메뉴 건너뛰기




Volumn 423, Issue 3, 2012, Pages 273-283

Protein folding: Adding a nucleus to guide helix docking reduces landscape roughness

Author keywords

energy landscape; helix bundle; minimal frustration; protein folding; value analysis

Indexed keywords

SOLVENT;

EID: 84867080086     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2012.08.003     Document Type: Article
Times cited : (15)

References (47)
  • 1
    • 77956208339 scopus 로고    scopus 로고
    • What lessons can be learned from studying the folding of homologous proteins?
    • A.A. Nickson, and J. Clarke What lessons can be learned from studying the folding of homologous proteins? Methods 52 2010 38 50
    • (2010) Methods , vol.52 , pp. 38-50
    • Nickson, A.A.1    Clarke, J.2
  • 2
    • 0028947257 scopus 로고
    • Funnels, pathways, and the energy landscape of protein folding: A synthesis
    • J.D. Bryngleson, J.N. Onuchic, N.D. Socci, and P.G. Wolynes Funnels, pathways, and the energy landscape of protein folding: a synthesis Proteins 21 1995 167 195
    • (1995) Proteins , vol.21 , pp. 167-195
    • Bryngleson, J.D.1    Onuchic, J.N.2    Socci, N.D.3    Wolynes, P.G.4
  • 3
    • 7044226061 scopus 로고    scopus 로고
    • The folding of spectrin domains I: Wild-type domains have the same stability but very different kinetic properties
    • K.A. Scott, S. Batey, K.A. Hooton, and J. Clarke The folding of spectrin domains I: wild-type domains have the same stability but very different kinetic properties J. Mol. Biol. 344 2004 195 205
    • (2004) J. Mol. Biol. , vol.344 , pp. 195-205
    • Scott, K.A.1    Batey, S.2    Hooton, K.A.3    Clarke, J.4
  • 4
    • 7044222120 scopus 로고    scopus 로고
    • The folding of spectrin domains II: Value analysis of R16
    • K.A. Scott, L.G. Randles, and J. Clarke The folding of spectrin domains II: Value analysis of R16 J. Mol. Biol. 344 2004 207 221
    • (2004) J. Mol. Biol. , vol.344 , pp. 207-221
    • Scott, K.A.1    Randles, L.G.2    Clarke, J.3
  • 5
    • 33745899026 scopus 로고    scopus 로고
    • The folding pathway of spectrin R17 from experiment and simulation: Using experimentally validated MD simulations to characterize states hinted at by experiment
    • K.A. Scott, L.G. Randles, S.J. Moran, V. Daggett, and J. Clarke The folding pathway of spectrin R17 from experiment and simulation: using experimentally validated MD simulations to characterize states hinted at by experiment J. Mol. Biol. 359 2006 159 173
    • (2006) J. Mol. Biol. , vol.359 , pp. 159-173
    • Scott, K.A.1    Randles, L.G.2    Moran, S.J.3    Daggett, V.4    Clarke, J.5
  • 6
    • 76249117417 scopus 로고    scopus 로고
    • Experimental evidence for a frustrated energy landscape in a three-helix-bundle protein family
    • B.G. Wensley, S. Batey, F.A.C. Bone, Z.M. Chan, N.R. Tumelty, and A. Steward Experimental evidence for a frustrated energy landscape in a three-helix-bundle protein family Nature 463 2010 685 688
    • (2010) Nature , vol.463 , pp. 685-688
    • Wensley, B.G.1    Batey, S.2    Bone, F.A.C.3    Chan, Z.M.4    Tumelty, N.R.5    Steward, A.6
  • 7
    • 67649840692 scopus 로고    scopus 로고
    • Different members of a simple three-helix bundle protein family have very different folding rate constants and fold by different mechanisms
    • B.G. Wensley, M. Gärtner, W. Choo, S. Batey, and J. Clarke Different members of a simple three-helix bundle protein family have very different folding rate constants and fold by different mechanisms J. Mol. Biol. 390 2009 1074 1085
    • (2009) J. Mol. Biol. , vol.390 , pp. 1074-1085
    • Wensley, B.G.1    Gärtner, M.2    Choo, W.3    Batey, S.4    Clarke, J.5
  • 10
