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Volumn 156, Issue 2-3, 2011, Pages 115-127

The primary DNA-binding subsite of the rat pol β. Energetics of interactions of the 8-kDa domain of the enzyme with the ssDNA

Author keywords

DNA repair; DNA replication; Fluorescence titrations; Polymerases; Protein ssDNA interactions

Indexed keywords

DNA POLYMERASE; POLYMERASE BETA; SINGLE STRANDED DNA; UNCLASSIFIED DRUG; WATER;

EID: 79956104025     PISSN: 03014622     EISSN: 18734200     Source Type: Journal    
DOI: 10.1016/j.bpc.2011.01.006     Document Type: Article
Times cited : (2)

References (52)
  • 5
    • 0029028964 scopus 로고
    • Excision of deoxyribose phosphate residues by DNA polymerase beta during DNA repair
    • Y. Matsumoto, K. Kim, Excision of deoxyribose phosphate residues by DNA polymerase beta during DNA repair, Science 269 (1995) 699-702.
    • (1995) Science , vol.269 , pp. 699-702
    • Matsumoto, Y.1    Kim, K.2
  • 6
    • 0032485858 scopus 로고    scopus 로고
    • Catalytic center of DNA polymerase beta for excision of deoxyribose phosphate groups
    • DOI 10.1021/bi9727545
    • Y. Matsumoto, K. Kim, D.S. Katz, J.-A. Feng, Catalytic center of DNA polymerase beta for excision of deoxyribose phosphate groups, Biochemistry 37 (1998) 6456-6464. (Pubitemid 28213666)
    • (1998) Biochemistry , vol.37 , Issue.18 , pp. 6456-6464
    • Matsumoto, Y.1    Kim, K.2    Katz, D.S.3    Feng, J.-A.4
  • 7
    • 0025314841 scopus 로고
    • Mismatch-specific thymine DNA glycosylase and DNA polymerase beta mediate the correction of G.T mispairs in nuclear extracts from human cells
    • K. Wiebauer, J. Jiricny, Mismatch-specific thymine DNA glycosylase and DNA polymerase beta mediate the correction of G.T mispairs in nuclear extracts from human cells, Proc. Natl Acad. Sci. USA 87 (1990) 5842-5845.
    • (1990) Proc. Natl Acad. Sci. USA , vol.87 , pp. 5842-5845
    • Wiebauer, K.1    Jiricny, J.2
  • 8
    • 0030825134 scopus 로고    scopus 로고
    • DNA polymerases required for repair of UV-induced damage in Saccharomyces cerevisiae
    • M.E. Budd, J.L. Campbell, DNA polymerases required for repair of UV-induced damage in Saccharomyces cerevisiae, Mutat. Res. 384 (1997) 157-167.
    • (1997) Mutat. Res. , vol.384 , pp. 157-167
    • Budd, M.E.1    Campbell, J.L.2
  • 10
    • 0028136070 scopus 로고
    • Crystal structure of rat DNA polymerase beta: Evidence for a common polymerase mechanism
    • M.R. Sawaya, H. Pelletier, A. Kumar, S.H. Wilson, J.A. Kraut, Crystal structure of the rat DNA polymerase beta: evidence a common polymerase mechanism, Science 264 (1994) 1930-1935. (Pubitemid 24245639)
    • (1994) Science , vol.264 , Issue.5167 , pp. 1930-1935
    • Sawaya, M.R.1    Pelletier, H.2    Kumar, A.3    Wilson, S.H.4    Kraut, J.5
  • 11
    • 0032553313 scopus 로고    scopus 로고
    • Human DNA polymerase β recognizes single-stranded DNA using two different binding modes
    • S. Rajendran, M.J. Jezewska, W. Bujalowski, Human DNA polymerase β recognizes single-stranded DNA using two different binding modes, J. Biol. Chem. 273 (1998) 31021-31031.
