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Volumn 18, Issue 1, 2008, Pages 4-9

Combining experiment and simulation in protein folding: closing the gap for small model systems

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

EID: 39149104002     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.sbi.2007.11.007     Document Type: Review
Times cited : (89)

References (54)
  • 1
    • 0028143603 scopus 로고
    • Characterization of the transition state of protein unfolding by use of molecular dynamics: chymotrypsin inhibitor 2
    • Li A., and Daggett V. Characterization of the transition state of protein unfolding by use of molecular dynamics: chymotrypsin inhibitor 2. Proc Natl Acad Sci U S A 91 (1994) 10430-10434
    • (1994) Proc Natl Acad Sci U S A , vol.91 , pp. 10430-10434
    • Li, A.1    Daggett, V.2
  • 2
    • 2342451295 scopus 로고    scopus 로고
    • Transition states for protein folding have native topologies despite high structural variability
    • Lindorff-Larsen K., Vendruscolo M., Paci E., and Dobson C.M. Transition states for protein folding have native topologies despite high structural variability. Nat Struct Mol Biol 11 (2004) 443-449
    • (2004) Nat Struct Mol Biol , vol.11 , pp. 443-449
    • Lindorff-Larsen, K.1    Vendruscolo, M.2    Paci, E.3    Dobson, C.M.4
  • 3
    • 24644481440 scopus 로고    scopus 로고
    • A funneled energy landscape for cytochrome c directly predicts the sequential folding route inferred from hydrogen exchange experiments
    • Weinkam P., Zong C., and Wolynes P.G. A funneled energy landscape for cytochrome c directly predicts the sequential folding route inferred from hydrogen exchange experiments. Proc Natl Acad Sci 102 (2005) 12401-12406
    • (2005) Proc Natl Acad Sci , vol.102 , pp. 12401-12406
    • Weinkam, P.1    Zong, C.2    Wolynes, P.G.3
  • 4
    • 33747065536 scopus 로고    scopus 로고
    • Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: structure-based molecular dynamics simulations
    • Okazaki K.-i., Koga N., Takada S., Onuchic J.N., and Wolynes P.G. Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: structure-based molecular dynamics simulations. Proc Natl Acad Sci 103 (2006) 11844-11849
    • (2006) Proc Natl Acad Sci , vol.103 , pp. 11844-11849
    • Okazaki, K.-i.1    Koga, N.2    Takada, S.3    Onuchic, J.N.4    Wolynes, P.G.5
  • 5
    • 30044442528 scopus 로고    scopus 로고
    • High-resolution protein folding with a transferable potential
    • Hubner I.A., Deeds E.J., and Shakhnovich E.I. High-resolution protein folding with a transferable potential. Proc Natl Acad Sci 102 (2005) 18914-18919
    • (2005) Proc Natl Acad Sci , vol.102 , pp. 18914-18919
    • Hubner, I.A.1    Deeds, E.J.2    Shakhnovich, E.I.3
  • 6
    • 34547507851 scopus 로고    scopus 로고
    • Effects of crowding and confinement on the structures of the transition state ensemble in proteins
    • Cheung M.S., and Thirumalai D. Effects of crowding and confinement on the structures of the transition state ensemble in proteins. J Phys Chem B 111 (2007) 8250-8257
    • (2007) J Phys Chem B , vol.111 , pp. 8250-8257
    • Cheung, M.S.1    Thirumalai, D.2
  • 7
    • 4344707281 scopus 로고    scopus 로고
    • Unfolded proteins and protein folding studied by NMR
    • Dyson H.J., and Wright P.E. Unfolded proteins and protein folding studied by NMR. Chem Rev 104 (2004) 3607-3622
