메뉴 건너뛰기




Volumn 410, Issue 2, 2011, Pages 241-267

Nonspecific DNA binding and bending by HUαβ: Interfaces of the three binding modes characterized by salt-dependent thermodynamics

Author keywords

DNA bending; DNA binding mode; HU protein; isothermal titration calorimetry; salt concentration dependent thermodynamics

Indexed keywords

CURVED DNA; DNA DIRECTED DNA POLYMERASE BETA; HU PROTEIN; INTEGRATION HOST FACTOR; POLYCATION; POLYELECTROLYTE; SODIUM CHLORIDE;

EID: 79958732532     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2011.04.001     Document Type: Article
Times cited : (18)

References (106)
  • 1
    • 14244263426 scopus 로고    scopus 로고
    • Major nucleoid proteins in the structure and function of the Escherichia coli chromosome
    • (Higgins, N. P., ed.), ASM Press, Washington, DC
    • Johnson, R. C., Johnson, L. M., Schmidt, J. W. & Gardner, J. F. (2005). Major nucleoid proteins in the structure and function of the Escherichia coli chromosome. In The Bacterial Chromosome (Higgins, N. P., ed.), pp. 65-132, ASM Press, Washington, DC.
    • (2005) The Bacterial Chromosome , pp. 65-132
    • Johnson, R.C.1    Johnson, L.M.2    Schmidt, J.W.3    Gardner, J.F.4
  • 2
    • 0023413620 scopus 로고
    • Histonelike proteins of bacteria
    • Drlica, K. & Rouviere-Yaniv, J. (1987). Histonelike proteins of bacteria. Microbiol. Rev. 51, 301-319.
    • (1987) Microbiol. Rev. , vol.51 , pp. 301-319
    • Drlica, K.1    Rouviere-Yaniv, J.2
  • 3
    • 0034703060 scopus 로고    scopus 로고
    • Global gene expression profiling in Escherichia coli K12. The effects of integration host factor
    • Arfin, S. M., Long, A. D., Ito, E. T., Tolleri, L., Riehle, M. M., Paegle, E. S. & Hatfield, G. W. (2000). Global gene expression profiling in Escherichia coli K12. The effects of integration host factor. J. Biol. Chem. 275, 29672-29684.
    • (2000) J. Biol. Chem. , vol.275 , pp. 29672-29684
    • Arfin, S.M.1    Long, A.D.2    Ito, E.T.3    Tolleri, L.4    Riehle, M.M.5    Paegle, E.S.6    Hatfield, G.W.7
  • 4
    • 0024291348 scopus 로고
    • Integration host factor: A protein for all reasons
    • Friedman, D. I. (1988). Integration host factor: a protein for all reasons. Cell, 55, 545-554.
    • (1988) Cell , vol.55 , pp. 545-554
    • Friedman, D.I.1
  • 5
    • 34247517469 scopus 로고    scopus 로고
    • DNA-protein interactions and bacterial chromosome architecture
    • Stavans, J. & Oppenheim, A. (2006). DNA-protein interactions and bacterial chromosome architecture. Phys. Biol. 3, R1-R10.
    • (2006) Phys. Biol. , vol.3
    • Stavans, J.1    Oppenheim, A.2
  • 6
    • 1342324028 scopus 로고    scopus 로고
    • IHF and HU: Flexible architects of bent DNA
    • Swinger, K. K. & Rice, P. A. (2004). IHF and HU: flexible architects of bent DNA. Curr. Opin. Struct. Biol. 14, 28-35.
    • (2004) Curr. Opin. Struct. Biol. , vol.14 , pp. 28-35
    • Swinger, K.K.1    Rice, P.A.2
  • 7
    • 0032731196 scopus 로고    scopus 로고
    • Twelve species of the nucleoid-associated protein from Escherichia coli. Sequence recognition specificity and DNA binding affinity
    • Azam, T. A. & Ishihama, A. (1999). Twelve species of the nucleoid-associated protein from Escherichia coli. Sequence recognition specificity and DNA binding affinity. J. Biol. Chem. 274, 33105-33113.
    • (1999) J. Biol. Chem. , vol.274 , pp. 33105-33113
    • Azam, T.A.1    Ishihama, A.2
  • 8
    • 33750527566 scopus 로고    scopus 로고
    • The architectural role of nucleoid-associated proteins in the organization of bacterial chromatin: A molecular perspective
    • Luijsterburg, M. S., Noom, M. C., Wuite, G. J. & Dame, R. T. (2006). The architectural role of nucleoid-associated proteins in the organization of bacterial chromatin: a molecular perspective. J. Struct. Biol. 156, 262-272.
    • (2006) J. Struct. Biol. , vol.156 , pp. 262-272
    • Luijsterburg, M.S.1    Noom, M.C.2    Wuite, G.J.3    Dame, R.T.4
  • 9
    • 1842411320 scopus 로고    scopus 로고
    • Crystal structure of the nucleosome core particle at 2.8 Å resolution
    • DOI 10.1038/38444
    • Luger, K., Mader, A. W., Richmond, R. K., Sargent, D. F. & Richmond, T. J. (1997). Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature, 389, 251-260. (Pubitemid 27406632)
    • (1997) Nature , vol.389 , Issue.6648 , pp. 251-260
    • Luger, K.1    Mader, A.W.2    Richmond, R.K.3    Sargent, D.F.4    Richmond, T.J.5
  • 10
    • 52949086418 scopus 로고    scopus 로고
    • DNA binding mode transitions of Escherichia coli HU (alphabeta): Evidence for formation of a bent DNA-protein complex on intact, linear duplex DNA
    • Koh, J., Saecker, R. M. & Record, M. T., Jr (2008). DNA binding mode transitions of Escherichia coli HU (alphabeta): evidence for formation of a bent DNA-protein complex on intact, linear duplex DNA. J. Mol. Biol. 383, 324-346.
    • (2008) J. Mol. Biol. , vol.383 , pp. 324-346
    • Koh, J.1    Saecker, R.M.2    Record Jr., M.T.3
  • 11
    • 2342454974 scopus 로고    scopus 로고
    • Dual architectural roles of HU: Formation of flexible hinges and rigid filaments
    • van Noort, J., Verbrugge, S., Goosen, N., Dekker, C. & Dame, R. T. (2004). Dual architectural roles of HU: formation of flexible hinges and rigid filaments. Proc. Natl Acad. Sci. USA, 101, 6969-6974.
