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Volumn 85, Issue 3, 2000, Pages 123-131

Investigations on human immunodeficiency virus type 1 integrase/DNA binding interactions via molecular dynamics and electrostatics calculations

Author keywords

AIDS; Electrostatics; HIV 1 integrase; Integrase DNA interaction; Molecular dynamics

Indexed keywords

INTEGRASE; METAL ION;

EID: 0034104449     PISSN: 01637258     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0163-7258(99)00059-5     Document Type: Conference Paper
Times cited : (31)

References (51)
  • 2
    • 0029814410 scopus 로고    scopus 로고
    • Retroviral integrase, putting the pieces together
    • Andrake M.D., Skalka A.M. Retroviral integrase, putting the pieces together. J Biol Chem. 271:1996;19633-19636.
    • (1996) J Biol Chem , vol.271 , pp. 19633-19636
    • Andrake, M.D.1    Skalka, A.M.2
  • 4
    • 0032567350 scopus 로고    scopus 로고
    • Structural determinants of metal-induced conformational changes in HIV-1 integrase
    • Asante-Appiah E., Seeholzer S.H., Skalka A.M. Structural determinants of metal-induced conformational changes in HIV-1 integrase. J Biol Chem. 273:1998;35078-35087.
    • (1998) J Biol Chem , vol.273 , pp. 35078-35087
    • Asante-Appiah, E.1    Seeholzer, S.H.2    Skalka, A.M.3
  • 5
    • 0026612756 scopus 로고
    • a values of ionizable groups in bacteriorhodopsin
    • a values of ionizable groups in bacteriorhodopsin. J Mol Biol. 224:1992;473-486.
    • (1992) J Mol Biol , vol.224 , pp. 473-486
    • Bashford, D.1    Gerwert, K.2
  • 6
    • 0025197061 scopus 로고
    • a's of ionizable groups in proteins: Atomic detail from a continuum electrostatic model
    • a's of ionizable groups in proteins. atomic detail from a continuum electrostatic model Biochemistry. 29:1990;10219-10225.
    • (1990) Biochemistry , vol.29 , pp. 10219-10225
    • Bashford, D.1    Karplus, M.2
  • 8
    • 0033466532 scopus 로고    scopus 로고
    • Simulation of pH-dependent properties of proteins using mesoscopic models
    • K.B. Lipkowitz, & D.B. Boyd. New York: John Wiley & Sons
    • Briggs J., Antosiewicz J. Simulation of pH-dependent properties of proteins using mesoscopic models. Lipkowitz K.B., Boyd D.B. Reviews in Computational Chemistry. 1999;249-311 John Wiley & Sons, New York.
    • (1999) Reviews in Computational Chemistry , pp. 249-311
    • Briggs, J.1    Antosiewicz, J.2
  • 10
    • 0030566832 scopus 로고    scopus 로고
    • The catalytic domain of avian sarcoma virus integrase: Conformation of the active site residues in the presence of divalent cations
    • Bujacz G., Alexandratos J., Clement-Mella Q., Zhou-Liu C., Wlodawer A. The catalytic domain of avian sarcoma virus integrase. conformation of the active site residues in the presence of divalent cations FEBS Lett. 398:1996;175-178.
    • (1996) FEBS Lett , vol.398 , pp. 175-178
    • Bujacz, G.1    Alexandratos, J.2    Clement-Mella, Q.3    Zhou-Liu, C.4    Wlodawer, A.5
  • 11
    • 0030746054 scopus 로고    scopus 로고
    • Binding of different divalent cations to the active site of avian sarcoma virus integrase and their effects on enzymatic activity
    • Bujacz G., Alexandratos J., Wlodawer A., Merkel G., Andrake M., Katz R.A., Skalka A.M. Binding of different divalent cations to the active site of avian sarcoma virus integrase and their effects on enzymatic activity. J Biol Chem. 272:1997;18161-18168.
