across protein fold space using the Dynameomics database, which represents the largest existing data set of protein MD simulations for representatives of essentially all known protein folds. We provide an overview of MD-derived entropies accounting for all possible degrees of dihedral freedom on an unprecedented scale. Although different side chains might be expected to impose varying restrictions on the conformational space that the backbone canmore »« less
Cited by 17
https://doi.org/10.1021/acs.jpcb.7b00577

Full Text Available
Wang-Landau density of states based study of the folding-unfolding transition in the mini-protein Trp-cage (TC5b)

Journal Article Singh, Priya ; Sarkar, Subir K. ; Bandyopadhyay, Pradipta - Journal of Chemical Physics

We present the results of a high-statistics equilibrium study of the folding/unfolding transition for the 20-residue mini-protein Trp-cage (TC5b) in water. The ECEPP/3 force field is used and the interaction with water is treated by a solvent-accessible surface area method. A Wang-Landau type simulation is used to calculate the density of states and the conditional probabilities for the various values of the radius of gyration and the number of native contacts at fixed values of energy—along with a systematic check on their convergence. All thermodynamic quantities of interest are calculated from this information. The folding-unfolding transition corresponds to a peakmore »« less
https://doi.org/10.1063/1.4885726
Protein folding from heterogeneous unfolded state revealed by time-resolved X-ray solution scattering

Journal Article Kim, Tae Wu ; Lee, Sang Jin ; Jo, Junbeom ; ... - Proceedings of the National Academy of Sciences of the United States of America

One of the most challenging tasks in biological science is to understand how a protein folds. In theoretical studies, the hypothesis adopting a funnel-like free-energy landscape has been recognized as a prominent scheme for explaining protein folding in views of both internal energy and conformational heterogeneity of a protein. Despite numerous experimental efforts, however, comprehensively studying protein folding with respect to its global conformational changes in conjunction with the heterogeneity has been elusive. Here we investigate the redox-coupled folding dynamics of equine heart cytochrome c (cyt-c) induced by external electron injection by using time-resolved X-ray solution scattering. A systematic kineticmore »« less
Cited by 29
https://doi.org/10.1073/pnas.1913442117

Full Text Available
Properties of protein unfolded states suggest broad selection for expanded conformational ensembles

Journal Article Bowman, Micayla A. ; Riback, Joshua A. ; Rodriguez, Anabel ; ... - Proceedings of the National Academy of Sciences of the United States of America

Much attention is being paid to conformational biases in the ensembles of intrinsically disordered proteins. However, it is currently unknown whether or how conformational biases within the disordered ensembles of foldable proteins affect function in vivo. Recently, we demonstrated that water can be a good solvent for unfolded polypeptide chains, even those with a hydrophobic and charged sequence composition typical of folded proteins. These results run counter to the generally accepted model that protein folding begins with hydrophobicity-driven chain collapse. Here we investigate what other features, beyond amino acid composition, govern chain collapse. We found that local clustering of hydrophobicmore »« less
https://doi.org/10.1073/pnas.2003773117
Local conformational relaxations and protein folding-unfolding transition

Journal Article Tsong, T Y ; Kanehisa, M I - Biophys. J.; (United States)

A protein molecule is a small system; as such its conformation constantly fluctuates. These events cover a broad time range: picoseconds for bond vibrations, oscillations and rotation, nanoseconds to microseconds for chain motions at a local level, and milliseconds to seconds for folding-unfolding transition. In a recent study we examined how events associated with rapid intramolecular motions or local conformational relaxations might affect the dynamics of the chain folding. We have proposed a cluster model which postulates that a peptide chain folds, under a favorable solvent condition, by first forming structural nuclei at locals, and second, merging or coalescing thesemore »« less
https://doi.org/10.1016/S0006-3495(80)84966-6

Similar Records

Title: Dynameomics: A Consensus View of the Protein Unfolding/Folding Transition State Ensemble across a Diverse Set of Protein Folds

