메뉴 건너뛰기




Volumn 117, Issue 47, 2013, Pages 14688-14696

Assessment of local friction in protein folding dynamics using a helix cross-linker

Author keywords

[No Author keywords available]

Indexed keywords

CONFORMATIONAL TRANSITIONS; ENERGY LANDSCAPE; EXCLUDED VOLUME EFFECTS; EXPERIMENTAL ASSESSMENT; FOLDING KINETICS; PROTEIN FOLDING DYNAMICS; PROTEIN STABILITY; STERIC HINDRANCES;

EID: 84891360974     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp409334h     Document Type: Article
Times cited : (11)

References (96)
  • 2
    • 0000710672 scopus 로고    scopus 로고
    • Diffusive dynamics of the reaction coordinate for protein folding funnels
    • Socci, N. D.; Onuchic, J. N.; Wolynes, P. G. Diffusive Dynamics of the Reaction Coordinate for Protein Folding Funnels. J. Chem. Phys. 1996, 104, 5860-5868.
    • (1996) J Chem. Phys. , vol.104 , pp. 5860-5868
    • Socci, N.D.1    Onuchic, J.N.2    Wolynes, P.G.3
  • 3
    • 1842298212 scopus 로고    scopus 로고
    • From levinthal to pathways to funnels
    • Dill, K. A.; Chan, H. S. From Levinthal to Pathways to Funnels. Nat. Struct. Biol. 1997, 4, 10-19.
    • (1997) Nat. Struct. Biol. , vol.4 , pp. 10-19
    • Dill, K.A.1    Chan, H.S.2
  • 5
    • 0033607208 scopus 로고    scopus 로고
    • Exploring the origins of topological frustration: Design of a minimally frustrated model of fragment b of protein a
    • Shea, J. E.; Onuchic, J. N.; Brooks, C. L. Exploring the Origins of Topological Frustration: Design of a Minimally Frustrated Model of Fragment B of Protein A. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 12512-12517.
    • (1999) Proc. Natl. Acad. Sci. U.S.A. , vol.96 , pp. 12512-12517
    • Shea, J.E.1    Onuchic, J.N.2    Brooks, C.L.3
  • 7
    • 77951711256 scopus 로고    scopus 로고
    • Topological frustration in beta alpha-repeat proteins: Sequence diversity modulates the conserved folding mechanisms of alpha/beta/alpha sandwich proteins
    • Hills, R. D.; Kathuria, S. V.; Wallace, L. A.; Day, I. J.; Brooks, C. L.; Matthews, C. R. Topological Frustration in Beta Alpha-Repeat Proteins: Sequence Diversity Modulates the Conserved Folding Mechanisms of Alpha/Beta/Alpha Sandwich Proteins. J. Mol. Biol. 2010, 398, 332-350.
    • (2010) J. Mol. Biol. , vol.398 , pp. 332-350
    • Hills, R.D.1    Kathuria, S.V.2    Wallace, L.A.3    Day, I.J.4    Brooks, C.L.5    Matthews, C.R.6
  • 9
    • 0032853084 scopus 로고    scopus 로고
    • Diffusional barrier crossing in a two-state protein folding reaction
    • Jacob, M.; Geeves, M.; Holtermann, G.; Schmid, F. X. Diffusional Barrier Crossing in a Two-State Protein Folding Reaction. Nat. Struct. Biol. 1999, 6, 923-926.
    • (1999) Nat. Struct. Biol. , vol.6 , pp. 923-926
    • Jacob, M.1    Geeves, M.2    Holtermann, G.3    Schmid, F.X.4
  • 10
    • 1642379707 scopus 로고    scopus 로고
    • A limiting speed for protein folding at low solvent viscosity
    • Qiu, L.; Hagen, S. J. A Limiting Speed for Protein Folding at Low Solvent Viscosity. J. Am. Chem. Soc. 2004, 126, 3398-3399.
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 3398-3399
    • Qiu, L.1    Hagen, S.J.2
  • 11
    • 24144469761 scopus 로고    scopus 로고
    • Diffusional limits to the speed of protein folding: Fact or friction?
    • Hagen, S. J.; Qiu, L. L.; Pabit, S. A. Diffusional Limits to the Speed of Protein Folding: Fact or Friction? J. Phys.: Condens. Matter 2005, 17, S1503-S1514.
    • (2005) J. Phys.: Condens. Matter , vol.17
    • Hagen, S.J.1    Qiu, L.L.2    Pabit, S.A.3
  • 13
    • 0032506017 scopus 로고    scopus 로고
    • Limited internal friction in the rate-limiting step of a two-state protein folding reaction
    • Plaxco, K. W.; Baker, D. Limited Internal Friction in the Rate-Limiting Step of a Two-State Protein Folding Reaction. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 13591-13596.
