메뉴 건너뛰기




Volumn 418, Issue 5, 2012, Pages 300-315

Mapping the transition state for DNA bending by IHF

Author keywords

DNA bending dynamics; FRET measurements; integration host factor; laser temperature jump; protein DNA interactions

Indexed keywords

CURVED DNA; INTEGRATION HOST FACTOR;

EID: 84859714414     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2012.02.028     Document Type: Article
Times cited : (24)

References (84)
  • 1
    • 0030798605 scopus 로고    scopus 로고
    • Clues and consequences of DNA bending in transcription
    • DOI 10.1146/annurev.micro.51.1.593
    • Perez-Martin, J. & de Lorenzo, V. (1997). Clues and consequences of DNA bending in transcription. Annu. Rev. Microbiol. 51, 593-628. (Pubitemid 27433060)
    • (1997) Annual Review of Microbiology , vol.51 , pp. 593-628
    • Perez-Martin, J.1    De Lorenzo, V.2
  • 3
    • 0030451819 scopus 로고    scopus 로고
    • Crystal structure of an IHF-DNA complex: A protein-induced DNA U-turn
    • DOI 10.1016/S0092-8674(00)81824-3
    • Rice, P. A., Yang, S., Mizuuchi, K. & Nash, H. A. (1996). Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn. Cell, 87, 1295-1306. (Pubitemid 27010112)
    • (1996) Cell , vol.87 , Issue.7 , pp. 1295-1306
    • Rice, P.A.1    Yang, S.-W.2    Mizuuchi, K.3    Nash, H.A.4
  • 4
    • 0029938053 scopus 로고    scopus 로고
    • Crystal structure of the lactose operon repressor and its complexes with DNA and inducer
    • Lewis, M., Chang, G., Horton, N. C., Kercher, M. A., Pace, H. C., Schumacher, M. A. et al. (1996). Crystal structure of the lactose operon repressor and its complexes with DNA and inducer. Science, 271, 1247-1254.
    • (1996) Science , vol.271 , pp. 1247-1254
    • Lewis, M.1    Chang, G.2    Horton, N.C.3    Kercher, M.A.4    Pace, H.C.5    Schumacher, M.A.6
  • 5
    • 0027504913 scopus 로고
    • Crystal structure of a yeast TBP/TATA-box complex
    • DOI 10.1038/365512a0
    • Kim, Y., Geiger, J. H., Hahn, S. & Sigler, P. B. (1993). Crystal structure of a yeast TBP/TATA-box complex. Nature, 365, 512-520. (Pubitemid 23317770)
    • (1993) Nature , vol.365 , Issue.6446 , pp. 512-520
    • Kim, Y.1    Geiger, J.H.2    Hahn, S.3    Sigler, P.B.4
  • 7
    • 0034641938 scopus 로고    scopus 로고
    • Crystal structures of mismatch repair protein MutS and its complex with a substrate DNA
    • Obmolova, G., Ban, C., Hsieh, P. & Yang, W. (2000). Crystal structures of mismatch repair protein MutS and its complex with a substrate DNA. Nature, 407, 703-710.
    • (2000) Nature , vol.407 , pp. 703-710
    • Obmolova, G.1    Ban, C.2    Hsieh, P.3    Yang, W.4
  • 8
    • 0034641947 scopus 로고    scopus 로고
    • The crystal structure of DNA mismatch repair protein MutS binding to a G x T mismatch
    • Lamers, M. H., Perrakis, A., Enzlin, J. H., Winterwerp, H. H., de Wind, N. & Sixma, T. K. (2000). The crystal structure of DNA mismatch repair protein MutS binding to a G x T mismatch. Nature, 407, 711-717.
    • (2000) Nature , vol.407 , pp. 711-717
    • Lamers, M.H.1    Perrakis, A.2    Enzlin, J.H.3    Winterwerp, H.H.4    De Wind, N.5    Sixma, T.K.6
  • 9
    • 60149104870 scopus 로고    scopus 로고
    • Indirect readout of DNA sequence by proteins
    • (Rice, P. A. & Correll, C. C., eds), Royal Society of Chemistry, Cambridge, UK
    • Lawson, C. L. & Berman, H. M. (2008). Indirect readout of DNA sequence by proteins. In Protein-Nucleic Acid Interactions (Rice, P. A. & Correll, C. C., eds), Royal Society of Chemistry, Cambridge, UK.
    • (2008) Protein-Nucleic Acid Interactions
    • Lawson, C.L.1    Berman, H.M.2
  • 10
    • 23444450909 scopus 로고
    • Coupling of local folding to site-specific binding of proteins to DNA
    • Spolar, R. S. & Record, M. T., Jr (1994). Coupling of local folding to site-specific binding of proteins to DNA. Science, 263, 777-784. (Pubitemid 24093205)
    • (1994) Science , vol.263 , Issue.5148 , pp. 777-784
    • Spolar, R.S.1    Record Jr., M.T.2
  • 11
    • 0030593036 scopus 로고    scopus 로고
    • Assembly of a ribonucleoprotein catalyst by tertiary structure capture
    • Weeks, K. M. & Cech, T. R. (1996). Assembly of a ribonucleoprotein catalyst by tertiary structure capture. Science, 271, 345-348.