    • (1998) J. Biol. Chem. , vol.273 , pp. 31021-31031
    • Rajendran, S.1    Jezewska, M.J.2    Bujalowski, W.3
  • 12
    • 0032509151 scopus 로고    scopus 로고
    • Transition between different binding modes in rat DNA polymerase β-ssDNA complexes
    • M.J. Jezewska, S. Rajendran, W. Bujalowski, Transition between different binding modes in rat DNA polymerase β-ssDNA complexes, J. Mol. Biol. 284 (28) (1998) 1113-1131.
    • (1998) J. Mol. Biol. , vol.284 , Issue.28 , pp. 1113-1131
    • Jezewska, M.J.1    Rajendran, S.2    Bujalowski, W.3
  • 13
    • 0035804927 scopus 로고    scopus 로고
    • Recognition of template primer and gapped DNA substrates by human DNA polymerase β
    • S. Rajendran, M.J. Jezewska, W. Bujalowski, Recognition of template primer and gapped DNA substrates by human DNA polymerase β, J. Mol. Biol. 308 (2001) 477-500.
    • (2001) J. Mol. Biol. , vol.308 , pp. 477-500
    • Rajendran, S.1    Jezewska, M.J.2    Bujalowski, W.3
  • 14
    • 0035844159 scopus 로고    scopus 로고
    • Energetics and specificity of rat DNA polymerase β interactions with template-primer and gapped DNA substrates
    • M.J. Jezewska, S. Rajendran, W. Bujalowski, Energetics and specificity of rat DNA polymerase β interactions with template-primer and gapped DNA substrates, J. Biol. Chem. 276 (2001) 16123-16136.
    • (2001) J. Biol. Chem. , vol.276 , pp. 16123-16136
    • Jezewska, M.J.1    Rajendran, S.2    Bujalowski, W.3
  • 15
    • 0035916918 scopus 로고    scopus 로고
    • Interactions of the 8-kDa domain of rat DNA polymerase β with DNA
    • DOI 10.1021/bi002749s
    • M.J. Jezewska, S. Rajendran, W. Bujalowski, Interactions of the 8-kDa domain of rat DNA polymerase β with ssDNA, Biochemistry 40 (2001) 3295-3307. (Pubitemid 32221631)
    • (2001) Biochemistry , vol.40 , Issue.11 , pp. 3295-3307
    • Jezewska, M.J.1    Rajendran, S.2    Bujalowski, W.3
  • 16
    • 0141885289 scopus 로고    scopus 로고
    • Tertiary conformation of the template-primer and gapped DNA substrates in complexes with rat polymerase β. Fluorescence energy transfer studies using the multiple donor-acceptor approach
    • DOI 10.1021/bi030111l
    • M.J. Jezewska, R. Galletto, W. Bujalowski, Tertiary conformation of the template-primer and gapped DNA substrates in complexes with rat polymerase β. Fluorescence energy transfer studies using the multiple donor-acceptor approach, Biochemistry 42 (2003) 11864-11878. (Pubitemid 37243648)
    • (2003) Biochemistry , vol.42 , Issue.40 , pp. 11864-11878
    • Jezewska, M.J.1    Galletto, R.2    Bujalowski, W.3
  • 17
    • 7244228547 scopus 로고    scopus 로고
    • 4 group and magnesium on the enzyme binding to the gapped DNAs with different ssDNA gaps
    • 4 group and magnesium on the enzyme binding to the gapped DNAs with different ssDNA gaps, Cell Biochem. Biophys. 38 (2003) 125-160.
    • (2003) Cell Biochem. Biophys. , vol.38 , pp. 125-160
    • Jezewska, M.J.1    Galletto, R.2    Bujalowski, W.3
  • 18
    • 0037036453 scopus 로고    scopus 로고
    • Dynamics of gapped DNA recognition by human polymerase β
    • W. Bujalowski, M.J. Jezewska, R. Galletto, Dynamics of gapped DNA recognition by human polymerase β, J. Biol. Chem. 277 (2002) 20316-20327.
