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Volumn 428, Issue 8, 2016, Pages 1617-1636

High-resolution mapping of the folding transition state of a WW domain

Author keywords

folding transition state; laser T jump; protein folding; WW domain; value analysis

Indexed keywords

HYDROGEN; PROTEIN; NIMA INTERACTING PEPTIDYLPROLYL ISOMERASE; PEPTIDYLPROLYL ISOMERASE; PHOSPHOPROTEIN; PIN1 PROTEIN, HUMAN; SIGNAL TRANSDUCING ADAPTOR PROTEIN; YAP1 (YES-ASSOCIATED) PROTEIN, HUMAN;

EID: 84961141561     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2016.02.008     Document Type: Article
Times cited : (21)

References (47)
  • 2
    • 39149104002 scopus 로고    scopus 로고
    • Combining experiment and simulation in protein folding: Closing the gap for small model systems
    • R.D. Schaeffer, A. Fersht, and V. Daggett Combining experiment and simulation in protein folding: closing the gap for small model systems Curr. Opin. Struct. Biol. 18 2008 4 9
    • (2008) Curr. Opin. Struct. Biol. , vol.18 , pp. 4-9
    • Schaeffer, R.D.1    Fersht, A.2    Daggett, V.3
  • 3
    • 33745714381 scopus 로고    scopus 로고
    • Testing simplified proteins models of the hPin1 WW domain
    • F. Cecconi, C. Guardiani, and R. Livi Testing simplified proteins models of the hPin1 WW domain Biophys. J. 91 2006 694 704
    • (2006) Biophys. J. , vol.91 , pp. 694-704
    • Cecconi, F.1    Guardiani, C.2    Livi, R.3
  • 4
  • 5
    • 0029099161 scopus 로고
    • The WW domain of Yes-associated protein binds a proline-rich ligand that differs from the consensus established for Src homology 3-binding modules
    • H.I. Chen, and M. Sudol The WW domain of Yes-associated protein binds a proline-rich ligand that differs from the consensus established for Src homology 3-binding modules Proc. Natl. Acad. Sci. U. S. A. 92 1995 7819 7823
    • (1995) Proc. Natl. Acad. Sci. U. S. A. , vol.92 , pp. 7819-7823
    • Chen, H.I.1    Sudol, M.2
  • 8
    • 84907573466 scopus 로고    scopus 로고
    • Understanding the frustration arising from the competition between function, misfolding, and aggregation in a globular protein
    • S. Gianni, C. Camilloni, R. Giri, A. Toto, D. Bonetti, A. Morrone, and et al. Understanding the frustration arising from the competition between function, misfolding, and aggregation in a globular protein Proc. Natl. Acad. Sci. U. S. A. 111 2014 14141 14146
    • (2014) Proc. Natl. Acad. Sci. U. S. A. , vol.111 , pp. 14141-14146
    • Gianni, S.1    Camilloni, C.2    Giri, R.3    Toto, A.4    Bonetti, D.5    Morrone, A.6
  • 9
    • 78650415889 scopus 로고    scopus 로고
    • Computational design and experimental testing of the fastest-folding β-sheet protein
    • S. Piana, K. Sarkar, K. Lindorff-Larsen, M. Guo, M. Gruebele, and D.E. Shaw Computational design and experimental testing of the fastest-folding β-sheet protein J. Mol. Biol. 405 2011 43 48
    • (2011) J. Mol. Biol. , vol.405 , pp. 43-48
    • Piana, S.1    Sarkar, K.2    Lindorff-Larsen, K.3    Guo, M.4    Gruebele, M.5    Shaw, D.E.6
  • 10
    • 67749090874 scopus 로고    scopus 로고
    • Sequence determinants of thermodynamic stability in a WW domain - An all-β-sheet protein
    • M. Jäger, M. Dendle, and J.W. Kelly Sequence determinants of thermodynamic stability in a WW domain - an all-β-sheet protein Protein Sci. 18 2009 1806 1813
    • (2009) Protein Sci. , vol.18 , pp. 1806-1813
    • Jäger, M.1    Dendle, M.2    Kelly, J.W.3
  • 11
    • 11244304395 scopus 로고    scopus 로고
    • Toward assessing the position-dependent contributions of backbone hydrogen bonding to β-sheet folding thermodynamics employing amide-to-ester perturbations
