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Volumn 387, Issue 4, 2009, Pages 993-1001

Downhill versus Barrier-Limited Folding of BBL. 3. Heterogeneity of the Native State of the BBL Peripheral Subunit Binding Domain and Its Implications for Folding Mechanisms

Author keywords

conformational heterogeneity; downhill; protein folding; simulation

Indexed keywords

BBL 3 PROTEIN; HISTIDINE; PROTEIN DERIVATIVE; PROTEIN SUBUNIT; PYRUVATE DEHYDROGENASE; SOLVENT; UNCLASSIFIED DRUG;

EID: 62649107589     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2009.02.014     Document Type: Article
Times cited : (14)

References (41)
  • 1
    • 0015859467 scopus 로고
    • Principles that govern folding of protein chains
    • Anfinsen C.B. Principles that govern folding of protein chains. Science 181 (1973) 223-230
    • (1973) Science , vol.181 , pp. 223-230
    • Anfinsen, C.B.1
  • 4
    • 3242677702 scopus 로고    scopus 로고
    • A simple thermodynamic test to discriminate between two-state and downhill folding
    • Oliva F.Y., and Munoz V. A simple thermodynamic test to discriminate between two-state and downhill folding. J. Am. Chem. Soc. 126 (2004) 8596-8597
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 8596-8597
    • Oliva, F.Y.1    Munoz, V.2
  • 5
    • 18844421130 scopus 로고    scopus 로고
    • Robustness of downhill folding: guidelines for the analysis of equilibrium folding experiments on small proteins
    • Naganathan A.N., Perez-Jimenez R., Sanchez-Ruiz J.M., and Munoz V. Robustness of downhill folding: guidelines for the analysis of equilibrium folding experiments on small proteins. Biochemistry 44 (2005) 7435-7449
    • (2005) Biochemistry , vol.44 , pp. 7435-7449
    • Naganathan, A.N.1    Perez-Jimenez, R.2    Sanchez-Ruiz, J.M.3    Munoz, V.4
  • 6
    • 33746102627 scopus 로고    scopus 로고
    • Atom-by-atom analysis of global downhill protein folding
    • Sadqi M., Fushman D., and Munoz V. Atom-by-atom analysis of global downhill protein folding. Nature 442 (2006) 317-321
    • (2006) Nature , vol.442 , pp. 317-321
    • Sadqi, M.1    Fushman, D.2    Munoz, V.3
  • 7
    • 0014958182 scopus 로고
    • Stereochemistry of cooperative effects in haemoglobin: haem-haem interaction and the problem of allostery
    • Perutz M.F. Stereochemistry of cooperative effects in haemoglobin: haem-haem interaction and the problem of allostery. Nature 228 (1970) 726-734
    • (1970) Nature , vol.228 , pp. 726-734
    • Perutz, M.F.1
  • 8
    • 0015223374 scopus 로고
    • Equilibrium and rate constants for the interconversion of two conformations of α-chymotrypsin: the existence of a catalytically inactive conformation at neutral pH
    • Fersht A.R., and Requena Y. Equilibrium and rate constants for the interconversion of two conformations of α-chymotrypsin: the existence of a catalytically inactive conformation at neutral pH. J. Mol. Biol. 60 (1971) 279-290
    • (1971) J. Mol. Biol. , vol.60 , pp. 279-290
    • Fersht, A.R.1    Requena, Y.2
  • 9
    • 0014757455 scopus 로고
    • Nuclear magnetic resonance studies of the structure and binding sites of enzymes: XII. A conformational equilibrium in staphylococcal nuclease involving a histidine residue
    • Markley J.L., Williams M.N., and Jardetzky O. Nuclear magnetic resonance studies of the structure and binding sites of enzymes: XII. A conformational equilibrium in staphylococcal nuclease involving a histidine residue. Proc. Natl Acad. Sci. USA 65 (1970) 645-651
    • (1970) Proc. Natl Acad. Sci. USA , vol.65 , pp. 645-651
    • Markley, J.L.1    Williams, M.N.2    Jardetzky, O.3
  • 10
    • 38049063892 scopus 로고    scopus 로고
    • Folding and unfolding mechanism of highly stable full-consensus ankyrin repeat proteins
    • Wetzel S.K., Settanni G., Kenig M., Binz H.K., and Plückthun A. Folding and unfolding mechanism of highly stable full-consensus ankyrin repeat proteins. J. Mol. Biol. 376 (2008) 241-257