    • (1998) Proc. Natl. Acad. Sci. U.S.A. , vol.95 , pp. 13591-13596
    • Plaxco, K.W.1    Baker, D.2
  • 14
    • 0033535951 scopus 로고    scopus 로고
    • Intermediates can accelerate protein folding
    • Wagner, C.; Kiefhaber, T. Intermediates can Accelerate Protein Folding. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 6716-6721.
    • (1999) Proc. Natl. Acad. Sci. U.S.A. , vol.96 , pp. 6716-6721
    • Wagner, C.1    Kiefhaber, T.2
  • 16
    • 0034321011 scopus 로고    scopus 로고
    • Energetic frustration and the nature of the transition state in protein folding
    • Shea, J. E.; Onuchic, J. N.; Brooks, C. L. Energetic Frustration and the Nature of the Transition State in Protein Folding. J. Chem. Phys. 2000, 113, 7663-7671.
    • (2000) J Chem. Phys. , vol.113 , pp. 7663-7671
    • Shea, J.E.1    Onuchic, J.N.2    Brooks, C.3
  • 17
    • 0035868526 scopus 로고    scopus 로고
    • Microscopic theory of protein folding rates. Ii. Local reaction coordinates and chain dynamics
    • Portman, J. J.; Takada, S.; Wolynes, P. G. Microscopic Theory of Protein Folding Rates. II. Local Reaction Coordinates and Chain Dynamics. J. Chem. Phys. 2001, 114, 5082-5096.
    • (2001) J Chem. Phys. , vol.114 , pp. 5082-5096
    • Portman, J.J.1    Takada, S.2    Wolynes, P.G.3
  • 18
    • 0037459035 scopus 로고    scopus 로고
    • Solvation effects and driving forces for protein thermodynamic and kinetic cooperativity: How adequate is native-centric topological modeling?
    • Kaya, H.; Chan, H. S. Solvation Effects and Driving Forces for Protein Thermodynamic and Kinetic Cooperativity: How Adequate is Native-Centric Topological Modeling? J. Mol. Biol. 2003, 326, 911-931.
    • (2003) J. Mol. Biol. , vol.326 , pp. 911-931
    • Kaya, H.1    Chan, H.2
  • 19
    • 0042561888 scopus 로고    scopus 로고
    • Solvent viscosity dependence of the folding rate of a small protein: Distributed computing study
    • Zagrovic, B.; Pande, V. Solvent Viscosity Dependence of the Folding Rate of a Small Protein: Distributed Computing Study. J. Comput. Chem. 2003, 24, 1432-1436.
    • (2003) J. Comput. Chem. , vol.24 , pp. 1432-1436
    • Zagrovic, B.1    Pande, V.2
  • 20
    • 33644554831 scopus 로고    scopus 로고
    • Role of unfolded state heterogeneity and en-route ruggedness in protein folding kinetics
    • Ellison, P. A.; Cavagnero, S. Role of Unfolded State Heterogeneity and En-Route Ruggedness in Protein Folding Kinetics. Protein Sci. 2006, 15, 564-582.
    • (2006) Protein sci , vol.15 , pp. 564-582
    • Ellison, P.A.1    Cavagnero, S.2
  • 21
    • 35548963462 scopus 로고    scopus 로고
    • Configuration-dependent diffusion can shift the kinetic transition state and barrier height of protein folding
    • Chahine, J.; Oliveira, R. J.; Leite, V. B. P.; Wang, J. Configuration-Dependent Diffusion can Shift the Kinetic Transition State and Barrier Height of Protein Folding. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 14646-14651.
    • (2007) Proc. Natl. Acad. Sci. U.S.A. , vol.104 , pp. 14646-14651
    • Chahine, J.1    Oliveira, R.J.2    Leite, V.B.P.3    Wang, J.4
  • 22
    • 68649085948 scopus 로고    scopus 로고
    • Internal friction and nonequilibrium unfolding of polymeric globules
    • Alexander-Katz, A.; Wada, H.; Netz, R. R. Internal Friction and Nonequilibrium Unfolding of Polymeric Globules. Phys. Rev. Lett. 2009, 103, 028102.
    • (2009) Phys. Rev. Lett. , vol.103 , pp. 028102
    • Alexander-Katz, A.1    Wada, H.2    Netz, R.R.3
  • 23
    • 84886662755 scopus 로고    scopus 로고
    • How well does a funneled energy landscape capture the folding mechanism of spectrin domains?
    • Best, R. B. How well does a Funneled Energy Landscape Capture the Folding Mechanism of Spectrin Domains? J. Phys. Chem. B 2013, 117, 13235-13244.
    • (2012) J. Phys. Chem. B , vol.117 , pp. 13235-13244
    • Best, R.B.1
  • 24
    • 84859565600 scopus 로고    scopus 로고
    • Peptide chain dynamics in light and heavy water: Zooming in on internal friction
    • Schulz, J. C.; Schmidt, L.; Best, R. B.; Dzubiella, J.; Netz, R. R. Peptide Chain Dynamics in Light and Heavy Water: Zooming in on Internal Friction. J. Am. Chem. Soc. 2012, 134, 6273-6279.