    • (2004) Chem Rev , vol.104 , pp. 3607-3622
    • Dyson, H.J.1    Wright, P.E.2
  • 9
    • 4644238629 scopus 로고    scopus 로고
    • On the interpretation of residual dipolar couplings as reporters of molecular dynamics
    • Fredriksson K., Louhivuori M., Permi P., and Annila A. On the interpretation of residual dipolar couplings as reporters of molecular dynamics. J Am Chem Soc 126 (2004) 12646-12650
    • (2004) J Am Chem Soc , vol.126 , pp. 12646-12650
    • Fredriksson, K.1    Louhivuori, M.2    Permi, P.3    Annila, A.4
  • 10
    • 0033654297 scopus 로고    scopus 로고
    • Generalized born models of macromolecular solvation effects
    • Bashford D., and Case D.A. Generalized born models of macromolecular solvation effects. Annu Rev Phys Chem 51 (2000) 129-152
    • (2000) Annu Rev Phys Chem , vol.51 , pp. 129-152
    • Bashford, D.1    Case, D.A.2
  • 11
    • 0032506017 scopus 로고    scopus 로고
    • Limited internal friction in the rate-limiting step of a two-state protein folding reaction
    • Plaxco K.W., and Baker D. Limited internal friction in the rate-limiting step of a two-state protein folding reaction. Proc Natl Acad Sci 95 (1998) 13591-13596
    • (1998) Proc Natl Acad Sci , vol.95 , pp. 13591-13596
    • Plaxco, K.W.1    Baker, D.2
  • 13
    • 33645722974 scopus 로고    scopus 로고
    • Convergence of replica exchange molecular dynamics
    • Zhang W., Wu C., and Duan Y. Convergence of replica exchange molecular dynamics. J Chem Phys 123 (2005)
    • (2005) J Chem Phys , vol.123
    • Zhang, W.1    Wu, C.2    Duan Y3
  • 14
    • 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. Formation of the folding nucleus of an SH3 domain investigated by loosely coupled molecular dynamics simulations. Biophys J 86 (2004) 1691-1701
    • (2004) Biophys J , vol.86 , pp. 1691-1701
    • Settanni, G.1    Gsponer, J.2    Caflisch, A.3
  • 17
    • 23744502246 scopus 로고    scopus 로고
    • Is there or isn't there? The case for (and against) residual structure in chemically denatured proteins
    • McCarney E.R., Kohn J.E., and Plaxco K.W. Is there or isn't there? The case for (and against) residual structure in chemically denatured proteins. Crit Rev Biochem Mol Biol 40 (2005) 181-189
    • (2005) Crit Rev Biochem Mol Biol , vol.40 , pp. 181-189
    • McCarney, E.R.1    Kohn, J.E.2    Plaxco, K.W.3
  • 18
    • 33846839535 scopus 로고    scopus 로고
    • Characterizing the unfolded states of proteins using single-molecule FRET spectroscopy and molecular simulations
    • Merchant K.A., Best R.B., Louis J.M., Gopich I.V., and Eaton W.A. Characterizing the unfolded states of proteins using single-molecule FRET spectroscopy and molecular simulations. Proc Natl Acad Sci U S A 104 (2007) 1528-1533
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 1528-1533
    • Merchant, K.A.1    Best, R.B.2    Louis, J.M.3    Gopich, I.V.4    Eaton, W.A.5
  • 19
    • 0032978994 scopus 로고    scopus 로고
    • Chain collapse can occur concomitantly with the rate-limiting step in protein folding
    • Plaxco K.W., Millett I.S., Segel D.J., Doniach S., and Baker D. Chain collapse can occur concomitantly with the rate-limiting step in protein folding. Nat Struct Mol Biol 6 (1999) 554-556
    • (1999) Nat Struct Mol Biol , vol.6 , pp. 554-556
    • Plaxco, K.W.1    Millett, I.S.2    Segel, D.J.3    Doniach, S.4    Baker, D.5
