메뉴 건너뛰기




Volumn 15, Issue 4, 2006, Pages 843-852

Solvation of the folding-transition state in Pseudomonas aeruginosa azurin is modulated by metal

Author keywords

Circular dichroism; Conformational changes; Fluorescence; Kinetics; Molecular mechanics dynamics; Protein structure folding; Stability and mutagenesis

Indexed keywords

AZURIN; METAL; THREONINE; VALINE; WATER; ZINC;

EID: 33645514416     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1110/ps.051838206     Document Type: Article
Times cited : (14)

References (58)
  • 1
    • 0026411154 scopus 로고
    • Copper protein structures
    • Adman, E.T. 1991. Copper protein structures. Adv. Protein Chem. 42: 145-197.
    • (1991) Adv. Protein Chem. , vol.42 , pp. 145-197
    • Adman, E.T.1
  • 2
    • 3042988525 scopus 로고
    • Conformational analysis 130. MM2. A hydrocarbon force field utilizing V1 and V2 torsional terms
    • Allinger, N.L. 1977. Conformational analysis 130. MM2. A hydrocarbon force field utilizing V1 and V2 torsional terms. J. Am. Chem. Soc. 99: 8127-8134.
    • (1977) J. Am. Chem. Soc. , vol.99 , pp. 8127-8134
    • Allinger, N.L.1
  • 3
    • 0035895436 scopus 로고    scopus 로고
    • Apparent two-state tendamistat folding is a sequential process along a defined route
    • Bachmann, A. and Kiefhaber, T. 2001. Apparent two-state tendamistat folding is a sequential process along a defined route. J. Mol. Biol. 306: 375-386.
    • (2001) J. Mol. Biol. , vol.306 , pp. 375-386
    • Bachmann, A.1    Kiefhaber, T.2
  • 4
  • 5
    • 0036183221 scopus 로고    scopus 로고
    • Im7 folding mechanism: Misfolding on a path to the native state
    • Capaldi, A.P., Kleanthous, C., and Radford, S.E. 2002. Im7 folding mechanism: Misfolding on a path to the native state. Nat. Struct. Biol. 9: 209-216.
    • (2002) Nat. Struct. Biol. , vol.9 , pp. 209-216
    • Capaldi, A.P.1    Kleanthous, C.2    Radford, S.E.3
  • 6
    • 0037154268 scopus 로고    scopus 로고
    • Protein folding mediated by solvation: Water expulsion and formation of the hydrophobic core occur after the structural collapse
    • Cheung, M.S., Garcia, A.E., and Onuchic, J.N. 2002. Protein folding mediated by solvation: Water expulsion and formation of the hydrophobic core occur after the structural collapse. Proc. Natl. Acad. Sci. 99: 685-690.
    • (2002) Proc. Natl. Acad. Sci. , vol.99 , pp. 685-690
    • Cheung, M.S.1    Garcia, A.E.2    Onuchic, J.N.3
  • 8
    • 0031043161 scopus 로고    scopus 로고
    • Nucleation mechanisms in protein folding
    • Fersht, A.R. 1997. Nucleation mechanisms in protein folding. Curr. Opin. Struct. Biol. 7: 3-9.
    • (1997) Curr. Opin. Struct. Biol. , vol.7 , pp. 3-9
    • Fersht, A.R.1
  • 10
    • 2542599277 scopus 로고    scopus 로고
    • Φ-Value analysis and the nature of protein-folding transition states
    • Fersht, A.R. and Sato, S. 2004. Φ-Value analysis and the nature of protein-folding transition states. Proc. Natl. Acad. Sci. 101: 7976-7981.
    • (2004) Proc. Natl. Acad. Sci. , vol.101 , pp. 7976-7981
    • Fersht, A.R.1    Sato, S.2
  • 11
    • 4444289990 scopus 로고    scopus 로고
    • Conformational changes in azurin from Pseudomona aeruginosa induced through chemical and physical protocols
    • Fuentes, L., Oyola, J., Fernandez, M., and Quinones, E. 2004. Conformational changes in azurin from Pseudomona aeruginosa induced through chemical and physical protocols. Biophys. J. 87: 1873-1880.
    • (2004) Biophys. J. , vol.87 , pp. 1873-1880
    • Fuentes, L.1    Oyola, J.2    Fernandez, M.3    Quinones, E.4
  • 12
    • 0032707954 scopus 로고    scopus 로고
    • Finding the right fold
    • Goldenberg, D.P. 1999. Finding the right fold. Nat. Struct. Biol. 6: 987-990.