    • (2012) J. Am. Chem. Soc. , vol.134 , pp. 6273-6279
    • Schulz, J.C.1    Schmidt, L.2    Best, R.B.3    Dzubiella, J.4    Netz, R.R.5
  • 25
    • 0035128362 scopus 로고    scopus 로고
    • Effect of viscosity on the kinetics of alpha-helix and beta-hairpin formation
    • Jas, G. S.; Eaton, W. A.; Hofrichter, J. Effect of Viscosity on the Kinetics of Alpha-Helix and Beta-Hairpin Formation. J. Phys. Chem. B 2001, 105, 261-272.
    • (2001) J. Phys. Chem. B , vol.105 , pp. 261-272
    • Jas, G.S.1    Eaton, W.A.2    Hofrichter, J.3
  • 26
    • 70450235210 scopus 로고    scopus 로고
    • The transition state transit time of ww domain folding is controlled by energy landscape roughness
    • Liu, F.; Nakaema, M.; Gruebele, M. The Transition State Transit Time of WW Domain Folding is Controlled by Energy Landscape Roughness. J. Chem. Phys. 2009, 131, 195101.
    • (2009) J Chem. Phys. , vol.131 , pp. 195101
    • Liu, F.1    Nakaema, M.2    Gruebele, M.3
  • 27
    • 77957916566 scopus 로고    scopus 로고
    • Solvent viscosity and friction in protein folding dynamics
    • Hagen, S. J. Solvent Viscosity and Friction in Protein Folding Dynamics. Curr. Protein Pept. Sci. 2010, 11, 385-395.
    • (2010) Curr. Protein Pept. Sci. , vol.11 , pp. 385-395
    • Hagen, S.1
  • 29
    • 84867092008 scopus 로고    scopus 로고
    • Separating the effects of internal friction and transition state energy to explain the slow, frustrated folding of spectrin domains
    • Wensley, B. G.; Kwa, L. G.; Shammas, S. L.; Rogers, J. M.; Browning, S.; Yang, Z. Q.; Clarke, J. Separating the Effects of Internal Friction and Transition State Energy to Explain the Slow, Frustrated Folding of Spectrin Domains. Proc. Natl. Acad. Sci. U.S.A. 2012, 109, 17795-17799.
    • (2012) Proc. Natl. Acad. Sci. U.S.A. , vol.109 , pp. 17795-17799
    • Wensley, B.G.1    Kwa, L.G.2    Shammas, S.L.3    Rogers, J.M.4    Browning, S.5    Yang, Z.Q.6    Clarke, J.7
  • 30
    • 84879993654 scopus 로고    scopus 로고
    • Defining a length scale for millisecond-timescale protein conformational exchange
    • Sekhar, A.; Vallurupalli, P.; Kay, L. E. Defining a Length Scale for Millisecond-Timescale Protein Conformational Exchange. Proc. Natl. Acad. Sci. U.S.A. 2013, 110, 11391-11396.
    • (2013) Proc. Natl. Acad. Sci. U.S.A. , vol.110 , pp. 11391-11396
    • Sekhar, A.1    Vallurupalli, P.2    Kay, L.E.3
  • 31
    • 0026636807 scopus 로고
    • The role of solvent viscosity in the dynamics of protein conformational changes
    • Ansari, A.; Jones, C. M.; Henry, E. R.; Hofrichter, J.; Eaton, W. A. The Role of Solvent Viscosity in the Dynamics of Protein Conformational Changes. Science 1992, 256, 1796-1798.
    • (1992) Science , vol.256 , pp. 1796-1798
    • Ansari, A.1    Jones, C.M.2    Henry, E.R.3    Hofrichter, J.4    Eaton, W.A.5
  • 32
    • 0034691198 scopus 로고    scopus 로고
    • Measuring the rate of intramolecular contact formation in polypeptides
    • Lapidus, L. J.; Eaton, W. A.; Hofrichter, J. Measuring the Rate of Intramolecular Contact Formation in Polypeptides. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 7220-7225.
    • (2000) Proc. Natl. Acad. Sci. U.S.A. , vol.97 , pp. 7220-7225
    • Lapidus, L.J.1    Eaton, W.A.2    Hofrichter, J.3
  • 33
    • 4744357562 scopus 로고    scopus 로고
    • Internal friction controls the speed of protein folding from a compact configuration
    • Pabit, S. A.; Roder, H.; Hagen, S. J. Internal Friction Controls the Speed of Protein Folding from a Compact Configuration. Biochemistry 2004, 43, 12532-12538.
    • (2004) Biochemistry , vol.43 , pp. 12532-12538
    • Pabit, S.A.1    Roder, H.2    Hagen, S.J.3
  • 35
    • 33646796290 scopus 로고    scopus 로고
    • Effects of denaturants on the dynamics of loop formation in polypeptides
    • Buscaglia, M.; Lapidus, L. J.; Eaton, W. A.; Hofrichter, J. Effects of Denaturants on the Dynamics of Loop Formation in Polypeptides. Biophys. J. 2006, 91, 276-288.