    • (2002) J. Biol. Chem. , vol.277 , pp. 20316-20327
    • Bujalowski, W.1    Jezewska, M.J.2    Galletto, R.3
  • 19
    • 0014109212 scopus 로고
    • Spectroscopic determination of tryptophan and tyrosine in proteins
    • H. Edelhoch, Spectroscopic determination of tryptophan and tyrosine in proteins, Biochemistry 6 (1967) 1948-1954.
    • (1967) Biochemistry , vol.6 , pp. 1948-1954
    • Edelhoch, H.1
  • 20
    • 0024448151 scopus 로고
    • Calculation of protein extinction coefficients from amino acid sequence data
    • S.C. Gill, P.H. von Hippel, Calculation of protein extinction coefficients from amino acid sequence data, Anal. Biochem. 182 (1989) 319-326.
    • (1989) Anal. Biochem. , vol.182 , pp. 319-326
    • Gill, S.C.1    Von Hippel, P.H.2
  • 21
    • 0017873807 scopus 로고
    • Base stacking in a fluorescent dinucleoside monophosphate: εApεA
    • B.M. Baker, J. Vanderkooi, N.R. Kallenbach, Base stacking in a fluorescent dinucleoside monophosphate: εApεA, Biopolymers 17 (1978) 1361-1372.
    • (1978) Biopolymers , vol.17 , pp. 1361-1372
    • Baker, B.M.1    Vanderkooi, J.2    Kallenbach, N.R.3
  • 22
    • 0016206255 scopus 로고
    • Chloroacetaldehyde-modified di-nucleoside phosphates. Dynamic fluorescence quenching and quenching due to intramolecular complexation
    • G.L. Tolman, J.R. Barrio, N.J. Leonard, Chloroacetaldehyde-modified di-nucleoside phosphates. Dynamic fluorescence quenching and quenching due to intramolecular complexation, Biochemistry 13 (1974) 4869-4878.
    • (1974) Biochemistry , vol.13 , pp. 4869-4878
    • Tolman, G.L.1    Barrio, J.R.2    Leonard, N.J.3
  • 23
    • 0026351773 scopus 로고
    • Thermodynamic methods for model-independent determination of equilibrium binding isotherms for protein-DNA interactions: Spectroscopic approaches to monitor binding
    • T.M. Lohman, W. Bujalowski, Thermodynamic methods for model-independent determination of equilibrium binding isotherms for protein-DNA interactions: spectroscopic approaches to monitor binding, Methods Enzymol. 208 (1991) 258-290.
    • (1991) Methods Enzymol. , vol.208 , pp. 258-290
    • Lohman, T.M.1    Bujalowski, W.2
  • 25
    • 33644632662 scopus 로고    scopus 로고
    • Thermodynamic and kinetic methods of analyses of protein-nucleic acid interactions. From simpler to more complex systems
    • W. Bujalowski, Thermodynamic and kinetic methods of analyses of protein-nucleic acid interactions. From simpler to more complex systems, Chem. Rev. 106 (2006) 556-606.
    • (2006) Chem. Rev. , vol.106 , pp. 556-606
    • Bujalowski, W.1
  • 26
    • 0030980795 scopus 로고    scopus 로고
    • Fluorescence resonance energy transfer as a probe of DNA structure and function
    • DOI 10.1016/S0076-6879(97)78022-4
    • M. Yang, D.P. Millar, Fluorescence resonance energy transfer as a probe of DNA structure and function, Methods Enzymol. 278 (1997) 417-444. (Pubitemid 27229931)
    • (1997) Methods in Enzymology , vol.278 , pp. 417-444
    • Yang, M.1    Millar, D.P.2
  • 27
    • 0344936650 scopus 로고
    • The helix-coil transition of DNA duplexes and hairpins observed by multiple fluorescence parameters
    • G. Vamosi, R.M. Clegg, The helix-coil transition of DNA duplexes and hairpins observed by multiple fluorescence parameters, Biochemistry 37 (1992) 14300-14316.