    • (1999) Nat. Struct. Biol. , vol.6 , pp. 987-990
    • Goldenberg, D.P.1
  • 13
    • 0031853167 scopus 로고    scopus 로고
    • Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain
    • 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: 714-720.
    • (1998) Nat. Struct. Biol. , vol.5 , pp. 714-720
    • Grantcharova, V.P.1    Riddle, D.S.2    Santiago, J.V.3    Baker, D.4
  • 15
    • 0031473847 scopus 로고    scopus 로고
    • SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling
    • Guex, N. and Peitsch, M.C. 1997. SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling. Electrophoresis 18: 2714-2723.
    • (1997) Electrophoresis , vol.18 , pp. 2714-2723
    • Guex, N.1    Peitsch, M.C.2
  • 16
    • 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: 61-69.
    • (2003) Biophys. J. , vol.85 , pp. 61-69
    • Guo, W.1    Lampoudi, S.2    Shea, J.E.3
  • 17
    • 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. 1995. 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: 260-288.
    • (1995) J. Mol. Biol. , vol.254 , pp. 260-288
    • Itzhaki, L.S.1    Otzen, D.E.2    Fersht, A.R.3
  • 18
    • 0031815749 scopus 로고    scopus 로고
    • How do small single-domain proteins fold?
    • Jackson, S.E. 1998. How do small single-domain proteins fold? Fold. Des. 3: R81-R91.
    • (1998) Fold. Des. , vol.3
    • Jackson, S.E.1
  • 19
    • 2542494929 scopus 로고    scopus 로고
    • Unification of the folding mechanisms of non-two-state and two-state proteins
    • Kamagata, K., Arai, M., and Kuwajima, K. 2004. Unification of the folding mechanisms of non-two-state and two-state proteins. J. Mol. Biol. 339: 951-965.
    • (2004) J. Mol. Biol. , vol.339 , pp. 951-965
    • Kamagata, K.1    Arai, M.2    Kuwajima, K.3
  • 20
    • 0034685619 scopus 로고    scopus 로고
    • A breakdown of symmetry in the folding transition state of protein L.
    • Kim, D.E., Fisher, C., and Baker, D. 2000. A breakdown of symmetry in the folding transition state of protein L. J. Mol. Biol. 298: 971-984.
    • (2000) J. Mol. Biol. , vol.298 , pp. 971-984
    • Kim, D.E.1    Fisher, C.2    Baker, D.3
  • 21
    • 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, B.B., Osmark, P., Neergaard, T.B., Schiodt, J., Kristiansen, K., Knudsen, J., and Poulsen, F.M. 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
  • 22
    • 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. 2004. Transition states for protein folding have native topologies despite high structural variability. Nat. Struct. Mol. Biol. 11: 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
  • 23
    • 0030334834 scopus 로고    scopus 로고
    • Structure of the transition state for folding of the 129 aa protein CheY resembles that of a smaller protein, CI-2
    • Lopez-Hernandez, E. and Serrano, L. 1996. Structure of the transition state for folding of the 129 aa protein CheY resembles that of a smaller protein, CI-2. Fold. Des. 1: 43-55.
    • (1996) Fold. Des. , vol.1 , pp. 43-55
    • Lopez-Hernandez, E.1    Serrano, L.2
  • 24
    • 2342485664 scopus 로고    scopus 로고
    • Methionine-121 coordination determines metal specificity in unfolded Pseudomonas aeruginosa azurin
    • Marks, J., Pozdnyakova, I., Guidry, J., and Wittung-Stafshede, P. 2004. Methionine-121 coordination determines metal specificity in unfolded Pseudomonas aeruginosa azurin. J. Biol. Inorg. Chem. 9: 281-288.
    • (2004) J. Biol. Inorg. Chem. , vol.9 , pp. 281-288
    • Marks, J.1    Pozdnyakova, I.2    Guidry, J.3    Wittung-Stafshede, P.4
  • 25
    • 0031825181 scopus 로고    scopus 로고
    • Obligatory steps in protein folding and the conformational diversity of the transition state
    • Martinez, J.C., Pisabarro, M.T., and Serrano, L. 1998. Obligatory steps in protein folding and the conformational diversity of the transition state. Nat. Struct. Biol. 5: 721-729.
    • (1998) Nat. Struct. Biol. , vol.5 , pp. 721-729
    • Martinez, J.C.1    Pisabarro, M.T.2    Serrano, L.3
  • 26
    • 0026354152 scopus 로고
    • Protein engineering in analysis of protein folding pathways and stability
    • Matouschek, A. and Fersht, A.R. 1991. Protein engineering in analysis of protein folding pathways and stability. Methods Enzymol. 202: 82-112.