    • (2006) Biophys. J. , vol.91 , pp. 276-288
    • Buscaglia, M.1    Lapidus, L.J.2    Eaton, W.A.3    Hofrichter, J.4
  • 36
    • 77956361829 scopus 로고    scopus 로고
    • Extremely slow intramolecular diffusion in unfolded protein l
    • Waldauer, S. A.; Bakajin, O.; Lapidus, L. J. Extremely Slow Intramolecular Diffusion in Unfolded Protein L. Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 13713-13717.
    • (2010) Proc. Natl. Acad. Sci. U.S.A. , vol.107 , pp. 13713-13717
    • Waldauer, S.A.1    Bakajin, O.2    Lapidus, L.J.3
  • 37
    • 84870835154 scopus 로고    scopus 로고
    • Localizing internal friction along the reaction coordinate of protein folding by combining ensemble and single-molecule fluorescence spectroscopy
    • Borgia, A.; Wensley, B. G.; Soranno, A.; Nettels, D.; Borgia, M. B.; Hoffmann, A.; Pfeil, S. H.; Lipman, E. A.; Clarke, J.; Schuler, B. Localizing Internal Friction Along the Reaction Coordinate of Protein Folding by Combining Ensemble and Single-Molecule Fluorescence Spectroscopy. Nat. Commun. 2012, 3, 1-9.
    • (2012) Nat. Commun. , vol.3 , pp. 1-9
    • Borgia, A.1    Wensley, B.G.2    Soranno, A.3    Nettels, D.4    Borgia, M.B.5    Hoffmann, A.6    Pfeil, S.H.7    Lipman, E.A.8    Clarke, J.9    Schuler, B.10
  • 42
    • 84875438723 scopus 로고    scopus 로고
    • Force-clamp experiments reveal the free-energy profile and diffusion coefficient of the collapse of protein molecules
    • Lannon, H.; Haghpanah, J. S.; Montclare, J. K.; Vanden-Eijnden, E.; Brujic, J. Force-Clamp Experiments Reveal the Free-Energy Profile and Diffusion Coefficient of the Collapse of Protein Molecules. Phys. Rev. Lett. 2013, 110, 128301.
    • (2013) Phys. Rev. Lett. , vol.110 , pp. 128301
    • Lannon, H.1    Haghpanah, J.S.2    Montclare, J.K.3    Vanden-Eijnden, E.4    Brujic, J.5
  • 45
    • 0034697986 scopus 로고    scopus 로고
    • What can disulfide bonds tell us about protein energetics, function and folding: Simulations and bioinformatics analysis
    • Abkevich, V. I.; Shakhnovich, E. I. What can Disulfide Bonds tell us about Protein Energetics, Function and Folding: Simulations and Bioinformatics Analysis. J. Mol. Biol. 2000, 300, 975-985.
    • (2000) J. Mol. Biol. , vol.300 , pp. 975-985
    • Abkevich, V.1    Shakhnovich, E.2
  • 47
    • 36849028572 scopus 로고    scopus 로고
    • Intramolecular cross-linking evaluated as a structural probe of the protein folding transition state
    • Shandiz, A. T.; Capraro, B. R.; Sosnick, T. R. Intramolecular Cross-Linking Evaluated as a Structural Probe of the Protein Folding Transition State. Biochemistry 2007, 46, 13711-13719.
    • (2007) Biochemistry , vol.46 , pp. 13711-13719
    • Shandiz, A.T.1    Capraro, B.R.2    Sosnick, T.R.3
  • 48
    • 0141885404 scopus 로고    scopus 로고
    • The kinetics of helix unfolding of an azobenzene cross-linked peptide probed by nanosecond time-resolved optical rotatory dispersion
    • Chen, E. F.; Kumita, J. R.; Woolley, G. A.; Kliger, D. S. The Kinetics of Helix Unfolding of an Azobenzene Cross-Linked Peptide Probed by Nanosecond Time-Resolved Optical Rotatory Dispersion. J. Am. Chem. Soc. 2003, 125, 12443-12449.
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 12443-12449
    • Chen, E.F.1    Kumita, J.R.2    Woolley, G.A.3    Kliger, D.S.4
  • 51
    • 65249101769 scopus 로고    scopus 로고
    • Bulky side chains and non-native salt bridges slow down the folding of a cross-linked helical peptide: A combined molecular dynamics and time-resolved infrared spectroscopy study
    • Paoli, B.; Seeber, M.; Backus, E. H. G.; Ihalainen, J. A.; Hamm, P.; Caflisch, A. Bulky Side Chains and Non-Native Salt Bridges Slow Down the Folding of a Cross-Linked Helical Peptide: a Combined Molecular Dynamics and Time-Resolved Infrared Spectroscopy Study. J. Phys. Chem. B 2009, 113, 4435-4442.