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 6969-6974
    • Van Noort, J.1    Verbrugge, S.2    Goosen, N.3    Dekker, C.4    Dame, R.T.5
  • 12
    • 7244245362 scopus 로고    scopus 로고
    • Micromechanical analysis of the binding of DNA-bending proteins HMGB1, NHP6A, and HU reveals their ability to form highly stable DNA-protein complexes
    • Skoko, D., Wong, B., Johnson, R. C. & Marko, J. F. (2004). Micromechanical analysis of the binding of DNA-bending proteins HMGB1, NHP6A, and HU reveals their ability to form highly stable DNA-protein complexes. Biochemistry, 43, 13867-13874.
    • (2004) Biochemistry , vol.43 , pp. 13867-13874
    • Skoko, D.1    Wong, B.2    Johnson, R.C.3    Marko, J.F.4
  • 13
    • 0037048702 scopus 로고    scopus 로고
    • HU: Promoting or counteracting DNA compaction?
    • Dame, R. T. & Goosen, N. (2002). HU: promoting or counteracting DNA compaction? FEBS Lett. 529, 151-156.
    • (2002) FEBS Lett. , vol.529 , pp. 151-156
    • Dame, R.T.1    Goosen, N.2
  • 14
    • 0026019440 scopus 로고
    • HU and IHF, two homologous histone-like proteins of Escherichia coli, form different protein - DNA complexes with short DNA fragments
    • Bonnefoy, E. & Rouviere-Yaniv, J. (1991). HU and IHF, two homologous histone-like proteins of Escherichia coli, form different protein-DNA complexes with short DNA fragments. EMBO J. 10, 687-696. (Pubitemid 21905524)
    • (1991) EMBO Journal , vol.10 , Issue.3 , pp. 687-696
    • Bonnefoy, E.1    Rouviere-Yaniv, J.2
  • 15
    • 0033515646 scopus 로고    scopus 로고
    • Differential binding of the Escherichia coli HU, homodimeric forms and heterodimeric form to linear, gapped and cruciform DNA
    • Pinson, V., Takahashi, M. & Rouviere-Yaniv, J. (1999). Differential binding of the Escherichia coli HU, homodimeric forms and heterodimeric form to linear, gapped and cruciform DNA. J. Mol. Biol. 287, 485-497.
    • (1999) J. Mol. Biol. , vol.287 , pp. 485-497
    • Pinson, V.1    Takahashi, M.2    Rouviere-Yaniv, J.3
  • 16
    • 79955878276 scopus 로고    scopus 로고
    • HU binding to DNA: Evidence for multiple complex formation and DNA bending
    • vol. 40, p. 2588, 2001
    • Wojtuszewski, K., Hawkins, M. E., Cole, J. L. & Mukerji, I. (2001). HU binding to DNA: evidence for multiple complex formation and DNA bending.; (vol. 40, p. 2588, 2001). Biochemistry, 40, 4892.
    • (2001) Biochemistry , vol.40 , pp. 4892
    • Wojtuszewski, K.1    Hawkins, M.E.2    Cole, J.L.3    Mukerji, I.4
  • 17
    • 0037452946 scopus 로고    scopus 로고
    • HU binding to bent DNA: A fluorescence resonance energy transfer and anisotropy study
    • DOI 10.1021/bi0264014
    • Wojtuszewski, K. & Mukerji, I. (2003). HU binding to bent DNA: a fluorescence resonance energy transfer and anisotropy study. Biochemistry, 42, 3096-3104. (Pubitemid 36331555)
    • (2003) Biochemistry , vol.42 , Issue.10 , pp. 3096-3104
    • Wojtuszewski, K.1    Mukerji, I.2
  • 18
    • 41149097061 scopus 로고    scopus 로고
    • Mechanisms of specific and nonspecific binding of architectural proteins in prokaryotic gene regulation
    • Benevides, J. M., Danahy, J., Kawakami, J. & Thomas, G. J., Jr (2008). Mechanisms of specific and nonspecific binding of architectural proteins in prokaryotic gene regulation. Biochemistry, 47, 3855-3862.
    • (2008) Biochemistry , vol.47 , pp. 3855-3862
    • Benevides, J.M.1    Danahy, J.2    Kawakami, J.3    Thomas Jr., G.J.4
  • 19
    • 0018405881 scopus 로고
    • E. coli DNA binding protein HU forms nucleosome like structure with circular double stranded DNA
    • Rouviere-Yaniv, J., Yaniv, M. & Germond, J. E. (1979). E. coli DNA binding protein HU forms nucleosome-like structure with circular double-stranded DNA. Cell, 17, 265-274. (Pubitemid 9230307)
    • (1979) Cell , vol.17 , Issue.2 , pp. 265-274
    • Rouviere-Yaniv, J.1    Yaniv, M.2    Germond, J.E.3
  • 20
    • 0023041804 scopus 로고
    • Interaction of the Escherichia coli HU protein with DNA. Evidence for formation of nucleosome-like structures with altered DNA helical pitch
    • Broyles, S. S. & Pettijohn, D. E. (1986). Interaction of the Escherichia coli HU protein with DNA. Evidence for formation of nucleosome-like structures with altered DNA helical pitch. J. Mol. Biol. 187, 47-60.
    • (1986) J. Mol. Biol. , vol.187 , pp. 47-60
    • Broyles, S.S.1    Pettijohn, D.E.2
  • 21
    • 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
  • 23
    • 0021286693 scopus 로고
    • 3-Å resolution structure of a protein with histone-like properties in prokaryotes
    • Tanaka, I., Appelt, K., Dijk, J., White, S. W. & Wilson, K. S. (1984). 3-Å resolution structure of a protein with histone-like properties in prokaryotes. Nature, 310, 376-381. (Pubitemid 14051101)
    • (1984) Nature , vol.310 , Issue.5976 , pp. 376-381
    • Tanaka, I.1    Appelt, K.2    Dijk, J.3
  • 24
    • 0024403429 scopus 로고
    • Negative cooperativity in Escherichia coli single strand binding protein-oligonucleotide interactions: I. Evidence and a quantitative model
    • Bujalowski, W. & Lohman, T. M. (1989). Negative cooperativity in Escherichia coli single strand binding protein-oligonucleotide interactions: I. Evidence and a quantitative model. J. Mol. Biol. 207, 249-268.
    • (1989) J. Mol. Biol. , vol.207 , pp. 249-268
    • Bujalowski, W.1    Lohman, T.M.2
  • 25
    • 0021920551 scopus 로고
    • Two binding modes in Escherichia coli single strand binding protein-single stranded DNA complexes. Modulation by NaCl concentration
    • Lohman, T. M. & Overman, L. B. (1985). Two binding modes in Escherichia coli single strand binding protein-single stranded DNA complexes. Modulation by NaCl concentration. J. Biol. Chem. 260, 3594-3603.