  • 20
    • 33846381622 scopus 로고    scopus 로고
    • Direct observation of microscopic reversibility in single-molecule protein folding
    • Day R., and Daggett V. Direct observation of microscopic reversibility in single-molecule protein folding. J Mol Biol 366 (2007) 677-686
    • (2007) J Mol Biol , vol.366 , pp. 677-686
    • Day, R.1    Daggett, V.2
  • 21
    • 26444608613 scopus 로고    scopus 로고
    • Ensemble versus single-molecule protein unfolding
    • Day R., and Daggett V. Ensemble versus single-molecule protein unfolding. Proc Natl Acad Sci U S A 102 (2005) 13445-13450
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 13445-13450
    • Day, R.1    Daggett, V.2
  • 22
    • 0032561237 scopus 로고    scopus 로고
    • Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
    • Duan Y., and Kollman P.A. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science 282 (1998) 740-744
    • (1998) Science , vol.282 , pp. 740-744
    • Duan, Y.1    Kollman, P.A.2
  • 23
    • 0038054301 scopus 로고    scopus 로고
    • Experimental tests of villin subdomain folding simulations
    • Kubelka J., Eaton W.A., and Hofrichter J. Experimental tests of villin subdomain folding simulations. J Mol Biol 329 (2003) 625-630
    • (2003) J Mol Biol , vol.329 , pp. 625-630
    • Kubelka, J.1    Eaton, W.A.2    Hofrichter, J.3
  • 24
    • 0037174385 scopus 로고    scopus 로고
    • All-atom structure prediction and folding simulations of a stable protein
    • Simmerling C., Strockbine B., and Roitberg A.E. All-atom structure prediction and folding simulations of a stable protein. J Am Chem Soc 124 (2002) 11258-11259
    • (2002) J Am Chem Soc , vol.124 , pp. 11258-11259
    • Simmerling, C.1    Strockbine, B.2    Roitberg, A.E.3
  • 25
    • 34249298006 scopus 로고    scopus 로고
    • Two-stage folding of HP-35 from ab initio simulations
    • Lei H., and Duan Y. Two-stage folding of HP-35 from ab initio simulations. J Mol Biol 370 (2007) 196-206
    • (2007) J Mol Biol , vol.370 , pp. 196-206
    • Lei, H.1    Duan, Y.2
  • 26
    • 0036180616 scopus 로고    scopus 로고
    • The role of aromatic residues in the hydrophobic core of the villin headpiece subdomain
    • Frank B.S., Vardar D., Buckley D.A., and McKnight C.J. The role of aromatic residues in the hydrophobic core of the villin headpiece subdomain. Protein Sci 11 (2002) 680-687
    • (2002) Protein Sci , vol.11 , pp. 680-687
    • Frank, B.S.1    Vardar, D.2    Buckley, D.A.3    McKnight, C.J.4
  • 27
    • 34249807361 scopus 로고    scopus 로고
    • Ab initio folding of albumin binding domain from all-atom molecular dynamics simulation
    • Lei H., and Duan Y. Ab initio folding of albumin binding domain from all-atom molecular dynamics simulation. J Phys Chem B 111 (2007) 5458-5463
    • (2007) J Phys Chem B , vol.111 , pp. 5458-5463
    • Lei, H.1    Duan, Y.2
  • 29
    • 35648943228 scopus 로고    scopus 로고
    • D.L. Ensign, P.M. Kasson, V.S. Pande: Heterogeneity even at the speed limit of folding: large-scale molecular dynamics study of a fast-folding variant of the villin headpiece. J Mol Biol 2007, 374:806-816.
    • D.L. Ensign, P.M. Kasson, V.S. Pande: Heterogeneity even at the speed limit of folding: large-scale molecular dynamics study of a fast-folding variant of the villin headpiece. J Mol Biol 2007, 374:806-816.