    • (2008) J. Mol. Biol. , vol.376 , pp. 241-257
    • Wetzel, S.K.1    Settanni, G.2    Kenig, M.3    Binz, H.K.4    Plückthun, A.5
  • 12
  • 14
    • 0026578578 scopus 로고
    • Three-dimensional solution structure of the E3-binding domain of the dihydrolipoamide succinyltransferase core from the 2-oxoglutarate dehydrogenase multienzyme complex of Escherichia coli
    • Robien M.A., Clore G.M., Omichinski J.G., Perham R.N., Appella E., Sakaguchi K., and Gronenborn A.M. Three-dimensional solution structure of the E3-binding domain of the dihydrolipoamide succinyltransferase core from the 2-oxoglutarate dehydrogenase multienzyme complex of Escherichia coli. Biochemistry 31 (1992) 3463-3471
    • (1992) Biochemistry , vol.31 , pp. 3463-3471
    • Robien, M.A.1    Clore, G.M.2    Omichinski, J.G.3    Perham, R.N.4    Appella, E.5    Sakaguchi, K.6    Gronenborn, A.M.7
  • 15
    • 34250012657 scopus 로고    scopus 로고
    • Downhill versus two-state protein folding in a statistical mechanical model
    • Bruscolini P., Pelizzola A., and Zamparo M. Downhill versus two-state protein folding in a statistical mechanical model. J. Chem. Phys. 126 (2007) 215103
    • (2007) J. Chem. Phys. , vol.126 , pp. 215103
    • Bruscolini, P.1    Pelizzola, A.2    Zamparo, M.3
  • 16
    • 40649105020 scopus 로고    scopus 로고
    • Cooperative folding kinetics of BBL protein and peripheral subunit-binding domain homologues
    • Yu W., Chung K., Cheon M., Heo M., Han K.H., Ham S., and Chang I. Cooperative folding kinetics of BBL protein and peripheral subunit-binding domain homologues. Proc. Natl Acad. Sci. USA 105 (2008) 2397-2402
    • (2008) Proc. Natl Acad. Sci. USA , vol.105 , pp. 2397-2402
    • Yu, W.1    Chung, K.2    Cheon, M.3    Heo, M.4    Han, K.H.5    Ham, S.6    Chang, I.7
  • 17
    • 33645019703 scopus 로고    scopus 로고
    • Folding with downhill behavior and low cooperativity of proteins
    • Zuo G.H., Wang J., and Wang W. Folding with downhill behavior and low cooperativity of proteins. Proteins: Struct., Funct., Bioinf. 63 (2006) 165-173
    • (2006) Proteins: Struct., Funct., Bioinf. , vol.63 , pp. 165-173
    • Zuo, G.H.1    Wang, J.2    Wang, W.3
  • 18
  • 19
    • 0029155772 scopus 로고
    • Impact of local and non-local interactions on thermodynamics and kinetics of protein folding
    • Abkevich V.I., Gutin A.M., and Shakhnovich E.I. Impact of local and non-local interactions on thermodynamics and kinetics of protein folding. J. Mol. Biol. 252 (1995) 460-471
    • (1995) J. Mol. Biol. , vol.252 , pp. 460-471
    • Abkevich, V.I.1    Gutin, A.M.2    Shakhnovich, E.I.3
  • 21
    • 45849119074 scopus 로고    scopus 로고
    • Observation of noncooperative folding thermodynamics in simulations of 1BBL
    • Pitera J.W., Swope W.C., and Abraham F.F. Observation of noncooperative folding thermodynamics in simulations of 1BBL. Biophys. J. 94 (2008) 4837-4846
    • (2008) Biophys. J. , vol.94 , pp. 4837-4846
    • Pitera, J.W.1    Swope, W.C.2    Abraham, F.F.3
  • 22
    • 0029619259 scopus 로고
    • Knowledge-based protein secondary structure assignment
    • Frishman D., and Argos P. Knowledge-based protein secondary structure assignment. Proteins: Struct., Funct., Bioinf. 23 (1995) 566-579
    • (1995) Proteins: Struct., Funct., Bioinf. , vol.23 , pp. 566-579
    • Frishman, D.1    Argos, P.2
  • 25
    • 0015505502 scopus 로고
    • Conformational equilibria in alpha-chymotrypsin and delta-chymotrypsin-energetics and importance of salt bridge
    • Fersht A.R. Conformational equilibria in alpha-chymotrypsin and delta-chymotrypsin-energetics and importance of salt bridge. J. Mol. Biol. 64 (1972) 497-509
    • (1972) J. Mol. Biol. , vol.64 , pp. 497-509
    • Fersht, A.R.1
  • 28
    • 62649174053 scopus 로고    scopus 로고
    • Downhill versus barrier-limited folding of BBL: 2. Mechanistic insights from kinetics of folding monitored by independent tryptophan probes