    • 0031592935 scopus 로고    scopus 로고
    • Solution structure of the spectrin repeat: A left-handed antiparallel triple-helical coiled-coil
    • J. Pascual, M. Pfuhl, D. Walther, M. Saraste, and M. Nilges Solution structure of the spectrin repeat: a left-handed antiparallel triple-helical coiled-coil J. Mol. Biol. 273 1997 740 751
    • (1997) J. Mol. Biol. , vol.273 , pp. 740-751
    • Pascual, J.1    Pfuhl, M.2    Walther, D.3    Saraste, M.4    Nilges, M.5
  • 11
    • 0029863942 scopus 로고    scopus 로고
    • The spectrin repeat folds into a three-helix bundle in solution
    • J. Pascual, M. Pfuhl, G. Rivas, A. Pastore, and M. Saraste The spectrin repeat folds into a three-helix bundle in solution FEBS Lett. 383 1996 201 207
    • (1996) FEBS Lett. , vol.383 , pp. 201-207
    • Pascual, J.1    Pfuhl, M.2    Rivas, G.3    Pastore, A.4    Saraste, M.5
  • 12
    • 7444232111 scopus 로고    scopus 로고
    • Independent movement, dimerization and stability of tandem repeats of chicken brain α-spectrin
    • H. Kusunoki, G. Minasov, R.I. Macdonald, and A. Mondragon Independent movement, dimerization and stability of tandem repeats of chicken brain α-spectrin J. Mol. Biol. 344 2004 495 511
    • (2004) J. Mol. Biol. , vol.344 , pp. 495-511
    • Kusunoki, H.1    Minasov, G.2    MacDonald, R.I.3    Mondragon, A.4
  • 13
    • 22444436625 scopus 로고    scopus 로고
    • Spectrin R16: Broad energy barrier or sequential transition states?
    • K.A. Scott, and J. Clarke Spectrin R16: broad energy barrier or sequential transition states? Protein Sci. 14 2005 1617 1629
    • (2005) Protein Sci. , vol.14 , pp. 1617-1629
    • Scott, K.A.1    Clarke, J.2
  • 14
    • 84867092008 scopus 로고    scopus 로고
    • Separating the effects of internal friction and transition state energy to explain the slow, frustrated folding of spectrin domains
    • 10.1073/pnas.1201793109 published ahead of print June 18
    • B.G. Wensley, L. Kwa, S.L. Shammas, J.M. Rogers, S. Browning, Z. Yang, and J. Clarke Separating the effects of internal friction and transition state energy to explain the slow, frustrated folding of spectrin domains Proc. Natl Acad. Sci. USA 18 2012 10.1073/pnas.1201793109 published ahead of print June 18
    • (2012) Proc. Natl Acad. Sci. USA , vol.18
    • Wensley, B.G.1    Kwa, L.2    Shammas, S.L.3    Rogers, J.M.4    Browning, S.5    Yang, Z.6    Clarke, J.7
  • 15
    • 0024733407 scopus 로고
    • Intermediates and barrier crossing in a random energy model (with applications to protein folding)
    • J.D. Bryngleson, and P.G. Wolynes Intermediates and barrier crossing in a random energy model (with applications to protein folding) J. Phys. Chem. 93 1989 6902 6915
    • (1989) J. Phys. Chem. , vol.93 , pp. 6902-6915
    • Bryngleson, J.D.1    Wolynes, P.G.2
  • 16
    • 0025214083 scopus 로고
    • Role of diffusion in the folding of the α subunit of tryptophan synthase from Escherischia coli
    • B.A. Chrunyk, and C.R. Mathews Role of diffusion in the folding of the α subunit of tryptophan synthase from Escherischia coli Biochemistry 29 1990 2149 2154
    • (1990) Biochemistry , vol.29 , pp. 2149-2154
    • Chrunyk, B.A.1    Mathews, C.R.2
  • 18
    • 0032506017 scopus 로고    scopus 로고
    • Limited internal friction in the rate-limiting step of a two-state protein folding reaction
    • K.W. Plaxco, and D. Baker Limited internal friction in the rate-limiting step of a two-state protein folding reaction Proc. Natl Acad. Sci. USA 95 1998 13591 13596
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 13591-13596
    • Plaxco, K.W.1    Baker, D.2
  • 19
    • 0033596697 scopus 로고    scopus 로고