    • (1996) Science , vol.271 , pp. 345-348
    • Weeks, K.M.1    Cech, T.R.2
  • 12
    • 0033784534 scopus 로고    scopus 로고
    • Induced fit in RNA-protein recognition
    • Williamson, J. R. (2000). Induced fit in RNA-protein recognition. Nat. Struct. Biol. 7, 834-837.
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 834-837
    • Williamson, J.R.1
  • 13
    • 0035838382 scopus 로고    scopus 로고
    • Current topics in RNA-protein recognition: Control of specificity and biological function through induced fit and conformational capture
    • DOI 10.1021/bi010680y
    • Leulliot, N. & Varani, G. (2001). Current topics in RNA-protein recognition: control of specificity and biological function through induced fit and conformational capture. Biochemistry, 40, 7947-7956. (Pubitemid 32641191)
    • (2001) Biochemistry , vol.40 , Issue.27 , pp. 7947-7956
    • Leulliot, N.1    Varani, G.2
  • 14
    • 33646768613 scopus 로고    scopus 로고
    • Poor base stacking at DNA lesions may initiate recognition by many repair proteins
    • Yang, W. (2006). Poor base stacking at DNA lesions may initiate recognition by many repair proteins. DNA Repair (Amst), 5, 654-666.
    • (2006) DNA Repair (Amst) , vol.5 , pp. 654-666
    • Yang, W.1
  • 15
    • 57549085374 scopus 로고    scopus 로고
    • Taking femtosecond snapshots of RNA conformational dynamics and complexity
    • Xia, T. (2008). Taking femtosecond snapshots of RNA conformational dynamics and complexity. Curr. Opin. Chem. Biol. 12, 604-611.
    • (2008) Curr. Opin. Chem. Biol. , vol.12 , pp. 604-611
    • Xia, T.1
  • 16
    • 70350091410 scopus 로고    scopus 로고
    • Domain-elongation NMR spectroscopy yields new insights into RNA dynamics and adaptive recognition
    • Zhang, Q. & Al-Hashimi, H. M. (2009). Domain-elongation NMR spectroscopy yields new insights into RNA dynamics and adaptive recognition. RNA, 15, 1941-1948.
    • (2009) RNA , vol.15 , pp. 1941-1948
    • Zhang, Q.1    Al-Hashimi, H.M.2
  • 17
    • 70350340728 scopus 로고    scopus 로고
    • The role of dynamic conformational ensembles in biomolecular recognition
    • Boehr, D. D., Nussinov, R. & Wright, P. E. (2009). The role of dynamic conformational ensembles in biomolecular recognition. Nat. Chem. Biol. 5, 789-796.
    • (2009) Nat. Chem. Biol. , vol.5 , pp. 789-796
    • Boehr, D.D.1    Nussinov, R.2    Wright, P.E.3
  • 18
    • 70149090164 scopus 로고    scopus 로고
    • The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding
    • Bakan, A. & Bahar, I. (2009). The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding. Proc. Natl Acad. Sci. USA, 106, 14349-14354.
    • (2009) Proc. Natl Acad. Sci. USA , vol.106 , pp. 14349-14354
    • Bakan, A.1    Bahar, I.2
  • 19
    • 0033603388 scopus 로고    scopus 로고
    • Intermediate species possessing bent DNA are present along the pathway to formation of a final TBP-TATA complex
    • DOI 10.1006/jmbi.1999.2835
    • Parkhurst, K. M., Richards, R. M., Brenowitz, M. & Parkhurst, L. J. (1999). Intermediate species possessing bent DNA are present along the pathway to formation of a final TBP-TATA complex. J. Mol. Biol. 289, 1327-1341. (Pubitemid 29296708)
    • (1999) Journal of Molecular Biology , vol.289 , Issue.5 , pp. 1327-1341
    • Parkhurst, K.M.1    Richards, R.M.2    Brenowitz, M.3    Parkhurst, L.J.4
  • 20
    • 0035839638 scopus 로고    scopus 로고
    • Marked Stepwise Differences within a Common Kinetic Mechanism Characterize TATA-binding Protein Interactions with Two Consensus Promoters
    • DOI 10.1074/jbc.M104099200
    • Powell, R. M., Parkhurst, K. M., Brenowitz, M. & Parkhurst, L. J. (2001). Marked stepwise differences within a common kinetic mechanism characterize TATA-binding protein interactions with two consensus promoters. J. Biol. Chem. 276, 29782-29791. (Pubitemid 37385047)
    • (2001) Journal of Biological Chemistry , vol.276 , Issue.32 , pp. 29782-29791
    • Powell, R.M.1    Parkhurst, K.M.2    Brenowitz, M.3    Parkhurst, L.J.4
  • 21
    • 64349107263 scopus 로고    scopus 로고
    • The TATA-binding protein core domain in solution variably bends TATA sequences via a three-step binding mechanism
    • Delgadillo, R. F., Whittington, J. E., Parkhurst, L. K. & Parkhurst, L. J. (2009). The TATA-binding protein core domain in solution variably bends TATA sequences via a three-step binding mechanism. Biochemistry, 48, 1801-1809.
