The folding mechanism of a -sheet: the WW domain1

The folding thermodynamics and kinetics of the Pin WW domain, a three-stranded antiparallel β-sheet, have been characterized extensively. Folding and activation free energies were determined as a function of temperature for 16 mutants, which sample all strands and turns of the molecule. The mutational phi value (Φm) diagram is a smooth function of sequence, indicating a prevalence of local interactions in the transition state (TS). At 37 °C, the diagram has a single pronounced maximum at turn 1: the rate-limiting step during folding is the formation of loop 1. In contrast, key residues for thermodynamic stability are located in the strand hydrophobic clusters, indicating that factors contributing to protein stability and folding kinetics are not correlated. The location of the TS along the entropic reaction coordinate ΦT, obtained by temperature-tuning the kinetics, reveals that sufficiently destabilizing mutants in loop 2 or in the Leu7-Trp11-Tyr24-Pro37 hydrophobic cluster can cause a switch to a late TS. Φm analysis is usually applied “perturbatively” (methyl truncation), but with ΦT to quantitatively assess TS shifts along a reaction coordinate, more severe mutations can be used to probe regions of the free energy surface beyond the TS.

[1]  H. Kramers.  Brownian motion in a field of force and the diffusion model of chemical reactions , 1940 .

[2]  J. Hofrichter,et al.  Laser temperature jump study of the helix<==>coil kinetics of an alanine peptide interpreted with a 'kinetic zipper' model. , 1997, Biochemistry.

[3]  R. Wade,et al.  Stability of the β-Sheet of the WW Domain: A Molecular Dynamics Simulation Study , 1999 .

[4]  Alternative Explanations for "Multistate" Kinetics in Protein Folding: Transient Aggregation and Changing Transition-State Ensembles , 1998 .

[5]  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.

[6]  D Thirumalai,et al.  Mechanisms and kinetics of beta-hairpin formation. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[7]  M. Oliveberg,et al.  High-energy channeling in protein folding. , 1997, Biochemistry.

[8]  M. Gruebele,et al.  Mapping the transition state of the WW domain β-sheet , 2000 .

[9]  J. Hofrichter,et al.  Fast events in protein folding. , 1996, Structure.

[10]  M. Gruebele,et al.  Observation of strange kinetics in protein folding. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[11]  P. Hänggi,et al.  Reaction-rate theory: fifty years after Kramers , 1990 .

[12]  A. Fersht,et al.  The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding. , 1992, Journal of molecular biology.

[13]  M. Sudol,et al.  WW: An isolated three‐stranded antiparallel β‐sheet domain that unfolds and refolds reversibly; evidence for a structured hydrophobic cluster in urea and GdnHCl and a disordered thermal unfolded state , 2008, Protein science : a publication of the Protein Society.

[14]  S. Khorasanizadeh,et al.  Evidence for a three-state model of protein folding from kinetic analysis of ubiquitin variants with altered core residues , 1996, Nature Structural Biology.

[15]  Tony Hunter,et al.  Structural basis for phosphoserine-proline recognition by group IV WW domains , 2000, Nature Structural Biology.

[16]  T. Oas,et al.  Submillisecond folding of monomeric lambda repressor. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[17]  M. Gruebele,et al.  The fast protein folding problem. , 2003, Annual review of physical chemistry.

[18]  M. Karplus,et al.  Understanding beta-hairpin formation. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[19]  P. Wolynes,et al.  Folding funnels and energy landscapes of larger proteins within the capillarity approximation. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[20]  R. Ranganathan,et al.  Structural and Functional Analysis of the Mitotic Rotamase Pin1 Suggests Substrate Recognition Is Phosphorylation Dependent , 1997, Cell.

[21]  Peter G. Wolynes,et al.  Role of explicitly cooperative interactions in protein folding funnels: A simulation study , 2001 .

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

[23]  J. Thornton,et al.  Analysis and prediction of the different types of β-turn in proteins , 1988 .

[24]  L. Regan,et al.  Guidelines for Protein Design: The Energetics of β Sheet Side Chain Interactions , 1995, Science.

[25]  H. Levine,et al.  How does a beta -hairpin fold/unfold? competition between topology and heterogeneity in a solvable model. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[26]  M. Gruebele,et al.  Direct observation of fast protein folding: the initial collapse of apomyoglobin. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[27]  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.

[28]  C. M. Jones,et al.  The role of solvent viscosity in the dynamics of protein conformational changes. , 1992, Science.

[29]  A. Fersht,et al.  The changing nature of the protein folding transition state: implications for the shape of the free-energy profile for folding. , 1998, Journal of molecular biology.

[30]  Shoji Takada,et al.  Variational Theory for Site Resolved Protein Folding Free Energy Surfaces , 1998, cond-mat/9805366.

[31]  P. Wolynes,et al.  Statistical mechanics of a correlated energy landscape model for protein folding funnels , 1996, cond-mat/9606159.