    • (2009) J. Phys. Chem. B , vol.113 , pp. 4435-4442
    • Paoli, B.1    Seeber, M.2    Backus, E.H.G.3    Ihalainen, J.A.4    Hamm, P.5    Caflisch, A.6
  • 52
    • 77149131234 scopus 로고    scopus 로고
    • Slow folding of cross-linked alpha-helical peptides due to steric hindrance
    • Paoli, B.; Pellarin, R.; Caflisch, A. Slow Folding of Cross-Linked Alpha-Helical Peptides due to Steric Hindrance. J. Phys. Chem. B 2010, 114, 2023-2027.
    • (2010) J. Phys. Chem. B , vol.114 , pp. 2023-2027
    • Paoli, B.1    Pellarin, R.2    Caflisch, A.3
  • 54
    • 8644246795 scopus 로고    scopus 로고
    • Internal friction in the ultrafast folding of the tryptophan cage
    • Qiu, L. L.; Hagen, S. J. Internal Friction in the Ultrafast Folding of the Tryptophan Cage. Chem. Phys. 2004, 307, 243-249.
    • (2004) Chem. Phys. , vol.307 , pp. 243-249
    • Qiu, L.L.1    Hagen, S.J.2
  • 55
    • 80855133540 scopus 로고    scopus 로고
    • Achieving secondary structural resolution in kinetic measurements of protein folding: A case study of the folding mechanism of trp-cage
    • Culik, R. M.; Serrano, A. L.; Bunagan, M. R.; Gai, F. Achieving Secondary Structural Resolution in Kinetic Measurements of Protein Folding: a Case Study of the Folding Mechanism of Trp-Cage. Angew. Chem., Int. Ed. 2011, 50, 10884-10887.
    • (2011) Angew. Chem., Int. Ed. , vol.50 , pp. 10884-10887
    • Culik, R.M.1    Serrano, A.L.2    Bunagan, M.R.3    Gai, F.4
  • 56
    • 84862274056 scopus 로고    scopus 로고
    • Conformational dynamics of the trp-cage miniprotein at its folding temperature
    • Halabis, A.; Zmudzinska, W.; Liwo, A.; Oldziej, S. Conformational Dynamics of the Trp-Cage Miniprotein at its Folding Temperature. J. Phys. Chem. B 2012, 116, 6898-6907.
    • (2012) J. Phys. Chem. B , vol.116 , pp. 6898-6907
    • Halabis, A.1    Zmudzinska, W.2    Liwo, A.3    Oldziej, S.4
  • 58
    • 0037065310 scopus 로고    scopus 로고
    • The trp cage: Folding kinetics and unfolded state topology via molecular dynamics simulations
    • Snow, C. D.; Zagrovic, B.; Pande, V. S. The Trp Cage: Folding Kinetics and Unfolded State Topology via Molecular Dynamics Simulations. J. Am. Chem. Soc. 2002, 124, 14548-14549.
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 14548-14549
    • Snow, C.D.1    Zagrovic, B.2    Pande, V.S.3
  • 59
    • 0037470691 scopus 로고    scopus 로고
    • Ab initio folding simulation of the trp-cage mini-protein approaches nmr resolution
    • Chowdhury, S.; Lee, M. C.; Xiong, G. M.; Duan, Y. Ab initio Folding Simulation of the Trp-Cage Mini-Protein Approaches NMR Resolution. J. Mol. Biol. 2003, 327, 711-717.
    • (2003) J. Mol. Biol. , vol.327 , pp. 711-717
    • Chowdhury, S.1    Lee, M.C.2    Xiong, G.M.3    Duan, Y.4
  • 61
    • 11244291006 scopus 로고    scopus 로고
    • Folding trp-cage to nmr resolution native structure using a coarse-grained protein model
    • Ding, F.; Buldyrev, S. V.; Dokholyan, N. V. Folding Trp-Cage to NMR Resolution Native Structure using a Coarse-Grained Protein Model. Biophys. J. 2005, 88, 147-155.
    • (2005) Biophys. J. , vol.88 , pp. 147-155
    • Ding, F.1    Buldyrev, S.V.2    Dokholyan, N.V.3
  • 62
    • 33745570919 scopus 로고    scopus 로고
    • The equilibrium properties and folding kinetics of an all-atom go model of the trp-cage
    • Linhananta, A.; Boer, J.; MacKay, I. The Equilibrium Properties and Folding Kinetics of an All-Atom Go Model of the Trp-Cage. J. Chem. Phys. 2005, 122, 114901.
    • (2005) J Chem. Phys. , vol.122 , pp. 114901
    • Linhananta, A.1    Boer, J.2    MacKay, I.3
  • 63
    • 33645408056 scopus 로고    scopus 로고
    • Balancing solvation interactions i. Toward a consistent generalized born force field
    • Chen, J. H.; Im, W. P.; Brooks, C. L. Balancing Solvation and Intramolecular Interactions: Toward a Consistent Generalized Born Force Field. J. Am. Chem. Soc. 2006, 128, 3728-3736.