    • (1991) Methods Enzymol. , vol.202 , pp. 82-112
    • Matouschek, A.1    Fersht, A.R.2
  • 27
    • 0025698613 scopus 로고
    • Transient folding intermediates characterized by protein engineering
    • Matouschek, A., Kellis Jr., J.T., Serrano, L., Bycroft, M., and Fersht, A.R. 1990. Transient folding intermediates characterized by protein engineering. Nature 346: 440-445.
    • (1990) Nature , vol.346 , pp. 440-445
    • Matouschek, A.1    Kellis Jr., J.T.2    Serrano, L.3    Bycroft, M.4    Fersht, A.R.5
  • 29
    • 0028882589 scopus 로고
    • P22 Arc repressor: Transition state properties inferred from mutational effects on the rates of protein unfolding and refolding
    • Milla, M.E., Brown, B.M., Waldburger, C.D., and Sauer, R.T. 1995. P22 Arc repressor: Transition state properties inferred from mutational effects on the rates of protein unfolding and refolding. Biochemistry 34: 13914-13919.
    • (1995) Biochemistry , vol.34 , pp. 13914-13919
    • Milla, M.E.1    Brown, B.M.2    Waldburger, C.D.3    Sauer, R.T.4
  • 30
    • 0026557819 scopus 로고
    • Characterization and crystal structure of zinc azurin, a by-product of heterologous expression in Escherichia coli of Pseudomonas aeruginosa copper azurin
    • Nar, H., Huber, R., Messerschmidt, A., Filippou, A.C., Barth, M., Jaquinod, M., van de Kamp, M., and Canters, G.W. 1992a. Characterization and crystal structure of zinc azurin, a by-product of heterologous expression in Escherichia coli of Pseudomonas aeruginosa copper azurin. Eur. J. Biochem. 205: 1123-1129.
    • (1992) Eur. J. Biochem. , vol.205 , pp. 1123-1129
    • Nar, H.1    Huber, R.2    Messerschmidt, A.3    Filippou, A.C.4    Barth, M.5    Jaquinod, M.6    Van De Kamp, M.7    Canters, G.W.8
  • 31
    • 0026642328 scopus 로고
    • Crystal structure of Pseudomonas aeruginosa apo-azurin at 1.85 Å resolution
    • Nar, H., Messerschmidt, A., Huber, R., van de Kamp, M., and Canters, G.W. 1992b. Crystal structure of Pseudomonas aeruginosa apo-azurin at 1.85 Å resolution. FEBS Lett. 306: 119-124.
    • (1992) FEBS Lett. , vol.306 , pp. 119-124
    • Nar, H.1    Messerschmidt, A.2    Huber, R.3    Van De Kamp, M.4    Canters, G.W.5
  • 32
    • 0036172116 scopus 로고    scopus 로고
    • Hydrophobic core packing in the SH3 domain folding transition state
    • Northey, J.G., Di Nardo, A.A., and Davidson, A.R. 2002. Hydrophobic core packing in the SH3 domain folding transition state. Nat. Struct. Biol. 9: 126-130.
    • (2002) Nat. Struct. Biol. , vol.9 , pp. 126-130
    • Northey, J.G.1    Di Nardo, A.A.2    Davidson, A.R.3
  • 33
    • 0033580679 scopus 로고    scopus 로고
    • Structural changes in the transition state of protein folding: Alternative interpretations of curved chevron plots
    • Otzen, D.E., Kristensen, O., Proctor, M., and Oliveberg, M. 1999. Structural changes in the transition state of protein folding: Alternative interpretations of curved chevron plots. Biochemistry 38: 6499-6511.
    • (1999) Biochemistry , vol.38 , pp. 6499-6511
    • Otzen, D.E.1    Kristensen, O.2    Proctor, M.3    Oliveberg, M.4
  • 34
    • 0033649068 scopus 로고    scopus 로고
    • Linear extrapolation method of analyzing solvent denaturation curves
    • Pace, C.N. and Shaw, K.L. 2000. Linear extrapolation method of analyzing solvent denaturation curves. Proteins Suppl. 4: 1-7.
    • (2000) Proteins , Issue.4 SUPPL. , pp. 1-7
    • Pace, C.N.1    Shaw, K.L.2
  • 35
    • 0035904453 scopus 로고    scopus 로고
    • Biological relevance of metal binding before protein folding
    • Pozdnyakova, I. and Wittung-Stafshede, P. 2001a. Biological relevance of metal binding before protein folding. J. Am. Chem. Soc. 123: 10135-10136.
