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Volumn 6, Issue 1, 2009, Pages

The effect of surface tethering on the folding of the src-SH3 protein domain

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN SH3; PROTEIN;

EID: 62449169742     PISSN: 14783967     EISSN: 14783975     Source Type: Journal    
DOI: 10.1088/1478-3975/6/1/015004     Document Type: Article
Times cited : (21)

References (53)
  • 2
    • 0034807927 scopus 로고    scopus 로고
    • Single-molecule fluorescence resonance energy transfer
    • DOI 10.1006/meth.2001.1217
    • Ha T 2001 Single-molecule fluorescence resonance energy transfer Methods 25 78-86 (Pubitemid 32905290)
    • (2001) Methods , vol.25 , Issue.1 , pp. 78-86
    • Ha, T.1
  • 3
    • 0035366378 scopus 로고    scopus 로고
    • Single-molecule fluorescence methods for the study of nucleic acids
    • DOI 10.1016/S0959-440X(00)00204-9
    • Ha T 2001 Single-molecule fluorescence methods for the study of nucleic acids Curr. Opin. Struct. Biol. 11 287-92 (Pubitemid 32568267)
    • (2001) Current Opinion in Structural Biology , vol.11 , Issue.3 , pp. 287-292
    • Ha, T.1
  • 4
    • 34247848007 scopus 로고    scopus 로고
    • Mg2+ -dependent folding of a Diels-Alderase ribozyme probed by single-molecule FRET analysis
    • DOI 10.1093/nar/gkm072
    • Kobitski A Y, Nierth A, Helm M, Jaschke A and Nienhaus G U 2007 Mg2+-dependent folding of a Diels-Alderase ribozyme probed by single-molecule FRET analysis Nucleic. Acids. Res. 35 2047-59 (Pubitemid 47061670)
    • (2007) Nucleic Acids Research , vol.35 , Issue.6 , pp. 2047-2059
    • Kobitski, A.Y.1    Nierth, A.2    Helm, M.3    Jaschke, A.4    Nienhaus, G.U.5
  • 5
    • 0041321045 scopus 로고    scopus 로고
    • Single-molecule measurement of protein folding kinetics
    • DOI 10.1126/science.1085399
    • Lipman E A, Schuler B, Bakajin O and Eaton W A 2003 Single-molecule measurement of protein folding kinetics Science 301 1233-5 (Pubitemid 37052211)
    • (2003) Science , vol.301 , Issue.5637 , pp. 1233-1235
    • Lipman, E.A.1    Schuler, B.2    Bakajin, O.3    Eaton, W.A.4
  • 7
    • 33646937406 scopus 로고    scopus 로고
    • Single-molecule fluorescence studies of protein folding and conformational dynamics
    • DOI 10.1021/cr0404343
    • Michalet X, Weiss S and Jager M 2006 Single-molecule fluorescence studies of protein folding and conformational dynamics Chem. Rev. 106 1785-813 (Pubitemid 43792781)
    • (2006) Chemical Reviews , vol.106 , Issue.5 , pp. 1785-1813
    • Michalet, X.1    Weiss, S.2    Jager, M.3
  • 8
    • 0028104148 scopus 로고
    • Probing individual molecules with confocal fluorescence microscopy
    • Nie S, Chiu D T and Zare R N 1994 Probing individual molecules with confocal fluorescence microscopy Science 266 1018-21 (Pubitemid 24373713)
    • (1994) Science , vol.266 , Issue.5187 , pp. 1018-1021
    • Nie, S.1    Chiu, D.T.2    Zare, R.N.3
  • 9
    • 0037126290 scopus 로고    scopus 로고
    • Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy
    • DOI 10.1038/nature01060
    • Schuler B, Lipman E A and Eaton W A 2002 Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy Nature 419 743-7 (Pubitemid 35177962)
    • (2002) Nature , vol.419 , Issue.6908 , pp. 743-747
    • Schuler, B.1    Lipman, E.A.2    Eaton, W.A.3
  • 10
    • 0033548686 scopus 로고    scopus 로고
    • Fluorescence spectroscopy of single biomolecules
    • Weiss S 1999 Fluorescence spectroscopy of single biomolecules Science 283 1676-83 (Pubitemid 129502047)
    • (1999) Science , vol.283 , Issue.5408 , pp. 1676-1683
    • Weiss, S.1
  • 11
    • 0033813064 scopus 로고    scopus 로고
    • Measuring conformational dynamics of biomolecules by single molecule fluorescence spectroscopy
    • Weiss S 2000 Measuring conformational dynamics of biomolecules by single molecule fluorescence spectroscopy Nat. Struct. Biol. 7 724-9
    • (2000) Nat. Struct. Biol. , vol.7 , Issue.9 , pp. 724-729
    • Weiss, S.1
  • 13