    • (1992) Biochemistry , vol.37 , pp. 14300-14316
    • Vamosi, G.1    Clegg, R.M.2
  • 29
    • 0032562822 scopus 로고    scopus 로고
    • Does ssDNA pass through the inner channel of the protein hexamer in the complex with the E. coli DnaB helicase? Fluorescence energy transfer studies
    • M.J. Jezewska, S. Rajendran, D. Bujalowska, W. Bujalowski, Does ssDNA pass through the inner channel of the protein hexamer in the complex with the E. coli DnaB helicase? Fluorescence energy transfer studies, J. Biol. Chem. 273 (1998) 10515-10529.
    • (1998) J. Biol. Chem. , vol.273 , pp. 10515-10529
    • Jezewska, M.J.1    Rajendran, S.2    Bujalowska, D.3    Bujalowski, W.4
  • 31
    • 0019323544 scopus 로고
    • Fluorescence energy transfer on acethylcholinesterase: Special relationship between peripheral site and active center
    • H.A. Berman, J. Yguerabide, P. Taylor, Fluorescence energy transfer on acethylcholinesterase: special relationship between peripheral site and active center, Biochemistry 19 (1980) 2226-2235.
    • (1980) Biochemistry , vol.19 , pp. 2226-2235
    • Berman, H.A.1    Yguerabide, J.2    Taylor, P.3
  • 32
    • 34548653578 scopus 로고    scopus 로고
    • Interactions of the DNA Polymerase X of African Swine Fever Virus with Double-stranded DNA. Functional Structure of the Complex
    • DOI 10.1016/j.jmb.2007.06.054, PII S0022283607008522
    • M.J. Jezewska, P.J. Bujalowski, W. Bujalowski, Interactions of the DNA polymerase X of African swine fever virus with double-stranded DNA. Functional structure of the complex, J. Mol. Biol. 373 (2007) 75-95. (Pubitemid 47407736)
    • (2007) Journal of Molecular Biology , vol.373 , Issue.1 , pp. 75-95
    • Jezewska, M.J.1    Bujalowski, P.J.2    Bujalowski, W.3
  • 33
    • 80053408529 scopus 로고    scopus 로고
    • Thermodynamic analysis of the structure-function relationship in the total DNA-binding site of enzyme-DNA complexes
    • W. Bujalowski, M.J. Jezewska, Thermodynamic analysis of the structure-function relationship in the total DNA-binding site of enzyme-DNA complexes, Methods Enzymol. 466 (2009) 294-324.
    • (2009) Methods Enzymol. , vol.466 , pp. 294-324
    • Bujalowski, W.1    Jezewska, M.J.2
  • 34
    • 0030030309 scopus 로고    scopus 로고
    • A general method of analysis of ligand binding to competing macromolecules using the spectroscopic signal originating from a reference macromolecule. Application to Escherichia coli replicative helicase DnaB protein-nucleic acid interactions
    • M.J. Jezewska, W. Bujalowski, A general method of analysis of ligand binding to competing macromolecules using the spectroscopic signal originating from a reference macromolecule. Application to Escherichia coli replicative helicase DnaB protein-nucleic acid interactions, Biochemistry 35 (1996) 2117-2128.
