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Volumn 331, Issue 1, 2003, Pages 89-99

A protein-DNA binding mechanism proceeds through multi-state or two-state parallel pathways

Author keywords

DNA binding; HPV E2; Protein DNA; Recognition; Stopped flow

Indexed keywords

DNA BASE; VIRUS PROTEIN;

EID: 0038161225     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(03)00720-4     Document Type: Article
Times cited : (36)

References (33)
  • 1
    • 0019887628 scopus 로고
    • Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory
    • Berg O.G., Winter R.B., von Hippel P.H. Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory. Biochemistry. 20:1981;6929-6948.
    • (1981) Biochemistry , vol.20 , pp. 6929-6948
    • Berg, O.G.1    Winter, R.B.2    Von Hippel, P.H.3
  • 2
    • 0014945567 scopus 로고
    • The lac repressor-operator interaction. 3. Kinetic studies
    • Riggs A.D., Bourgeois S., Cohn M. The lac repressor-operator interaction. 3. Kinetic studies. J. Mol. Biol. 53:1970;401-417.
    • (1970) J. Mol. Biol. , vol.53 , pp. 401-417
    • Riggs, A.D.1    Bourgeois, S.2    Cohn, M.3
  • 3
    • 0024531901 scopus 로고
    • Facilitated target location in biological systems
    • von Hippel P.H., Berg O.G. Facilitated target location in biological systems. J. Biol. Chem. 264:1989;675-678.
    • (1989) J. Biol. Chem. , vol.264 , pp. 675-678
    • Von Hippel, P.H.1    Berg, O.G.2
  • 4
    • 0019867850 scopus 로고
    • Diffusion-driven mechanisms of protein translocation on nucleic acids. 3. The Escherichia coli lac repressor-operator interaction: Kinetic measurements and conclusions
    • Winter R.B., Berg O.G., von Hippel P.H. Diffusion-driven mechanisms of protein translocation on nucleic acids. 3. The Escherichia coli lac repressor-operator interaction: kinetic measurements and conclusions. Biochemistry. 20:1981;6961-6977.
    • (1981) Biochemistry , vol.20 , pp. 6961-6977
    • Winter, R.B.1    Berg, O.G.2    Von Hippel, P.H.3
  • 5
    • 0023364022 scopus 로고
    • Computer simulations of the diffusion of a substrate to an active site of an enzyme
    • Sharp K., Fine R., Honig B. Computer simulations of the diffusion of a substrate to an active site of an enzyme. Science. 236:1987;1460-1463.
    • (1987) Science , vol.236 , pp. 1460-1463
    • Sharp, K.1    Fine, R.2    Honig, B.3
  • 6
    • 0026323912 scopus 로고
    • Analysis of equilibrium and kinetic measurements to determine thermodynamic origins of stability and specificity and mechanism of formation of site-specific complexes between proteins and helical DNA
    • Record M.T. Jr, Ha J.H., Fisher M.A. Analysis of equilibrium and kinetic measurements to determine thermodynamic origins of stability and specificity and mechanism of formation of site-specific complexes between proteins and helical DNA. Methods Enzymol. 208:1991;291-343.
    • (1991) Methods Enzymol. , vol.208 , pp. 291-343
    • Record M.T., Jr.1    Ha, J.H.2    Fisher, M.A.3
  • 7
    • 0032749078 scopus 로고    scopus 로고
    • Intrinsically unstructured proteins: Re-assessing the protein structure-function paradigm
    • Wright P.E., Dyson H.J. Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. J. Mol. Biol. 293:1999;321-331.
    • (1999) J. Mol. Biol. , vol.293 , pp. 321-331
    • Wright, P.E.1    Dyson, H.J.2
  • 8
    • 23444450909 scopus 로고
    • Coupling of local folding to site-specific binding of proteins to DNA
    • Spolar R.S., Record M.T. Jr. Coupling of local folding to site-specific binding of proteins to DNA. Science. 263:1994;777-784.
    • (1994) Science , vol.263 , pp. 777-784
    • Spolar, R.S.1    Record M.T., Jr.2
  • 9
