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Volumn 9, Issue 1, 2000, Pages 10-19

Folding and binding cascades: Dynamic landscapes and population shifts

Author keywords

Allostery; Binding; Biological pathways; Conformational ensembles; Dynamic landscapes; Folding; Funnels; Induced conformational change

Indexed keywords

ALLOSTERISM; BINDING AFFINITY; ENZYME CONFORMATION; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN FOLDING; REVIEW;

EID: 0033970020     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.9.1.10     Document Type: Review
Times cited : (527)

References (59)
  • 2
    • 0028286471 scopus 로고
    • Kinetics versus thermodynamics in protein folding
    • Baker D, Agard DA. 1994. Kinetics versus thermodynamics in protein folding. Biochemistry 33:7505-7509.
    • (1994) Biochemistry , vol.33 , pp. 7505-7509
    • Baker, D.1    Agard, D.A.2
  • 3
    • 0028776642 scopus 로고
    • Matching speed and stability
    • Baldwin RL. 1994. Matching speed and stability. Nature 369:183-184.
    • (1994) Nature , vol.369 , pp. 183-184
    • Baldwin, R.L.1
  • 4
    • 0029249945 scopus 로고
    • The nature of protein folding pathways: The classical versus the new view
    • Baldwin RL. 1995. The nature of protein folding pathways: The classical versus the new view. J Biomol NMR 5:103-109.
    • (1995) J Biomol NMR , vol.5 , pp. 103-109
    • Baldwin, R.L.1
  • 5
    • 0032972986 scopus 로고    scopus 로고
    • Is protein folding hierarchic? I. Local structure and peptide folding
    • Baldwin RL, Rose GD. 1999a. Is protein folding hierarchic? I. Local structure and peptide folding. Trends Biochem Sci 24:26-33.
    • (1999) Trends Biochem Sci , vol.24 , pp. 26-33
    • Baldwin, R.L.1    Rose, G.D.2
  • 6
    • 0033080081 scopus 로고    scopus 로고
    • Is protein folding hierarchic? II. Folding intermediates and transition states
    • Baldwin RL, Rose GD. 1999b. Is protein folding hierarchic? II. Folding intermediates and transition states. Trends Biochem Sci 24:77-84.
    • (1999) Trends Biochem Sci , vol.24 , pp. 77-84
    • Baldwin, R.L.1    Rose, G.D.2
  • 7
    • 0028204771 scopus 로고
    • Domain swapping: Entangling alliances between proteins
    • Bennett MJ, Choe S, Eisenberg D. 1994. Domain swapping: Entangling alliances between proteins. Proc Natl Acad Sci USA 97:3127-3131.
    • (1994) Proc Natl Acad Sci USA , vol.97 , pp. 3127-3131
    • Bennett, M.J.1    Choe, S.2    Eisenberg, D.3
  • 8
    • 0028865843 scopus 로고
    • 3D domain swapping: A mechanism for oligomer assembly
    • Bennett MJ, Schlunegger MP, Eisenberg D. 1995. 3D domain swapping: A mechanism for oligomer assembly. Protein Sci 4:2455-2468.
    • (1995) Protein Sci , vol.4 , pp. 2455-2468
    • Bennett, M.J.1    Schlunegger, M.P.2    Eisenberg, D.3
  • 11
    • 0029151245 scopus 로고
    • First principles calculation of the folding free energy for a three helix bundle protein
    • Bozko EM, Brooks CL III. 1995. First principles calculation of the folding free energy for a three helix bundle protein. Science 269:393-396.
    • (1995) Science , vol.269 , pp. 393-396
    • Bozko, E.M.1    Brooks C.L. III2
  • 12
    • 0024733407 scopus 로고
    • Intermediates and barrier crossing in a random energy model (with applications to protein folding)
    • Bryngelson JD, Wolynes PG. 1989. Intermediates and barrier crossing in a random energy model (with applications to protein folding). J Phys Chem 93:6902-6915.
    • (1989) J Phys Chem , vol.93 , pp. 6902-6915
    • Bryngelson, J.D.1    Wolynes, P.G.2
  • 13
    • 0027530108 scopus 로고
    • Protein docking algorithms: Simulating molecular recognition
    • Cherfils J, Janin J. 1993. Protein docking algorithms: Simulating molecular recognition. Curr Opin Struct Biol 3:265-269.