    • (1996) Biochemistry , vol.35 , pp. 2117-2128
    • Jezewska, M.J.1    Bujalowski, W.2
  • 35
    • 0034730112 scopus 로고    scopus 로고
    • Interactions of Escherichia coli replicative helicase PriA protein with single-stranded DNA
    • DOI 10.1021/bi001113y
    • M.J. Jezewska, S. Rajendran, W. Bujalowski, Interactions of Escherichia coli replicative helicase PriA protein with single-stranded DNA, Biochemistry 39 (2000) 10454-10467. (Pubitemid 30655922)
    • (2000) Biochemistry , vol.39 , Issue.34 , pp. 10454-10467
    • Jezewska, M.J.1    Bujalowski, W.2
  • 36
    • 0032478286 scopus 로고    scopus 로고
    • Complex of Escherichia coli primary replicative helicase DnaB protein with a replication fork: Recognition and structure
    • DOI 10.1021/bi972564u
    • M.J. Jezewska, S. Rajendran, W. Bujalowski, Complex of Escherichia coli primary replicative helicase DnaB protein with a replication fork. Recognition and structure, Biochemistry 37 (1998) 3116-3136. (Pubitemid 28145766)
    • (1998) Biochemistry , vol.37 , Issue.9 , pp. 3116-3136
    • Jezewska, M.J.1    Rajendran, S.2    Bujalowski, W.3
  • 37
    • 4644321099 scopus 로고    scopus 로고
    • Interactions of the RepA helicase hexamer of plasmid RSF1010 with the ssDNA. Quantitative analysis of stoichiometries, intrinsic affinities, cooperativities, and heterogeneity of the total ssDNA-binding site
    • M.J. Jezewska, R. Galletto, W. Bujalowski, Interactions of the RepA helicase hexamer of plasmid RSF1010 with the ssDNA. Quantitative analysis of stoichiometries, intrinsic affinities, cooperativities, and heterogeneity of the total ssDNA-binding site, J. Mol. Biol. 343 (2004) 115-136.
    • (2004) J. Mol. Biol. , vol.343 , pp. 115-136
    • Jezewska, M.J.1    Galletto, R.2    Bujalowski, W.3
  • 38
    • 77950858634 scopus 로고    scopus 로고
    • Interactions of the Escherichia coli primosomal PriB protein with the single-stranded DNA. Stoichiometries, intrinsic affinities, cooperativities, and base specificities
    • M.R. Szymanski, M.J. Jezewska, W. Bujalowski, Interactions of the Escherichia coli primosomal PriB protein with the single-stranded DNA. Stoichiometries, intrinsic affinities, cooperativities, and base specificities, J. Mol. Biol. 398 (2010) 8-25.
    • (2010) J. Mol. Biol. , vol.398 , pp. 8-25
    • Szymanski, M.R.1    Jezewska, M.J.2    Bujalowski, W.3
  • 39
    • 0016175370 scopus 로고
    • Theoretical aspects of DNA-protein interactions: Cooperative and noncooperative binding of large ligands to a one-dimensional homogeneous lattice
    • J.D. McGhee, P.H. von Hippel, Theoretical aspects of DNA-protein interactions: cooperative and noncooperative binding of large ligands to a one-dimensional homogeneous lattice, J. Mol. Biol. 86 (1974) 469-489.
    • (1974) J. Mol. Biol. , vol.86 , pp. 469-489
    • McGhee, J.D.1    Von Hippel, P.H.2
  • 40
    • 0018196563 scopus 로고
    • Cooperative and noncooperative binding of large ligands to a finite one-dimensional lattice. A model for ligand-oligonucleotide interactions
    • DOI 10.1016/0301-4622(78)80015-5
    • I.R. Epstein, Cooperative and non-cooperative binding of large ligands to a finite one-dimensional lattice. A model for ligand-oligonucleotide interactions, Biophys. Chem. 8 (1978) 327-339. (Pubitemid 9053702)
    • (1978) Biophysical Chemistry , vol.8 , Issue.4 , pp. 327-339
    • Epstein, I.R.1
  • 41
    • 0024730670 scopus 로고
    • On the cooperative binding of large ligands to a one-dimensional homogeneous lattice: The generalized three-state lattice model
    • W. Bujalowski, T.M. Lohman, C.F. Anderson, On the cooperative binding of large ligands to a one-dimensional homogeneous lattice: the generalized three-state lattice model, Biopolymers 28 (1989) 1637-1643.