    • S. Deechongkit, P.E. Dawson, and J.W. Kelly Toward assessing the position-dependent contributions of backbone hydrogen bonding to β-sheet folding thermodynamics employing amide-to-ester perturbations J. Am. Chem. Soc. 126 2004 16762 16771
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 16762-16771
    • Deechongkit, S.1    Dawson, P.E.2    Kelly, J.W.3
  • 12
    • 3042848873 scopus 로고    scopus 로고
    • Context-dependent contributions of backbone hydrogen bonding to beta-sheet folding energetics
    • S. Deechongkit, H. Nguyen, E.T. Powers, P.E. Dawson, M. Gruebele, and J.W. Kelly Context-dependent contributions of backbone hydrogen bonding to beta-sheet folding energetics Nature 430 2004 101
    • (2004) Nature , vol.430 , pp. 101
    • Deechongkit, S.1    Nguyen, H.2    Powers, E.T.3    Dawson, P.E.4    Gruebele, M.5    Kelly, J.W.6
  • 13
    • 0036296248 scopus 로고    scopus 로고
    • Protein folding kinetics beyond the Φ-value: Using multiple amino acid substitutions to investigate the structure of the SH3 domain folding transition state
    • J.G.B. Northey, K.L. Maxwell, and A.R. Davidson Protein folding kinetics beyond the Φ-value: using multiple amino acid substitutions to investigate the structure of the SH3 domain folding transition state J. Mol. Biol. 320 2002 389 402
    • (2002) J. Mol. Biol. , vol.320 , pp. 389-402
    • Northey, J.G.B.1    Maxwell, K.L.2    Davidson, A.R.3
  • 16
    • 80054929399 scopus 로고    scopus 로고
    • The free energy landscape analysis of protein (FIP35) folding dynamics
    • S.V. Krivov The free energy landscape analysis of protein (FIP35) folding dynamics J. Phys. Chem. B 115 2011 12315 12324
    • (2011) J. Phys. Chem. B , vol.115 , pp. 12315-12324
    • Krivov, S.V.1
  • 18
    • 33745606942 scopus 로고    scopus 로고
    • Phi-Analysis at the experimental limits: Mechanism of beta-hairpin formation
    • M. Petrovich, A.L. Jonsson, N. Ferguson, V. Daggett, and A.R. Fersht phi-Analysis at the experimental limits: mechanism of beta-hairpin formation J. Mol. Biol. 360 2006 865 881
    • (2006) J. Mol. Biol. , vol.360 , pp. 865-881
    • Petrovich, M.1    Jonsson, A.L.2    Ferguson, N.3    Daggett, V.4    Fersht, A.R.5
  • 19
    • 84889792013 scopus 로고    scopus 로고
    • A guide to measuring and interpreting phi-values
    • N.R. Guydosh, and A.R. Fersht A guide to measuring and interpreting phi-values Protein Folding Handbook 2005 445 453
    • (2005) Protein Folding Handbook , pp. 445-453
    • Guydosh, N.R.1    Fersht, A.R.2
  • 20
    • 38549170892 scopus 로고    scopus 로고
    • Transition states in protein folding kinetics: Modeling Φ-values of small β-sheet proteins
    • T.R. Weikl Transition states in protein folding kinetics: modeling Φ-values of small β-sheet proteins Biophys. J. 94 2008 929 937
    • (2008) Biophys. J. , vol.94 , pp. 929-937
    • Weikl, T.R.1
  • 22
    • 59449097753 scopus 로고    scopus 로고
    • Some recommendations for the practitioner to improve the precision of experimentally determined protein folding rates and Φ-values
    • I. Ruczinski, and K.W. Plaxco Some recommendations for the practitioner to improve the precision of experimentally determined protein folding rates and Φ-values Proteins 74 2009 461 474
    • (2009) Proteins , vol.74 , pp. 461-474
    • Ruczinski, I.1    Plaxco, K.W.2
  • 23
    • 33749322256 scopus 로고    scopus 로고
    • Methods for the accurate estimation of confidence intervals on protein folding Φ-values
    • I. Ruczinski, T.R. Sosnick, and K.W. Plaxco Methods for the accurate estimation of confidence intervals on protein folding Φ-values Protein Sci. 15 2006 2257 2264
    • (2006) Protein Sci. , vol.15 , pp. 2257-2264
    • Ruczinski, I.1    Sosnick, T.R.2    Plaxco, K.W.3