    • (2009) Biochemistry , vol.48 , pp. 1801-1809
    • Delgadillo, R.F.1    Whittington, J.E.2    Parkhurst, L.K.3    Parkhurst, L.J.4
  • 22
    • 0038161225 scopus 로고    scopus 로고
    • A protein-DNA binding mechanism proceeds through multi-state or two-state parallel pathways
    • DOI 10.1016/S0022-2836(03)00720-4
    • Ferreiro, D. U. & de Prat-Gay, G. (2003). A protein-DNA binding mechanism proceeds through multi-state or two-state parallel pathways. J. Mol. Biol. 331, 89-99. (Pubitemid 36870779)
    • (2003) Journal of Molecular Biology , vol.331 , Issue.1 , pp. 89-99
    • Ferreiro, D.U.1    De Prat-Gay, G.2
  • 25
    • 0023204437 scopus 로고
    • Importance of DNA stiffness in protein-DNA binding specificity
    • DOI 10.1038/329263a0
    • Hogan, M. E. & Austin, R. H. (1987). Importance of DNA stiffness in protein-DNA binding specificity. Nature, 329, 263-266. (Pubitemid 17128973)
    • (1987) Nature , vol.329 , Issue.6136 , pp. 263-266
    • Hogan, M.E.1    Austin, R.H.2
  • 26
    • 0026766290 scopus 로고
    • Protein-induced bending and DNA cyclization
    • Kahn, J. D. & Crothers, D. M. (1992). Protein-induced bending and DNA cyclization. Proc. Natl Acad. Sci. USA, 89, 6343-6347.
    • (1992) Proc. Natl Acad. Sci. USA , vol.89 , pp. 6343-6347
    • Kahn, J.D.1    Crothers, D.M.2
  • 27
    • 0028289189 scopus 로고
    • Detection of localized DNA flexibility
    • DOI 10.1038/368163a0
    • Kahn, J. D., Yun, E. & Crothers, D. M. (1994). Detection of localized DNA flexibility. Nature, 368, 163-166. (Pubitemid 24101530)
    • (1994) Nature , vol.368 , Issue.6467 , pp. 163-166
    • Kahn, J.D.1    Yun, E.2    Crothers, D.M.3
  • 28
    • 0028919503 scopus 로고
    • Pre-bending of a promoter sequence enhances affinity for the TATA-binding factor
    • Parvin, J. D., McCormick, R. J., Sharp, P. A. & Fisher, D. E. (1995). Pre-bending of a promoter sequence enhances affinity for the TATA-binding factor. Nature, 373, 724-727.
    • (1995) Nature , vol.373 , pp. 724-727
    • Parvin, J.D.1    McCormick, R.J.2    Sharp, P.A.3    Fisher, D.E.4
  • 29
    • 0029127570 scopus 로고
    • DNA bending is an important component of site-specific recognition by the TATA binding protein
    • Starr, D. B., Hoopes, B. C. & Hawley, D. K. (1995). DNA bending is an important component of site-specific recognition by the TATA binding protein. J. Mol. Biol. 250, 434-446.
    • (1995) J. Mol. Biol. , vol.250 , pp. 434-446
    • Starr, D.B.1    Hoopes, B.C.2    Hawley, D.K.3
  • 30
    • 0030581147 scopus 로고    scopus 로고
    • Localized DNA flexibility contributes to target site selection by DNA-bending proteins
    • DOI 10.1006/jmbi.1996.0386
    • Grove, A., Galeone, A., Mayol, L. & Geiduschek, E. P. (1996). Localized DNA flexibility contributes to target site selection by DNA-bending proteins. J. Mol. Biol. 260, 120-125. (Pubitemid 26245353)
    • (1996) Journal of Molecular Biology , vol.260 , Issue.2 , pp. 120-125
    • Grove, A.1    Galeone, A.2    Mayol, L.3    Geiduschek, E.P.4
  • 31
    • 0032475962 scopus 로고    scopus 로고
    • Affinity, stability and polarity of binding of the TATA binding protein governed by flexure at the TATA box
    • DOI 10.1006/jmbi.1998.2058
    • Grove, A., Galeone, A., Yu, E., Mayol, L. & Geiduschek, E. P. (1998). Affinity, stability and polarity of binding of the TATA binding protein governed by flexure at the TATA Box. J. Mol. Biol. 282, 731-739. (Pubitemid 28442342)
    • (1998) Journal of Molecular Biology , vol.282 , Issue.4 , pp. 731-739
    • Grove, A.1    Galeone, A.2    Yu, E.3    Mayol, L.4    Geiduschek, E.P.5
  • 32
    • 0345604432 scopus 로고    scopus 로고
    • Solution measurement of DNA curvature in papillomavirus E2 binding sites
    • DOI 10.1093/nar/gkg697
    • Zimmerman, J. M. & Maher, L. J., 3rd (2003). Solution measurement of DNA curvature in papillomavirus E2 binding sites. Nucleic Acids Res. 31, 5134-5139. (Pubitemid 37441880)
    • (2003) Nucleic Acids Research , vol.31 , Issue.17 , pp. 5134-5139
    • Zimmerman, J.M.1    Maher III, L.J.2
  • 34
    • 0029008807 scopus 로고
    • Yeast TATA binding protein interaction with DNA: Fluorescence determination of oligomeric state, equilibrium binding, on-rate, and dissociation kinetics
    • Perez-Howard, G. M., Weil, P. A. & Beechem, J. M. (1995). Yeast TATA binding protein interaction with DNA: fluorescence determination of oligomeric state, equilibrium binding, on-rate, and dissociation kinetics. Biochemistry, 34, 8005-8017.