    • (1985) J. Biol. Chem. , vol.260 , pp. 3594-3603
    • Lohman, T.M.1    Overman, L.B.2
  • 26
    • 0023040461 scopus 로고
    • Escherichia coli single-strand binding protein forms multiple, distinct complexes with single-stranded DNA
    • Bujalowski, W. & Lohman, T. M. (1986). Escherichia coli single-strand binding protein forms multiple, distinct complexes with single-stranded DNA. Biochemistry, 25, 7799-7802.
    • (1986) Biochemistry , vol.25 , pp. 7799-7802
    • Bujalowski, W.1    Lohman, T.M.2
  • 27
    • 0023916373 scopus 로고
    • Binding mode transitions of Escherichia coli single strand binding protein-single-stranded DNA complexes. Cation, anion, pH, and binding density effects
    • Bujalowski, W., Overman, L. B. & Lohman, T. M. (1988). Binding mode transitions of Escherichia coli single strand binding protein-single-stranded DNA complexes. Cation, anion, pH, and binding density effects. J. Biol. Chem. 263, 4629-4640.
    • (1988) J. Biol. Chem. , vol.263 , pp. 4629-4640
    • Bujalowski, W.1    Overman, L.B.2    Lohman, T.M.3
  • 28
    • 0028246888 scopus 로고
    • Escherichia coli single-stranded DNA-binding protein: Multiple DNA-binding modes and cooperativities
    • Lohman, T. M. & Ferrari, M. E. (1994). Escherichia coli single-stranded DNA-binding protein: multiple DNA-binding modes and cooperativities. Annu. Rev. Biochem. 63, 527-570.
    • (1994) Annu. Rev. Biochem. , vol.63 , pp. 527-570
    • Lohman, T.M.1    Ferrari, M.E.2
  • 29
    • 33749354956 scopus 로고    scopus 로고
    • Saccharomyces cerevisiae replication protein A binds to single-stranded DNA in multiple salt-dependent modes
    • DOI 10.1021/bi060994r
    • Kumaran, S., Kozlov, A. G. & Lohman, T. M. (2006). Saccharomyces cerevisiae replication protein A binds to single-stranded DNA in multiple salt-dependent modes. Biochemistry, 45, 11958-11973. (Pubitemid 44497821)
    • (2006) Biochemistry , vol.45 , Issue.39 , pp. 11958-11973
    • Kumaran, S.1    Kozlov, A.G.2    Lohman, T.M.3
  • 30
    • 0032553313 scopus 로고    scopus 로고
    • Human DNA polymerase beta recognizes single-stranded DNA using two different binding modes
    • Rajendran, S., Jezewska, M. J. & Bujalowski, W. (1998). Human DNA polymerase beta recognizes single-stranded DNA using two different binding modes. J. Biol. Chem. 273, 31021-31031.
    • (1998) J. Biol. Chem. , vol.273 , pp. 31021-31031
    • Rajendran, S.1    Jezewska, M.J.2    Bujalowski, W.3
  • 31
    • 0032509151 scopus 로고    scopus 로고
    • Transition between different binding modes in rat DNA polymerase beta-ssDNA complexes
    • Jezewska, M. J., Rajendran, S. & Bujalowski, W. (1998). Transition between different binding modes in rat DNA polymerase beta-ssDNA complexes. J. Mol. Biol. 284, 1113-1131.
    • (1998) J. Mol. Biol. , vol.284 , pp. 1113-1131
    • Jezewska, M.J.1    Rajendran, S.2    Bujalowski, W.3
  • 32
    • 0031776135 scopus 로고    scopus 로고
    • Analysis of effects of salts and uncharged solutes on protein and nucleic acid equilibria and processes: A practical guide to recognizing and interpreting polyelectrolyte effects, Hofmeister effects, and osmotic effects of salts
    • Record, M. T., Jr, Zhang, W. & Anderson, C. F. (1998). Analysis of effects of salts and uncharged solutes on protein and nucleic acid equilibria and processes: a practical guide to recognizing and interpreting polyelectrolyte effects, Hofmeister effects, and osmotic effects of salts. Adv. Protein Chem. 51, 281-353.
    • (1998) Adv. Protein Chem. , vol.51 , pp. 281-353
    • Record Jr., M.T.1    Zhang, W.2    Anderson, C.F.3
  • 33
    • 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
    • Record, M. T., Jr, Anderson, C. F. & Lohman, T. M. (1978). 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, 103-178.
    • (1978) Q. Rev. Biophys. , vol.11 , pp. 103-178
    • Record Jr., M.T.1    Anderson, C.F.2    Lohman, T.M.3
  • 34
    • 39649115803 scopus 로고    scopus 로고
    • Formation of a wrapped DNA-protein interface: Experimental characterization and analysis of the large contributions of ions and water to the thermodynamics of binding IHF to H′ DNA
    • Vander Meulen, K. A., Saecker, R. M. & Record, M. T., Jr (2008). Formation of a wrapped DNA-protein interface: experimental characterization and analysis of the large contributions of ions and water to the thermodynamics of binding IHF to H′ DNA. J. Mol. Biol. 377, 9-27.
    • (2008) J. Mol. Biol. , vol.377 , pp. 9-27
    • Vander Meulen, K.A.1    Saecker, R.M.2    Record Jr., M.T.3
  • 35
    • 49649112395 scopus 로고    scopus 로고
    • Thermodynamic origin of Hofmeister ion effects
    • Pegram, L. M. & Record, M. T., Jr (2008). Thermodynamic origin of Hofmeister ion effects. J. Phys. Chem. B, 112, 9428-9436.
    • (2008) J. Phys. Chem. B , vol.112 , pp. 9428-9436
    • Pegram, L.M.1    Record Jr., M.T.2
  • 36
    • 0017146579 scopus 로고
    • Ion effects on ligand-nucleic acid interactions
    • Record, M. T., Jr, Lohman, M. L. & De Haseth, P. (1976). Ion effects on ligand-nucleic acid interactions. J. Mol. Biol. 107, 145-158.
    • (1976) J. Mol. Biol. , vol.107 , pp. 145-158
    • Record Jr., M.T.1    Lohman, M.L.2    De Haseth, P.3
  • 37
    • 0025264701 scopus 로고
    • Thermodynamic extent of counterion release upon binding oligolysines to single-stranded nucleic acids
    • Mascotti, D. P. & Lohman, T. M. (1990). Thermodynamic extent of counterion release upon binding oligolysines to single-stranded nucleic acids. Proc. Natl Acad. Sci. USA, 87, 3142-3146.
    • (1990) Proc. Natl Acad. Sci. USA , vol.87 , pp. 3142-3146
    • Mascotti, D.P.1    Lohman, T.M.2
  • 39
    • 0029047968 scopus 로고
    • On the magnitude of the electrostatic contribution to ligand-DNA interactions
    • Misra, V. K. & Honig, B. (1995). On the magnitude of the electrostatic contribution to ligand-DNA interactions. Proc. Natl Acad. Sci. USA, 92, 4691-4695.
