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Volumn 5, Issue 1, 1996, Pages 62-71

Simulations of CRP:(cAMP)2 in noncrystalline environments show a subunit transition from the open to the closed conformation

Author keywords

allosteric interactions; cAMP; CRP; molecular dynamics simulation in solution; molecular dynamics simulation in vacuo; molecule optimal dynamic coordinates; nonlinear dynamics; subunit reorientation

Indexed keywords

CYCLIC AMP; CYCLIC AMP BINDING PROTEIN; DNA;

EID: 0030068480     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1002/pro.5560050108     Document Type: Article
Times cited : (48)

References (29)
  • 1
    • 0020490340 scopus 로고
    • Molecular cloning and sequencing of the gene for E. coli cAMP receptor protein
    • Aiba H, Fujimoto S, Ozaki N. 1982. Molecular cloning and sequencing of the gene for E. coli cAMP receptor protein. Nucleic Acids Res 10:1345-1362.
    • (1982) Nucleic Acids Res , vol.10 , pp. 1345-1362
    • Aiba, H.1    Fujimoto, S.2    Ozaki, N.3
  • 4
    • 0001031179 scopus 로고
    • Proteins: A theoretical perspective of dynamics, structure, and thermodynamics
    • New York: Wiley
    • Brooks CL, Karplus M, Montgomery-Pettitt BM. 1988. Proteins: A theoretical perspective of dynamics, structure, and thermodynamics. In: Advances in chemical physics, vol LXXI. New York: Wiley.
    • (1988) Advances in Chemical Physics , vol.71
    • Brooks, C.L.1    Karplus, M.2    Montgomery-Pettitt, B.M.3
  • 5
    • 0028061282 scopus 로고
    • Promoter structure, promoter recognition, and transcription activation in prokaryotes
    • Busby S, Ebright RH. 1994. Promoter structure, promoter recognition, and transcription activation in prokaryotes. Cell 79:743-746.
    • (1994) Cell , vol.79 , pp. 743-746
    • Busby, S.1    Ebright, R.H.2
  • 7
    • 0020417679 scopus 로고
    • Proton nuclear magnetic resonance study of the histidine residues of the Escherichia coli adenosine 3′,5′-phosphate receptor protein. pH titration behavior, deuterium exchange and partial assignments
    • Clore GM, Gronenborn AM. 1982. Proton nuclear magnetic resonance study of the histidine residues of the Escherichia coli adenosine 3′,5′-phosphate receptor protein. pH titration behavior, deuterium exchange and partial assignments. Biochemistry 21:4048-4053.
    • (1982) Biochemistry , vol.21 , pp. 4048-4053
    • Clore, G.M.1    Gronenborn, A.M.2
  • 8
    • 0020490341 scopus 로고
    • Cloning and sequencing of the crp gene of Escherichia coli K12
    • Cossart P, Gicquel-Sanzey B. 1982. Cloning and sequencing of the crp gene of Escherichia coli K12. Nucleic Acids Res 10:1363-1378.
    • (1982) Nucleic Acids Res , vol.10 , pp. 1363-1378
    • Cossart, P.1    Gicquel-Sanzey, B.2
  • 9
    • 0027225271 scopus 로고
    • Transcription activation at class I CAP-dependent promoters
    • Ebright RH. 1993. Transcription activation at class I CAP-dependent promoters. Mol Microbiol 8:797-802.
    • (1993) Mol Microbiol , vol.8 , pp. 797-802
    • Ebright, R.H.1
  • 10
    • 0026320866 scopus 로고
    • The energy landscapes and motions in proteins
    • Frauenfelder H, Sligar SG, Wolynes PG. 1991. The energy landscapes and motions in proteins. Science 254:1598-1601.
    • (1991) Science , vol.254 , pp. 1598-1601
    • Frauenfelder, H.1    Sligar, S.G.2    Wolynes, P.G.3
  • 11
    • 0000577041 scopus 로고
    • Non-linear dynamics of proteins
    • García AE. 1992. Non-linear dynamics of proteins. Phys Rev Lett 68:2696-2699.
    • (1992) Phys Rev Lett , vol.68 , pp. 2696-2699
    • García, A.E.1
  • 12
    • 0011479901 scopus 로고
    • Multi-basin dynamics of a protein in aqueous solution
    • Peyrard M, ed. Berlin: Les Editions de Physique, Springer
    • García AE. 1995. Multi-basin dynamics of a protein in aqueous solution. In: Peyrard M, ed. Nonlinear excitations in biomolecules. Berlin: Les Editions de Physique, Springer. pp 191-206.
    • (1995) Nonlinear Excitations in Biomolecules
    • García, A.E.1
  • 13
    • 0028363352 scopus 로고
    • Dynamics and relative stability of parallel- and antiparallel-stranded DNA duplexes
    • García AE. Soumpasis DM, Jovin TM. 1994. Dynamics and relative stability of parallel- and antiparallel-stranded DNA duplexes. Biophys J 66: 1742-1755.
    • (1994) Biophys J , vol.66 , pp. 1742-1755
    • García, A.E.1    Soumpasis, D.M.2    Jovin, T.M.3
  • 14
    • 0026651748 scopus 로고
    • DNA sequence determinants for binding of the Escherichia coli catabolite gene activator protein
    • Gunasekera A, Ebright YW, Ebright RH. 1992. DNA sequence determinants for binding of the Escherichia coli catabolite gene activator protein. J Biol Chem 21:14713-14720.
    • (1992) J Biol Chem , vol.21 , pp. 14713-14720
    • Gunasekera, A.1    Ebright, Y.W.2    Ebright, R.H.3
  • 15
    • 0024462882 scopus 로고