    • (1995) Biochemistry , vol.34 , pp. 8005-8017
    • Perez-Howard, G.M.1    Weil, P.A.2    Beechem, J.M.3
  • 35
    • 0029943025 scopus 로고    scopus 로고
    • Simultaneous binding and bending of promoter DNA by the TATA binding protein: Real time kinetic measurements
    • DOI 10.1021/bi9530301
    • Parkhurst, K. M., Brenowitz, M. & Parkhurst, L. J. (1996). Simultaneous binding and bending of promoter DNA by the TATA binding protein: real time kinetic measurements. Biochemistry, 35, 7459-7465. (Pubitemid 26189811)
    • (1996) Biochemistry , vol.35 , Issue.23 , pp. 7459-7465
    • Parkhurst, K.M.1    Brenowitz, M.2    Parkhurst, L.J.3
  • 36
    • 0036304119 scopus 로고    scopus 로고
    • Concerted binding and bending of DNA by Eschericia coli integration host factor
    • DOI 10.1006/jmbi.2001.5303
    • Dhavan, G. M., Crothers, D. M., Chance, M. R. & Brenowitz, M. (2002). Concerted binding and bending of DNA by Escherichia coli integration host factor. J. Mol. Biol. 315, 1027-1037. (Pubitemid 34729284)
    • (2002) Journal of Molecular Biology , vol.315 , Issue.5 , pp. 1027-1037
    • Dhavan, G.M.1    Crothers, D.M.2    Chance, M.R.3    Brenowitz, M.4
  • 37
    • 0346220020 scopus 로고    scopus 로고
    • Simultaneous DNA Binding and Bending by EcoRV Endonuclease Observed by Real-Time Fluorescence
    • DOI 10.1021/bi035520w
    • Hiller, D. A., Fogg, J. M., Martin, A. M., Beechem, J. M., Reich, N. O. & Perona, J. J. (2003). Simultaneous DNA binding and bending by EcoRV endonuclease observed by real-time fluorescence. Biochemistry, 42, 14375-14385. (Pubitemid 37531983)
    • (2003) Biochemistry , vol.42 , Issue.49 , pp. 14375-14385
    • Hiller, D.A.1    Fogg, J.M.2    Martin, A.M.3    Beechem, J.M.4    Reich, N.O.5    Perona, J.J.6
  • 38
    • 33846610053 scopus 로고    scopus 로고
    • The Effects of Nucleotides on MutS-DNA Binding Kinetics Clarify the Role of MutS ATPase Activity in Mismatch Repair
    • DOI 10.1016/j.jmb.2006.11.092, PII S002228360601655X
    • Jacobs-Palmer, E. & Hingorani, M. M. (2007). The effects of nucleotides on MutS-DNA binding kinetics clarify the role of MutS ATPase activity in mismatch repair. J. Mol. Biol. 366, 1087-1098. (Pubitemid 46186387)
    • (2007) Journal of Molecular Biology , vol.366 , Issue.4 , pp. 1087-1098
    • Jacobs-Palmer, E.1    Hingorani, M.M.2
  • 39
    • 54249112805 scopus 로고    scopus 로고
    • The role of nucleotide cofactor binding in cooperativity and specificity of MutS recognition
    • Huang, S. N. & Crothers, D. M. (2008). The role of nucleotide cofactor binding in cooperativity and specificity of MutS recognition. J. Mol. Biol. 384, 31-47.