  • 30
    • 35448930794 scopus 로고    scopus 로고
    • Molecular dynamics simulations from putative transition states of alpha-spectrin SH3 domain
    • Periole X., Vendruscolo M., and Mark A.E. Molecular dynamics simulations from putative transition states of alpha-spectrin SH3 domain. Proteins: Struct, Funct Bioinformat 69 (2007) 536-550
    • (2007) Proteins: Struct, Funct Bioinformat , vol.69 , pp. 536-550
    • Periole, X.1    Vendruscolo, M.2    Mark, A.E.3
  • 32
    • 33745606942 scopus 로고    scopus 로고
    • Phi-analysis at the experimental limits: mechanism of beta-hairpin formation
    • Petrovich M., Jonsson A.L., Ferguson N., Daggett V., and Fersht A.R. 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
  • 33
    • 34748919075 scopus 로고    scopus 로고
    • The role of the turn in beta-hairpin formation during WW domain folding
    • Sharpe T., Jonsson A.L., Rutherford T.J., Daggett V., and Fersht A.R. The role of the turn in beta-hairpin formation during WW domain folding. Protein Sci 16 (2007) 2233-2239
    • (2007) Protein Sci , vol.16 , pp. 2233-2239
    • Sharpe, T.1    Jonsson, A.L.2    Rutherford, T.J.3    Daggett, V.4    Fersht, A.R.5
  • 35
  • 36
    • 34748874234 scopus 로고    scopus 로고
    • A cross-strand Trp Trp pair stabilizes the hPin1 WW domain at the expense of function
    • Jager M., Dendle M., Fuller A.A., and Kelly J.W. A cross-strand Trp Trp pair stabilizes the hPin1 WW domain at the expense of function. Protein Sci 16 (2007) 2306-2313
    • (2007) Protein Sci , vol.16 , pp. 2306-2313
    • Jager, M.1    Dendle, M.2    Fuller, A.A.3    Kelly, J.W.4
  • 38
    • 0037221599 scopus 로고    scopus 로고
    • Is there a unifying mechanism for protein folding?
    • Daggett V., and Fersht A.R. Is there a unifying mechanism for protein folding?. Trends Biochem Sci 28 (2003) 18-25
    • (2003) Trends Biochem Sci , vol.28 , pp. 18-25
    • Daggett, V.1    Fersht, A.R.2
  • 39
    • 20544462511 scopus 로고    scopus 로고
    • Simulation and experiment conspire to reveal cryptic intermediates and a slide from the nucleation-condensation to framework mechanism of folding
    • White G.W., Gianni S., Grossmann J.G., Jemth P., Fersht A.R., and Daggett V. Simulation and experiment conspire to reveal cryptic intermediates and a slide from the 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.1    Gianni, S.2    Grossmann, J.G.3    Jemth, P.4    Fersht, A.R.5    Daggett, V.6
  • 40
    • 27144532135 scopus 로고    scopus 로고
    • Solution structure of a protein denatured state and folding intermediate
    • Religa T.L., Markson J.S., Mayor U., Freund S.M., and Fersht A.R. 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
  • 41
    • 34547151184 scopus 로고    scopus 로고
    • The helix-turn-helix motif as an ultrafast independently folding domain: the pathway of folding of Engrailed homeodomain
    • Religa T.L., Johnson C.M., Vu D.M., Brewer S.H., Dyer R.B., and Fersht A.R. The helix-turn-helix motif as an ultrafast independently folding domain: the pathway of folding of Engrailed homeodomain. Proc Natl Acad Sci U S A 104 (2007) 9272-9277
    • (2007) Proc Natl Acad Sci U S A , 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
  • 42
    • 33845189399 scopus 로고    scopus 로고
    • Understanding ensemble protein folding at atomic detail
    • Hubner I.A., Deeds E.J., and Shakhnovich E.I. Understanding ensemble protein folding at atomic detail. Proc Natl Acad Sci 103 (2006) 17747-17752