    • (2006) J. Am. Chem. Soc. , vol.128 , pp. 3728-3736
    • Chen, J.H.1    Im, W.P.2    Brooks, C.L.3
  • 64
    • 55849087551 scopus 로고    scopus 로고
    • Calculation of the free energy and cooperativity of protein folding
    • Kentsis, A.; Gindin, T.; Mezei, M.; Osman, R. Calculation of the Free Energy and Cooperativity of Protein Folding. PLoS One 2007, 2, 1-10.
    • (2007) PLoS One , vol.2 , pp. 1-10
    • Kentsis, A.1    Gindin, T.2    Mezei, M.3    Osman, R.4
  • 65
    • 33847254549 scopus 로고    scopus 로고
    • Replica exchange simulation of reversible folding/unfolding of the trp-cage miniprotein in explicit solvent: On the structure and possible role of internal water
    • Paschek, D.; Nymeyer, H.; Garcia, A. E. Replica Exchange Simulation of Reversible Folding/Unfolding of the Trp-Cage Miniprotein in Explicit Solvent: On the Structure and Possible Role of Internal Water. J. Struct. Biol. 2007, 157, 524-533.
    • (2007) J. Struct. Biol. , vol.157 , pp. 524-533
    • Paschek, D.1    Nymeyer, H.2    Garcia, A.E.3
  • 66
    • 34249071886 scopus 로고    scopus 로고
    • A bias-exchange approach to protein folding
    • Piana, S.; Laio, A. A Bias-Exchange Approach to Protein Folding. J. Phys. Chem. B 2007, 111, 4553-4559.
    • (2007) J. Phys. Chem. B , vol.111 , pp. 4553-4559
    • Piana, S.1    Laio, A.2
  • 67
    • 34047148428 scopus 로고    scopus 로고
    • Application of the accelerated molecular dynamics simulations to the folding of a small protein
    • Yang, L. J.; Grubb, M. P.; Gao, Y. Q. Application of the Accelerated Molecular Dynamics Simulations to the Folding of a Small Protein. J. Chem. Phys. 2007, 126, 125102.
    • (2007) J Chem. Phys. , vol.126 , pp. 125102
    • Yang, L.J.1    Grubb, M.P.2    Gao, Y.Q.3
  • 68
    • 58149146888 scopus 로고    scopus 로고
    • Rate constant and reaction coordinate of trp-cage folding in explicit
    • Juraszek, J.; Bolhuis, P. G. Rate Constant and Reaction Coordinate of Trp-Cage Folding in Explicit Water. Biophys. J. 2008, 95, 4246-4257.
    • (2008) Water. Biophys. J. , vol.95 , pp. 4246-4257
    • Juraszek, J.1    Bolhuis, P.2
  • 69
    • 56649083699 scopus 로고    scopus 로고
    • Computing the stability diagram of the trp-cage miniprotein
    • Paschek, D.; Hempel, S.; Garcia, A. E. Computing the Stability Diagram of the Trp-Cage Miniprotein. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 17754-17759.
    • (2008) Proc. Natl. Acad. Sci. U.S.A. , vol.105 , pp. 17754-17759
    • Paschek, D.1    Hempel, S.2    Garcia, A.E.3
  • 70
    • 51649103970 scopus 로고    scopus 로고
    • Ab initio folding simulation of trpcage by replica exchange with hybrid hamiltonian
    • Xu, W. X.; Mu, Y. G. Ab Initio Folding Simulation of Trpcage by Replica Exchange with Hybrid Hamiltonian. Biophys. Chem. 2008, 137, 116-125.
    • (2008) Biophys. Chem. , vol.137 , pp. 116-125
    • Xu, W.X.1    Mu, Y.G.2
  • 71
    • 66349120814 scopus 로고    scopus 로고
    • Loss of dispersion energy changes the stability and folding/unfolding equilibrium of the trp-cage protein
    • Cerny, J.; Vondrasek, J.; Hobza, P. Loss of Dispersion Energy Changes the Stability and Folding/Unfolding Equilibrium of the Trp-Cage Protein. J. Phys. Chem. B 2009, 113, 5657-5660.
    • (2009) J. Phys. Chem. B , vol.113 , pp. 5657-5660
    • Cerny, J.1    Vondrasek, J.2    Hobza, P.3
  • 72
    • 67650230368 scopus 로고    scopus 로고
    • Folding simulations of trp-cage mini protein in explicit solvent using biasing potential replica-exchange molecular dynamics simulations
    • Kannan, S.; Zacharias, M. Folding Simulations of Trp-Cage Mini Protein in Explicit Solvent using Biasing Potential Replica-Exchange Molecular Dynamics Simulations. Proteins: Struct., Funct., Bioinf. 2009, 76, 448-460.
