메뉴 건너뛰기




Volumn 336, Issue 4, 2004, Pages 829-842

Heat Capacity Effects of Water Molecules and Ions at a Protein-DNA Interface

Author keywords

Heat capacity change; Interfacial ions; Isothermal titration calorimetry; Protein DNA interaction; Water molecules

Indexed keywords

BACTERIAL DNA; BACTERIAL PROTEIN; ION; WATER;

EID: 1042298819     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2003.12.061     Document Type: Article
Times cited : (108)

References (55)
  • 1
    • 0025098571 scopus 로고
    • Common features of protein unfolding and dissolution of hydrophobic compounds
    • Murphy K.P., Privalov P.L., Gill S.J. Common features of protein unfolding and dissolution of hydrophobic compounds. Science. 247:1990;559-561.
    • (1990) Science , vol.247 , pp. 559-561
    • Murphy, K.P.1    Privalov, P.L.2    Gill, S.J.3
  • 2
    • 0342656167 scopus 로고    scopus 로고
    • Characterization of sequence-specific DNA binding by the transcription factor Oct-1
    • Lundbäck T., Chang J.-F., Phillips K., Luisi B., Ladbury J.E. Characterization of sequence-specific DNA binding by the transcription factor Oct-1. Biochemistry. 39:2000;7570-7579.
    • (2000) Biochemistry , vol.39 , pp. 7570-7579
    • Lundbäck, T.1    Chang, J.-F.2    Phillips, K.3    Luisi, B.4    Ladbury, J.E.5
  • 3
    • 23444450909 scopus 로고
    • Coupling of local folding to site-specific binding of proteins to DNA
    • Spolar R.S., Record J.M.T. Coupling of local folding to site-specific binding of proteins to DNA. Science. 263:1994;777-784.
    • (1994) Science , vol.263 , pp. 777-784
    • Spolar, R.S.1    Record, J.M.T.2
  • 4
    • 0032570633 scopus 로고    scopus 로고
    • Thermodynamics of specific and non-specific DNA binding by the c-Myb DNA-binding domain
    • Oda M., Furukawa K., Ogata K., Sarai A., Nakamura H. Thermodynamics of specific and non-specific DNA binding by the c-Myb DNA-binding domain. J. Mol. Biol. 276:1998;571-590.
    • (1998) J. Mol. Biol. , vol.276 , pp. 571-590
    • Oda, M.1    Furukawa, K.2    Ogata, K.3    Sarai, A.4    Nakamura, H.5
  • 5
    • 0026498015 scopus 로고
    • Thermodynamic stoichiometries of participation of water, cations and anions in specific and non-specific binding of lac repressor to DNA. Possible thermodynamic origins of the "glutamate effect" on protein-DNA interactions
    • Ha J.-H., Capp M.W., Hohenwalter M.D., Baskerville M., Record M.T. Jr. Thermodynamic stoichiometries of participation of water, cations and anions in specific and non-specific binding of lac repressor to DNA. Possible thermodynamic origins of the "glutamate effect" on protein-DNA interactions. J. Mol. Biol. 228:1992;252-264.
    • (1992) J. Mol. Biol. , vol.228 , pp. 252-264
    • Ha, J.-H.1    Capp, M.W.2    Hohenwalter, M.D.3    Baskerville, M.4    Record Jr., M.T.5
  • 6
    • 0032577337 scopus 로고    scopus 로고
    • The effects of salt on the TATA binding protein-DNA interaction from a hyperthermophilic archaeon
    • O'Brien R., DeDecker B., Fleming K.G., Sigler P.B., Ladbury J.E. The effects of salt on the TATA binding protein-DNA interaction from a hyperthermophilic archaeon. J. Mol. Biol. 279:1998;117-125.
    • (1998) J. Mol. Biol. , vol.279 , pp. 117-125
    • O'Brien, R.1    Dedecker, B.2    Fleming, K.G.3    Sigler, P.B.4    Ladbury, J.E.5
  • 7
    • 0029860343 scopus 로고    scopus 로고
    • Water-mediated protein-DNA interactions: The relationship of thermodynamics to structural detail
    • Morton C.J., Ladbury J.E. Water-mediated protein-DNA interactions: the relationship of thermodynamics to structural detail. Protein Sci. 5:1996;2115-2118.