    • 0035830451 scopus 로고    scopus 로고
    • Kinetic studies of Fos·Jun·DNA complex formation: DNA binding prior to dimerization
    • Kohler J.J., Schepartz A. Kinetic studies of Fos·Jun·DNA complex formation: DNA binding prior to dimerization. Biochemistry. 40:2001;130-142.
    • (2001) Biochemistry , vol.40 , pp. 130-142
    • Kohler, J.J.1    Schepartz, A.2
  • 10
    • 0035839638 scopus 로고    scopus 로고
    • Marked stepwise differences within a common kinetic mechanism characterize TATA-binding protein interactions with two consensus promoters
    • Powell R.M., Parkhurst K.M., Brenowitz M., Parkhurst L.J. Marked stepwise differences within a common kinetic mechanism characterize TATA-binding protein interactions with two consensus promoters. J. Biol. Chem. 276:2001;29782-29791.
    • (2001) J. Biol. Chem. , vol.276 , pp. 29782-29791
    • Powell, R.M.1    Parkhurst, K.M.2    Brenowitz, M.3    Parkhurst, L.J.4
  • 11
    • 0037040899 scopus 로고    scopus 로고
    • Comparison of TATA-binding protein recognition of a variant and consensus DNA promoters
    • Powell R.M., Parkhurst K.M., Parkhurst L.J. Comparison of TATA-binding protein recognition of a variant and consensus DNA promoters. J. Biol. Chem. 277:2002;7776-7784.
    • (2002) J. Biol. Chem. , vol.277 , pp. 7776-7784
    • Powell, R.M.1    Parkhurst, K.M.2    Parkhurst, L.J.3
  • 12
    • 0036086459 scopus 로고    scopus 로고
    • The papillomavirus E2 proteins: Structure, function, and biology
    • Hegde R.S. The papillomavirus E2 proteins: structure, function, and biology. Annu. Rev. Biophys. Biomol. Struct. 31:2002;343-360.
    • (2002) Annu. Rev. Biophys. Biomol. Struct. , vol.31 , pp. 343-360
    • Hegde, R.S.1
  • 13
    • 0025953354 scopus 로고
    • The papillomavirus E2 regulatory proteins
    • McBride A., Romanczuk H., Howley P. The papillomavirus E2 regulatory proteins. J. Biol. Chem. 266:1991;18411-18414.
    • (1991) J. Biol. Chem. , vol.266 , pp. 18411-18414
    • McBride, A.1    Romanczuk, H.2    Howley, P.3
  • 14
    • 0026656038 scopus 로고
    • Crystal structure at 1.7 Å of the bovine papillomavirus-1 E2 DNA-binding domain bound to its DNA target
    • Hegde R., Grossman S., Laimins L., Sigler P. Crystal structure at 1.7 Å of the bovine papillomavirus-1 E2 DNA-binding domain bound to its DNA target. Nature. 359:1992;505-512.
    • (1992) Nature , vol.359 , pp. 505-512
    • Hegde, R.1    Grossman, S.2    Laimins, L.3    Sigler, P.4
  • 15
    • 0029863788 scopus 로고    scopus 로고
    • Crystal structure of the DNA-binding domain of the Epstein-Barr virus origin-binding protein EBNA1, bound to DNA
    • Bochkarev A., Barwell J.A., Pfuetzner R.A., Bochkareva E., Frappier L., Edwards A.M. Crystal structure of the DNA-binding domain of the Epstein-Barr virus origin-binding protein EBNA1, bound to DNA. Cell. 84:1996;791-800.
    • (1996) Cell , vol.84 , pp. 791-800
    • Bochkarev, A.1    Barwell, J.A.2    Pfuetzner, R.A.3    Bochkareva, E.4    Frappier, L.5    Edwards, A.M.6
  • 16
    • 0029761636 scopus 로고    scopus 로고
    • The dimeric DNA binding domain of the human papillomavirus E2 protein folds through a monomeric intermediate which cannot be native-like
    • Mok Y.K., Bycroft M., de Prat-Gay G. The dimeric DNA binding domain of the human papillomavirus E2 protein folds through a monomeric intermediate which cannot be native-like. Nature Struct. Biol. 3:1996;711-717.
    • (1996) Nature Struct. Biol. , vol.3 , pp. 711-717
    • Mok, Y.K.1    Bycroft, M.2    De Prat-Gay, G.3
  • 17
    • 0034727658 scopus 로고    scopus 로고
    • Distinctive cognate sequence discrimination, bound DNA conformation, and binding modes in the E2 C-terminal domains from prototype human and bovine papillomaviruses