    • (1993) Curr Opin Struct Biol , vol.3 , pp. 265-269
    • Cherfils, J.1    Janin, J.2
  • 14
    • 0029190841 scopus 로고
    • Oligomer evolution in action
    • D'Alessio G. 1995. Oligomer evolution in action. Nat Struct Biol 2:11-13.
    • (1995) Nat Struct Biol , vol.2 , pp. 11-13
    • D'Alessio, G.1
  • 15
    • 0032993447 scopus 로고    scopus 로고
    • Polymer principles and protein folding
    • Dill KA. 1999. Polymer principles and protein folding. Protein Sci 8:1166-1180.
    • (1999) Protein Sci , vol.8 , pp. 1166-1180
    • Dill, K.A.1
  • 16
    • 1842298212 scopus 로고    scopus 로고
    • From Levinthal to pathways to funnels
    • Dill KA, Chan HS. 1997. From Levinthal to pathways to funnels. Nat Struct Biol 4:10-19.
    • (1997) Nat Struct Biol , vol.4 , pp. 10-19
    • Dill, K.A.1    Chan, H.S.2
  • 17
    • 0031883764 scopus 로고    scopus 로고
    • Steric chaperones
    • Ellis RJ. 1998. Steric chaperones. Trends Biochem Sci 23:43-45.
    • (1998) Trends Biochem Sci , vol.23 , pp. 43-45
    • Ellis, R.J.1
  • 18
    • 0027943261 scopus 로고
    • Conformational isomerism and the diversity of antibodies
    • Foote J, Milstein C. 1994. Conformational isomerism and the diversity of antibodies. Proc Natl Acad Sci USA 91:10370-10374.
    • (1994) Proc Natl Acad Sci USA , vol.91 , pp. 10370-10374
    • Foote, J.1    Milstein, C.2
  • 19
    • 0026320866 scopus 로고
    • The energy landscapes and motions of proteins
    • Frauenfelder H, Sugar SG, Wolynes PG. 1991. The energy landscapes and motions of proteins. Science 254:1598-1603.
    • (1991) Science , vol.254 , pp. 1598-1603
    • Frauenfelder, H.1    Sugar, S.G.2    Wolynes, P.G.3
  • 20
    • 0033621118 scopus 로고    scopus 로고
    • The propagation of binding interactions to remote sites in proteins: Analysis of the binding of the monoclonal antibody D1.3 to lysozyme
    • Freire E. 1999. The propagation of binding interactions to remote sites in proteins: Analysis of the binding of the monoclonal antibody D1.3 to lysozyme. Proc Natl Acad Sci USA 96:10118-10122.
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 10118-10122
    • Freire, E.1
  • 21
    • 0032530836 scopus 로고    scopus 로고
    • A database of macromolecular motions
    • Gerstein M, Krebs W. 1998. A database of macromolecular motions. Nucl Acids Res 26:4280-4290.
    • (1998) Nucl Acids Res , vol.26 , pp. 4280-4290
    • Gerstein, M.1    Krebs, W.2
  • 23
    • 0031856887 scopus 로고    scopus 로고
    • Satisfying turns in folding transitions
    • Gruebele M, Wolynes P. 1998. Satisfying turns in folding transitions. Nut Struct Biol 5:662-665.
    • (1998) Nut Struct Biol , vol.5 , pp. 662-665
    • Gruebele, M.1    Wolynes, P.2
  • 24
    • 0028023724 scopus 로고
    • Statistical mechanics of kinetic proofreading in protein folding in vivo
    • Gulukota K, Wolynes P. 1994. Statistical mechanics of kinetic proofreading in protein folding in vivo. Proc Natl Acad Sci USA 91:9292-9296.
    • (1994) Proc Natl Acad Sci USA , vol.91 , pp. 9292-9296
    • Gulukota, K.1    Wolynes, P.2
  • 25
    • 0002724139 scopus 로고
    • The role of induced fit and conformational changes of enzymes in specificity and catalysis
    • Herschlag D. 1988. The role of induced fit and conformational changes of enzymes in specificity and catalysis. Bioorg Chem 16:62-96.