  • 24
    • 77952730001 scopus 로고    scopus 로고
    • Insights into protein folding mechanisms from large scale analysis of mutational effects
    • A.N. Naganathan, and V. Muñoz Insights into protein folding mechanisms from large scale analysis of mutational effects Proc. Natl. Acad. Sci. 107 2010 8611 8616
    • (2010) Proc. Natl. Acad. Sci. , vol.107 , pp. 8611-8616
    • Naganathan, A.N.1    Muñoz, V.2
  • 25
    • 0034718553 scopus 로고    scopus 로고
    • Folding simulations of a three-stranded antiparallel beta-sheet peptide
    • P. Ferrara, and A. Caflisch Folding simulations of a three-stranded antiparallel beta-sheet peptide Proc. Natl. Acad. Sci. 97 2000 10780 10785
    • (2000) Proc. Natl. Acad. Sci. , vol.97 , pp. 10780-10785
    • Ferrara, P.1    Caflisch, A.2
  • 26
    • 84919884353 scopus 로고    scopus 로고
    • Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements
    • R. Zhou, G.G. Maisuradze, D. Suñol, T. Todorovski, M.J. Macias, Y. Xiao, and et al. Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements Proc. Natl. Acad. Sci. 111 2014 18243 18248
    • (2014) Proc. Natl. Acad. Sci. , vol.111 , pp. 18243-18248
    • Zhou, R.1    Maisuradze, G.G.2    Suñol, D.3    Todorovski, T.4    MacIas, M.J.5    Xiao, Y.6
  • 29
    • 61449176137 scopus 로고    scopus 로고
    • The osmolyte trimethylamine-N-oxide stabilizes the Fyn SH3 domain without altering the structure of its folding transition state
    • S.L. Lin, A. Zarrine-Afsar, and A.R. Davidson The osmolyte trimethylamine-N-oxide stabilizes the Fyn SH3 domain without altering the structure of its folding transition state Protein Sci. 18 2009 526 536
    • (2009) Protein Sci. , vol.18 , pp. 526-536
    • Lin, S.L.1    Zarrine-Afsar, A.2    Davidson, A.R.3
  • 31
    • 0036037586 scopus 로고    scopus 로고
    • Quantifying protein folding transition states with Φ(T)
    • J. Ervin, and M. Gruebele Quantifying protein folding transition states with Φ(T) J. Biol. Phys. 28 2002 115 128
    • (2002) J. Biol. Phys. , vol.28 , pp. 115-128
    • Ervin, J.1    Gruebele, M.2
  • 32
    • 0034724566 scopus 로고    scopus 로고
    • Mapping the transition state of the WW domain β-sheet1
    • J.C. Crane, E.K. Koepf, J.W. Kelly, and M. Gruebele Mapping the transition state of the WW domain β-sheet1 J. Mol. Biol. 298 2000 283 292
    • (2000) J. Mol. Biol. , vol.298 , pp. 283-292
    • Crane, J.C.1    Koepf, E.K.2    Kelly, J.W.3    Gruebele, M.4
  • 33
  • 34
    • 2542599277 scopus 로고    scopus 로고
    • Φ-value analysis and the nature of protein-folding transition states
    • A.R. Fersht, and S. Sato Φ-value analysis and the nature of protein-folding transition states Proc. Natl. Acad. Sci. U. S. A. 101 2004 7976 7981
    • (2004) Proc. Natl. Acad. Sci. U. S. A. , vol.101 , pp. 7976-7981
    • Fersht, A.R.1    Sato, S.2
  • 35
    • 0036160702 scopus 로고    scopus 로고
    • NMR solution structure of the isolated Apo Pin1 WW domain: Comparison to the x-ray crystal structures of Pin1
    • J.A. Kowalski, K. Liu, and J.W. Kelly NMR solution structure of the isolated Apo Pin1 WW domain: comparison to the x-ray crystal structures of Pin1 Biopolymers 63 2002 111 121
    • (2002) Biopolymers , vol.63 , pp. 111-121
    • Kowalski, J.A.1    Liu, K.2    Kelly, J.W.3
  • 36
    • 67649412164 scopus 로고    scopus 로고
    • The Fip35 WW domain folds with structural and mechanistic heterogeneity in molecular dynamics simulations
    • D.L. Ensign, and V.S. Pande The Fip35 WW domain folds with structural and mechanistic heterogeneity in molecular dynamics simulations Biophys. J. 96 2009 L53 L55
    • (2009) Biophys. J. , vol.96 , pp. L53-L55
    • Ensign, D.L.1    Pande, V.S.2
  • 37