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 10135-10136
    • Pozdnyakova, I.1    Wittung-Stafshede, P.2
  • 36
    • 0035856539 scopus 로고    scopus 로고
    • Copper binding before polypeptide folding speeds up formation of active (holo) Pseudomonas aeruginosa azurin
    • _. 2001b. Copper binding before polypeptide folding speeds up formation of active (holo) Pseudomonas aeruginosa azurin. Biochemistry 40: 13728-13733.
    • (2001) Biochemistry , vol.40 , pp. 13728-13733
  • 37
    • 1242341404 scopus 로고    scopus 로고
    • Approaching the speed limit for Greek Key β-barrel formation: Transition-state movement tunes folding rate of zinc-substituted azurin
    • _. 2003. Approaching the speed limit for Greek Key β-barrel formation: Transition-state movement tunes folding rate of zinc-substituted azurin. Biochim. Biophys. Acta 1651: 1-4.
    • (2003) Biochim. Biophys. Acta , vol.1651 , pp. 1-4
  • 39
    • 0036225868 scopus 로고    scopus 로고
    • Studies of Pseudomonas aeruginosa azurin mutants: Cavities in β-barrel do not affect refolding speed
    • _. 2002. Studies of Pseudomonas aeruginosa azurin mutants: Cavities in β-barrel do not affect refolding speed. Biophys. J. 82: 2645-2651.
    • (2002) Biophys. J. , vol.82 , pp. 2645-2651
  • 42
    • 0037225280 scopus 로고    scopus 로고
    • Evidence for sequential barriers and obligatory intermediates in apparent two-state protein folding
    • Sanchez, I.E. and Kiefhaber, T. 2003a. Evidence for sequential barriers and obligatory intermediates in apparent two-state protein folding. J. Mol. Biol. 325: 367-376.
    • (2003) J. Mol. Biol. , vol.325 , pp. 367-376
    • Sanchez, I.E.1    Kiefhaber, T.2
  • 43
    • 0037418635 scopus 로고    scopus 로고
    • Hammond behavior versus ground state effects in protein folding: Evidence for narrow free energy barriers and residual structure in unfolded states
    • _. 2003b. Hammond behavior versus ground state effects in protein folding: Evidence for narrow free energy barriers and residual structure in unfolded states. J. Mol. Biol. 327: 867-884.
    • (2003) J. Mol. Biol. , vol.327 , pp. 867-884
  • 44
    • 0037438623 scopus 로고    scopus 로고
    • Non-linear rate-equilibrium free energy relationships and Hammond behavior in protein folding
    • _. 2003c. Non-linear rate-equilibrium free energy relationships and Hammond behavior in protein folding. Biophys. Chem. 100: 397-407.
    • (2003) Biophys. Chem. , vol.100 , pp. 397-407
  • 45
    • 0345304461 scopus 로고    scopus 로고
    • Origin of unusual φ-values in protein folding: Evidence against specific nucleation sites
    • _. 2003d. Origin of unusual φ-values in protein folding: Evidence against specific nucleation sites. J. Mol. Biol. 334: 1077-1085.
    • (2003) J. Mol. Biol. , vol.334 , pp. 1077-1085
  • 46
    • 0042622380 scopus 로고    scopus 로고
    • SWISS-MODEL: An automated protein homology-modeling server
    • Schwede, T., Kopp, J., Guex, N., and Peitsch, M.C. 2003. SWISS-MODEL: An automated protein homology-modeling server. Nucleic Acids Res. 31: 3381-3385.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3381-3385
    • Schwede, T.1    Kopp, J.2    Guex, N.3    Peitsch, M.C.4
  • 47
    • 0026553768 scopus 로고
    • The folding of an enzyme. II. Substructure of barnase and the contribution of different interactions to protein stability
    • Serrano, L., Kellis Jr., J.T., Cann, P., Matouschek, A., and Fersht, A.R. 1992. The folding of an enzyme. II. Substructure of barnase and the contribution of different interactions to protein stability. J. Mol. Biol. 224: 783-804.
    • (1992) J. Mol. Biol. , vol.224 , pp. 783-804
    • Serrano, L.1    Kellis Jr., J.T.2    Cann, P.3    Matouschek, A.4    Fersht, A.R.5
  • 48
    • 14144255497 scopus 로고    scopus 로고
    • Value analysis by molecular dynamics simulations of reversible folding
    • Settanni, G., Rao, F., and Caflisch, A. 2005. φ-Value analysis by molecular dynamics simulations of reversible folding. Proc. Natl. Acad. Sci. 102: 628-633.