    • (2008) J. Mol. Biol. , vol.384 , pp. 31-47
    • Huang, S.N.1    Crothers, D.M.2
  • 40
    • 0002480960 scopus 로고    scopus 로고
    • The HU and IHF proteins: Accessory factors for complex protein-DNA assemblies
    • (Lin, E. S. & Lynch, A. S., eds), Chapman and Hall, New York, NY
    • Nash, H. A. (1996). The HU and IHF proteins: accessory factors for complex protein-DNA assemblies. In Regulation of Gene Expression in E. coli (Lin, E. S. & Lynch, A. S., eds), Chapman and Hall, New York, NY.
    • (1996) Regulation of Gene Expression in E. Coli
    • Nash, H.A.1
  • 41
    • 0019783899 scopus 로고
    • Purification and properties of the Escherichia coli protein factor required for lambda integrative recombination
    • Nash, H. A. & Robertson, C. A. (1981). Purification and properties of the Escherichia coli protein factor required for lambda integrative recombination. J. Biol. Chem. 256, 9246-9253. (Pubitemid 12208316)
    • (1981) Journal of Biological Chemistry , vol.256 , Issue.17 , pp. 9246-9253
    • Nash, H.A.1    Robertson, C.A.2
  • 42
    • 0025282704 scopus 로고
    • Characterization of the integration host factor binding site in the ilvPG1 promoter region of the ilvGMEDA operon of Escherichia coli
    • Winkelman, J. W. & Hatfield, G. W. (1990). Characterization of the integration host factor binding site in the ilvPG1 promoter region of the ilvGMEDA operon of Escherichia coli. J. Biol. Chem. 265, 10055-10060.
    • (1990) J. Biol. Chem. , vol.265 , pp. 10055-10060
    • Winkelman, J.W.1    Hatfield, G.W.2
  • 43
    • 0030782227 scopus 로고    scopus 로고
    • Role of architectural elements in combinatorial regulation of initiation of DNA replication in Escherichia coli
    • Polaczek, P., Kwan, K., Liberies, D. A. & Campbell, J. L. (1997). Role of architectural elements in combinatorial regulation of initiation of DNA replication in Escherichia coli. Mol. Microbiol. 26, 261-275. (Pubitemid 27483676)
    • (1997) Molecular Microbiology , vol.26 , Issue.2 , pp. 261-275
    • Polaczek, P.1    Kwan, K.2    Liberles, D.A.3    Campbell, J.L.4
  • 44
    • 0027208111 scopus 로고
    • Function of IHF in lambda DNA packaging. I. Identification of the strong binding site for integration host factor and the locus for intrinsic bending in cosB
    • DOI 10.1006/jmbi.1993.1166
    • Xin, W. & Feiss, M. (1993). Function of IHF in lambda DNA packaging. I. Identification of the strong binding site for integration host factor and the locus for intrinsic bending in cosB. J. Mol. Biol. 230, 492-504. (Pubitemid 23161359)
    • (1993) Journal of Molecular Biology , vol.230 , Issue.2 , pp. 492-504
    • Xin, W.1    Feiss, M.2
  • 46
    • 1342324028 scopus 로고    scopus 로고
    • IHF and HU: Flexible architects of bent DNA
    • DOI 10.1016/j.sbi.2003.12.003
    • Swinger, K. K. & Rice, P. A. (2004). IHF and HU: flexible architects of bent DNA. Curr. Opin. Struct. Biol. 14, 28-35. (Pubitemid 38249589)
    • (2004) Current Opinion in Structural Biology , vol.14 , Issue.1 , pp. 28-35
    • Swinger, K.K.1    Rice, P.A.2
  • 47
    • 84859719786 scopus 로고    scopus 로고
    • Dynamics and mechanism of DNA-bending proteins in binding site recognition
    • (Williams, M. C. & Maher, L. J., eds), Springer, New York, NY
    • Ansari, A. & Kuznetsov, S. V. (2010). Dynamics and mechanism of DNA-bending proteins in binding site recognition. In Biophysics of DNA-Protein Interactions (Williams, M. C. & Maher, L. J., eds), pp. 107-142, Springer, New York, NY.
    • (2010) Biophysics of DNA-Protein Interactions , pp. 107-142
    • Ansari, A.1    Kuznetsov, S.V.2
  • 50
    • 44949085459 scopus 로고    scopus 로고
    • New insights into the transition pathway from nonspecific to specific complex of DNA with Escherichia coli integration host factor
    • Vivas, P., Kuznetsov, S. V. & Ansari, A. (2008). New insights into the transition pathway from nonspecific to specific complex of DNA with Escherichia coli integration host factor. J. Phys. Chem. B, 112, 5997-6007.