    • Neuweiler H., Sharpe T.D., Johnson C.M., Teufel D.P., Ferguson N., and Fersht A.R. Downhill versus barrier-limited folding of BBL: 2. Mechanistic insights from kinetics of folding monitored by independent tryptophan probes. J. Mol. Biol. 387 (2009) 975-985
    • (2009) J. Mol. Biol. , vol.387 , pp. 975-985
    • Neuweiler, H.1    Sharpe, T.D.2    Johnson, C.M.3    Teufel, D.P.4    Ferguson, N.5    Fersht, A.R.6
  • 29
    • 11144223201 scopus 로고    scopus 로고
    • Exploring protein-folding ensembles: a variable-barrier model for the analysis of equilibrium unfolding experiments
    • Munoz V., and Sanchez-Ruiz J.M. Exploring protein-folding ensembles: a variable-barrier model for the analysis of equilibrium unfolding experiments. Proc. Natl Acad. Sci. USA 101 (2004) 17646-17651
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 17646-17651
    • Munoz, V.1    Sanchez-Ruiz, J.M.2
  • 30
    • 57049130977 scopus 로고    scopus 로고
    • Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multienzyme complex
    • Pei X.Y., Titman C.M., Frank R.A., Leeper F.J., and Luisi B.F. Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multienzyme complex. Structure 16 (2008) 1860-1872
    • (2008) Structure , vol.16 , pp. 1860-1872
    • Pei, X.Y.1    Titman, C.M.2    Frank, R.A.3    Leeper, F.J.4    Luisi, B.F.5
  • 32
    • 0035789518 scopus 로고    scopus 로고
    • GROMACS 3.0: a package for molecular simulation and trajectory analysis
    • Lindahl E., Hess B., and van der Spoel D. GROMACS 3.0: a package for molecular simulation and trajectory analysis. J. Mol. Med. 7 (2001) 306-317
    • (2001) J. Mol. Med. , vol.7 , pp. 306-317
    • Lindahl, E.1    Hess, B.2    van der Spoel, D.3
  • 33
    • 0029912748 scopus 로고    scopus 로고
    • Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
    • Jorgensen W.L., Maxwell D.S., and Tirado-Rives J. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J. Am. Chem. Soc. 118 (1996) 11225-11236
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 11225-11236
    • Jorgensen, W.L.1    Maxwell, D.S.2    Tirado-Rives, J.3
  • 34
    • 1242346370 scopus 로고
    • The missing term in effective pair potentials
    • Grigera J.R., and Straatsma T.P. The missing term in effective pair potentials. J. Phys. Chem. 91 (1987) 6269-6271
    • (1987) J. Phys. Chem. , vol.91 , pp. 6269-6271
    • Grigera, J.R.1    Straatsma, T.P.2
  • 35
    • 33846823909 scopus 로고
    • Particle mesh Ewald-an N·log(N) method for Ewald sums in large systems
    • Darden T., York D., and Pedersen L. Particle mesh Ewald-an N·log(N) method for Ewald sums in large systems. J. Chem. Phys. 98 (1993) 10089-10092
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 39
    • 35748935079 scopus 로고    scopus 로고
    • Wordom: a program for efficient analysis of molecular dynamics simulations
    • Seeber M., Cecchini M., Rao F., Settanni G., and Caflisch A. Wordom: a program for efficient analysis of molecular dynamics simulations. Bioinformatics 23 (2007) 2625-2627
    • (2007) Bioinformatics , vol.23 , pp. 2625-2627
    • Seeber, M.1    Cecchini, M.2    Rao, F.3    Settanni, G.4    Caflisch, A.5
  • 40
    • 0036428782 scopus 로고    scopus 로고
    • Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing
    • Zagrovic B., Snow C.D., Shirts M.R., and Pande V.S. Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing. J. Mol. Biol. 323 (2002) 927-937
    • (2002) J. Mol. Biol. , vol.323 , pp. 927-937
    • Zagrovic, B.1    Snow, C.D.2    Shirts, M.R.3    Pande, V.S.4
  • 41
    • 44849116304 scopus 로고    scopus 로고
    • High temperature unfolding simulations of the TRPZ1 peptide
    • Settanni G., and Fersht A.R. High temperature unfolding simulations of the TRPZ1 peptide. Biophys. J. 94 (2008) 4444-4453
    • (2008) Biophys. J. , vol.94 , pp. 4444-4453
    • Settanni, G.1    Fersht, A.R.2


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