    • (1997) J Biol Chem , vol.272 , pp. 18161-18168
    • Bujacz, G.1    Alexandratos, J.2    Wlodawer, A.3    Merkel, G.4    Andrake, M.5    Katz, R.A.6    Skalka, A.M.7
  • 12
    • 0027456715 scopus 로고
    • Domains of the integrase protein of human immunodeficiency virus type 1 responsible for polynucleotidyl transfer and zinc binding
    • Bushman F.D., Engelman A., Palmer I., Wingfield P., Cragie R. Domains of the integrase protein of human immunodeficiency virus type 1 responsible for polynucleotidyl transfer and zinc binding. Proc Natl Acad Sci USA. 90:1993;3428-3432.
    • (1993) Proc Natl Acad Sci USA , vol.90 , pp. 3428-3432
    • Bushman, F.D.1    Engelman, A.2    Palmer, I.3    Wingfield, P.4    Cragie, R.5
  • 14
    • 0026549933 scopus 로고
    • Reversal of integration and DNA splicing mediated by integrase of human immunodeficiency virus
    • Chow S.A., Vincent K.A., Ellison V., Brown P.O. Reversal of integration and DNA splicing mediated by integrase of human immunodeficiency virus. Science. 255:1992;723-726.
    • (1992) Science , vol.255 , pp. 723-726
    • Chow, S.A.1    Vincent, K.A.2    Ellison, V.3    Brown, P.O.4
  • 16
    • 0026124585 scopus 로고
    • Electrostatics and diffusion of molecules in solution - simulations with the University-of-Houston-Brownian Dynamics program
    • Davis M.E., Madura J.D., Luty B.A., McCammon J.A. Electrostatics and diffusion of molecules in solution - simulations with the University-of-Houston-Brownian Dynamics program. Comp Phys Commun. 62:1991;187-197.
    • (1991) Comp Phys Commun , vol.62 , pp. 187-197
    • Davis, M.E.1    Madura, J.D.2    Luty, B.A.3    McCammon, J.A.4
  • 18
    • 0028584269 scopus 로고
    • Crystal structure of the catalytic domain of HIV-1 integrase: Similarity to other polynucleotidyl transferases
    • Dyda F., Hickman A.B., Jenkins T.M., Engelman A., Cragie R., Davies D.R. Crystal structure of the catalytic domain of HIV-1 integrase. similarity to other polynucleotidyl transferases Science. 266:1994;1981-1986.
    • (1994) Science , vol.266 , pp. 1981-1986
    • Dyda, F.1    Hickman, A.B.2    Jenkins, T.M.3    Engelman, A.4    Cragie, R.5    Davies, D.R.6
  • 21
    • 0026649557 scopus 로고
    • Identification of amino acid residues critical for human immunodeficiency virus type 1 protein in vitro
    • Engelman A., Cragie R. Identification of amino acid residues critical for human immunodeficiency virus type 1 protein in vitro. J Virol. 66:1992;6361-6369.
    • (1992) J Virol , vol.66 , pp. 6361-6369
    • Engelman, A.1    Cragie, R.2
  • 22
    • 0028067324 scopus 로고
    • The core end carboxyl-terminal domains of the integrase protein of human immunodeficiency virus type 1 each contribute to non-specific DNA binding
    • Engelman A., Hickman A.B., Cragie R. The core end carboxyl-terminal domains of the integrase protein of human immunodeficiency virus type 1 each contribute to non-specific DNA binding. J Virol. 68:1994;5911-5917.
    • (1994) J Virol , vol.68 , pp. 5911-5917
    • Engelman, A.1    Hickman, A.B.2    Cragie, R.3
  • 23
    • 0032189652 scopus 로고    scopus 로고
    • Sequence specificity of viral end DNA binding by HIV-1 integrase reveals critical regions for protein-DNA interaction
    • Esposito D., Craigie R. Sequence specificity of viral end DNA binding by HIV-1 integrase reveals critical regions for protein-DNA interaction. EMBO J. 17:1998;5832-5843.