    • Escherichia coli cAMP receptor protein: Evidence for three protein conformational states with different promoter binding affinities
    • Heyduk T, Lee JC. 1989. Escherichia coli cAMP receptor protein: Evidence for three protein conformational states with different promoter binding affinities. Biochemistry 28:6914-6924.
    • (1989) Biochemistry , vol.28 , pp. 6914-6924
    • Heyduk, T.1    Lee, J.C.2
  • 16
    • 0004016501 scopus 로고
    • Comparison of simple potential functions for simulating liquid water
    • Jorgensen WL, Chandrasekhar J, Madura JD. 1983. Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926-935.
    • (1983) J Chem Phys , vol.79 , pp. 926-935
    • Jorgensen, W.L.1    Chandrasekhar, J.2    Madura, J.D.3
  • 17
    • 33645941402 scopus 로고
    • The OPLS potential functions for proteins. Energy minimizations for crystals of cyclic peptides and crambin
    • Jorgensen WL, Tirado-Rives J. 1988. The OPLS potential functions for proteins. Energy minimizations for crystals of cyclic peptides and crambin. J Am Chem Soc 110:1657-1666.
    • (1988) J Am Chem Soc , vol.110 , pp. 1657-1666
    • Jorgensen, W.L.1    Tirado-Rives, J.2
  • 18
    • 0000127140 scopus 로고
    • Method for estimating the configurational entropy of macromolecules
    • Karplus M, Kushick JN. 1981. Method for estimating the configurational entropy of macromolecules. Macromolecules 14:325-332.
    • (1981) Macromolecules , vol.14 , pp. 325-332
    • Karplus, M.1    Kushick, J.N.2
  • 19
    • 0027236999 scopus 로고
    • Transcriptional control by cAMP and its receptor protein
    • Kolb A, Busby S, Buc H, Garges S, Adhya S. 1993. Transcriptional control by cAMP and its receptor protein. Annu Rev Biochem 62:749-795.
    • (1993) Annu Rev Biochem , vol.62 , pp. 749-795
    • Kolb, A.1    Busby, S.2    Buc, H.3    Garges, S.4    Adhya, S.5
  • 20
    • 0000910556 scopus 로고
    • Molecular dynamics of macromolecules in water
    • Levitt M. 1989. Molecular dynamics of macromolecules in water. Chemica Scripta 29A:197-203.
    • (1989) Chemica Scripta , vol.29 A , pp. 197-203
    • Levitt, M.1
  • 21
    • 0018350099 scopus 로고
    • Least square fitting of two structures. Appendix in gene duplication in the structural evolution of chymotrypsin
    • McLachalan J. 1979. Least square fitting of two structures. Appendix in gene duplication in the structural evolution of chymotrypsin. J Mol Biol 128: 49-79.
    • (1979) J Mol Biol , vol.128 , pp. 49-79
    • McLachalan, J.1
  • 23
    • 0025914242 scopus 로고
    • Crystal structure of a CAP-DNA complex: The DNA is bent by 90 degrees
    • Schultz SC, Shields GC, Steitz TA. 1991. Crystal structure of a CAP-DNA complex: The DNA is bent by 90 degrees. Science 253:1001-1007.
    • (1991) Science , vol.253 , pp. 1001-1007
    • Schultz, S.C.1    Shields, G.C.2    Steitz, T.A.3
  • 24
    • 23444450909 scopus 로고
    • Coupling of local folding to site-specific binding of proteins to DNA
    • Spolar RS, Record MT. 1994. Coupling of local folding to site-specific binding of proteins to DNA. Science 263:777-784.
    • (1994) Science , vol.263 , pp. 777-784
    • Spolar, R.S.1    Record, M.T.2
  • 25
    • 84946450438 scopus 로고
    • Algorithms for macromolecular dynamics and constraint dynamics
    • van Gunsteren WF, Berendsen HJC. 1977. Algorithms for macromolecular dynamics and constraint dynamics. Mol Phys 34:1111-641.
    • (1977) Mol Phys , vol.34 , pp. 1111-1641
    • Van Gunsteren, W.F.1    Berendsen, H.J.C.2
  • 26
    • 0023661228 scopus 로고
    • Structure of a complex of catabolite gene activator protein and cyclic AMP refined at 2.5 Å resolution
    • Weber IT, Steitz TA. 1987. Structure of a complex of catabolite gene activator protein and cyclic AMP refined at 2.5 Å resolution. J Mol Biol 198:311-326.
    • (1987) J Mol Biol , vol.198 , pp. 311-326
    • Weber, I.T.1    Steitz, T.A.2
  • 28
    • 84988053694 scopus 로고
    • An all atom force field for simulations of proteins and nucleic acids
    • Weiner SC, Kollman PA, Nguyen DT, Case DA. 1986. An all atom force field for simulations of proteins and nucleic acids. J Comput Chem 7: 230-252.
    • (1986) J Comput Chem , vol.7 , pp. 230-252
    • Weiner, S.C.1    Kollman, P.A.2    Nguyen, D.T.3    Case, D.A.4
  • 29
    • 0027161386 scopus 로고
    • Identification of the activating region of catabolite gene activator protein (CAP): Isolation and characterization of mutants of CAP specifically defective in transcription activation
    • Zhou Y, Zhang X, Ebrigh RH. 1993. Identification of the activating region of catabolite gene activator protein (CAP): Isolation and characterization of mutants of CAP specifically defective in transcription activation. Proc Natl Acad Sci USA 90:6081-6085.
    • (1993) Proc Natl Acad Sci USA , vol.90 , pp. 6081-6085
    • Zhou, Y.1    Zhang, X.2    Ebrigh, R.H.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.