Citation Formats

Folding Dynamics of the src SH3 Domain journal, December 1997

Microscopic Reversibility of Protein Folding in Molecular Dynamics Simulations of the Engrailed Homeodomain † journal, July 2008

Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution journal, September 1995

The Structure of the Major Transition State for Folding of an FF Domain from Experiment and Simulation journal, July 2005

The Folding Kinetics and Thermodynamics of the Fyn-SH3 Domain journal, February 1998

Simulation and Experiment at High Temperatures: Ultrafast Folding of a Thermophilic Protein by Nucleation-condensation journal, April 2005

Structure of the Transition State for Folding of a Protein Derived from Experiment and Simulation journal, March 1996

How do small single-domain proteins fold? journal, August 1998

The molecular basis for the chemical denaturation of proteins by urea journal, April 2003

Is there a unifying mechanism for protein folding? journal, January 2003

Cutoff Size Need Not Strongly Influence Molecular Dynamics Results for Solvated Polypeptides † journal, January 2005

Increasing Temperature Accelerates Protein Unfolding Without Changing the Pathway of Unfolding journal, September 2002

Folding studies of immunoglobulin-like β-sandwich proteins suggest that they share a common folding pathway journal, September 1999

Calibration and Testing of a Water Model for Simulation of the Molecular Dynamics of Proteins and Nucleic Acids in Solution journal, June 1997

Identification and Characterization of the Unfolding Transition State of Chymotrypsin Inhibitor 2 by Molecular Dynamics Simulations journal, March 1996

The Structure of the Transition State for Folding of Chymotrypsin Inhibitor 2 Analysed by Protein Engineering Methods: Evidence for a Nucleation-condensation Mechanism for Protein Folding journal, November 1995

Using flexible loop mimetics to extend Φ-value analysis to secondary structure interactions journal, October 2001

Diffusing and Colliding: The Atomic Level Folding/Unfolding Pathway of a Small Helical Protein journal, August 2004

CATH – a hierarchic classification of protein domain structures journal, August 1997

Families and the structural relatedness among globular proteins journal, June 1993

Stability and folding properties of a model β-sheet protein, Escherichia coli CspA journal, February 1998

Hierarchy of structure loss in MD simulations of src SH3 domain unfolding journal, September 1999

Mapping the Interactions Present in the Transition State for Unfolding/Folding of FKBP12 journal, August 1999

Φ-Analysis at the Experimental Limits: Mechanism of β-Hairpin Formation journal, July 2006

The Folding Pathway of Spectrin R17 from Experiment and Simulation: Using Experimentally Validated MD Simulations to Characterize States Hinted at by Experiment journal, May 2006

The role of the turn in β-hairpin formation during WW domain folding journal, October 2007

Direct Observation of Microscopic Reversibility in Single-molecule Protein Folding journal, February 2007

Characterization of the transition state of protein unfolding by use of molecular dynamics: chymotrypsin inhibitor 2. journal, October 1994

Synergy between simulation and experiment in describing the energy landscape of protein folding journal, July 1998

Role of native topology investigated by multiple unfolding simulations of four SH3 domains journal, May 2001

The intrinsic conformational propensities of the 20 naturally occurring amino acids and reflection of these propensities in proteins journal, August 2008

Structural Analysis of the Rate-limiting Transition States in the Folding of Im7 and Im9: Similarities and Differences in the Folding of Homologous Proteins journal, February 2003

Simulation and Experiment Conspire to Reveal Cryptic Intermediates and a Slide from the Nucleation-condensation to Framework Mechanism of Folding journal, July 2005

SCOP: A structural classification of proteins database for the investigation of sequences and structures journal, April 1995

A consensus view of fold space: Combining SCOP, CATH, and the Dali Domain Dictionary journal, October 2003

Methods for molecular dynamics simulations of protein folding/unfolding in solution journal, September 2004

Testing protein-folding simulations by experiment: B domain of protein A journal, April 2004