    • (1998) EMBO J , vol.17 , pp. 5832-5843
    • Esposito, D.1    Craigie, R.2
  • 25
    • 0031949592 scopus 로고    scopus 로고
    • Effects of mutations in residues near the active site of human immunodeficiency virus type 1 integrase on specific enzyme substrate interactions
    • Gerton J.L., Ohgi S., Olsen M., Derise J., Brown P.O. Effects of mutations in residues near the active site of human immunodeficiency virus type 1 integrase on specific enzyme substrate interactions. J Virol. 72:1998;5046-5055.
    • (1998) J Virol , vol.72 , pp. 5046-5055
    • Gerton, J.L.1    Ohgi, S.2    Olsen, M.3    Derise, J.4    Brown, P.O.5
  • 26
    • 0032483022 scopus 로고    scopus 로고
    • Three new structures of the core domain of HIV-1 integrase: An active site that bindings magnesium
    • Goldgur Y., Dyda F., Hickman A.B., Jenkins T.M., Craigie R., Davies D.R. Three new structures of the core domain of HIV-1 integrase. an active site that bindings magnesium Proc Natl Acad Sci USA. 95:1998;9150-9154.
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 9150-9154
    • Goldgur, Y.1    Dyda, F.2    Hickman, A.B.3    Jenkins, T.M.4    Craigie, R.5    Davies, D.R.6
  • 27
    • 0033551443 scopus 로고    scopus 로고
    • The mobility of an HIV-1 integrase active site loop is correlated with catalytic activity
    • Greenwald J., Le V., Butler S.L., Bushman F., Choe S. The mobility of an HIV-1 integrase active site loop is correlated with catalytic activity. Biochemistry. 38:1999;8892-8898.
    • (1999) Biochemistry , vol.38 , pp. 8892-8898
    • Greenwald, J.1    Le, V.2    Butler, S.L.3    Bushman, F.4    Choe, S.5
  • 29
    • 0030875813 scopus 로고    scopus 로고
    • Mapping features of HIV-1 integrase near selected sites on viral and target DNA molecules in an active site enzyme-DNA complex by photo-cross-linking
    • Heuer T.S., Brown P.O. Mapping features of HIV-1 integrase near selected sites on viral and target DNA molecules in an active site enzyme-DNA complex by photo-cross-linking. Biochemistry. 36:1997;10655-10665.
    • (1997) Biochemistry , vol.36 , pp. 10655-10665
    • Heuer, T.S.1    Brown, P.O.2
  • 30
    • 0032510707 scopus 로고    scopus 로고
    • Photo-cross-linking studies suggest a model for the architecture of an active human immunodeficiency virus type 1 integrase-DNA complex
    • Heuer T.S., Brown P.O. Photo-cross-linking studies suggest a model for the architecture of an active human immunodeficiency virus type 1 integrase-DNA complex. Biochemistry. 37:1998;6667-6678.
    • (1998) Biochemistry , vol.37 , pp. 6667-6678
    • Heuer, T.S.1    Brown, P.O.2
  • 31
    • 0030828521 scopus 로고    scopus 로고
    • Critical contacts between HIV-1 integrase and viral DNA identified by structure-based analysis and photo-cross-linking
    • Jenkins T.M., Esposito D., Engelman A., Cragie R. Critical contacts between HIV-1 integrase and viral DNA identified by structure-based analysis and photo-cross-linking. EMBO J. 16:1997;6849-6859.
    • (1997) EMBO J , vol.16 , pp. 6849-6859
    • Jenkins, T.M.1    Esposito, D.2    Engelman, A.3    Cragie, R.4
  • 32
    • 0026035178 scopus 로고
    • Retroviral integrase domains: DNA binding and the recognition of LTR sequence
    • Khan E., Mack J.P.G., Katz R.A., Kulkosky J., Skalka A.M. Retroviral integrase domains. DNA binding and the recognition of LTR sequence Nucleic Acids Res. 19:1991;851-860.