    • Ferreiro D.U., Lima L.M., Nadra A.D., Alonso L.G., Goldbaum F.A., de Prat-Gay G. Distinctive cognate sequence discrimination, bound DNA conformation, and binding modes in the E2 C-terminal domains from prototype human and bovine papillomaviruses. Biochemistry. 39:2000;14692-14701.
    • (2000) Biochemistry , vol.39 , pp. 14692-14701
    • Ferreiro, D.U.1    Lima, L.M.2    Nadra, A.D.3    Alonso, L.G.4    Goldbaum, F.A.5    De Prat-Gay, G.6
  • 18
    • 0030064186 scopus 로고    scopus 로고
    • Equilibrium dissociation and unfolding of the dimeric human papillomavirus strain-16 E2 DNA-binding domain
    • Mok Y.K., de Prat Gay G., Butler P.J., Bycroft M. Equilibrium dissociation and unfolding of the dimeric human papillomavirus strain-16 E2 DNA-binding domain. Protein Sci. 5:1996;310-319.
    • (1996) Protein Sci. , vol.5 , pp. 310-319
    • Mok, Y.K.1    De Prat Gay, G.2    Butler, P.J.3    Bycroft, M.4
  • 19
    • 0041884902 scopus 로고
    • Binding of synthetic lactose operator DNAs to lactose represessors
    • Goeddel D.V., Yansura D.G., Caruthers M.H. Binding of synthetic lactose operator DNAs to lactose represessors. Proc. Natl Acad. Sci. USA. 74:1977;3292-3296.
    • (1977) Proc. Natl Acad. Sci. USA , vol.74 , pp. 3292-3296
    • Goeddel, D.V.1    Yansura, D.G.2    Caruthers, M.H.3
  • 20
    • 0025166415 scopus 로고
    • The DNA-binding domain of HPV-16 E2 protein interaction with the viral enhancer: Protein-induced DNA bending and role of the nonconserved core sequence in binding site affinity
    • Bedrosian C.L., Bastia D. The DNA-binding domain of HPV-16 E2 protein interaction with the viral enhancer: protein-induced DNA bending and role of the nonconserved core sequence in binding site affinity. Virology. 174:1990;557-575.
    • (1990) Virology , vol.174 , pp. 557-575
    • Bedrosian, C.L.1    Bastia, D.2
  • 21
    • 0032489497 scopus 로고    scopus 로고
    • DNA structure and flexibility in the sequence-specific binding of papillomavirus E2 proteins
    • Hines C.S., Meghoo C., Shetty S., Biburger M., Brenowitz M., Hegde R.S. DNA structure and flexibility in the sequence-specific binding of papillomavirus E2 proteins. J. Mol. Biol. 276:1998;809-818.
    • (1998) J. Mol. Biol. , vol.276 , pp. 809-818
    • Hines, C.S.1    Meghoo, C.2    Shetty, S.3    Biburger, M.4    Brenowitz, M.5    Hegde, R.S.6
  • 22
    • 0034613274 scopus 로고    scopus 로고
    • The structural basis of DNA target discrimination by papillomavirus E2 proteins
    • Kim S.S., Tam J.K., Wang A.F., Hegde R.S. The structural basis of DNA target discrimination by papillomavirus E2 proteins. J. Biol. Chem. 275:2000;31245-31254.
    • (2000) J. Biol. Chem. , vol.275 , pp. 31245-31254
    • Kim, S.S.1    Tam, J.K.2    Wang, A.F.3    Hegde, R.S.4
  • 23
    • 0032489427 scopus 로고    scopus 로고
    • Subunit rearrangement accompanies sequence-specific DNA binding by the bovine papillomavirus-1 E2 protein
    • Hegde R.S., Wang A.F., Kim S.S., Schapira M. Subunit rearrangement accompanies sequence-specific DNA binding by the bovine papillomavirus-1 E2 protein. J. Mol. Biol. 276:1998;797-808.
    • (1998) J. Mol. Biol. , vol.276 , pp. 797-808
    • Hegde, R.S.1    Wang, A.F.2    Kim, S.S.3    Schapira, M.4
  • 24
    • 0030876594 scopus 로고    scopus 로고
    • Conformational changes and stabilization induced by ligand binding in the DNA-binding domain of the E2 protein from human papillomavirus
    • Lima L.M., de Prat-Gay G. Conformational changes and stabilization induced by ligand binding in the DNA-binding domain of the E2 protein from human papillomavirus. J. Biol. Chem. 272:1997;19295-19303.