    • 0034674420 scopus 로고    scopus 로고
    • A single-molecule study of RNA catalysis and folding
    • DOI 10.1126/science.288.5473.2048
    • Zhuang X, Bartley L E, Babcock H P, Russell R, Ha T, Herschlag D and Chu S 2000 A single-molecule study of RNA catalysis and folding Science 288 2048-51 (Pubitemid 30397686)
    • (2000) Science , vol.288 , Issue.5473 , pp. 2048-2051
    • Zhuang, X.1    Bartley, L.E.2    Babcock, H.P.3    Russell, R.4    Ha, T.5    Herschlag, D.6    Chu, S.7
  • 14
    • 7544225920 scopus 로고    scopus 로고
    • Vesicle encapsulation studies reveal that single molecule ribozyme heterogeneities are intrinsic
    • Okumus B, Wilson T J, Lilley D M and Ha T 2004 Vesicle encapsulation studies reveal that single molecule ribozyme heterogeneities are intrinsic Biophys J. 87 2798-806
    • (2004) Biophys J. , vol.87 , Issue.4 , pp. 2798-2806
    • Okumus, B.1    Wilson, T.J.2    Lilley, D.M.3    Ha, T.4
  • 15
    • 10044255342 scopus 로고    scopus 로고
    • Probing the kinetics of single molecule protein folding
    • DOI 10.1529/biophysj.104.046243
    • Leite V B, Onuchic J N, Stell G and Wang J 2004 Probing the kinetics of single molecule protein folding Biophys J. 87 3633-41 (Pubitemid 39602874)
    • (2004) Biophysical Journal , vol.87 , Issue.6 , pp. 3633-3641
    • Leite, V.B.P.1    Onuchic, J.N.2    Stell, G.3    Wang, J.4
  • 16
    • 23744433971 scopus 로고    scopus 로고
    • Surfaces and orientations: Much to FRET about?
    • Rasnik I, McKinney S A and Ha T 2005 Surfaces and orientations: much to FRET about? Acc. Chem. Res. 38 542-8
    • (2005) Acc. Chem. Res. , vol.38 , Issue.7 , pp. 542-548
    • Rasnik, I.1    McKinney, S.A.2    Ha, T.3
  • 19
    • 33847737459 scopus 로고    scopus 로고
    • Stability of a protein tethered to a surface
    • DOI 10.1063/1.2464114
    • Friedel M, Baumketner A and Shea J E 2007 Stability of a protein tethered to a surface J. Chem. Phys. 126 095101 (Pubitemid 46385645)
    • (2007) Journal of Chemical Physics , vol.126 , Issue.9 , pp. 095101
    • Friedel, M.1    Baumketner, A.2    Shea, J.-E.3
  • 20
    • 44849123226 scopus 로고    scopus 로고
    • An entropic perspective of protein stability on surfaces
    • Knotts T A t, Rathore N and de Pablo J J 2008 An entropic perspective of protein stability on surfaces Biophys J. 94 4473-83
    • (2008) Biophys J. , vol.94 , Issue.11 , pp. 4473-4483
    • Knotts, T.A.T.1    Rathore, N.2    De Pablo, J.J.3
  • 21
    • 0027335694 scopus 로고
    • 1 H and 15 N assignments and secondary structure of the Src SH3 domain
    • Yu H, Rosen M K and Schreiber S L 1993 1 H and 15 N assignments and secondary structure of the Src SH3 domain FEBS Lett 324 87-92
    • (1993) FEBS Lett , vol.324 , Issue.1 , pp. 87-92
    • Yu, H.1    Rosen, M.K.2    Schreiber, S.L.3
  • 22
    • 4444358276 scopus 로고    scopus 로고
    • Transition states for folding of circular-permuted proteins
    • DOI 10.1002/prot.20175
    • Chen J, Wang J and Wang W 2004 Transition states for folding of circular-permuted proteins Proteins 57 153-71 (Pubitemid 39198960)
    • (2004) Proteins: Structure, Function and Genetics , vol.57 , Issue.1 , pp. 153-171
    • Chen, J.1    Wang, J.2    Wang, W.3
  • 23
    • 21744452297 scopus 로고    scopus 로고
    • Reconstruction of the src-SH3 protein domain transition state ensemble using multiscale molecular dynamics simulations
    • DOI 10.1016/j.jmb.2005.05.017, PII S0022283605005486
    • Ding F, Guo W, Dokholyan N V, Shakhnovich E I and Shea J E 2005 Reconstruction of the src-SH3 protein domain transition state ensemble using multiscale molecular dynamics simulations J. Mol. Biol. 350 1035-50 (Pubitemid 40943460)
    • (2005) Journal of Molecular Biology , vol.350 , Issue.5 , pp. 1035-1050
    • Ding, F.1    Guo, W.2    Dokholyan, N.V.3    Shakhnovich, E.I.4    Shea, J.-E.5
  • 24
    • 0031444104 scopus 로고    scopus 로고
    • Folding dynamics of the src SH3 domain
    • DOI 10.1021/bi971786p