    • (1996) Protein Sci. , vol.5 , pp. 2115-2118
    • Morton, C.J.1    Ladbury, J.E.2
  • 8
    • 0028157348 scopus 로고
    • Mutagenesis supports water mediated recognition in the trp repressor-operator system
    • Joachimiak A., Haran T.E., Sigler P.B. Mutagenesis supports water mediated recognition in the trp repressor-operator system. EMBO J. 13:1994;367-372.
    • (1994) EMBO J. , vol.13 , pp. 367-372
    • Joachimiak, A.1    Haran, T.E.2    Sigler, P.B.3
  • 9
    • 0028607523 scopus 로고
    • Cavities and packing at protein interfaces
    • Hubbard S.J., Argos P. Cavities and packing at protein interfaces. Protein Sci. 3:1994;2194-2206.
    • (1994) Protein Sci. , vol.3 , pp. 2194-2206
    • Hubbard, S.J.1    Argos, P.2
  • 10
    • 0029450365 scopus 로고
    • Hydration in drug design.1. Multiple hydrogen-bonding features of water molecules in mediating protein-ligand interactions
    • Poornima C.S., Dean P.M. Hydration in drug design.1. Multiple hydrogen-bonding features of water molecules in mediating protein-ligand interactions. J. Comp.-Aided Mol. Des. 9:1995;500-512.
    • (1995) J. Comp.-Aided Mol. Des. , vol.9 , pp. 500-512
    • Poornima, C.S.1    Dean, P.M.2
  • 11
    • 0035976713 scopus 로고    scopus 로고
    • Do water molecules mediate protein-DNA recognition?
    • Reddy C.K., Das A., Jayaram B. Do water molecules mediate protein-DNA recognition? J. Mol. Biol. 314:2001;619-632.
    • (2001) J. Mol. Biol. , vol.314 , pp. 619-632
    • Reddy, C.K.1    Das, A.2    Jayaram, B.3
  • 12
    • 0030466444 scopus 로고    scopus 로고
    • Just add water! the effect of water on the specificity of protein-ligand binding sites with applications to drug design
    • Ladbury J.E. Just add water! The effect of water on the specificity of protein-ligand binding sites with applications to drug design. Chem. Biol. 3:1996;973-980.
    • (1996) Chem. Biol. , vol.3 , pp. 973-980
    • Ladbury, J.E.1
  • 13
    • 0030471364 scopus 로고    scopus 로고
    • The role of water in sequence-independent ligand binding by an oligopeptide transporter protein
    • Tame J.R.H., Sleigh S.H., Wilkinson A.J., Ladbury J.E. The role of water in sequence-independent ligand binding by an oligopeptide transporter protein. Nature Struct. Biol. 3:1996;998-1001.
    • (1996) Nature Struct. Biol. , vol.3 , pp. 998-1001
    • Tame, J.R.H.1    Sleigh, S.H.2    Wilkinson, A.J.3    Ladbury, J.E.4
  • 14
    • 0002638463 scopus 로고
    • Heat capacity and entropy changes in processes involving proteins
    • Sturtevant J.M. Heat capacity and entropy changes in processes involving proteins. Proc. Natl Acad. Sci. USA. 74:1977;2236-2240.
    • (1977) Proc. Natl Acad. Sci. USA , vol.74 , pp. 2236-2240
    • Sturtevant, J.M.1
  • 17
    • 0031562901 scopus 로고    scopus 로고
    • The 2.1 Å crystal structure of an archeal preinitiation complex TATA-binding protein/transcription factor (II)B core/TATA-Box
    • Kosa P.F., Gosh G., DeDecker B.S., Sigler P.B. The 2.1 Å crystal structure of an archeal preinitiation complex TATA-binding protein/ transcription factor (II)B core/TATA-Box. Proc. Natl Acad. Sci. USA. 94:1997;6042-6047.
