Dynameomics: a consensus view of the protein unfolding/folding transition state ensemble across a diverse set of protein folds.

The Dynameomics project aims to simulate a representative sample of all globular protein metafolds under both native and unfolding conditions. We have identified protein unfolding transition state (TS) ensembles from multiple molecular dynamics simulations of high-temperature unfolding in 183 structurally distinct proteins. These data can be used to study individual proteins and individual protein metafolds and to mine for TS structural features common across all proteins. Separating the TS structures into four different fold classes (all proteins, all-alpha, all-beta, and mixed alpha/beta and alpha +beta) resulted in no significant difference in the overall protein properties. The residues with the most contacts in the native state lost the most contacts in the TS ensemble. On average, residues beginning in an alpha-helix maintained more structure in the TS ensemble than did residues starting in beta-strands or any other conformation. The metafolds studied here represent 67% of all known protein structures, and this is, to our knowledge, the largest, most comprehensive study of the protein folding/unfolding TS ensemble to date. One might have expected broad distributions in the average global properties of the TS relative to the native state, indicating variability in the amount of structure present in the TS. Instead, the average global properties converged with low standard deviations across metafolds, suggesting that there are general rules governing the structure and properties of the TS.

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

[2]  Amanda L. Jonsson,et al.  Φ-Analysis at the Experimental Limits: Mechanism of β-Hairpin Formation , 2006 .

[3]  Stephen J. Moran,et al.  The folding pathway of spectrin R17 from experiment and simulation: using experimentally validated MD simulations to characterize States hinted at by experiment. , 2006, Journal of molecular biology.

[4]  A. Fersht,et al.  Testing protein-folding simulations by experiment: B domain of protein A. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[5]  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.

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

[7]  R Dustin Schaeffer,et al.  Dynameomics: mass annotation of protein dynamics and unfolding in water by high-throughput atomistic molecular dynamics simulations. , 2008, Protein engineering, design & selection : PEDS.

[8]  A. Fersht,et al.  Structure of the transition state for the folding/unfolding of the barley chymotrypsin inhibitor 2 and its implications for mechanisms of protein folding. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[9]  W. Kabsch,et al.  Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.

[10]  David C. Jones,et al.  CATH--a hierarchic classification of protein domain structures. , 1997, Structure.

[11]  Jörg Gsponer,et al.  Molecular dynamics simulations of protein folding from the transition state , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[12]  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.

[13]  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.

[14]  E. Cota,et al.  Folding studies of immunoglobulin-like beta-sandwich proteins suggest that they share a common folding pathway. , 1999, Structure.

[15]  V. Daggett,et al.  Mapping the interactions present in the transition state for unfolding/folding of FKBP12. , 1999, Journal of molecular biology.

[16]  V. Daggett,et al.  Can non-mechanical proteins withstand force? Stretching barnase by atomic force microscopy and molecular dynamics simulation. , 2001, Biophysical journal.

[17]  V. Daggett,et al.  Diffusing and colliding: the atomic level folding/unfolding pathway of a small helical protein. , 2004, Journal of molecular biology.

[18]  Valerie Daggett,et al.  The intrinsic conformational propensities of the 20 naturally occurring amino acids and reflection of these propensities in proteins , 2008, Proceedings of the National Academy of Sciences.

[19]  Valerie Daggett,et al.  Dynameomics: a multi-dimensional analysis-optimized database for dynamic protein data. , 2008, Protein engineering, design & selection : PEDS.

[20]  L. Gregoret,et al.  Stability and folding properties of a model β‐sheet protein, Escherichia coli CspA , 1998, Protein science : a publication of the Protein Society.

[21]  D. Yee,et al.  DILL Families and the structural relatedness among globular proteins data , 1993 .

[22]  A. Fersht,et al.  The structure of the major transition state for folding of an FF domain from experiment and simulation. , 2005, Journal of molecular biology.

[23]  Sheena E Radford,et al.  Structural analysis of the rate-limiting transition states in the folding of Im7 and Im9: similarities and differences in the folding of homologous proteins. , 2003, Journal of molecular biology.

[24]  A Caflisch,et al.  Role of native topology investigated by multiple unfolding simulations of four SH3 domains. , 2001, Journal of molecular biology.

[25]  A G Murzin,et al.  SCOP: a structural classification of proteins database for the investigation of sequences and structures. , 1995, Journal of molecular biology.

[26]  David A. C. Beck,et al.  Microscopic reversibility of protein folding in molecular dynamics simulations of the engrailed homeodomain. , 2008, Biochemistry.

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

[28]  D Baker,et al.  Folding dynamics of the src SH3 domain. , 1997, Biochemistry.

[29]  S. Jackson,et al.  How do small single-domain proteins fold? , 1998, Folding & design.

[30]  Valerie Daggett,et al.  The molecular basis for the chemical denaturation of proteins by urea , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[31]  I D Campbell,et al.  The folding kinetics and thermodynamics of the Fyn-SH3 domain. , 1998, Biochemistry.

[32]  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 .

[33]  Ryan Day,et al.  Direct observation of microscopic reversibility in single-molecule protein folding. , 2007, Journal of molecular biology.

[34]  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.

[35]  S. Pongor,et al.  A normalized root‐mean‐spuare distance for comparing protein three‐dimensional structures , 2001, Protein science : a publication of the Protein Society.

[36]  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.

[37]  David Baker,et al.  Experiment and theory highlight role of native state topology in SH3 folding , 1999, Nature Structural Biology.

[38]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[39]  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.

[40]  David A C Beck,et al.  Methods for molecular dynamics simulations of protein folding/unfolding in solution. , 2004, Methods.

[41]  David Baker,et al.  Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain , 1998, Nature Structural &Molecular Biology.

[42]  Luis Serrano,et al.  The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved , 1999, Nature Structural Biology.

[43]  Valerie Daggett,et al.  Dynameomics: design of a computational lab workflow and scientific data repository for protein simulations. , 2008, Protein engineering, design & selection : PEDS.

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

[45]  V. Daggett,et al.  Staphylococcal protein A: unfolding pathways, unfolded states, and differences between the B and E domains. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

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

[47]  Ryan Day,et al.  A consensus view of fold space: Combining SCOP, CATH, and the Dali Domain Dictionary , 2003, Protein science : a publication of the Protein Society.

[48]  Valerie Daggett,et al.  Dynameomics: Large‐scale assessment of native protein flexibility , 2008, Protein science : a publication of the Protein Society.

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

[50]  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 .

[51]  Alan R. Davidson,et al.  Hydrophobic core packing in the SH3 domain folding transition state , 2002, Nature Structural Biology.

[52]  M Levitt,et al.  Hierarchy of structure loss in MD simulations of src SH3 domain unfolding. , 1999, Journal of molecular biology.

[53]  Amanda L. Jonsson,et al.  The role of the turn in β‐hairpin formation during WW domain folding , 2007 .

[54]  Valerie Daggett,et al.  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 , 1998 .

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

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

[57]  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.

[58]  L. Gierasch,et al.  Keeping it in the family: folding studies of related proteins. , 2001, Current opinion in structural biology.

[59]  A. Fersht,et al.  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. , 1995, Journal of molecular biology.

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

[61]  A. Fersht,et al.  Demonstration of a low-energy on-pathway intermediate in a fast-folding protein by kinetics, protein engineering, and simulation. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[62]  A. R. Fersht,et al.  Solution structure of a protein denatured state and folding intermediate , 2005, Nature.