Dynameomics: Large‐scale assessment of native protein flexibility journal, December 2008

Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features journal, December 1983

Structure of the transition state for the folding/unfolding of the barley chymotrypsin inhibitor 2 and its implications for mechanisms of protein folding. journal, October 1994

Demonstration of a low-energy on-pathway intermediate in a fast-folding protein by kinetics, protein engineering, and simulation journal, April 2004

Dynameomics: mass annotation of protein dynamics and unfolding in water by high-throughput atomistic molecular dynamics simulations journal, April 2008

Sensitivity of the folding/unfolding transition state ensemble of chymotrypsin inhibitor 2 to changes in temperature and solvent journal, May 2005

Dynameomics: design of a computational lab workflow and scientific data repository for protein simulations journal, April 2008

Dynameomics: a multi-dimensional analysis-optimized database for dynamic protein data journal, April 2008

Molecular dynamics simulations of protein folding from the transition state journal, April 2002

Keeping it in the family: folding studies of related proteins journal, February 2001

A normalized root-mean-spuare distance for comparing protein three-dimensional structures journal, December 2008

Folding of chymotrypsin inhibitor 2. 1. Evidence for a two-state transition journal, October 1991

Combined Molecular Dynamics and Φ-Value Analysis of Structure−Reactivity Relationships in the Transition State and Unfolding Pathway of Barnase: Structural Basis of Hammond and Anti-Hammond Effects journal, December 1998

Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain journal, August 1998

Staphylococcal protein A: Unfolding pathways, unfolded states, and differences between the B and E domains journal, January 2000

The Protein Data Bank journal, January 2000

Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation journal, November 2000

Hydrophobic core packing in the SH3 domain folding transition state journal, January 2002

The complete folding pathway of a protein from nanoseconds to microseconds journal, February 2003

Solution structure of a protein denatured state and folding intermediate journal, October 2005

Unifying features in protein-folding mechanisms journal, October 2003

Folding Dynamics of the src SH3 Domain
journal, December 1997

Microscopic Reversibility of Protein Folding in Molecular Dynamics Simulations of the Engrailed Homeodomain ^†
journal, July 2008

Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution
journal, September 1995

The Structure of the Major Transition State for Folding of an FF Domain from Experiment and Simulation
journal, July 2005

The Folding Kinetics and Thermodynamics of the Fyn-SH3 Domain
journal, February 1998

Simulation and Experiment at High Temperatures: Ultrafast Folding of a Thermophilic Protein by Nucleation-condensation
journal, April 2005

Structure of the Transition State for Folding of a Protein Derived from Experiment and Simulation
journal, March 1996

How do small single-domain proteins fold?
journal, August 1998

The molecular basis for the chemical denaturation of proteins by urea
journal, April 2003

Is there a unifying mechanism for protein folding?
journal, January 2003

Cutoff Size Need Not Strongly Influence Molecular Dynamics Results for Solvated Polypeptides ^†
journal, January 2005

Increasing Temperature Accelerates Protein Unfolding Without Changing the Pathway of Unfolding
journal, September 2002

Folding studies of immunoglobulin-like β-sandwich proteins suggest that they share a common folding pathway
journal, September 1999

Calibration and Testing of a Water Model for Simulation of the Molecular Dynamics of Proteins and Nucleic Acids in Solution
journal, June 1997

Identification and Characterization of the Unfolding Transition State of Chymotrypsin Inhibitor 2 by Molecular Dynamics Simulations
journal, March 1996

The Structure of the Transition State for Folding of Chymotrypsin Inhibitor 2 Analysed by Protein Engineering Methods: Evidence for a Nucleation-condensation Mechanism for Protein Folding
journal, November 1995

Using flexible loop mimetics to extend Φ-value analysis to secondary structure interactions
journal, October 2001

Diffusing and Colliding: The Atomic Level Folding/Unfolding Pathway of a Small Helical Protein
journal, August 2004

CATH – a hierarchic classification of protein domain structures
journal, August 1997