    • (1995) Proc. Natl Acad. Sci. USA , vol.92 , pp. 4691-4695
    • Misra, V.K.1    Honig, B.2
  • 40
    • 0029038105 scopus 로고
    • Salt effects on polyelectrolyte-ligand binding: Comparison of Poisson-Boltzmann, and limiting law/counterion binding models
    • Sharp, K. A., Friedman, R. A., Misra, V., Hecht, J. & Honig, B. (1995). Salt effects on polyelectrolyte-ligand binding: comparison of Poisson-Boltzmann, and limiting law/counterion binding models. Biopolymers, 36, 245-262.
    • (1995) Biopolymers , vol.36 , pp. 245-262
    • Sharp, K.A.1    Friedman, R.A.2    Misra, V.3    Hecht, J.4    Honig, B.5
  • 41
    • 0019330787 scopus 로고
    • Pentalysine-deoxyribonucleic acid interactions: A model for the general effects of ion concentrations on the interactions of proteins with nucleic acids
    • Lohman, T. M., deHaseth, P. L. & Record, M. T., Jr (1980). Pentalysine-deoxyribonucleic acid interactions: a model for the general effects of ion concentrations on the interactions of proteins with nucleic acids. Biochemistry, 19, 3522-3530.
    • (1980) Biochemistry , vol.19 , pp. 3522-3530
    • Lohman, T.M.1    DeHaseth, P.L.2    Record Jr., M.T.3
  • 42
    • 0019942441 scopus 로고
    • Equilibrium dialysis studies of polyamine binding to DNA
    • Braunlin, W. H., Strick, T. J. & Record, M. T., Jr (1982). Equilibrium dialysis studies of polyamine binding to DNA. Biopolymers, 21, 1301-1314.
    • (1982) Biopolymers , vol.21 , pp. 1301-1314
    • Braunlin, W.H.1    Strick, T.J.2    Record Jr., M.T.3
  • 43
    • 0026730188 scopus 로고
    • Thermodynamics of single-stranded RNA binding to oligolysines containing tryptophan
    • Mascotti, D. P. & Lohman, T. M. (1992). Thermodynamics of single-stranded RNA binding to oligolysines containing tryptophan. Biochemistry, 31, 8932-8946.
    • (1992) Biochemistry , vol.31 , pp. 8932-8946
    • Mascotti, D.P.1    Lohman, T.M.2
  • 44
    • 0027379588 scopus 로고
    • Thermodynamics of single-stranded RNA and DNA interactions with oligolysines containing tryptophan. Effects of base composition
    • Mascotti, D. P. & Lohman, T. M. (1993). Thermodynamics of single-stranded RNA and DNA interactions with oligolysines containing tryptophan. Effects of base composition. Biochemistry, 32, 10568-10579.
    • (1993) Biochemistry , vol.32 , pp. 10568-10579
    • Mascotti, D.P.1    Lohman, T.M.2
  • 45
    • 0030920231 scopus 로고    scopus 로고
    • Thermodynamics of oligoarginines binding to RNA and DNA
    • DOI 10.1021/bi970272n
    • Mascotti, D. P. & Lohman, T. M. (1997). Thermodynamics of oligoarginines binding to RNA and DNA. Biochemistry, 36, 7272-7279. (Pubitemid 27258144)
    • (1997) Biochemistry , vol.36 , Issue.23 , pp. 7272-7279
    • Mascotti, D.P.1    Lohman, T.M.2
  • 46
    • 0031576995 scopus 로고    scopus 로고
    • Thermodynamics of the interactions of lac repressor with variants of the symmetric lac operator: Effects of converting a consensus site to a non-specific site
    • Frank, D. E., Saecker, R. M., Bond, J. P., Capp, M. W., Tsodikov, O. V., Melcher, S. E. et al. (1997). Thermodynamics of the interactions of lac repressor with variants of the symmetric lac operator: effects of converting a consensus site to a non-specific site. J. Mol. Biol. 267, 1186-1206.
    • (1997) J. Mol. Biol. , vol.267 , pp. 1186-1206
    • Frank, D.E.1    Saecker, R.M.2    Bond, J.P.3    Capp, M.W.4    Tsodikov, O.V.5    Melcher, S.E.6
  • 47
    • 0029883976 scopus 로고    scopus 로고
    • Equilibrium DNA binding of Sac7d protein from the hyperthermophile Sulfolobus acidocaldarius: Fluorescence and circular dichroism studies
    • DOI 10.1021/bi952555q
    • McAfee, J. G., Edmondson, S. P., Zegar, I. & Shriver, J. W. (1996). Equilibrium DNA binding of Sac7d protein from the hyperthermophile Sulfolobus acidocaldarius: fluorescence and circular dichroism studies. Biochemistry, 35, 4034-4045. (Pubitemid 26113460)
    • (1996) Biochemistry , vol.35 , Issue.13 , pp. 4034-4045
    • McAfee, J.G.1    Edmondson, S.P.2    Zegar, I.3    Shriver, J.W.4
  • 48
    • 0032510217 scopus 로고    scopus 로고
    • The hyperthermophile chromsomal protein Sac7d sharply kinks DNA
    • DOI 10.1038/32455
    • Robinson, H., Gao, Y. G., McCrary, B. S., Edmondson, S. P., Shriver, J. W. & Wang, A. H. (1998). The hyperthermophile chromosomal protein Sac7d sharply kinks DNA. Nature, 392, 202-205. (Pubitemid 28162796)
    • (1998) Nature , vol.392 , Issue.6672 , pp. 202-205
    • Robinson, H.1    Gao, Y.-G.2    McCrary, B.S.3    Edmondson, S.P.4    Shriver, J.W.5    Wang, A.H.-J.6
  • 49
    • 0000162429 scopus 로고    scopus 로고
    • Salt dependence of the free energy, enthalpy, and entropy of nonsequence specific DNA binding
    • Lundback, T. & Hard, T. (1996). Salt dependence of the free energy, enthalpy, and entropy of nonsequence specific DNA binding. J. Phys. Chem. 100, 17690-17695.
    • (1996) J. Phys. Chem. , vol.100 , pp. 17690-17695
    • Lundback, T.1    Hard, T.2
  • 50
    • 0031718377 scopus 로고    scopus 로고
    • The crystal structure of the hyperthermophile chromosomal protein Sso7d bound to DNA
    • Gao, Y. G., Su, S. Y., Robinson, H., Padmanabhan, S., Lim, L., McCrary, B. S. et al. (1998). The crystal structure of the hyperthermophile chromosomal protein Sso7d bound to DNA. Nat. Struct. Biol. 5, 782-786.