    • Viscosity dependence of the folding kinetics of a dimeric and monomeric coiled coil
    • R.P. Bhattacharyya, and T.R. Sosnick Viscosity dependence of the folding kinetics of a dimeric and monomeric coiled coil Biochemistry 38 1999 2601 2609
    • (1999) Biochemistry , vol.38 , pp. 2601-2609
    • Bhattacharyya, R.P.1    Sosnick, T.R.2
  • 20
    • 33846617642 scopus 로고    scopus 로고
    • Diffusional barrier in the unfolding of a small protein
    • L. Pradeep, and J.B. Udgaonkar Diffusional barrier in the unfolding of a small protein J. Mol. Biol. 366 2007 1016 1028
    • (2007) J. Mol. Biol. , vol.366 , pp. 1016-1028
    • Pradeep, L.1    Udgaonkar, J.B.2
  • 21
    • 33748472551 scopus 로고    scopus 로고
    • Internal friction in the ultrafast folding of the trpyophan cage
    • L.L. Qiu, and S.J. Hagen Internal friction in the ultrafast folding of the trpyophan cage Chem. Phys. 312 2004 327 333
    • (2004) Chem. Phys. , vol.312 , pp. 327-333
    • Qiu, L.L.1    Hagen, S.J.2
  • 23
    • 1842450320 scopus 로고    scopus 로고
    • Structural insights into the stability and flexibility of unusual erythroid spectrin repeats
    • H. Kusunoki, R.I. MacDonald, and A. Mondragon Structural insights into the stability and flexibility of unusual erythroid spectrin repeats Structure 12 2004 645 656
    • (2004) Structure , vol.12 , pp. 645-656
    • Kusunoki, H.1    MacDonald, R.I.2    Mondragon, A.3
  • 24
    • 34547275473 scopus 로고
    • Brownian motion in a field of force and the diffusion model of chemical reactions
    • H.A. Kramers Brownian motion in a field of force and the diffusion model of chemical reactions Physica 7 1940 284 304
    • (1940) Physica , vol.7 , pp. 284-304
    • Kramers, H.A.1
  • 25
    • 0026636807 scopus 로고
    • The role of solvent viscosity in the dynamics of protein conformational changes
    • A. Ansari, C.M. Jones, E.R. Henry, J. Hofrichter, and W.A. Eaton The role of solvent viscosity in the dynamics of protein conformational changes Science 256 1992 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
  • 27
    • 0027310845 scopus 로고
    • The control of protein stability and association by weak interactions with water: How do solvents affect these processes?
    • S.N. Timasheff The control of protein stability and association by weak interactions with water: how do solvents affect these processes? Annu. Rev. Biophys. Biomol. Struct. 22 1993 67 97
    • (1993) Annu. Rev. Biophys. Biomol. Struct. , vol.22 , pp. 67-97
    • Timasheff, S.N.1
  • 28
    • 0035128362 scopus 로고    scopus 로고
    • Effect of viscosity on the kinetics of α-helix and β-hairpin formation
    • G.S. Jas, W.A. Eaton, and J. Hofrichter Effect of viscosity on the kinetics of α-helix and β-hairpin formation J. Phys. Chem. B 105 2001 261 272
    • (2001) J. Phys. Chem. B , vol.105 , pp. 261-272
    • Jas, G.S.1    Eaton, W.A.2    Hofrichter, J.3
  • 29
    • 0031576337 scopus 로고    scopus 로고
    • Glutamine, alanine or glycine repeats inserted into the loop of a protein have minimal effects on stability and folding rates
    • A.G. Ladurner, and A.R. Fersht Glutamine, alanine or glycine repeats inserted into the loop of a protein have minimal effects on stability and folding rates J. Mol. Biol. 273 1997 330 337
    • (1997) J. Mol. Biol. , vol.273 , pp. 330-337
    • Ladurner, A.G.1    Fersht, A.R.2
  • 30
    • 0029041315 scopus 로고
    • Exploring the energy surface of protein folding by structure-reactivity relationships and engineered proteins: Observation of Hammond behavior for the gross structure of the transition state and anti-Hammond behavior for structural elements for unfolding/folding of barnase