    • 70450255797 scopus 로고    scopus 로고
    • Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations
    • F. Noé, C. Schütte, E. Vanden-Eijnden, L. Reich, and T.R. Weikl Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations Proc. Natl. Acad. Sci. U. S. A. 106 2009 19011 19016
    • (2009) Proc. Natl. Acad. Sci. U. S. A. , vol.106 , pp. 19011-19016
    • Noé, F.1    Schütte, C.2    Vanden-Eijnden, E.3    Reich, L.4    Weikl, T.R.5
  • 38
    • 80755172456 scopus 로고    scopus 로고
    • Markov state model reveals folding and functional dynamics in ultra-long MD trajectories
    • T.J. Lane, G.R. Bowman, K. Beauchamp, V.A. Voelz, and V.S. Pande Markov state model reveals folding and functional dynamics in ultra-long MD trajectories J. Am. Chem. Soc. 133 2011 18413 18419
    • (2011) J. Am. Chem. Soc. , vol.133 , pp. 18413-18419
    • Lane, T.J.1    Bowman, G.R.2    Beauchamp, K.3    Voelz, V.A.4    Pande, V.S.5
  • 39
    • 5244245983 scopus 로고
    • A correlation of reaction rates
    • G.S. Hammond A correlation of reaction rates J. Am. Chem. Soc. 77 1955 334 338
    • (1955) J. Am. Chem. Soc. , vol.77 , pp. 334-338
    • Hammond, G.S.1
  • 40
    • 0030961726 scopus 로고    scopus 로고
    • Entropy in protein folding and in protein-protein interactions
    • G.P. Brady, and K.A. Sharp Entropy in protein folding and in protein-protein interactions Curr. Opin. Struct. Biol. 7 1997 215 221
    • (1997) Curr. Opin. Struct. Biol. , vol.7 , pp. 215-221
    • Brady, G.P.1    Sharp, K.A.2
  • 41
    • 42749106226 scopus 로고    scopus 로고
    • Finite size effects on thermal denaturation of globular proteins
    • M.S. Li, D.K. Klimov, and D. Thirumalai Finite size effects on thermal denaturation of globular proteins Phys. Rev. Lett. 93 2004 268107
    • (2004) Phys. Rev. Lett. , vol.93 , pp. 268107
    • Li, M.S.1    Klimov, D.K.2    Thirumalai, D.3
  • 42
    • 84862195114 scopus 로고    scopus 로고
    • Effects of mutation, truncation, and temperature on the folding kinetics of a WW domain
    • G.G. Maisuradze, R. Zhou, A. Liwo, Y. Xiao, and H.A. Scheraga Effects of mutation, truncation, and temperature on the folding kinetics of a WW domain J. Mol. Biol. 420 2012 350 365
    • (2012) J. Mol. Biol. , vol.420 , pp. 350-365
    • Maisuradze, G.G.1    Zhou, R.2    Liwo, A.3    Xiao, Y.4    Scheraga, H.A.5
  • 44
    • 84935912411 scopus 로고    scopus 로고
    • Comparing fast pressure Jump and temperature Jump protein folding experiments and simulations
    • A.J. Wirth, Y. Liu, M.B. Prigozhin, K. Schulten, and M. Gruebele Comparing fast pressure Jump and temperature Jump protein folding experiments and simulations J. Am. Chem. Soc. 137 2015 7152 7159
    • (2015) J. Am. Chem. Soc. , vol.137 , pp. 7152-7159
    • Wirth, A.J.1    Liu, Y.2    Prigozhin, M.B.3    Schulten, K.4    Gruebele, M.5
  • 45
    • 0001261542 scopus 로고    scopus 로고
    • A single-sweep, nanosecond time resolution laser temperature-jump apparatus
    • R.M. Ballew, J. Sabelko, C. Reiner, and M. Gruebele A single-sweep, nanosecond time resolution laser temperature-jump apparatus Rev. Sci. Instrum. 67 1996 3694
    • (1996) Rev. Sci. Instrum. , vol.67 , pp. 3694
    • Ballew, R.M.1    Sabelko, J.2    Reiner, C.3    Gruebele, M.4
  • 46
    • 0033996482 scopus 로고    scopus 로고
    • Submicrosecond real-time fluorescence sampling: Application to protein folding
    • J. Ervin, J. Sabelko, and M. Gruebele Submicrosecond real-time fluorescence sampling: application to protein folding J. Photochem. Photobiol. B Biol. 54 2000 1 15
    • (2000) J. Photochem. Photobiol. B Biol. , vol.54 , pp. 1-15
    • Ervin, J.1    Sabelko, J.2    Gruebele, M.3


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