    • (1997) Proc. Natl Acad. Sci. USA , vol.94 , pp. 6042-6047
    • Kosa, P.F.1    Gosh, G.2    Dedecker, B.S.3    Sigler, P.B.4
  • 18
    • 0035957083 scopus 로고    scopus 로고
    • Site-specific cation binding mediates TATA binding protein-DNA interaction from a hyperthermophilic archaeon
    • Bergqvist S., O'Brien R., Ladbury J.E. Site-specific cation binding mediates TATA binding protein-DNA interaction from a hyperthermophilic archaeon. Biochemistry. 40:2001;2419-2425.
    • (2001) Biochemistry , vol.40 , pp. 2419-2425
    • Bergqvist, S.1    O'Brien, R.2    Ladbury, J.E.3
  • 19
    • 0036106350 scopus 로고    scopus 로고
    • Reversal of protein halophilicity by limited mutation strategy
    • Bergqvist S., Williams M.A., O'Brien R., Ladbury J.E. Reversal of protein halophilicity by limited mutation strategy. Structure. 10:2002;629-637.
    • (2002) Structure , vol.10 , pp. 629-637
    • Bergqvist, S.1    Williams, M.A.2    O'Brien, R.3    Ladbury, J.E.4
  • 21
    • 0024378717 scopus 로고
    • Role of the hydrophobic effect in stability of site-specific protein-DNA complexes
    • Ha J.H., Spolar R.S., Record M.T. Jr. Role of the hydrophobic effect in stability of site-specific protein-DNA complexes. J. Mol. Biol. 209:1989;801-816.
    • (1989) J. Mol. Biol. , vol.209 , pp. 801-816
    • Ha, J.H.1    Spolar, R.S.2    Record Jr., M.T.3
  • 22
    • 0000866128 scopus 로고
    • Hydrophobic effect in protein folding and other noncovalent processes involving proteins
    • Spolar R.S., Ha J.H., Record T.M. Jr. Hydrophobic effect in protein folding and other noncovalent processes involving proteins. Proc. Natl Acad. Sci. USA. 86:1989;8382-8385.
    • (1989) Proc. Natl Acad. Sci. USA , vol.86 , pp. 8382-8385
    • Spolar, R.S.1    Ha, J.H.2    Record Jr., T.M.3
  • 23
    • 0028946647 scopus 로고
    • Thermodynamic evaluation of binding interactions in the methionine repressor system of Escherichia coli using isothermal titration calorimetry
    • Hyre D.E., Spicer L.D. Thermodynamic evaluation of binding interactions in the methionine repressor system of Escherichia coli using isothermal titration calorimetry. Biochemistry. 34:1995;3212-3221.
    • (1995) Biochemistry , vol.34 , pp. 3212-3221
    • Hyre, D.E.1    Spicer, L.D.2
  • 24
    • 0000162429 scopus 로고    scopus 로고
    • Salt dependence of the free energy, enthalpy, and entropy of non-sequence specific DNA binding
    • Lundbäck T., Härd T. Salt dependence of the free energy, enthalpy, and entropy of non-sequence specific DNA binding. J. Phys. Chem. 100:1996;17690-17695.
    • (1996) J. Phys. Chem. , vol.100 , pp. 17690-17695
    • Lundbäck, T.1    Härd, T.2
  • 25
    • 0033544727 scopus 로고    scopus 로고
    • The energetics of HMG Box interactions with DNA: Thermodynamics of the DNA binding of the HMG Box from mouse Sox-5
    • Privalov P.L., Jelesarov I., Read C.M., Dragan A.I., Crane-Robinson C. The energetics of HMG Box interactions with DNA: thermodynamics of the DNA binding of the HMG Box from mouse Sox-5. J. Mol. Biol. 294:1999;997-1013.
    • (1999) J. Mol. Biol. , vol.294 , pp. 997-1013
    • Privalov, P.L.1    Jelesarov, I.2    Read, C.M.3    Dragan, A.I.4    Crane-Robinson, C.5
  • 29
    • 0025906146 scopus 로고
    • Contribution to the thermodynamics of protein folding from the reduction in water-accessible nonpolar surface area
    • Livingstone J.R., Spolar R.S., Record M.T. Jr. Contribution to the thermodynamics of protein folding from the reduction in water-accessible nonpolar surface area. Biochemistry. 30:1991;4237-4244.