    • (2009) Proteins: Struct., Funct., Bioinf. , vol.76 , pp. 448-460
    • Kannan, S.1    Zacharias, M.2
  • 73
    • 69049099679 scopus 로고    scopus 로고
    • A kinetic model of trp-cage folding from multiple biased molecular dynamics simulations
    • Marinelli, F.; Pietrucci, F.; Laio, A.; Piana, S. A Kinetic Model of Trp-Cage Folding from Multiple Biased Molecular Dynamics Simulations. PLoS Comput. Biol. 2009, 5, 1-18.
    • (2009) PLoS Comput. Biol. , vol.5 , pp. 1-18
    • Marinelli, F.1    Pietrucci, F.2    Laio, A.3    Piana, S.4
  • 74
    • 77954320896 scopus 로고    scopus 로고
    • Balance between alpha and beta structures in ab initio protein folding
    • Best, R. B.; Mittal, J. Balance Between Alpha and Beta Structures in Ab Initio Protein Folding. J. Phys. Chem. B 2010, 114, 8790-8798.
    • (2010) J. Phys. Chem. B , vol.114 , pp. 8790-8798
    • Best, R.B.1    Mittal, J.2
  • 75
    • 84867027679 scopus 로고    scopus 로고
    • Enhanced sampling molecular dynamics simulation captures eperimentally suggested intermediate and unfolded states in the folding pathway of trp-cage miniprotein
    • Shao, Q.; Shi, J. Y.; Zhu, W. L. Enhanced Sampling Molecular Dynamics Simulation Captures Eperimentally Suggested Intermediate and Unfolded States in the Folding Pathway of Trp-Cage Miniprotein. J. Chem. Phys. 2012, 137, 125103.
    • (2012) J Chem. Phys. , vol.137 , pp. 125103
    • Shao, Q.1    Shi, J.Y.2    Zhu, W.3
  • 76
    • 84874844718 scopus 로고    scopus 로고
    • Efficient numerical reconstruction of protein folding kinetics with partial path sampling and pathlike variables
    • Juraszek, J.; Saladino, G.; van Erp, T. S.; Gervasio, F. L. Efficient Numerical Reconstruction of Protein Folding Kinetics with Partial Path Sampling and Pathlike Variables. Phys. Rev. Lett. 2013, 110, 108106.
    • (2013) Phys. Rev. Lett. , vol.110 , pp. 108106
    • Juraszek, J.1    Saladino, G.2    Van Erp, T.S.3    Gervasio, F.L.4
  • 77
    • 84880168392 scopus 로고    scopus 로고
    • Dynamic folding pathway models of the trp-cage protein
    • Lee, I. H.; Kim, S. Y. Dynamic Folding Pathway Models of the Trp-Cage Protein. . Res. Int. 2013, 2013, 1-9.
    • (2013) Res. Int. , vol.2013 , pp. 1-9
    • Lee, I.H.1    Kim, S.Y.2
  • 78
    • 84883607162 scopus 로고    scopus 로고
    • Following easy slope paths on a free energy landscape: The case study of the trp-cage folding mechanism
    • Marinelli, F. Following Easy Slope Paths on a Free Energy Landscape: the Case Study of the Trp-Cage Folding Mechanism. Biophys. J. 2013, 105, 1236-1247.
    • (2013) Biophys. J. , vol.105 , pp. 1236-1247
    • Marinelli, F.1
  • 80
    • 0035955148 scopus 로고    scopus 로고
    • Temperature-dependent helix-coil transition of an alanine based peptide
    • Huang, C.-Y.; Klemke, J. W.; Getahun, Z.; DeGrado, W. F.; Gai, F. Temperature-Dependent Helix-Coil Transition of an Alanine Based Peptide. J. Am. Chem. Soc. 2001, 123, 9235-9238.
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 9235-9238
    • Huang, C.-Y.1    Klemke, J.W.2    Getahun, Z.3    DeGrado, W.F.4    Gai, F.5
  • 84
  • 85
    • 33947209951 scopus 로고    scopus 로고
    • Unfolding thermodynamics of trp-cage, a 20 residue miniprotein, studied by differential scanning calorimetry and circular dichroism spectroscopy
    • Streicher, W. W.; Makhatadze, G. I. Unfolding Thermodynamics of Trp-Cage, a 20 residue Miniprotein, studied by Differential Scanning Calorimetry and Circular Dichroism Spectroscopy. Biochemistry 2007, 46, 2876-2880.
    • (2007) Biochemistry , vol.46 , pp. 2876-2880
    • Streicher, W.W.1    Makhatadze, G.I.2
  • 86
    • 23744503388 scopus 로고    scopus 로고
    • Uv-resonance raman thermal unfolding study of trp-cage shows that it is not a simple two-state miniprotein
    • Ahmed, Z.; Beta, I. A.; Mikhonin, A. V.; Asher, S. A. UV-Resonance Raman Thermal Unfolding Study of Trp-Cage shows that it is not a Simple Two-State Miniprotein. J. Am. Chem. Soc. 2005, 127, 10943-10950.