    • (2008) J. Phys. Chem. B , vol.112 , pp. 5997-6007
    • Vivas, P.1    Kuznetsov, S.V.2    Ansari, A.3
  • 51
    • 0033006629 scopus 로고    scopus 로고
    • Decreased imino proton exchange and base-pair opening in the IHF-DNA complex measured by NMR
    • DOI 10.1006/jmbi.1999.2690
    • Dhavan, G. M., Lapham, J., Yang, S. & Crothers, D. M. (1999). Decreased imino proton exchange and basepair opening in the IHF-DNA complex measured by NMR. J. Mol. Biol. 288, 659-671. (Pubitemid 29240524)
    • (1999) Journal of Molecular Biology , vol.288 , Issue.4 , pp. 659-671
    • Dhavan, G.M.1    Lapham, J.2    Yang, S.3    Crothers, D.M.4
  • 52
    • 27744578574 scopus 로고    scopus 로고
    • A nuclear magnetic resonance investigation of the energetics of basepair opening pathways in DNA
    • DOI 10.1529/biophysj.105.065763
    • Coman, D. & Russu, I. M. (2005). A nuclear magnetic resonance investigation of the energetics of basepair opening pathways in DNA. Biophys. J. 89, 3285-3292. (Pubitemid 41636083)
    • (2005) Biophysical Journal , vol.89 , Issue.5 , pp. 3285-3292
    • Coman, D.1    Russu, I.M.2
  • 54
    • 0032884399 scopus 로고    scopus 로고
    • Mutants of ETS domain PU.1 and GGAA/T recognition: Free energies and kinetics
    • Pio, F., Assa-Munt, N., Yguerabide, J. & Maki, R. A. (1999). Mutants of ETS domain PU.1 and GGAA/T recognition: free energies and kinetics. Protein Sci. 8, 2098-2109. (Pubitemid 29489938)
    • (1999) Protein Science , vol.8 , Issue.10 , pp. 2098-2109
    • Pio, F.1    Assa-Munt, N.2    Yguerabide, J.3    Maki, R.A.4
  • 55
    • 0034601780 scopus 로고    scopus 로고
    • Interaction of the Escherichia coli replication terminator protein (Tus) with DNA: A model derived from DNA-binding studies of mutant proteins by surface plasmon resonance
    • Neylon, C., Brown, S. E., Kralicek, A. V., Miles, C. S., Love, C. A. & Dixon, N. E. (2000). Interaction of the Escherichia coli replication terminator protein (Tus) with DNA: a model derived from DNA-binding studies of mutant proteins by surface plasmon resonance. Biochemistry, 39, 11989-11999.
    • (2000) Biochemistry , vol.39 , pp. 11989-11999
    • Neylon, C.1    Brown, S.E.2    Kralicek, A.V.3    Miles, C.S.4    Love, C.A.5    Dixon, N.E.6
  • 56
    • 0038206541 scopus 로고    scopus 로고
    • Mechanism of DNA binding by the ADR1 zinc finger transcription factor as determined by SPR
    • DOI 10.1016/S0022-2836(03)00550-3
    • Schaufler, L. E. & Klevit, R. E. (2003). Mechanism of DNA binding by the ADR1 zinc finger transcription factor as determined by SPR. J. Mol. Biol. 329, 931-939. (Pubitemid 36683150)
    • (2003) Journal of Molecular Biology , vol.329 , Issue.5 , pp. 931-939
    • Schaufler, L.E.1    Klevit, R.E.2
  • 57
    • 0034721922 scopus 로고    scopus 로고
    • Specific recognition of DNA by integration host factor. Glutamic acid 44 of the beta-subunit specifies the discrimination of a T:A from an A:T base pair without directly contacting the DNA
    • Read, E. K., Gumport, R. I. & Gardner, J. F. (2000). Specific recognition of DNA by integration host factor. Glutamic acid 44 of the beta-subunit specifies the discrimination of a T:A from an A:T base pair without directly contacting the DNA. J. Biol. Chem. 275, 33759-33764.
    • (2000) J. Biol. Chem. , vol.275 , pp. 33759-33764
    • Read, E.K.1    Gumport, R.I.2    Gardner, J.F.3
  • 58
    • 0038047138 scopus 로고    scopus 로고
    • Integration host factor: Putting a twist on protein-DNA recognition
    • DOI 10.1016/S0022-2836(03)00529-1
    • Lynch, T. W., Read, E. K., Mattis, A. N., Gardner, J. F. & Rice, P. A. (2003). Integration host factor: putting a twist on protein-DNA recognition. J. Mol. Biol. 330, 493-502. (Pubitemid 36808683)
    • (2003) Journal of Molecular Biology , vol.330 , Issue.3 , pp. 493-502
    • Lynch, T.W.1    Read, E.K.2    Mattis, A.N.3    Gardner, J.F.4    Rice, P.A.5
  • 59
    • 0033485813 scopus 로고    scopus 로고
    • Global structure similarities of intact and nicked DNA complexed with IHF measured in solution by fluorescence resonance energy transfer
    • Lorenz, M., Hillisch, A., Goodman, S. D. & Diekmann, S. (1999). Global structure similarities of intact and nicked DNA complexed with IHF measured in solution by fluorescence resonance energy transfer. Nucleic Acids Res. 27, 4619-4625.