    • (1991) Biochemistry , vol.30 , pp. 4237-4244
    • Livingstone, J.R.1    Spolar, R.S.2    Record Jr., M.T.3
  • 30
    • 0026684671 scopus 로고
    • Use of liquid hydrocarbon and amide transfer data to estimate contributions to thermodynamic functions of protein folding from the removal of nonpolar and polar surface from water
    • Spolar R.S., Livingstone J.R., Record M.T. Jr. Use of liquid hydrocarbon and amide transfer data to estimate contributions to thermodynamic functions of protein folding from the removal of nonpolar and polar surface from water. Biochemistry. 31:1992;3947-3955.
    • (1992) Biochemistry , vol.31 , pp. 3947-3955
    • Spolar, R.S.1    Livingstone, J.R.2    Record Jr., M.T.3
  • 31
    • 0026756702 scopus 로고
    • Thermodynamics of structural stability and cooperative folding behavior in proteins
    • Murphy K.P., Freire E. Thermodynamics of structural stability and cooperative folding behavior in proteins. Advan. Protein Chem. 43:1992;313-361.
    • (1992) Advan. Protein Chem. , vol.43 , pp. 313-361
    • Murphy, K.P.1    Freire, E.2
  • 32
    • 0029080864 scopus 로고
    • Thermodynamic mapping of the inhibitor site of the aspartic protease endothiapepsin
    • Gomez J., Freire E. Thermodynamic mapping of the inhibitor site of the aspartic protease endothiapepsin. J. Mol. Biol. 252:1995;337-350.
    • (1995) J. Mol. Biol. , vol.252 , pp. 337-350
    • Gomez, J.1    Freire, E.2
  • 33
    • 0029958659 scopus 로고    scopus 로고
    • Structure-based thermodynamic scale of α-helical propensities of amino acids
    • Luque I., Mayorga O.L., Freire E. Structure-based thermodynamic scale of α-helical propensities of amino acids. Biochemistry. 35:1996;13681-13688.
    • (1996) Biochemistry , vol.35 , pp. 13681-13688
    • Luque, I.1    Mayorga, O.L.2    Freire, E.3
  • 34
    • 0029941271 scopus 로고    scopus 로고
    • Energetics of hydrogen bonding in proteins: A model compound study
    • Habermann S.M., Murphy K.P. Energetics of hydrogen bonding in proteins: a model compound study. Protein Sci. 5:1996;1229-1239.
    • (1996) Protein Sci. , vol.5 , pp. 1229-1239
    • Habermann, S.M.1    Murphy, K.P.2
  • 36
    • 0036836538 scopus 로고    scopus 로고
    • Structural parameterization of the binding enthalpy of small ligands
    • Luque I., Freire E. Structural parameterization of the binding enthalpy of small ligands. Proteins: Struct. Funct. Genet. 49:2002;181-190.
    • (2002) Proteins: Struct. Funct. Genet. , vol.49 , pp. 181-190
    • Luque, I.1    Freire, E.2
  • 37
    • 0030758672 scopus 로고    scopus 로고
    • The entropic penalty of ordered water accounts for weaker binding of the antibiotic novobiocin to a resistant mutant of DNA gyrase: A thermodynamic and crystallographic study
    • Holdgate G.A., Tunnicliffe A., Ward W.H.J., Weston S.A., Rosenbrock G., Barth P.T., et al. The entropic penalty of ordered water accounts for weaker binding of the antibiotic novobiocin to a resistant mutant of DNA gyrase: a thermodynamic and crystallographic study. Biochemistry. 36:1997;9663-9673.
    • (1997) Biochemistry , vol.36 , pp. 9663-9673
    • Holdgate, G.A.1    Tunnicliffe, A.2    Ward, W.H.J.3    Weston, S.A.4    Rosenbrock, G.5    Barth, P.T.6
  • 39
    • 0027504913 scopus 로고
    • Crystal structure of YTBP/TATA-box complex
    • Kim Y., Geiger J.H., Hahn S., Sigler P.B. Crystal structure of YTBP/TATA-box complex. Nature. 365:1993;512-520.