    • Grantcharova V P and Baker D 1997 Folding dynamics of the src SH3 domain Biochemistry 36 15685-92 (Pubitemid 28027367)
    • (1997) Biochemistry , vol.36 , Issue.50 , pp. 15685-15692
    • Grantcharova, V.P.1    Baker, D.2
  • 25
    • 0035936689 scopus 로고    scopus 로고
    • Circularization changes the folding transition state of the src SH3 domain
    • DOI 10.1006/jmbi.2000.4352
    • Grantcharova V P and Baker D 2001 Circularization changes the folding transition state of the src SH3 domain J. Mol. Biol. 306 555-63 (Pubitemid 33027722)
    • (2001) Journal of Molecular Biology , vol.306 , Issue.3 , pp. 555-563
    • Grantcharova, V.P.1    Baker, D.2
  • 27
    • 0031853167 scopus 로고    scopus 로고
    • Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain
    • DOI 10.1038/1412
    • Grantcharova V P, Riddle D S, Santiago J V and Baker D 1998 Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain Nat. Struct. Biol. 5 714-20 (Pubitemid 28359808)
    • (1998) Nature Structural Biology , vol.5 , Issue.8 , pp. 714-720
    • Grantcharova, V.P.1    Riddle, D.S.2    Santiago, J.V.3    Baker, D.4
  • 28
    • 0037974485 scopus 로고    scopus 로고
    • Posttransition state desolvation of the hydrophobic core of the src-SH3 protein domain
    • Guo W, Lampoudi S and Shea J E 2003 Posttransition state desolvation of the hydrophobic core of the src-SH3 protein domain Biophys J. 85 61-9 (Pubitemid 36753616)
    • (2003) Biophysical Journal , vol.85 , Issue.1 , pp. 61-69
    • Guo, W.1    Lampoudi, S.2    Shea, J.-E.3
  • 29
    • 1842584557 scopus 로고    scopus 로고
    • Temperature Dependence of the Free Energy Landscape of the src-SH3 Protein Domain
    • DOI 10.1002/prot.20053
    • Guo W, Lampoudi S and Shea J E 2004 Temperature dependence of the free energy landscape of the src-SH3 protein domain Proteins 55 395-406 (Pubitemid 38437496)
    • (2004) Proteins: Structure, Function and Genetics , vol.55 , Issue.2 , pp. 395-406
    • Guo, W.1    Lampoudi, S.2    Shea, J.-E.3
  • 31
    • 33748474227 scopus 로고    scopus 로고
    • Transition state of a SH3 domain detected with principle component analysis and a charge-neutralized all-atom protein model
    • DOI 10.1002/prot.21069
    • Mitomo D, Nakamura H K, Ikeda K, Yamagishi A and Higo J 2006 Transition state of a SH3 domain detected with principle component analysis and a charge-neutralized all-atom protein model Proteins 64 883-94 (Pubitemid 44420930)
    • (2006) Proteins: Structure, Function and Genetics , vol.64 , Issue.4 , pp. 883-894
    • Mitomo, D.1    Nakamura, H.K.2    Ikeda, K.3    Yamagishi, A.4    Higo, J.5
  • 32
    • 43949124462 scopus 로고    scopus 로고
    • Folding of the alphaII-spectrin SH3 domain under physiological salt conditions
    • Petzold K, Ohman A and Backman L 2008 Folding of the alphaII-spectrin SH3 domain under physiological salt conditions Arch. Biochem. Biophys. 474 39-47
    • (2008) Arch. Biochem. Biophys. , vol.474 , Issue.1 , pp. 39-47
    • Petzold, K.1    Ohman, A.2    Backman, L.3
  • 35
    • 33646872629 scopus 로고    scopus 로고
    • Characterization of the hydrodynamic properties of the folding transition state of an SH3 domain by magnetization transfer NMR spectroscopy
    • DOI 10.1021/bi060268o
    • Tollinger M, Neale C, Kay L E and Forman-Kay J D 2006 Characterization of the hydrodynamic properties of the folding transition state of an SH3 domain by magnetization transfer NMR spectroscopy Biochemistry 45 6434-45 (Pubitemid 43787809)
    • (2006) Biochemistry , vol.45 , Issue.20 , pp. 6434-6445
    • Tollinger, M.1    Neale, C.2    Kay, L.E.3    Forman-Kay, J.D.4
  • 36
    • 33645954277 scopus 로고    scopus 로고
    • Hydration and packing along the folding pathway of SH3 domains by pressure-dependent NMR
    • Bezsonova I, Korzhnev D M, Prosser R S, Forman-Kay J D and Kay L E 2006 Hydration and packing along the folding pathway of SH3 domains by pressure-dependent NMR Biochemistry 45 4711-9