    • (1988) Bioorg Chem , vol.16 , pp. 62-96
    • Herschlag, D.1
  • 26
    • 0030821162 scopus 로고    scopus 로고
    • Evolutionary chemistry: Getting there from here
    • Joyce GF. 1997. Evolutionary chemistry: Getting there from here. Science 276:1658-1659.
    • (1997) Science , vol.276 , pp. 1658-1659
    • Joyce, G.F.1
  • 27
    • 0030626588 scopus 로고    scopus 로고
    • The Levinthal paradox: Yesterday and today
    • Karplus M. 1997. The Levinthal paradox: Yesterday and today. Fold Des 2:S69-S75.
    • (1997) Fold Des , vol.2
    • Karplus, M.1
  • 28
    • 0028929204 scopus 로고
    • Comment: Kinetics of protein folding
    • Karplus M, Sali A. Shakhnovilch H. 1995. Comment: Kinetics of protein folding. Nature 373:664-665.
    • (1995) Nature , vol.373 , pp. 664-665
    • Karplus, M.1    Sali, A.2    Shakhnovilch, H.3
  • 29
    • 0002770218 scopus 로고
    • Protein folding: Theoretical studies of thermodynamics and dynamics
    • Creighton T, ed. New York: Freeman & Sons
    • Karplus M, Shakhnovitch EI. 1992. Protein folding: Theoretical studies of thermodynamics and dynamics. In: Creighton T, ed. Protein folding. New York: Freeman & Sons. pp 127-195.
    • (1992) Protein Folding , pp. 127-195
    • Karplus, M.1    Shakhnovitch, E.I.2
  • 30
    • 0001858251 scopus 로고
    • Application of a theory of enzyme specificity to protein synthesis
    • Koshland DE Jr. 1958. Application of a theory of enzyme specificity to protein synthesis. Proc Natl Acad Sci USA 44:98-123.
    • (1958) Proc Natl Acad Sci USA , vol.44 , pp. 98-123
    • Koshland D.E., Jr.1
  • 31
    • 0033015989 scopus 로고    scopus 로고
    • The formation of a native-like structure containing eight conserved hydrophobic residues is rate limiting in two-state protein folding of ACBP
    • Kragelund BB, Osmark P, Neergaard TB, Schiodt J, Kristiansen K, Knudsen J, Poulsen FM. 1999. The formation of a native-like structure containing eight conserved hydrophobic residues is rate limiting in two-state protein folding of ACBP. Nat Struct Biol. 6:594-601.
    • (1999) Nat Struct Biol. , vol.6 , pp. 594-601
    • Kragelund, B.B.1    Osmark, P.2    Neergaard, T.B.3    Schiodt, J.4    Kristiansen, K.5    Knudsen, J.6    Poulsen, F.M.7
  • 32
    • 0032614825 scopus 로고    scopus 로고
    • Folding funnels and conformational transitions via hinge-bending motions
    • Kumar S, Ma B, Tsai CJ, Wolfson H, Nussinov R. 1999. Folding funnels and conformational transitions via hinge-bending motions. Cell Biochem Biophys 31:141-164.
    • (1999) Cell Biochem Biophys , vol.31 , pp. 141-164
    • Kumar, S.1    Ma, B.2    Tsai, C.J.3    Wolfson, H.4    Nussinov, R.5
  • 33
    • 0031465967 scopus 로고    scopus 로고
    • "New view" of protein folding reconciled with the old through multiple unfolding simulations
    • Lazaridis T, Karplus M. 1997. "New view" of protein folding reconciled with the old through multiple unfolding simulations. Science 278: 1928-1931.
    • (1997) Science , vol.278 , pp. 1928-1931
    • Lazaridis, T.1    Karplus, M.2
  • 35
    • 0033534360 scopus 로고    scopus 로고
    • Conformational changes affect binding and catalysis by ester-hydrolysing antibodies
    • Lindner AB, Eshhar Z, Tawfik DS. 1999. Conformational changes affect binding and catalysis by ester-hydrolysing antibodies. J Mol Biol 285:421-430.