    • (1998) Nat. Struct. Biol. , vol.5 , pp. 782-786
    • Gao, Y.G.1    Su, S.Y.2    Robinson, H.3    Padmanabhan, S.4    Lim, L.5    McCrary, B.S.6
  • 51
    • 0037459241 scopus 로고    scopus 로고
    • The energetics of specific binding of AT-hooks from HMGA1 to target DNA
    • Dragan, A. I., Liggins, J. R., Crane-Robinson, C. & Privalov, P. L. (2003). The energetics of specific binding of AT-hooks from HMGA1 to target DNA. J. Mol. Biol. 327, 393-411.
    • (2003) J. Mol. Biol. , vol.327 , pp. 393-411
    • Dragan, A.I.1    Liggins, J.R.2    Crane-Robinson, C.3    Privalov, P.L.4
  • 52
    • 0042166066 scopus 로고    scopus 로고
    • DNA binding of a non-sequence-specific HMG-D protein is entropy driven with a substantial non-electrostatic contribution
    • Dragan, A. I., Klass, J., Read, C., Churchill, M. E., Crane-Robinson, C. & Privalov, P. L. (2003). DNA binding of a non-sequence-specific HMG-D protein is entropy driven with a substantial non-electrostatic contribution. J. Mol. Biol. 331, 795-813.
    • (2003) J. Mol. Biol. , vol.331 , pp. 795-813
    • Dragan, A.I.1    Klass, J.2    Read, C.3    Churchill, M.E.4    Crane-Robinson, C.5    Privalov, P.L.6
  • 54
    • 0026253640 scopus 로고
    • Importance of oligoelectrolyte end effects for the thermodynamics of conformational transitions of nucleic acid oligomers: A grand canonical Monte Carlo analysis
    • Olmsted, M. C., Anderson, C. F. & Record, M. T., Jr (1991). Importance of oligoelectrolyte end effects for the thermodynamics of conformational transitions of nucleic acid oligomers: a grand canonical Monte Carlo analysis. Biopolymers, 31, 1593-1604.
    • (1991) Biopolymers , vol.31 , pp. 1593-1604
    • Olmsted, M.C.1    Anderson, C.F.2    Record Jr., M.T.3
  • 55
    • 0029864013 scopus 로고    scopus 로고
    • Large electrostatic differences in the binding thermodynamics of a cationic peptide to oligomeric and polymeric DNA
    • Zhang, W., Bond, J. P., Anderson, C. F., Lohman, T. M. & Record, M. T., Jr (1996). Large electrostatic differences in the binding thermodynamics of a cationic peptide to oligomeric and polymeric DNA. Proc. Natl Acad. Sci. USA, 93, 2511-2516.
    • (1996) Proc. Natl Acad. Sci. USA , vol.93 , pp. 2511-2516
    • Zhang, W.1    Bond, J.P.2    Anderson, C.F.3    Lohman, T.M.4    Record Jr., M.T.5
  • 57
    • 3042626449 scopus 로고    scopus 로고
    • Interactions of the KWK6 cationic peptide with short nucleic acid oligomers: Demonstration of large coulombic end effects on binding at 0.1-0.2 M salt
    • Ballin, J. D., Shkel, I. A. & Record, M. T., Jr (2004). Interactions of the KWK6 cationic peptide with short nucleic acid oligomers: demonstration of large coulombic end effects on binding at 0.1-0.2 M salt. Nucleic Acids. Res. 32, 3271-3281.
    • (2004) Nucleic Acids. Res. , vol.32 , pp. 3271-3281
    • Ballin, J.D.1    Shkel, I.A.2    Record Jr., M.T.3
  • 58
    • 33745823525 scopus 로고    scopus 로고
    • Interactions of cationic ligands and proteins with small nucleic acids: Analytic treatment of the large coulombic end effect on binding free energy as a function of salt concentration
    • Shkel, I. A., Ballin, J. D. & Record, M. T., Jr (2006). Interactions of cationic ligands and proteins with small nucleic acids: analytic treatment of the large coulombic end effect on binding free energy as a function of salt concentration. Biochemistry, 45, 8411-8426.
    • (2006) Biochemistry , vol.45 , pp. 8411-8426
    • Shkel, I.A.1    Ballin, J.D.2    Record Jr., M.T.3
  • 59
    • 0000014960 scopus 로고
    • Monte Carlo description of oligoelectrolyte properties of DNA oligomers: Range of the end effect and the approach of molecular and thermodynamic properties to the polyelectrolyte limits
    • Olmsted, M. C., Anderson, C. F. & Record, M. T., Jr (1989). Monte Carlo description of oligoelectrolyte properties of DNA oligomers: range of the end effect and the approach of molecular and thermodynamic properties to the polyelectrolyte limits. Proc. Natl Acad. Sci. USA, 86, 7766-7770.
    • (1989) Proc. Natl Acad. Sci. USA , vol.86 , pp. 7766-7770
    • Olmsted, M.C.1    Anderson, C.F.2    Record Jr., M.T.3
  • 61
    • 0037823447 scopus 로고    scopus 로고
    • Evidence of a thermal unfolding dimeric intermediate for the Escherichia coli histone-like HU proteins: Thermodynamics and structure
    • Ramstein, J., Hervouet, N., Coste, F., Zelwer, C., Oberto, J. & Castaing, B. (2003). Evidence of a thermal unfolding dimeric intermediate for the Escherichia coli histone-like HU proteins: thermodynamics and structure. J. Mol. Biol. 331, 101-121.
    • (2003) J. Mol. Biol. , vol.331 , pp. 101-121
    • Ramstein, J.1    Hervouet, N.2    Coste, F.3    Zelwer, C.4    Oberto, J.5    Castaing, B.6
  • 63
    • 0016175370 scopus 로고
    • Theoretical aspects of DNA-protein interactions: Co-operative and non-co-operative binding of large ligands to a one-dimensional homogeneous lattice
    • McGhee, J. D. & von Hippel, P. H. (1974). Theoretical aspects of DNA-protein interactions: co-operative and non-co-operative binding of large ligands to a one-dimensional homogeneous lattice. J. Mol. Biol. 86, 469-489.
    • (1974) J. Mol. Biol. , vol.86 , pp. 469-489
    • McGhee, J.D.1    Von Hippel, P.H.2
  • 64
    • 0018196563 scopus 로고
    • Cooperative and non-cooperative binding of large ligands to a finite one-dimensional lattice. A model for ligand-oligonucleotide interactions
    • Epstein, I. R. (1978). Cooperative and non-cooperative binding of large ligands to a finite one-dimensional lattice. A model for ligand-oligonucleotide interactions. Biophys. Chem. 8, 327-339.