[32]  M. Gruebele,et al.  Submicrosecond real-time fluorescence sampling: application to protein folding. , 2000, Journal of photochemistry and photobiology. B, Biology.

[33]  E. Powers,et al.  Incorporating beta-turns and a turn mimetic out of context in loop 1 of the WW domain affords cooperatively folded beta-sheets. , 2001, Journal of the American Chemical Society.

[34]  Martin Gruebele,et al.  Observation of distinct nanosecond and microsecond protein folding events , 1996, Nature Structural Biology.

[35]  Lisa J. Lapidus,et al.  Measuring the rate of intramolecular contact formation in polypeptides. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[36]  W. DeGrado,et al.  In vitro evolution of thermodynamically stable turns , 1996, Nature Structural Biology.

[37]  T. Kiefhaber,et al.  The speed limit for protein folding measured by triplet-triplet energy transfer. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[38]  M. Macias,et al.  Structural analysis of WW domains and design of a WW prototype , 2000, Nature Structural Biology.

[39]  H. Edelhoch,et al.  Spectroscopic determination of tryptophan and tyrosine in proteins. , 1967, Biochemistry.

[40]  V. Muñoz,et al.  Kinetics and Dynamics of Loops, α-Helices, β-Hairpins, and Fast-Folding Proteins , 1998 .

[41]  R. Dyer,et al.  Fast events in protein folding: helix melting and formation in a small peptide. , 1996, Biochemistry.

[42]  Carl Frieden,et al.  Turn scanning by site‐directed mutagenesis: Application to the protein folding problem using the intestinal fatty acid binding protein , 1998, Protein science : a publication of the Protein Society.

[43]  Martin Gruebele,et al.  Transition from Exponential to Nonexponential Kinetics during Formation of a Nonbiological Helix , 2000 .

[44]  C. Pace,et al.  Polar group burial contributes more to protein stability than nonpolar group burial. , 2001, Biochemistry.

[45]  M. Sudol.  The WW module competes with the SH3 domain? , 1996, Trends in biochemical sciences.

[46]  L. Serrano,et al.  Obligatory steps in protein folding and the conformational diversity of the transition state , 1998, Nature Structural &Molecular Biology.

[47]  V. Muñoz,et al.  A statistical mechanical model for β-hairpin kinetics , 1998 .

[48]  M. A. Wouters,et al.  An analysis of side chain interactions and pair correlations within antiparallel β‐sheets: The differences between backbone hydrogen‐bonded and non‐hydrogen‐bonded residue pairs , 1995, Proteins.

[49]  S. Ramakumar,et al.  π‐Turns in proteins and peptides: Classification, conformation, occurrence, hydration and sequence , 1996, Protein science : a publication of the Protein Society.

[50]  M. Gruebele,et al.  A single‐sweep, nanosecond time resolution laser temperature‐jump apparatus , 1996 .

[51]  D. Rousseau,et al.  Hierarchical folding of intestinal fatty acid binding protein. , 2001, Biochemistry.

[52]  B. L. Sibanda,et al.  [5] Conformation of β hairpins in protein structures: Classification and diversity in homologous structures , 1991 .

[53]  V. Muñoz,et al.  Folding dynamics and mechanism of β-hairpin formation , 1997, Nature.

[54]  T. Hunter,et al.  NeW Wrinkles for an Old Domain , 2000, Cell.

[55]  A. H. Wang,et al.  Molecular Dynamics Simulations of Three-Strand β-Sheet Folding , 2000 .

[56]  A. Fersht,et al.  Mapping the transition state and pathway of protein folding by protein engineering , 1989, Nature.

[57]  J. Hofrichter,et al.  Rate of Intrachain Diffusion of Unfolded Cytochrome c , 1997 .

[58]  T. Kiefhaber,et al.  Intermediates can accelerate protein folding. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[59]  J. Onuchic,et al.  Protein folding funnels: the nature of the transition state ensemble. , 1996, Folding & design.

[60]  D. Turner,et al.  Dimerization of Proflavin by the Laser Raman Temperature-Jump Method , 1972, Nature.

[61]  V S Pande,et al.  Molecular dynamics simulations of unfolding and refolding of a beta-hairpin fragment of protein G. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[62]  H. M. Petrassi,et al.  Characterization of the structure and function of W --> F WW domain variants: identification of a natively unfolded protein that folds upon ligand binding. , 1999, Biochemistry.

[63]  D. Thirumalai,et al.  Viscosity Dependence of the Folding Rates of Proteins , 1997, cond-mat/9705309.

[64]  M. Gruebele,et al.  Laser Temperature Jump Induced Protein Refolding , 1998 .

[65]  J. Richardson,et al.  Amino acid preferences for specific locations at the ends of alpha helices. , 1988, Science.

[66]  J. Holzwarth,et al.  Nanosecond Temperature-Jump Technique with an Iodine Laser , 1977 .

[67]  J. Onuchic,et al.  Toward an outline of the topography of a realistic protein-folding funnel. , 1995, Proceedings of the National Academy of Sciences of the United States of America.