Families and the structural relatedness among globular proteins
journal, June 1993

Stability and folding properties of a model β-sheet protein, Escherichia coli CspA
journal, February 1998

Hierarchy of structure loss in MD simulations of src SH3 domain unfolding
journal, September 1999

Mapping the Interactions Present in the Transition State for Unfolding/Folding of FKBP12
journal, August 1999

Φ-Analysis at the Experimental Limits: Mechanism of β-Hairpin Formation
journal, July 2006

The Folding Pathway of Spectrin R17 from Experiment and Simulation: Using Experimentally Validated MD Simulations to Characterize States Hinted at by Experiment
journal, May 2006

The role of the turn in β-hairpin formation during WW domain folding
journal, October 2007

Direct Observation of Microscopic Reversibility in Single-molecule Protein Folding
journal, February 2007

Characterization of the transition state of protein unfolding by use of molecular dynamics: chymotrypsin inhibitor 2.
journal, October 1994

Synergy between simulation and experiment in describing the energy landscape of protein folding
journal, July 1998

Role of native topology investigated by multiple unfolding simulations of four SH3 domains
journal, May 2001

The intrinsic conformational propensities of the 20 naturally occurring amino acids and reflection of these propensities in proteins
journal, August 2008

Structural Analysis of the Rate-limiting Transition States in the Folding of Im7 and Im9: Similarities and Differences in the Folding of Homologous Proteins
journal, February 2003

Simulation and Experiment Conspire to Reveal Cryptic Intermediates and a Slide from the Nucleation-condensation to Framework Mechanism of Folding
journal, July 2005

SCOP: A structural classification of proteins database for the investigation of sequences and structures
journal, April 1995

A consensus view of fold space: Combining SCOP, CATH, and the Dali Domain Dictionary
journal, October 2003

Methods for molecular dynamics simulations of protein folding/unfolding in solution
journal, September 2004

Testing protein-folding simulations by experiment: B domain of protein A
journal, April 2004

Dynameomics: Large‐scale assessment of native protein flexibility
journal, December 2008

Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
journal, December 1983

Structure of the transition state for the folding/unfolding of the barley chymotrypsin inhibitor 2 and its implications for mechanisms of protein folding.
journal, October 1994

Demonstration of a low-energy on-pathway intermediate in a fast-folding protein by kinetics, protein engineering, and simulation
journal, April 2004

Dynameomics: mass annotation of protein dynamics and unfolding in water by high-throughput atomistic molecular dynamics simulations
journal, April 2008

Sensitivity of the folding/unfolding transition state ensemble of chymotrypsin inhibitor 2 to changes in temperature and solvent
journal, May 2005

Dynameomics: design of a computational lab workflow and scientific data repository for protein simulations
journal, April 2008

Dynameomics: a multi-dimensional analysis-optimized database for dynamic protein data
journal, April 2008

Molecular dynamics simulations of protein folding from the transition state
journal, April 2002

Keeping it in the family: folding studies of related proteins
journal, February 2001

A normalized root-mean-spuare distance for comparing protein three-dimensional structures
journal, December 2008

Folding of chymotrypsin inhibitor 2. 1. Evidence for a two-state transition
journal, October 1991

Combined Molecular Dynamics and Φ-Value Analysis of Structure−Reactivity Relationships in the Transition State and Unfolding Pathway of Barnase: Structural Basis of Hammond and Anti-Hammond Effects
journal, December 1998

Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain
journal, August 1998

Staphylococcal protein A: Unfolding pathways, unfolded states, and differences between the B and E domains
journal, January 2000

The Protein Data Bank
journal, January 2000

Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation
journal, November 2000

Hydrophobic core packing in the SH3 domain folding transition state
journal, January 2002

The complete folding pathway of a protein from nanoseconds to microseconds
journal, February 2003

Solution structure of a protein denatured state and folding intermediate
journal, October 2005

Unifying features in protein-folding mechanisms
journal, October 2003