    • (1978) Biophys. Chem. , vol.8 , pp. 327-339
    • Epstein, I.R.1
  • 65
    • 78049422210 scopus 로고    scopus 로고
    • Modulation of HU-DNA interactions by salt concentration and applied force
    • Xiao, B., Johnson, R. C. & Marko, J. F. (2010). Modulation of HU-DNA interactions by salt concentration and applied force. Nucleic Acids Res. 38, 6176-6185.
    • (2010) Nucleic Acids Res. , vol.38 , pp. 6176-6185
    • Xiao, B.1    Johnson, R.C.2    Marko, J.F.3
  • 66
    • 0028175289 scopus 로고
    • Co-operative binding of Escherichia coli SSB tetramers to single-stranded DNA in the (SSB)35 binding mode
    • Ferrari, M. E., Bujalowski, W. & Lohman, T. M. (1994). Co-operative binding of Escherichia coli SSB tetramers to single-stranded DNA in the (SSB)35 binding mode. J. Mol. Biol. 236, 106-123.
    • (1994) J. Mol. Biol. , vol.236 , pp. 106-123
    • Ferrari, M.E.1    Bujalowski, W.2    Lohman, T.M.3
  • 67
    • 0024356728 scopus 로고
    • Negative cooperativity in Escherichia coli single strand binding protein-oligonucleotide interactions: II. Salt, temperature and oligonucleotide length effects
    • Bujalowski, W. & Lohman, T. M. (1989). Negative cooperativity in Escherichia coli single strand binding protein-oligonucleotide interactions: II. Salt, temperature and oligonucleotide length effects. J. Mol. Biol. 207, 269-288.
    • (1989) J. Mol. Biol. , vol.207 , pp. 269-288
    • Bujalowski, W.1    Lohman, T.M.2
  • 68
    • 0028791330 scopus 로고
    • Mechanism of protein access to specific DNA sequences in chromatin: A dynamic equilibrium model for gene regulation
    • Polach, K. J. & Widom, J. (1995). Mechanism of protein access to specific DNA sequences in chromatin: a dynamic equilibrium model for gene regulation. J. Mol. Biol. 254, 130-149.
    • (1995) J. Mol. Biol. , vol.254 , pp. 130-149
    • Polach, K.J.1    Widom, J.2
  • 69
    • 3542998667 scopus 로고    scopus 로고
    • Nucleosomes facilitate their own invasion
    • Li, G. & Widom, J. (2004). Nucleosomes facilitate their own invasion. Nat. Struct. Mol. Biol. 11, 763-769.
    • (2004) Nat. Struct. Mol. Biol. , vol.11 , pp. 763-769
    • Li, G.1    Widom, J.2
  • 71
    • 0033772098 scopus 로고    scopus 로고
    • Thermodynamic analysis of interactions between denaturants and protein surface exposed on unfolding: Interpretation of urea and guanidinium chloride m-values and their correlation with changes in accessible surface area (ASA) using preferential interaction coefficients and the local-bulk domain model
    • Courtenay, E. S., Capp, M. W., Saecker, R. M. & Record, M. T., Jr (2000). Thermodynamic analysis of interactions between denaturants and protein surface exposed on unfolding: interpretation of urea and guanidinium chloride m-values and their correlation with changes in accessible surface area (ASA) using preferential interaction coefficients and the local-bulk domain model. Proteins, 4, 72-85.
    • (2000) Proteins , vol.4 , pp. 72-85
    • Courtenay, E.S.1    Capp, M.W.2    Saecker, R.M.3    Record Jr., M.T.4
  • 72
    • 0035176391 scopus 로고    scopus 로고
    • Thermodynamics of interactions of urea and guanidinium salts with protein surface: Relationship between solute effects on protein processes and changes in water-accessible surface area
    • DOI 10.1110/ps.ps.20801
    • Courtenay, E. S., Capp, M. W. & Record, M. T., Jr (2001). Thermodynamics of interactions of urea and guanidinium salts with protein surface: relationship between solute effects on protein processes and changes in water-accessible surface area. Protein Sci. 10, 2485-2497. (Pubitemid 33091572)
    • (2001) Protein Science , vol.10 , Issue.12 , pp. 2485-2497
    • Courtenay, E.S.1    Capp, M.W.2    Record Jr., M.T.3
  • 73
    • 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. W., 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
  • 74
    • 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
  • 76
    • 0030424782 scopus 로고    scopus 로고
    • Structure and dynamics of the DNA binding protein HU from Bacillus stearothermophilus by NMR spectroscopy
    • Boelens, R., Vis, H., Vorgias, C. E., Wilson, K. S. & Kaptein, R. (1996). Structure and dynamics of the DNA binding protein HU from Bacillus stearothermophilus by NMR spectroscopy. Biopolymers, 40, 553-559.
    • (1996) Biopolymers , vol.40 , pp. 553-559
    • Boelens, R.1    Vis, H.2    Vorgias, C.E.3    Wilson, K.S.4    Kaptein, R.5
  • 78
    • 0033119773 scopus 로고    scopus 로고
    • The high-resolution structure of DNA-binding protein HU from Bacillus stearothermophilus
    • White, S. W., Wilson, K. S., Appelt, K. & Tanaka, I. (1999). The high-resolution structure of DNA-binding protein HU from Bacillus stearothermophilus. Acta. Crystallogr. Sect. D, 55, 801-809.
    • (1999) Acta. Crystallogr. Sect. D , vol.55 , pp. 801-809
    • White, S.W.1    Wilson, K.S.2    Appelt, K.3    Tanaka, I.4
  • 79
    • 0041821240 scopus 로고    scopus 로고
    • High-resolution X-ray structure of the DMA-binding protein HU from the hyper-thermophilic Thermotoga maritima and the determinants of its thermostability
    • DOI 10.1007/s00792-002-0302-7
    • Christodoulou, E., Rypniewski, W. R. & Vorgias, C. R. (2003). High-resolution X-ray structure of the DNA-binding protein HU from the hyper-thermophilic Thermotoga maritima and the determinants of its thermostability. Extremophiles, 7, 111-122. (Pubitemid 40924480)
    • (2003) Extremophiles , vol.7 , Issue.2 , pp. 111-122
    • Christodoulou, E.1    Rypniewski, W.R.2    Vorgias, C.E.3
  • 80
    • 0035964342 scopus 로고    scopus 로고
    • Electrostatics of nanosystems: Application to microtubules and the ribosome
    • Baker, N. A., Sept, D., Joseph, S., Holst, M. J. & McCammon, J. A. (2001). Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl Acad. Sci. USA, 98, 10037-10041.