    • (1989) Biopolymers , vol.28 , pp. 1637-1643
    • Bujalowski, W.1    Lohman, T.M.2    Anderson, C.F.3
  • 44
    • 0014674115 scopus 로고
    • Extension of the theory of linked functions to incorporate the effects of protein hydration
    • C. Tanford, Extension of the theory of linked functions to incorporate the effects of protein hydration, J. Mol. Biol. 39 (1969) 539-544.
    • (1969) J. Mol. Biol. , vol.39 , pp. 539-544
    • Tanford, C.1
  • 45
    • 0037162456 scopus 로고    scopus 로고
    • Protein-solvent interactions, protein hydration, and modulation of biochemical reactions by solvent components
    • S.N. Timasheff, Protein-solvent interactions, protein hydration, and modulation of biochemical reactions by solvent components, Proc. Natl Acad. Sci. USA 99 (2002) 9721-9726.
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 9721-9726
    • Timasheff, S.N.1
  • 46
    • 0034635965 scopus 로고    scopus 로고
    • Osmotic stress, crowding, preferential hydration, and binding: A comparison of perspectives
    • V.A. Parsegian, R.P. Rand, D.C. Rau, Osmotic stress, crowding, preferential hydration, and binding: a comparison of perspectives, Proc. Natl Acad. Sci. USA 97 (2000) 3987-3992.
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 3987-3992
    • Parsegian, V.A.1    Rand, R.P.2    Rau, D.C.3
  • 48
    • 0017820499 scopus 로고
    • Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: The roles of ion association or release, screening, and ion effects on water activity
    • M.T. Record Jr., C.F. Anderson, T.M. Lohman, Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity, Q. Rev. Biophys. 11 (1978) 103-178.
    • (1978) Q. Rev. Biophys. , vol.11 , pp. 103-178
    • Record Jr., M.T.1    Anderson, C.F.2    Lohman, T.M.3
  • 49
    • 70350513011 scopus 로고    scopus 로고
    • Interactions of the osmolyte glycine betaine with molecular surfaces in water: Thermodynamics, structural interpretation, and prediction of m-values
    • M.W. Capp, L.M. Pegram, R.M. Saecker, M. Kratz, D. Riccardi, T. Wendorff, J.G. Cannon, M.T. Record Jr., Interactions of the osmolyte glycine betaine with molecular surfaces in water: thermodynamics, structural interpretation, and prediction of m-values, Biochemistry 43 (2009) 4810372-4810379.
    • (2009) Biochemistry , vol.43 , pp. 4810372-4810379
    • Capp, M.W.1    Pegram, L.M.2    Saecker, R.M.3    Kratz, M.4    Riccardi, D.5    Wendorff, T.6    Cannon, J.G.7    Record Jr., M.T.8
  • 50
    • 62649089074 scopus 로고    scopus 로고
    • Quantifying the roles of water and solutes (denaturants, osmolytes, and Hofmeister salts) in protein and model processes using the solute partitioning model
    • L.M. Pegram, M.T. Record Jr., Quantifying the roles of water and solutes (denaturants, osmolytes, and Hofmeister salts) in protein and model processes using the solute partitioning model, Meth. Mol. Biol. 490 (2009) 179-193.
    • (2009) Meth. Mol. Biol. , vol.490 , pp. 179-193
    • Pegram, L.M.1    Record Jr., M.T.2
  • 51
    • 0034711010 scopus 로고    scopus 로고
    • Functional hydrogen-bonding map of the minor groove binding tracks of six DNA polymerases
    • J.C. Morales, E.T. Kool, functional hydrogen-bonding map of the minor groove binding tracks of six DNA polymerases, Biochemistry 39 (2000) 12979-12988.
    • (2000) Biochemistry , vol.39 , pp. 12979-12988
    • Morales, J.C.1    Kool, E.T.2


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