    • (1999) J Mol Biol , vol.285 , pp. 421-430
    • Lindner, A.B.1    Eshhar, Z.2    Tawfik, D.S.3
  • 37
    • 0031837984 scopus 로고    scopus 로고
    • Hinge bending within the cytokine receptor superfamily revealed by the 2.4 Å crystal structure of the extracellular domain of the rabbit tissue factor
    • Muller Y, Kelley RF, De Vos AM. 1998. Hinge bending within the cytokine receptor superfamily revealed by the 2.4 Å crystal structure of the extracellular domain of the rabbit tissue factor. Protein Sci 7:1106-1115.
    • (1998) Protein Sci , vol.7 , pp. 1106-1115
    • Muller, Y.1    Kelley, R.F.2    De Vos, A.M.3
  • 38
    • 0033603002 scopus 로고    scopus 로고
    • Stopped-flow kinetic analysis of the ligand-induced coil-helix transition in glutathione S-transferase A1-I: Evidence for a persistent denatured state
    • Nieslanik BS, Dabrowski MJ, Lyon RP, Atkins WM. 1999. Stopped-flow kinetic analysis of the ligand-induced coil-helix transition in glutathione S-transferase A1-I: Evidence for a persistent denatured state. Biochemistry 38:6971-6980.
    • (1999) Biochemistry , vol.38 , pp. 6971-6980
    • Nieslanik, B.S.1    Dabrowski, M.J.2    Lyon, R.P.3    Atkins, W.M.4
  • 39
    • 0029089732 scopus 로고
    • Molecular surface complementarity at protein-protein interfaces: The critical role played by surface normals at well placed, sparse, points in docking
    • Norel R, Lin SL, Wolfson H, Nussinov R. 1995. Molecular surface complementarity at protein-protein interfaces: The critical role played by surface normals at well placed, sparse, points in docking. J Mol Biol 252:263-273.
    • (1995) J Mol Biol , vol.252 , pp. 263-273
    • Norel, R.1    Lin, S.L.2    Wolfson, H.3    Nussinov, R.4
  • 40
    • 0033566576 scopus 로고    scopus 로고
    • Examination of shape complementarity in docking of unbound proteins
    • Norel R, Petrey D, Wolfson H, Nussinov R. 1999. Examination of shape complementarity in docking of unbound proteins. Proteins 36:307-317.
    • (1999) Proteins , vol.36 , pp. 307-317
    • Norel, R.1    Petrey, D.2    Wolfson, H.3    Nussinov, R.4
  • 41
    • 0030322669 scopus 로고
    • Protein folding funnels: The nature of the transition state ensemble
    • Onuchic JN, Socci ND, Luthey-Schulten Z, Wolynes PG. 1446. Protein folding funnels: The nature of the transition state ensemble. Fold Des 1:441-450.
    • (1446) Fold Des , vol.1 , pp. 441-450
    • Onuchic, J.N.1    Socci, N.D.2    Luthey-Schulten, Z.3    Wolynes, P.G.4
  • 43
    • 0032502839 scopus 로고    scopus 로고
    • Contact order, transition state placement and the refolding rates of single domain proteins
    • Plaxco KW, Simons KT, Baker D. 1998. Contact order, transition state placement and the refolding rates of single domain proteins. J. Mol Biol 277:985-994.
    • (1998) J. Mol Biol , vol.277 , pp. 985-994
    • Plaxco, K.W.1    Simons, K.T.2    Baker, D.3
  • 44
    • 0032989351 scopus 로고    scopus 로고
    • Observations of strange kinetics in protein folding
    • Sabelko J, Ervin J, Gruebele M. 1999. Observations of strange kinetics in protein folding. Proc Natl Acad Sci USA 96:6031-6036.
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 6031-6036
    • Sabelko, J.1    Ervin, J.2    Gruebele, M.3
  • 46
    • 0030756534 scopus 로고    scopus 로고
    • Protein memory through altered folding mediated by intramolecular chaperones
    • Shinde UP, Liu JJ, Inoye M. 1997. Protein memory through altered folding mediated by intramolecular chaperones. Nature 389:520-522.