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 10037-10041
    • Baker, N.A.1    Sept, D.2    Joseph, S.3    Holst, M.J.4    McCammon, J.A.5
  • 81
    • 0011219932 scopus 로고
    • Proteins from the prokaryotic nucleoid. The interaciton between protein NS and DNA involves the oligomeric form of the protein and at least one Arg residue
    • Lammi, M., Paci, M. & Gualerzi, C. O. (1984). Proteins from the prokaryotic nucleoid. The interaciton between protein NS and DNA involves the oligomeric form of the protein and at least one Arg residue. FEBS Lett. 170, 99-104.
    • (1984) FEBS Lett. , vol.170 , pp. 99-104
    • Lammi, M.1    Paci, M.2    Gualerzi, C.O.3
  • 82
    • 0027201673 scopus 로고
    • Proton NMR study on a histone-like protein, HU alpha, from Escherichia coli and its complex with oligo DNAs
    • Shindo, H., Kurumizaka, H., Furubayashi, A., Sakuma, C., Matsumoto, U., Yanagida, A. et al. (1993). Proton NMR study on a histone-like protein, HU alpha, from Escherichia coli and its complex with oligo DNAs. Biol. Pharm. Bull. 16, 437-443.
    • (1993) Biol. Pharm. Bull. , vol.16 , pp. 437-443
    • Shindo, H.1    Kurumizaka, H.2    Furubayashi, A.3    Sakuma, C.4    Matsumoto, U.5    Yanagida, A.6
  • 83
    • 0033251310 scopus 로고    scopus 로고
    • Arginine-55 in the beta-arm is essential for the activity of DNA-binding protein HU from Bacillus stearothermophilus
    • Saitoh, F., Kawamura, S., Yamasaki, N., Tanaka, I. & Kimura, M. (1999). Arginine-55 in the beta-arm is essential for the activity of DNA-binding protein HU from Bacillus stearothermophilus. Biosci. Biotechnol. Biochem. 63, 2232-2235.
    • (1999) Biosci. Biotechnol. Biochem. , vol.63 , pp. 2232-2235
    • Saitoh, F.1    Kawamura, S.2    Yamasaki, N.3    Tanaka, I.4    Kimura, M.5
  • 84
    • 0025610965 scopus 로고
    • HU-1 mutants of Escherichia coli deficient in DNA binding
    • Goshima, N., Kohno, K., Imamoto, F. & Kano, Y. (1990). HU-1 mutants of Escherichia coli deficient in DNA binding. Gene, 96, 141-145.
    • (1990) Gene , vol.96 , pp. 141-145
    • Goshima, N.1    Kohno, K.2    Imamoto, F.3    Kano, Y.4
  • 85
    • 0032557719 scopus 로고    scopus 로고
    • Calorimetric studies of E. coli SSB protein single-stranded DNA interactions. Effects of monovalent salts on binding enthalpy
    • Kozlov, A. G. & Lohman, T. M. (1998). Calorimetric studies of E. coli SSB protein single-stranded DNA interactions. Effects of monovalent salts on binding enthalpy. J. Mol. Biol. 278, 999-1014.
    • (1998) J. Mol. Biol. , vol.278 , pp. 999-1014
    • Kozlov, A.G.1    Lohman, T.M.2
  • 86
    • 33645971001 scopus 로고    scopus 로고
    • Effects of monovalent anions on a temperature-dependent heat capacity change for Escherichia coli SSB tetramer binding to single-stranded DNA
    • Kozlov, A. G. & Lohman, T. M. (2006). Effects of monovalent anions on a temperature-dependent heat capacity change for Escherichia coli SSB tetramer binding to single-stranded DNA. Biochemistry, 45, 5190-5205.
    • (2006) Biochemistry , vol.45 , pp. 5190-5205
    • Kozlov, A.G.1    Lohman, T.M.2
  • 87
    • 0029933128 scopus 로고    scopus 로고
    • A highly salt-dependent enthalpy change for Escherichia coli SSB protein-nucleic acid binding due to ion-protein interactions
    • Lohman, T. M., Overman, L. B., Ferrari, M. E. & Kozlov, A. G. (1996). A highly salt-dependent enthalpy change for Escherichia coli SSB protein-nucleic acid binding due to ion-protein interactions. Biochemistry, 35, 5272-5279.
    • (1996) Biochemistry , vol.35 , pp. 5272-5279
    • Lohman, T.M.1    Overman, L.B.2    Ferrari, M.E.3    Kozlov, A.G.4
  • 88
    • 0035816212 scopus 로고    scopus 로고
    • Specific and non-specific interactions of integration host factor with DNA: Thermodynamic evidence for disruption of multiple IHF surface salt-bridges coupled to DNA binding
    • Holbrook, J. A., Tsodikov, O. V., Saecker, R. M. & Record, M. T., Jr (2001). Specific and non-specific interactions of integration host factor with DNA: thermodynamic evidence for disruption of multiple IHF surface salt-bridges coupled to DNA binding. J. Mol. Biol. 310, 379-401.
    • (2001) J. Mol. Biol. , vol.310 , pp. 379-401
    • Holbrook, J.A.1    Tsodikov, O.V.2    Saecker, R.M.3    Record Jr., M.T.4
  • 89
    • 0034435652 scopus 로고    scopus 로고
    • Structural and thermodynamic strategies for site-specific DNA binding proteins
    • DOI 10.1016/S0969-2126(00)00501-3, PII S0969212600005013
    • Jen-Jacobson, L., Engler, L. E. & Jacobson, L. A. (2000). Structural and thermodynamic strategies for site-specific DNA binding proteins. Structure, 8, 1015-1023. (Pubitemid 32667465)
    • (2000) Structure , vol.8 , Issue.10 , pp. 1015-1023
    • Jen-Jacobson, L.1    Engler, L.E.2    Jacobson, L.A.3
  • 90
    • 0033614819 scopus 로고    scopus 로고
    • Enthalpy and heat capacity changes for formation of an oligomeric DNA duplex: Interpretation in terms of coupled processes of formation and association of single-stranded helices
    • Holbrook, J. A., Capp, M. W., Saecker, R. M. & Record, M. T., Jr (1999). Enthalpy and heat capacity changes for formation of an oligomeric DNA duplex: interpretation in terms of coupled processes of formation and association of single-stranded helices. Biochemistry, 38, 8409-8422.
    • (1999) Biochemistry , vol.38 , pp. 8409-8422
    • Holbrook, J.A.1    Capp, M.W.2    Saecker, R.M.3    Record Jr., M.T.4
  • 92
    • 0027510369 scopus 로고
    • In vivo thermodynamic analysis of repression with and without looping in lac constructs. Estimates of free and local lac repressor concentrations and of physical properties of a region of supercoiled plasmid DNA in vivo
    • Law, S. M., Bellomy, G. R., Schlax, P. J. & Record, M. T., Jr (1993). In vivo thermodynamic analysis of repression with and without looping in lac constructs. Estimates of free and local lac repressor concentrations and of physical properties of a region of supercoiled plasmid DNA in vivo. J. Mol. Biol. 230, 161-173.