    • (2006) Proc Natl Acad Sci , vol.103 , pp. 17747-17752
    • Hubner, I.A.1    Deeds, E.J.2    Shakhnovich, E.I.3
  • 43
    • 0034610360 scopus 로고    scopus 로고
    • Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation
    • Mayor U., Johnson C.M., Daggett V., and Fersht A.R. Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation. Proc Natl Acad Sci U S A 97 (2000) 13518-13522
    • (2000) Proc Natl Acad Sci U S A , vol.97 , pp. 13518-13522
    • Mayor, U.1    Johnson, C.M.2    Daggett, V.3    Fersht, A.R.4
  • 44
    • 0028868995 scopus 로고
    • The structure of the transition state for folding of chymotrypsin inhibitor 2 analysed by protein engineering methods: evidence for a nucleation-condensation mechanism for protein folding
    • Itzhaki L.S., Otzen D.E., and Fersht A.R. The structure of the transition state for folding of chymotrypsin inhibitor 2 analysed by protein engineering methods: evidence for a nucleation-condensation mechanism for protein folding. J Mol Biol 254 (1995) 260-288
    • (1995) J Mol Biol , vol.254 , pp. 260-288
    • Itzhaki, L.S.1    Otzen, D.E.2    Fersht, A.R.3
  • 45
    • 0027948175 scopus 로고
    • Structure of the transition state for the folding/unfolding of the barley chymotrypsin inhibitor 2 and its implications for mechanisms of protein folding
    • Otzen D.E., Itzhaki L.S., ElMasry N.F., Jackson S.E., and Fersht A.R. Structure of the transition state for the folding/unfolding of the barley chymotrypsin inhibitor 2 and its implications for mechanisms of protein folding. Proc Natl Acad Sci 91 (1994) 10422-10425
    • (1994) Proc Natl Acad Sci , vol.91 , pp. 10422-10425
    • Otzen, D.E.1    Itzhaki, L.S.2    ElMasry, N.F.3    Jackson, S.E.4    Fersht, A.R.5
  • 48
    • 4143080376 scopus 로고    scopus 로고
    • Trapping the on-pathway folding intermediate of Im7 at equilibrium
    • Spence G.R., Capaldi A.P., and Radford S.E. Trapping the on-pathway folding intermediate of Im7 at equilibrium. J Mol Biol 341 (2004) 215-226
    • (2004) J Mol Biol , vol.341 , pp. 215-226
    • Spence, G.R.1    Capaldi, A.P.2    Radford, S.E.3
  • 51
    • 27444434259 scopus 로고    scopus 로고
    • Directed evolution of highly homologous proteins with different folds by phage display: implications for the protein folding code
    • Alexander P.A., Rozak D.A., Orban J., and Bryan P.N. Directed evolution of highly homologous proteins with different folds by phage display: implications for the protein folding code. Biochemistry 44 (2005) 14045-14054
    • (2005) Biochemistry , vol.44 , pp. 14045-14054
    • Alexander, P.A.1    Rozak, D.A.2    Orban, J.3    Bryan, P.N.4
  • 52
    • 33846985596 scopus 로고    scopus 로고
    • Folding mechanisms of proteins with high sequence identity but different folds
    • Scott K.A., and Daggett V. Folding mechanisms of proteins with high sequence identity but different folds. Biochemistry 46 (2007) 1545-1556
    • (2007) Biochemistry , vol.46 , pp. 1545-1556
    • Scott, K.A.1    Daggett, V.2
  • 54
    • 33745764034 scopus 로고    scopus 로고
    • Structural comparison of the two alternative transition states for folding of TI I27
    • Geierhaas C.D., Best R.B., Paci E., Vendruscolo M., and Clarke J. Structural comparison of the two alternative transition states for folding of TI I27. Biophys J 91 (2006) 263-275
    • (2006) Biophys J , vol.91 , pp. 263-275
    • Geierhaas, C.D.1    Best, R.B.2    Paci, E.3    Vendruscolo, M.4    Clarke, J.5


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