    • (1999) Nucleic Acids Res. , vol.27 , pp. 4619-4625
    • Lorenz, M.1    Hillisch, A.2    Goodman, S.D.3    Diekmann, S.4
  • 61
    • 33845796196 scopus 로고    scopus 로고
    • Structure-based Analysis of HU-DNA Binding
    • DOI 10.1016/j.jmb.2006.10.024, PII S0022283606013623
    • Swinger, K. K. & Rice, P. A. (2007). Structure-based analysis of HU-DNA binding. J. Mol. Biol. 365, 1005-1016. (Pubitemid 46014175)
    • (2007) Journal of Molecular Biology , vol.365 , Issue.4 , pp. 1005-1016
    • Swinger, K.K.1    Rice, P.A.2
  • 62
    • 33646205283 scopus 로고    scopus 로고
    • Microsecond dynamics of protein-DNA interactions: Direct observation of the wrapping/unwrapping kinetics of single-stranded DNA around the E. coli SSB tetramer
    • Kuznetsov, S. V., Kozlov, A. G., Lohman, T. M. & Ansari, A. (2006). Microsecond dynamics of protein-DNA interactions: direct observation of the wrapping/unwrapping kinetics of single-stranded DNA around the E. coli SSB tetramer. J. Mol. Biol. 359, 55-65.
    • (2006) J. Mol. Biol. , vol.359 , pp. 55-65
    • Kuznetsov, S.V.1    Kozlov, A.G.2    Lohman, T.M.3    Ansari, A.4
  • 64
    • 0041312645 scopus 로고    scopus 로고
    • Flexible DNA bending in HU-DNA cocrystal structures
    • DOI 10.1093/emboj/cdg351
    • Swinger, K. K., Lemberg, K. M., Zhang, Y. & Rice, P. A. (2003). Flexible DNA bending in HU-DNA cocrystal structures. EMBO J. 22, 3749-3760. (Pubitemid 36898351)
    • (2003) EMBO Journal , vol.22 , Issue.14 , pp. 3749-3760
    • Swinger, K.K.1    Lemberg, K.M.2    Zhang, Y.3    Rice, P.A.4
  • 65
    • 33846954751 scopus 로고    scopus 로고
    • Shaping the Borrelia burgdorferi genome: Crystal structure and binding properties of the DNA-bending Hbb
    • Mouw, K. M. & Rice, P. A. (2007). Shaping the Borrelia burgdorferi genome: crystal structure and binding properties of the DNA-bending Hbb. Mol. Microbiol. 63, 1319-1330.
    • (2007) Mol. Microbiol. , vol.63 , pp. 1319-1330
    • Mouw, K.M.1    Rice, P.A.2
  • 67
    • 0028301832 scopus 로고
    • Electrophoretic evidence that single-stranded regions of one or more nucleotides dramatically increase the flexibility of DNA
    • Mills, J. B., Cooper, J. P. & Hagerman, P. J. (1994). Electrophoretic evidence that single-stranded regions of one or more nucleotides dramatically increase the flexibility of DNA. Biochemistry, 33, 1797-1803. (Pubitemid 24089708)
    • (1994) Biochemistry , vol.33 , Issue.7 , pp. 1797-1803
    • Mills, J.B.1    Cooper, J.P.2    Hagerman, P.J.3
  • 69
    • 4444260310 scopus 로고    scopus 로고
    • Stacked-unstacked equilibrium at the nick site of DNA
    • DOI 10.1016/j.jmb.2004.07.075, PII S0022283604009167
    • Protozanova, E., Yakovchuk, P. & Frank-Kamenetskii, M. D. (2004). Stacked-unstacked equilibrium at the nick site of DNA. J. Mol. Biol. 342, 775-785. (Pubitemid 39165649)
    • (2004) Journal of Molecular Biology , vol.342 , Issue.3 , pp. 775-785
    • Protozanova, E.1    Yakovchuk, P.2    Frank-Kamenetskii, M.D.3
  • 70
    • 19544379865 scopus 로고    scopus 로고
    • Localized single-stranded bubble mechanism for cyclization of short double helix DNA
    • Yan, J. & Marko, J. F. (2004). Localized single-stranded bubble mechanism for cyclization of short double helix DNA. Phys. Rev. Lett. 93, 108108.
    • (2004) Phys. Rev. Lett. , vol.93 , pp. 108108
    • Yan, J.1    Marko, J.F.2
  • 71
    • 41349084347 scopus 로고    scopus 로고
    • Exact theory of kinkable elastic polymers
    • Wiggins, P. A., Phillips, R. & Nelson, P. C. (2005). Exact theory of kinkable elastic polymers. Phys. Rev. E, 71, 021909.