    • J.M. Matthews, and A.R. Fersht Exploring the energy surface of protein folding by structure-reactivity relationships and engineered proteins: observation of Hammond behavior for the gross structure of the transition state and anti-Hammond behavior for structural elements for unfolding/folding of barnase Biochemistry 34 1995 6805 6814
    • (1995) Biochemistry , vol.34 , pp. 6805-6814
    • Matthews, J.M.1    Fersht, A.R.2
  • 32
    • 0034610360 scopus 로고    scopus 로고
    • Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation
    • U. Mayor, C.M. Johnson, V. Daggett, and A.R. Fersht Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation Proc. Natl Acad. Sci. USA 97 2000 13518 13522
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 13518-13522
    • Mayor, U.1    Johnson, C.M.2    Daggett, V.3    Fersht, A.R.4
  • 33
    • 0142185492 scopus 로고    scopus 로고
    • The denatured state of Engrailed Homeodomain under denaturing and native conditions
    • U. Mayor, J.G. Grossmann, N.W. Foster, S.M. Freund, and A.R. Fersht The denatured state of Engrailed Homeodomain under denaturing and native conditions J. Mol. Biol. 333 2003 977 991
    • (2003) J. Mol. Biol. , vol.333 , pp. 977-991
    • Mayor, U.1    Grossmann, J.G.2    Foster, N.W.3    Freund, S.M.4    Fersht, A.R.5
  • 34
    • 27144532135 scopus 로고    scopus 로고
    • Solution structure of a protein denatured state and folding intermediate
    • T.L. Religa, J.S. Markson, U. Mayor, S.M. Freund, and A.R. Fersht Solution structure of a protein denatured state and folding intermediate Nature 437 2005 1053 1056
    • (2005) Nature , vol.437 , pp. 1053-1056
    • Religa, T.L.1    Markson, J.S.2    Mayor, U.3    Freund, S.M.4    Fersht, A.R.5
  • 35
    • 20544462511 scopus 로고    scopus 로고
    • Simulation and experiment conspire to reveal cryptic intermediates and a slide from nucleation-condensation to framework mechanism of folding
    • G.W.N. White, S. Gianni, J.G. Grossmann, P. Jemth, A.R. Fersht, and V. Daggett Simulation and experiment conspire to reveal cryptic intermediates and a slide from nucleation-condensation to framework mechanism of folding J. Mol. Biol. 350 2005 757 775
    • (2005) J. Mol. Biol. , vol.350 , pp. 757-775
    • White, G.W.N.1    Gianni, S.2    Grossmann, J.G.3    Jemth, P.4    Fersht, A.R.5    Daggett, V.6
  • 36
    • 34547151184 scopus 로고    scopus 로고
    • The helix-turn-helix motif as an ultrafast independently folding domain: The pathway of folding of Engrailed homeodomain
    • T.L. Religa, C.M. Johnson, D.M. Vu, S.H. Brewer, R.B. Dyer, and A.R. Fersht The helix-turn-helix motif as an ultrafast independently folding domain: the pathway of folding of Engrailed homeodomain Proc. Natl Acad. Sci. USA 104 2007 9272 9277
    • (2007) Proc. Natl Acad. Sci. USA , vol.104 , pp. 9272-9277
    • Religa, T.L.1    Johnson, C.M.2    Vu, D.M.3    Brewer, S.H.4    Dyer, R.B.5    Fersht, A.R.6
  • 37
    • 0036183221 scopus 로고    scopus 로고
    • Im7 folding mechanism: Misfolding on a path to the native state
    • A.P. Capaldi, C. Kleanthous, and S.E. Radford Im7 folding mechanism: misfolding on a path to the native state Nat. Struct. Biol. 9 2002 209 216
    • (2002) Nat. Struct. Biol. , vol.9 , pp. 209-216
    • Capaldi, A.P.1    Kleanthous, C.2    Radford, S.E.3
  • 38
    • 0042093787 scopus 로고    scopus 로고
    • Origins of chevron rollovers in non-two-state protein folding kinetics
    • H. Kaya, and H.S. Chan Origins of chevron rollovers in non-two-state protein folding kinetics Phys. Rev. Lett. 90 2003 258104
    • (2003) Phys. Rev. Lett. , vol.90 , pp. 258104
    • Kaya, H.1    Chan, H.S.2
  • 39
    • 0022555885 scopus 로고
    • Determination and analysis of urea and guanidine hydrochloride denaturation curves