    • (1993) Nature , vol.365 , pp. 512-520
    • Kim, Y.1    Geiger, J.H.2    Hahn, S.3    Sigler, P.B.4
  • 40
    • 0033573008 scopus 로고    scopus 로고
    • TATA element recognition by the TATA box-binding protein has been conserved throughout evolution
    • Patikoglou G.A., Kim J.L., Sun L., Yang S.-H., Kodadek T., Burley S.K. TATA element recognition by the TATA box-binding protein has been conserved throughout evolution. Genes Dev. 13:1999;3217-3230.
    • (1999) Genes Dev. , vol.13 , pp. 3217-3230
    • Patikoglou, G.A.1    Kim, J.L.2    Sun, L.3    Yang, S.-H.4    Kodadek, T.5    Burley, S.K.6
  • 41
    • 0037378942 scopus 로고    scopus 로고
    • Energetics of sequence-specific protein-DNA association: Binding of integrase Tn916 to its target DNA
    • Milev S., Gorfe A.A., Karshikoff A., Clubb R.T., Bosshard H.R., Jelesarov I. Energetics of sequence-specific protein-DNA association: binding of integrase Tn916 to its target DNA. Biochemistry. 42:2003;3481-3491.
    • (2003) Biochemistry , vol.42 , pp. 3481-3491
    • Milev, S.1    Gorfe, A.A.2    Karshikoff, A.3    Clubb, R.T.4    Bosshard, H.R.5    Jelesarov, I.6
  • 42
    • 0000562369 scopus 로고    scopus 로고
    • Water and monovalent ions in the minor groove of B-DNA oligonucleotides as seen by NMR
    • Halle B., Denisov V.P. Water and monovalent ions in the minor groove of B-DNA oligonucleotides as seen by NMR. Biopolymers. 48:1998;210-233.
    • (1998) Biopolymers , vol.48 , pp. 210-233
    • Halle, B.1    Denisov, V.P.2
  • 43
    • 0000616995 scopus 로고
    • Apparent molar heat capacities of amino-acids and other organic compounds
    • Edsall J.T. Apparent molar heat capacities of amino-acids and other organic compounds. J. Am. Chem. Soc. 57:1935;1506-1507.
    • (1935) J. Am. Chem. Soc. , vol.57 , pp. 1506-1507
    • Edsall, J.T.1
  • 44
    • 0038115064 scopus 로고    scopus 로고
    • Negligible effect of ions on the hydrogen-bond structure of liquid water
    • Otma A.W., Kropman M.F., Woutersen S., Bakker H.J. Negligible effect of ions on the hydrogen-bond structure of liquid water. Science. 301:2003;347-349.
    • (2003) Science , vol.301 , pp. 347-349
    • Otma, A.W.1    Kropman, M.F.2    Woutersen, S.3    Bakker, H.J.4
  • 45
    • 0030036162 scopus 로고    scopus 로고
    • Large heat capacity change in a protein-monovalent cation interaction
    • Guinto E.R., Di Cera E. Large heat capacity change in a protein-monovalent cation interaction. Biochemistry. 35:1996;8800-8804.
    • (1996) Biochemistry , vol.35 , pp. 8800-8804
    • Guinto, E.R.1    Di Cera, E.2
  • 46
    • 0035805184 scopus 로고    scopus 로고
    • Water at hydrophobic surfaces: Weak hydrogen bonding and strong orientation effects
    • Scatena L.F., Brown M.G., Richmond G.L. Water at hydrophobic surfaces: weak hydrogen bonding and strong orientation effects. Science. 292:2001;908-911.
    • (2001) Science , vol.292 , pp. 908-911
    • Scatena, L.F.1    Brown, M.G.2    Richmond, G.L.3
  • 48
    • 0001307815 scopus 로고    scopus 로고
    • The cost of releasing site-specific, bound water molecules from proteins: Towards a quantitative guide for structure-based drug design
    • J.E. Ladbury, & P.R. Connelly. Berlin: Springer
    • Connelly P.R. The cost of releasing site-specific, bound water molecules from proteins: towards a quantitative guide for structure-based drug design. Ladbury J.E., Connelly P.R. Structure-based Drug Design: Thermodynamics, Modelling and Strategy. 1997;Springer, Berlin.