    • (2005) J. Am. Chem. Soc. , vol.127 , pp. 10943-10950
    • Ahmed, Z.1    Beta, I.A.2    Mikhonin, A.V.3    Asher, S.A.4
  • 88
    • 77953508894 scopus 로고    scopus 로고
    • Microsecond simulations of the foldingunfolding thermodynamics of the trp-cage miniprotein
    • Day, R.; Paschek, D.; Garcia, A. E. Microsecond Simulations of the Folding/Unfolding Thermodynamics of the Trp-Cage Miniprotein. Proteins: Struct., Funct., Bioinf. 2010, 78, 1889-1899.
    • (2010) Proteins: Struct. Funct. Bioinf. , vol.78 , pp. 1889-1899
    • Day, R.1    Paschek, D.2    Garcia, A.E.3
  • 89
    • 70349232202 scopus 로고    scopus 로고
    • Effect of macromolecular crowding on protein folding dynamics at the secondary structure level
    • Mukherjee, S.; Waegele, M. M.; Chowdhury, P.; Guo, L.; Gai, F. Effect of Macromolecular Crowding on Protein Folding Dynamics at the Secondary Structure Level. J. Mol. Biol. 2009, 393, 227-236.
    • (2009) J. Mol. Biol. , vol.393 , pp. 227-236
    • Mukherjee, S.1    Waegele, M.M.2    Chowdhury, P.3    Guo, L.4    Gai, F.5
  • 90
    • 84885625540 scopus 로고    scopus 로고
    • Using d-amino acids to delineate the mechanism of protein folding: Application to trp-cage
    • Culik, R. M.; Annavarapu, S.; Nanda, V.; Gai, F. Using D-Amino Acids to Delineate the Mechanism of Protein Folding: Application to Trp-Cage. Chem. Phys. 2013, 422, 131-134.
    • (2013) Chem. Phys. , vol.422 , pp. 131-134
    • Culik, R.M.1    Annavarapu, S.2    Nanda, V.3    Gai, F.4
  • 91
    • 0024121530 scopus 로고
    • Diffusion in a rough potential
    • Zwanzig, R. Diffusion in a Rough Potential. Proc. Natl. Acad. Sci. U.S.A. 1988, 85, 2029-2030.
    • (1988) Proc. Natl. Acad. Sci. U.S.A. , vol.85 , pp. 2029-2030
    • Zwanzig, R.1
  • 92
    • 0034321095 scopus 로고    scopus 로고
    • Time scales and pathways for kinetic energy relaxation in solvated proteins: Application to carbonmonoxy myoglobin
    • Sagnella, D. E.; Straub, J. E.; Thirumalai, D. Time Scales and Pathways for Kinetic Energy Relaxation in Solvated Proteins: Application to Carbonmonoxy Myoglobin. J. Chem. Phys. 2000, 113, 7702-7711.
    • (2000) J Chem. Phys. , vol.113 , pp. 7702-7711
    • Sagnella, D.E.1    Straub, J.E.2    Thirumalai, D.3
  • 93
    • 0041335634 scopus 로고    scopus 로고
    • Can energy landscape roughness of proteins and rna be measured by using mechanical unfolding experiments?
    • Hyeon, C. B.; Thirumalai, D. Can Energy Landscape Roughness of Proteins and RNA be Measured by using Mechanical Unfolding Experiments? Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 10249-10253.
    • (2003) Proc. Natl. Acad. Sci. U.S.A. , vol.100 , pp. 10249-10253
    • Hyeon, C.B.1    Thirumalai, D.2
  • 94
    • 80053220763 scopus 로고    scopus 로고
    • Diffusion models of protein folding
    • Best, R. B.; Hummer, G. Diffusion Models of Protein Folding. Phys. Chem. Chem. Phys. 2011, 13, 16902-16911.
    • (2011) Phys. Chem Chem. Phys. , vol.13 , pp. 16902-16911
    • Best, R.B.1    Hummer, G.2
  • 95
    • 84877078222 scopus 로고    scopus 로고
    • Netz, roland r. Confinement-dependent friction in peptide bundles
    • Erbas, A. Netz, Roland R. Confinement-Dependent Friction in Peptide Bundles. Biophys. J. 2013, 104, 1285-1295.
    • (2013) Biophys. J. , vol.104 , pp. 1285-1295
    • Erbas, A.1
  • 96
    • 33750468665 scopus 로고    scopus 로고
    • Sampling the multiple folding mechanisms of trp-cage in explicit solvent
    • Juraszek, J.; Bolhuis, P. G. Sampling the Multiple Folding Mechanisms of Trp-Cage in Explicit solvent. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 15859-15864.
    • (2006) Proc. Natl. Acad. Sci. U.S.A. , vol.103 , pp. 15859-15864
    • Juraszek, J.1    Bolhuis, P.G.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.