    • (1997) Nature , vol.389 , pp. 520-522
    • Shinde, U.P.1    Liu, J.J.2    Inoye, M.3
  • 48
    • 0032948128 scopus 로고    scopus 로고
    • Analysis of long-range interactions in a model denatured state of staphylococcal nuclease based on correlated changes in backbone dynamics
    • Sinclair JF, Shortle D. 1999. Analysis of long-range interactions in a model denatured state of staphylococcal nuclease based on correlated changes in backbone dynamics. Protein Sci 8:991-1000.
    • (1999) Protein Sci , vol.8 , pp. 991-1000
    • Sinclair, J.F.1    Shortle, D.2
  • 49
    • 0030920782 scopus 로고    scopus 로고
    • G protein mechanisms: Insights from structural analysis
    • Sprang SR. 1997. G protein mechanisms: Insights from structural analysis. Ann Rev Biochem 66:639-678.
    • (1997) Ann Rev Biochem , vol.66 , pp. 639-678
    • Sprang, S.R.1
  • 51
    • 0033181015 scopus 로고    scopus 로고
    • The effects of inhibitor binding on the structural stability and cooperatively of the HIV-1 protease
    • Todd MJ, Freire E. 1999. The effects of inhibitor binding on the structural stability and cooperatively of the HIV-1 protease. Proteins 36:147-156.
    • (1999) Proteins , vol.36 , pp. 147-156
    • Todd, M.J.1    Freire, E.2
  • 52
    • 0033056708 scopus 로고    scopus 로고
    • Folding funnels, binding funnels and protein function
    • Tsai CJ, Kumar S, Ma B, Nussinov R. 1999a. Folding funnels, binding funnels and protein function. Protein Sci 8:1181-1190.
    • (1999) Protein Sci , vol.8 , pp. 1181-1190
    • Tsai, C.J.1    Kumar, S.2    Ma, B.3    Nussinov, R.4
  • 53
    • 0033621104 scopus 로고    scopus 로고
    • Folding and binding cascades: Shifts in energy landscapes
    • Tsai CJ, Ma B, Nussinov R. 1999b. Folding and binding cascades: Shifts in energy landscapes. Proc Natl Acad Sci USA 96:9970-9972.
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 9970-9972
    • Tsai, C.J.1    Ma, B.2    Nussinov, R.3
  • 54
    • 0032777204 scopus 로고    scopus 로고
    • Distinguishing between sequential and nonsequentially folded proteins: Implications for folding and misfolding
    • Tsai CJ, Maizel JV, Nussinov R. 1999c. Distinguishing between sequential and nonsequentially folded proteins: Implications for folding and misfolding. Protein Sci 8:1591-1604.
    • (1999) Protein Sci , vol.8 , pp. 1591-1604
    • Tsai, C.J.1    Maizel, J.V.2    Nussinov, R.3
  • 55
    • 0031868211 scopus 로고    scopus 로고
    • Protein folding via binding, and vice versa
    • Tsai CJ, Xu D, Nussinov R. 1998. Protein folding via binding, and vice versa. Fold Des 3:R71-R80.
    • (1998) Fold Des , vol.3
    • Tsai, C.J.1    Xu, D.2    Nussinov, R.3
  • 56
    • 0029644728 scopus 로고
    • Movie of the structural changes during a catalytic cycle of nucleoside monophosphate kinases
    • Vonrhein C, Schlauderer GJ, Schulz GE. 1995. Movie of the structural changes during a catalytic cycle of nucleoside monophosphate kinases. Structure 3:483-490.
    • (1995) Structure , vol.3 , pp. 483-490
    • Vonrhein, C.1    Schlauderer, G.J.2    Schulz, G.E.3
  • 58
    • 0029968247 scopus 로고    scopus 로고
    • Global changes in amide hydrogen exchange rates for a protein antigen in complex with three different antibodies
    • Williams DC, Benjamin DC, Poljak RJ, Rule GS. 1996. Global changes in amide hydrogen exchange rates for a protein antigen in complex with three different antibodies. J Mol Biol 257:866-876.
    • (1996) J Mol Biol , vol.257 , pp. 866-876
    • Williams, D.C.1    Benjamin, D.C.2    Poljak, R.J.3    Rule, G.S.4


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