    • (2005) Phys. Rev. E , vol.71 , pp. 021909
    • Wiggins, P.A.1    Phillips, R.2    Nelson, P.C.3
  • 73
    • 33749259954 scopus 로고    scopus 로고
    • Kinking Occurs during Molecular Dynamics Simulations of Small DNA Minicircles
    • DOI 10.1016/j.str.2006.08.004, PII S0969212606003522
    • Lankas, F., Lavery, R. & Maddocks, J. H. (2006). Kinking occurs during molecular dynamics simulations of small DNA minicircles. Structure, 14, 1527-1534. (Pubitemid 44486810)
    • (2006) Structure , vol.14 , Issue.10 , pp. 1527-1534
    • Lankas, F.1    Lavery, R.2    Maddocks, J.H.3
  • 74
    • 2342518189 scopus 로고    scopus 로고
    • Spontaneous sharp bending of double-stranded DNA
    • DOI 10.1016/S1097-2765(04)00210-2, PII S1097276504002102
    • Cloutier, T. E. & Widom, J. (2004). Spontaneous sharp bending of double-stranded DNA. Mol. Cell, 14, 355-362. (Pubitemid 38591406)
    • (2004) Molecular Cell , vol.14 , Issue.3 , pp. 355-362
    • Cloutier, T.E.1    Widom, J.2
  • 76
    • 40249090005 scopus 로고    scopus 로고
    • Kinking the double helix by bending deformation
    • DOI 10.1093/nar/gkm1125
    • Du, Q., Kotlyar, A. & Vologodskii, A. (2008). Kinking the double helix by bending deformation. Nucleic Acids Res. 36, 1120-1128. (Pubitemid 351330930)
    • (2008) Nucleic Acids Research , vol.36 , Issue.4 , pp. 1120-1128
    • Du, Q.1    Kotlyar, A.2    Vologodskii, A.3
  • 77
    • 17844406392 scopus 로고    scopus 로고
    • Induced fit and the entropy of structural adaptation in the complexation of CAP and lambda-repressor with cognate DNA sequences
    • DOI 10.1529/biophysj.104.053843
    • Dixit, S. B., Andrews, D. Q. & Beveridge, D. L. (2005). Induced fit and the entropy of structural adaptation in the complexation of CAP and lambda-repressor with cognate DNA sequences. Biophys. J. 88, 3147-3157. (Pubitemid 40586568)
    • (2005) Biophysical Journal , vol.88 , Issue.5 , pp. 3147-3157
    • Dixit, S.B.1    Andrews, D.Q.2    Beveridge, D.L.3
  • 78
    • 0029080688 scopus 로고
    • Thermodynamic and kinetic characterization of the binding of the TATA binding protein to the adenovirus E4 promoter
    • Petri, V., Hsieh, M. & Brenowitz, M. (1995). Thermodynamic and kinetic characterization of the binding of the TATA binding protein to the adenovirus E4 promoter. Biochemistry, 34, 9977-9984.
    • (1995) Biochemistry , vol.34 , pp. 9977-9984
    • Petri, V.1    Hsieh, M.2    Brenowitz, M.3
  • 81
    • 0030985132 scopus 로고    scopus 로고
    • Rapid-reaction analysis of plasmid DNA cleavage by the EcoRV restriction endonuclease
    • DOI 10.1021/bi970155s
    • Erskine, S. G., Baldwin, G. S. & Halford, S. E. (1997). Rapid-reaction analysis of plasmid DNA cleavage by the EcoRV restriction endonuclease. Biochemistry, 36, 7567-7576. (Pubitemid 27262383)
    • (1997) Biochemistry , vol.36 , Issue.24 , pp. 7567-7576
    • Erskine, S.G.1    Baldwin, G.S.2    Halford, S.E.3
  • 82
    • 65549171477 scopus 로고    scopus 로고
    • An end to 40 years of mistakes in DNA-protein association kinetics?
    • Halford, S. E. (2009). An end to 40 years of mistakes in DNA-protein association kinetics? Biochem. Soc. Trans. 37, 343-348.
    • (2009) Biochem. Soc. Trans. , vol.37 , pp. 343-348
    • Halford, S.E.1
  • 83
    • 33749039501 scopus 로고    scopus 로고
    • Positively charged C-terminal subdomains of EcoRV endonuclease: Contributions to DNA binding, bending, and cleavage
    • DOI 10.1021/bi0606400
    • Hiller, D. A. & Perona, J. J. (2006). Positively charged C-terminal subdomains of EcoRV endonuclease: contributions to DNA binding, bending, and cleavage. Biochemistry, 45, 11453-11463. (Pubitemid 44453993)
    • (2006) Biochemistry , vol.45 , Issue.38 , pp. 11453-11463
    • Hiller, D.A.1    Perona, J.J.2
  • 84
    • 84863903852 scopus 로고    scopus 로고
    • How proteins slide on DNA
    • (Williams, M. C. & Maher, L. J., eds), Springer, New York, NY
    • Barsky, D., Laurence, T. A. & Venclovas, C. (2010). How proteins slide on DNA. In Biophysics of DNA-Protein Interactions (Williams, M. C. & Maher, L. J., eds), pp. 39-68, Springer, New York, NY.
    • (2010) Biophysics of DNA-Protein Interactions , pp. 39-68
    • Barsky, D.1    Laurence, T.A.2    Venclovas, C.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.