    • (1997) Structure-based Drug Design: Thermodynamics, Modelling and Strategy
    • Connelly, P.R.1
  • 49
    • 0034842061 scopus 로고    scopus 로고
    • Influence of Glu-376→Gln mutation on enthalpy and heat capacity changes for the binding of slightly altered ligands to medium chain acyl-CoA dehydrogenase
    • Peterson K.M., Gopalan K.V., Nandy A., Srivastava D.K. Influence of Glu-376→Gln mutation on enthalpy and heat capacity changes for the binding of slightly altered ligands to medium chain acyl-CoA dehydrogenase. Protein Sci. 10:2001;1822-1834.
    • (2001) Protein Sci. , vol.10 , pp. 1822-1834
    • Peterson, K.M.1    Gopalan, K.V.2    Nandy, A.3    Srivastava, D.K.4
  • 50
    • 0024356301 scopus 로고
    • Rapid measurement of binding constants and heats of binding using a new titration calorimeter
    • Wiseman T., Williston S., Brandts J.F., Lin L.N. Rapid measurement of binding constants and heats of binding using a new titration calorimeter. Anal. Biochem. 179:1989;131-137.
    • (1989) Anal. Biochem. , vol.179 , pp. 131-137
    • Wiseman, T.1    Williston, S.2    Brandts, J.F.3    Lin, L.N.4
  • 51
    • 0032480810 scopus 로고    scopus 로고
    • Calorimetric investigation of proton linkage by monitoring both the enthalpy and association constant of binding: Application to the interaction of the src SH2 Domain with a high-affinity tyrosyl phosphopeptide
    • Bradshaw J.M., Waksman G. Calorimetric investigation of proton linkage by monitoring both the enthalpy and association constant of binding: application to the interaction of the src SH2 Domain with a high-affinity tyrosyl phosphopeptide. Biochemistry. 37:1998;15400-15407.
    • (1998) Biochemistry , vol.37 , pp. 15400-15407
    • Bradshaw, J.M.1    Waksman, G.2
  • 52
    • 0003742069 scopus 로고
    • University College London: Department of Biochemistry and Molecular Biology
    • Hubbard S.J., Thornton J.M. NACCESS, Computer Program. 1993;Department of Biochemistry and Molecular Biology, University College London.
    • (1993) NACCESS, Computer Program
    • Hubbard, S.J.1    Thornton, J.M.2
  • 53
    • 0015222647 scopus 로고
    • The interpretation of protein structures: Estimation of static accessibility
    • Lee B., Richards F.M. The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55:1971;379-400.
    • (1971) J. Mol. Biol. , vol.55 , pp. 379-400
    • Lee, B.1    Richards, F.M.2
  • 54
    • 0035812654 scopus 로고    scopus 로고
    • Intrinsic bending and deformability at the T-A step of CCTTTAAAGG: A comparative analysis of T-A and A-T steps within A-tracts
    • Mack D.R., Chiu T.K., Dickerson R.E. Intrinsic bending and deformability at the T-A step of CCTTTAAAGG: a comparative analysis of T-A and A-T steps within A-tracts. J. Mol. Biol. 312:2001;1037-1049.
    • (2001) J. Mol. Biol. , vol.312 , pp. 1037-1049
    • MacK, D.R.1    Chiu, T.K.2    Dickerson, R.E.3
  • 55
    • 0034698001 scopus 로고    scopus 로고
    • A-DNA conformational motifs in ligand-bound double helices
    • Lu X.-J., Shakked Z., Olsen W.K. A-DNA conformational motifs in ligand-bound double helices. J. Mol. Biol. 300:2000;819-840.
    • (2000) J. Mol. Biol. , vol.300 , pp. 819-840
    • Lu, X.-J.1    Shakked, Z.2    Olsen, W.K.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.