    • (1993) J. Mol. Biol. , vol.230 , pp. 161-173
    • Law, S.M.1    Bellomy, G.R.2    Schlax, P.J.3    Record Jr., M.T.4
  • 93
    • 0030928287 scopus 로고    scopus 로고
    • Repressor induced site-specific binding of HU for transcriptional regulation
    • DOI 10.1093/emboj/16.12.3666
    • Aki, T. & Adhya, S. (1997). Repressor induced site-specific binding of HU for transcriptional regulation. EMBO J. 16, 3666-3674. (Pubitemid 27250059)
    • (1997) EMBO Journal , vol.16 , Issue.12 , pp. 3666-3674
    • Aki, T.1    Adhya, S.2
  • 94
    • 0029973105 scopus 로고    scopus 로고
    • Anatomy of a flexer-DNA complex inside a higher-order transposition intermediate
    • DOI 10.1016/S0092-8674(00)81241-6
    • Lavoie, B. D., Shaw, G. S., Millner, A. & Chaconas, G. (1996). Anatomy of a flexer-DNA complex inside a higher-order transposition intermediate. Cell, 85, 761-771. (Pubitemid 26181054)
    • (1996) Cell , vol.85 , Issue.5 , pp. 761-771
    • Lavoie, B.D.1    Shaw, G.S.2    Millner, A.M.3    Chaconas, G.4
  • 95
    • 0023724433 scopus 로고
    • DNA dynamic flexibility and protein recognition: Differential stimulation by bacterial histone-like protein HU
    • Flashner, Y. & Gralla, J. D. (1988). DNA dynamic flexibility and protein recognition: differential stimulation by bacterial histone-like protein HU. Cell, 54, 713-721.
    • (1988) Cell , vol.54 , pp. 713-721
    • Flashner, Y.1    Gralla, J.D.2
  • 96
    • 52949113483 scopus 로고    scopus 로고
    • Microcal, LLC. Microcal, LLC, Northampton, MA
    • Microcal, LLC. (2004). In ITC Data Analysis in Origin, pp. 104-106, Microcal, LLC, Northampton, MA.
    • (2004) ITC Data Analysis in Origin , pp. 104-106
  • 97
    • 77957095245 scopus 로고
    • Nonlinear least-squares analysis
    • Johnson, M. L. & Frasier, S. G. (1985). Nonlinear least-squares analysis. Methods Enzymol. 117, 301-342.
    • (1985) Methods Enzymol. , vol.117 , pp. 301-342
    • Johnson, M.L.1    Frasier, S.G.2
  • 98
    • 0345983583 scopus 로고    scopus 로고
    • Modeling unusual nucleic acid structures
    • Molecular Modeling of Nucleic Acids (Leontes, N. B. & SantaLucia, J., Jr, eds), American Chemical Society, Washington, DC
    • Macke, T. & Case, D. A. (1998). Modeling unusual nucleic acid structures. In Molecular Modeling of Nucleic Acids (Leontes, N. B. & SantaLucia, J., Jr, eds), Molecular Modeling of Nucleic Acids, pp. 379-393, American Chemical Society, Washington, DC.
    • (1998) Molecular Modeling of Nucleic Acids , pp. 379-393
    • Macke, T.1    Case, D.A.2
  • 99
    • 33749173463 scopus 로고    scopus 로고
    • Second derivatives in generalized Born theory
    • Brown, R. A. & Case, D. A. (2006). Second derivatives in generalized Born theory. J. Comput. Chem. 27, 1662-1675.
    • (2006) J. Comput. Chem. , vol.27 , pp. 1662-1675
    • Brown, R.A.1    Case, D.A.2
  • 100
    • 32144432437 scopus 로고    scopus 로고
    • The SWISS-MODEL workspace: A web-based environment for protein structure homology modelling
    • DOI 10.1093/bioinformatics/bti770
    • Arnold, K., Bordoli, L., Kopp, J. & Schwede, T. (2006). The SWISS-MODEL workspace: a Web-based environment for protein structure homology modelling. Bioinformatics, 22, 195-201. (Pubitemid 43205406)
    • (2006) Bioinformatics , vol.22 , Issue.2 , pp. 195-201
    • Arnold, K.1    Bordoli, L.2    Kopp, J.3    Schwede, T.4
  • 102
    • 0037197254 scopus 로고    scopus 로고
    • Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature
    • Tsodikov, O. V., Record, M. T., Jr & Sergeev, Y. V. (2002). Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature. J. Comput. Chem. 23, 600-609.
    • (2002) J. Comput. Chem. , vol.23 , pp. 600-609
    • Tsodikov, O.V.1    Record Jr., M.T.2    Sergeev, Y.V.3
  • 103
    • 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 (1991). Contribution to the thermodynamics of protein folding from the reduction in water-accessible nonpolar surface area. Biochemistry, 30, 4237-4244.
    • (1991) Biochemistry , vol.30 , pp. 4237-4244
    • Livingstone, J.R.1    Spolar, R.S.2    Record Jr., M.T.3
  • 104
    • 34248370213 scopus 로고    scopus 로고
    • Spiral structure of Escherichia coli HUalphabeta provides foundation for DNA supercoiling
    • Guo, F. & Adhya, S. (2007). Spiral structure of Escherichia coli HUalphabeta provides foundation for DNA supercoiling. Proc. Natl Acad. Sci. USA, 104, 4309-4314.
    • (2007) Proc. Natl Acad. Sci. USA , vol.104 , pp. 4309-4314
    • Guo, F.1    Adhya, S.2
  • 105
    • 34547559704 scopus 로고    scopus 로고
    • PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations
    • Dolinsky, T. J., Czodrowski, P., Li, H., Nielsen, J. E., Jensen, J. H., Klebe, G. & Baker, N. A. (2007). PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res. 35, W522-W525.
    • (2007) Nucleic Acids Res. , vol.35
    • Dolinsky, T.J.1    Czodrowski, P.2    Li, H.3    Nielsen, J.E.4    Jensen, J.H.5    Klebe, G.6    Baker, N.A.7
  • 106
    • 77955900720 scopus 로고    scopus 로고
    • Coulombic free energy of polymeric nucleic acid: Low- and high-salt analytical approximations for the cylindrical Poisson-Boltzmann model
    • Shkel, I. A. (2010). Coulombic free energy of polymeric nucleic acid: low- and high-salt analytical approximations for the cylindrical Poisson-Boltzmann model. J. Phys. Chem. B, 114, 10793-10803.
    • (2010) J. Phys. Chem. B , vol.114 , pp. 10793-10803
    • Shkel, I.A.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.