    • (1997) J. Biol. Chem. , vol.272 , pp. 19295-19303
    • Lima, L.M.1    De Prat-Gay, G.2
  • 25
    • 0034435652 scopus 로고    scopus 로고
    • Structural and thermodynamic strategies for site-specific DNA binding proteins
    • Jen-Jacobson L., Engler L.E., Jacobson L.A. Structural and thermodynamic strategies for site-specific DNA binding proteins. Struct. Fold. Des. 8:2000;1015-1023.
    • (2000) Struct. Fold. Des. , vol.8 , pp. 1015-1023
    • Jen-Jacobson, L.1    Engler, L.E.2    Jacobson, L.A.3
  • 26
    • 0034255123 scopus 로고    scopus 로고
    • Speeding molecular recognition by using the folding funnel: The fly-casting mechanism
    • Shoemaker B.A., Portman J.J., Wolynes P.G. Speeding molecular recognition by using the folding funnel: the fly-casting mechanism. Proc. Natl Acad. Sci. USA. 97:2000;8868-8873.
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 8868-8873
    • Shoemaker, B.A.1    Portman, J.J.2    Wolynes, P.G.3
  • 27
    • 0034049693 scopus 로고    scopus 로고
    • Thermodynamic and kinetic analyses for understanding sequence-specific DNA recognition
    • Oda M., Nakamura H. Thermodynamic and kinetic analyses for understanding sequence-specific DNA recognition. Genes Cells. 5:2000;319-326.
    • (2000) Genes Cells , vol.5 , pp. 319-326
    • Oda, M.1    Nakamura, H.2
  • 28
    • 0025906146 scopus 로고
    • Contribution to the thermodynamics of protein folding from the reduction in water-accessible nonpolar surface area
    • Livingstone J.R., Spolar R.S., Record M.T. Jr. Contribution to the thermodynamics of protein folding from the reduction in water-accessible nonpolar surface area. Biochemistry. 30:1991;4237-4244.
    • (1991) Biochemistry , vol.30 , pp. 4237-4244
    • Livingstone, J.R.1    Spolar, R.S.2    Record M.T., Jr.3
  • 29
    • 0002638463 scopus 로고
    • Heat capacity and entropy changes in processes involving proteins
    • Sturtevant J.M. Heat capacity and entropy changes in processes involving proteins. Proc. Natl Acad. Sci. USA. 74:1977;2236-2240.
    • (1977) Proc. Natl Acad. Sci. USA , vol.74 , pp. 2236-2240
    • Sturtevant, J.M.1
  • 31
    • 0029910813 scopus 로고    scopus 로고
    • Differences in water release for the binding of EcoRI to specific and nonspecific DNA sequences
    • Sidorova N.Y., Rau D.C. Differences in water release for the binding of EcoRI to specific and nonspecific DNA sequences. Proc. Natl Acad. Sci. USA. 93:1996;12272-12277.
    • (1996) Proc. Natl Acad. Sci. USA , vol.93 , pp. 12272-12277
    • Sidorova, N.Y.1    Rau, D.C.2
  • 32
    • 0035919819 scopus 로고    scopus 로고
    • Linkage of EcoRI dissociation from its specific DNA recognition site to water activity, salt concentration, and pH: Separating their roles in specific and non-specific binding
    • Sidorova N.Y., Rau D.C. Linkage of EcoRI dissociation from its specific DNA recognition site to water activity, salt concentration, and pH: separating their roles in specific and non-specific binding. J. Mol. Biol. 310:2001;801-816.
    • (2001) J. Mol. Biol. , vol.310 , pp. 801-816
    • Sidorova, N.Y.1    Rau, D.C.2
  • 33
    • 0028271856 scopus 로고
    • Thermodynamic properties of the transition state for the rate-limiting step in the folding of the alpha subunit of tryptophan synthase
    • Chen X., Matthews C.R. Thermodynamic properties of the transition state for the rate-limiting step in the folding of the alpha subunit of tryptophan synthase. Biochemistry. 33:1994;6356-6362.
    • (1994) Biochemistry , vol.33 , pp. 6356-6362
    • Chen, X.1    Matthews, C.R.2


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