    • (2005) Proc. Natl. Acad. Sci. , vol.102 , pp. 628-633
    • Settanni, G.1    Rao, F.2    Caflisch, A.3
  • 49
    • 0014364651 scopus 로고
    • Protein denaturation
    • Tanford, C. 1968. Protein denaturation. Adv. Protein Chem. 23: 121-282.
    • (1968) Adv. Protein Chem. , vol.23 , pp. 121-282
    • Tanford, C.1
  • 50
    • 0014718113 scopus 로고
    • Protein denaturation. C. Theoretical models for the mechanism of denaturation
    • _. 1970. Protein denaturation. C. Theoretical models for the mechanism of denaturation. Adv. Protein Chem. 24: 1-95.
    • (1970) Adv. Protein Chem. , vol.24 , pp. 1-95
  • 51
    • 0025896727 scopus 로고
    • Water-protein interactions: Theory and experiment
    • Teeter, M.M. 1991. Water-protein interactions: Theory and experiment. Annu. Rev. Biophys. Biophys. Chem. 20: 577-600.
    • (1991) Annu. Rev. Biophys. Biophys. Chem. , vol.20 , pp. 577-600
    • Teeter, M.M.1
  • 52
    • 0037076337 scopus 로고    scopus 로고
    • Drying-induced hydrophobic polymer collapse
    • ten Wolde, P.R. and Chandler, D. 2002. Drying-induced hydrophobic polymer collapse. Proc. Natl. Acad. Sci. 99: 6539-6543.
    • (2002) Proc. Natl. Acad. Sci. , vol.99 , pp. 6539-6543
    • Ten Wolde, P.R.1    Chandler, D.2
  • 53
    • 0033592876 scopus 로고    scopus 로고
    • From snapshot to movie: φ Analysis of protein folding transition states taken one step further
    • Ternstrom, T.A, Mayor, U., Akke, M., and Oliveberg, M. 1999. From snapshot to movie: φ Analysis of protein folding transition states taken one step further. Proc. Natl. Acad. Sci. 96: 14854-14859.
    • (1999) Proc. Natl. Acad. Sci. , vol.96 , pp. 14854-14859
    • Ternstrom, T.A.1    Mayor, U.2    Akke, M.3    Oliveberg, M.4
  • 54
    • 0022340115 scopus 로고
    • The environment of the tryptophan residue in Pseudomonas aeruginosa azurin and its fluorescence properties
    • Turoverov, K.K., Kuznetsova, I.M., and Zaitsev, V.N. 1985. The environment of the tryptophan residue in Pseudomonas aeruginosa azurin and its fluorescence properties. Biophys. Chem. 23: 79-89.
    • (1985) Biophys. Chem. , vol.23 , pp. 79-89
    • Turoverov, K.K.1    Kuznetsova, I.M.2    Zaitsev, V.N.3
  • 55
    • 15244355262 scopus 로고    scopus 로고
    • Role of structural determinants in folding of the sandwich-like protein Pseudomonas aeruginosa azurin
    • Wilson, C.J. and Wittung-Stafshede, P. 2005a. Role of structural determinants in folding of the sandwich-like protein Pseudomonas aeruginosa azurin. Proc. Natl. Acad. Sci. 102: 3984-3987.
    • (2005) Proc. Natl. Acad. Sci. , vol.102 , pp. 3984-3987
    • Wilson, C.J.1    Wittung-Stafshede, P.2
  • 56
    • 23044514304 scopus 로고    scopus 로고
    • Snapshots of a dynamic folding nucleus in zinc-substituted Pseudomonas aeruginosa azurin
    • _. 2005b. Snapshots of a dynamic folding nucleus in zinc-substituted Pseudomonas aeruginosa azurin. Biochemistry 44: 10054-10062.
    • (2005) Biochemistry , vol.44 , pp. 10054-10062
  • 57
    • 10044257577 scopus 로고    scopus 로고
    • Role of cofactors in folding of the blue-copper protein azurin
    • Wittung-Stafshede, P. 2004. Role of cofactors in folding of the blue-copper protein azurin. Inorg. Chem. 43: 7926-7933.
    • (2004) Inorg. Chem. , vol.43 , pp. 7926-7933
    • Wittung-Stafshede, P.1
  • 58
    • 0141704162 scopus 로고    scopus 로고
    • Free energy landscape of protein folding in water: Explicit vs. implicit solvent
    • Zhou, R. 2003. Free energy landscape of protein folding in water: Explicit vs. implicit solvent. Proteins 53: 148-161.
    • (2003) Proteins , vol.53 , pp. 148-161
    • Zhou, R.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.