    • (2006) Biochemistry , vol.45 , Issue.15 , pp. 4711-4719
    • Bezsonova, I.1    Korzhnev, D.M.2    Prosser, R.S.3    Forman-Kay, J.D.4    Kay, L.E.5
  • 37
    • 1542345514 scopus 로고    scopus 로고
    • Formation of the Folding Nucleus of an SH3 Domain Investigated by Loosely Coupled Molecular Dynamics Simulations
    • Settanni G, Gsponer J and Caflisch A 2004 Formation of the folding nucleus of an SH3 domain investigated by loosely coupled molecular dynamics simulations Biophys J. 86 1691-701 (Pubitemid 38295604)
    • (2004) Biophysical Journal , vol.86 , Issue.3 , pp. 1691-1701
    • Settanni, G.1    Gsponer, J.2    Caflisch, A.3
  • 38
    • 33646144221 scopus 로고    scopus 로고
    • Confinement effects on the thermodynamics of protein folding: Monte Carlo simulations
    • Rathore N, Knotts T A t and de Pablo J J 2006 Confinement effects on the thermodynamics of protein folding: Monte Carlo simulations Biophys J. 90 1767-73
    • (2006) Biophys J. , vol.90 , Issue.5 , pp. 1767-1773
    • Rathore, N.1    Knotts, T.A.T.2    De Pablo, J.J.3
  • 40
    • 34447515841 scopus 로고    scopus 로고
    • From coarse-grain to all-atom: Toward multiscale analysis of protein landscapes
    • DOI 10.1002/prot.21371
    • Heath A P, Kavraki L E and Clementi C 2007 From coarse-grain to all-atom: toward multiscale analysis of protein landscapes Proteins 68 646-61 (Pubitemid 47068305)
    • (2007) Proteins: Structure, Function and Genetics , vol.68 , Issue.3 , pp. 646-661
    • Heath, A.P.1    Kavraki, L.E.2    Clementi, C.3
  • 41
    • 0034685604 scopus 로고    scopus 로고
    • Topological and energetic factors: What determines the structural details of the transition state ensemble and 'en-route' intermediates for protein folding? An investigation for small globular proteins
    • Clementi C, Nymeyer H and Onuchic J N 2000 Topological and energetic factors: what determines the structural details of the transition state ensemble and 'en-route' intermediates for protein folding? An investigation for small globular proteins J. Mol. Biol. 298 937-53
    • (2000) J. Mol. Biol. , vol.298 , Issue.5 , pp. 937-953
    • Clementi, C.1    Nymeyer, H.2    Onuchic, J.N.3
  • 44
    • 18844459862 scopus 로고    scopus 로고
    • Nucleation and the transition state of the SH3 domain
    • DOI 10.1016/j.jmb.2005.03.050, PII S002228360500330X
    • Hubner I A, Edmonds K A and Shakhnovich E I 2005 Nucleation and the transition state of the SH3 domain J. Mol. Biol. 349 424-34 (Pubitemid 40693760)
    • (2005) Journal of Molecular Biology , vol.349 , Issue.2 , pp. 424-434
    • Hubner, I.A.1    Edmonds, K.A.2    Shakhnovich, E.I.3
  • 48
    • 4243819810 scopus 로고
    • New Monte Carlo technique for studying phase transitions
    • Ferrenberg A M and Swendsen R H 1988 New Monte Carlo technique for studying phase transitions Phys. Rev. Lett. 61 2635-8
    • (1988) Phys. Rev. Lett. , vol.61 , Issue.23 , pp. 2635-2638
    • Ferrenberg, A.M.1    And Swendsen, R.H.2
  • 50
    • 84986519238 scopus 로고
    • The weighted histogram analysis method for free-energy calculations on biomolecules. I: The method
    • Kumar S, Bouzida D, Swendsen R H, Kollman P A and Rosenberg J M 1992 The weighted histogram analysis method for free-energy calculations on biomolecules. I: the method J. Comput. Chem. 13 11
    • (1992) J. Comput. Chem. , vol.13 , Issue.8 , pp. 1011
    • Kumar, S.1    Bouzida, D.2    Swendsen, R.H.3    Kollman, P.A.4    Rosenberg, J.M.5
  • 51
    • 0032872786 scopus 로고    scopus 로고
    • Amphitropic proteins: Regulation by reversible membrane interactions
    • DOI 10.1080/096876899294544
    • Johnson J E and Cornell R B 1999 Amphitropic proteins: regulation by reversible membrane interactions (review) Mol. Membr. Biol. 16 217-35 (Pubitemid 29419697)
    • (1999) Molecular Membrane Biology , vol.16 , Issue.3 , pp. 217-235
    • Johnson, J.E.1    Cornell, R.B.2


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