    • C.N. Pace Determination and analysis of urea and guanidine hydrochloride denaturation curves Methods Enzymol. 131 1986 266 280
    • (1986) Methods Enzymol. , vol.131 , pp. 266-280
    • Pace, C.N.1
  • 40
    • 0035895436 scopus 로고    scopus 로고
    • Apparent two-state tendamistat folding is a sequential process along a defined route
    • A. Bachmann, and T. Kiefhaber Apparent two-state tendamistat folding is a sequential process along a defined route J. Mol. Biol. 306 2001 375 386
    • (2001) J. Mol. Biol. , vol.306 , pp. 375-386
    • Bachmann, A.1    Kiefhaber, T.2
  • 41
    • 85012750408 scopus 로고
    • Kinetic characterisation of complex reaction systems
    • C.H. Bamford, C.F.H. Tipper, Elsevier Amsterdam, The Netherlands
    • Z.G. Szabo Kinetic characterisation of complex reaction systems C.H. Bamford, C.F.H. Tipper, Comprehensive Chemical Kinetics 2 1969 Elsevier Amsterdam, The Netherlands 1 81
    • (1969) Comprehensive Chemical Kinetics , vol.2 , pp. 1-81
    • Szabo, Z.G.1
  • 42
    • 0033592876 scopus 로고    scopus 로고
    • From snapshot to movie: Analysis of protein folding transition states taken one step further
    • T. Ternstrom, U. Mayor, M. Akke, and M. Oliveberg From snapshot to movie: Analysis of protein folding transition states taken one step further Proc. Natl Acad. Sci. USA 96 1999 14854 14859
    • (1999) Proc. Natl Acad. Sci. USA , vol.96 , pp. 14854-14859
    • Ternstrom, T.1    Mayor, U.2    Akke, M.3    Oliveberg, M.4
  • 43
    • 0032503027 scopus 로고    scopus 로고
    • The changing nature of the protein folding transition state: Implications for the shape of the free-energy profile for folding
    • M. Oliveberg, Y.J. Tan, M. Silow, and A.R. Fersht The changing nature of the protein folding transition state: implications for the shape of the free-energy profile for folding J. Mol. Biol. 277 1998 933 943
    • (1998) J. Mol. Biol. , vol.277 , pp. 933-943
    • Oliveberg, M.1    Tan, Y.J.2    Silow, M.3    Fersht, A.R.4
  • 44
    • 0033580679 scopus 로고    scopus 로고
    • Structural changes in the transition state of protein folding: Alternative interpretations of curved chevron plots
    • D.E. Otzen, O. Kristensen, M. Proctor, and M. Oliveberg Structural changes in the transition state of protein folding: alternative interpretations of curved chevron plots Biochemistry 38 1999 6499 6511
    • (1999) Biochemistry , vol.38 , pp. 6499-6511
    • Otzen, D.E.1    Kristensen, O.2    Proctor, M.3    Oliveberg, M.4
  • 45
    • 0035252685 scopus 로고    scopus 로고
    • Characterisation of the transition states for protein folding: Towards a new level of mechanistic detail in protein engineering analysis
    • M. Oliveberg Characterisation of the transition states for protein folding: towards a new level of mechanistic detail in protein engineering analysis Curr. Opin. Struct. Biol. 11 2001 94 100
    • (2001) Curr. Opin. Struct. Biol. , vol.11 , pp. 94-100
    • Oliveberg, M.1
  • 46
    • 0030750236 scopus 로고    scopus 로고
    • High-energy channeling in protein folding
    • M. Silow, and M. Oliveberg High-energy channeling in protein folding Biochemistry 36 1997 7633 7637
    • (1997) Biochemistry , vol.36 , pp. 7633-7637
    • Silow, M.1    Oliveberg, M.2
  • 47
    • 0026511656 scopus 로고
    • The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding
    • A.R. Fersht, A. Matouschek, and L. Serrano The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding J. Mol. Biol. 224 1992 771 782
    • (1992) J. Mol. Biol. , vol.224 , pp. 771-782
    • Fersht, A.R.1    Matouschek, A.2    Serrano, L.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.