    • (1991) Nucleic Acids Res , vol.19 , pp. 851-860
    • Khan, E.1    MacK, J.P.G.2    Katz, R.A.3    Kulkosky, J.4    Skalka, A.M.5
  • 33
    • 0026719238 scopus 로고
    • Residues critical for retroviral integrative recombination in a region that is highly conserved among retroviral/retrotransposons, integrases and bacterial insertion sequence transponsons
    • Kulkosky J., Jones K.S., Katz R.A., Mack J.P.G., Skalka A.M. Residues critical for retroviral integrative recombination in a region that is highly conserved among retroviral/retrotransposons, integrases and bacterial insertion sequence transponsons. Mol Cell Biol. 12:1992;2331-2338.
    • (1992) Mol Cell Biol , vol.12 , pp. 2331-2338
    • Kulkosky, J.1    Jones, K.S.2    Katz, R.A.3    MacK, J.P.G.4    Skalka, A.M.5
  • 34
    • 0030614408 scopus 로고    scopus 로고
    • Zn promotes the self-association of human immunodeficiency virus integrase in vitro
    • Lee S.P., Xiao J., Knutson J.R., Lewis M.S., Han M.K. Zn promotes the self-association of human immunodeficiency virus integrase in vitro. Biochemistry. 36:1997;173-180.
    • (1997) Biochemistry , vol.36 , pp. 173-180
    • Lee, S.P.1    Xiao, J.2    Knutson, J.R.3    Lewis, M.S.4    Han, M.K.5
  • 38
    • 0001166515 scopus 로고    scopus 로고
    • Structure-based mutation analysis of the C-terminal DNA-binding domain of human immunodeficiency virus type 1 integrase: Critical residues for protein oligomerization and protein binding
    • Lutzke R.A.P., Plasterk R.H.A. Structure-based mutation analysis of the C-terminal DNA-binding domain of human immunodeficiency virus type 1 integrase. critical residues for protein oligomerization and protein binding J Virol. 72:1998;4841-4848.
    • (1998) J Virol , vol.72 , pp. 4841-4848
    • Lutzke, R.A.P.1    Plasterk, R.H.A.2
  • 39
    • 0028034050 scopus 로고
    • Characterization of the minimal DNA-binding domain of the HIV integrase protein
    • Lutzke R.A.P., Vink C., Plasterk R.H.A. Characterization of the minimal DNA-binding domain of the HIV integrase protein. Nucleic Acids Res. 22:1994;4125-4131.
    • (1994) Nucleic Acids Res , vol.22 , pp. 4125-4131
    • Lutzke, R.A.P.1    Vink, C.2    Plasterk, R.H.A.3
  • 40
    • 0026124585 scopus 로고
    • Electrostatics and diffusion of molecules in solution - simulations with the University of Houston Brownian Dynamics program
    • Madura J.D., Briggs J.M., Wade R.C., Davis M.E., Luty B.A., Ilin A., McCammon J.A. Electrostatics and diffusion of molecules in solution - simulations with the University of Houston Brownian Dynamics program. Comput Phys Commun. 62:1995;187-197.
    • (1995) Comput Phys Commun , vol.62 , pp. 187-197
    • Madura, J.D.1    Briggs, J.M.2    Wade, R.C.3    Davis, M.E.4    Luty, B.A.5    Ilin, A.6    McCammon, J.A.7
  • 41
    • 0032544311 scopus 로고    scopus 로고
    • Crystal structures of the catalytic domain of HIV-1 integrase free and complexed with its cofactor: High level of similarity of the active site with other viral integrases
    • Maignan S., Guilloteau J.-P., Zhou-Liu Q., Clement-Mella C., Mikol V. Crystal structures of the catalytic domain of HIV-1 integrase free and complexed with its cofactor. high level of similarity of the active site with other viral integrases J Mol Biol. 282:1998;359-368.
    • (1998) J Mol Biol , vol.282 , pp. 359-368
    • Maignan, S.1    Guilloteau, J.-P.2    Zhou-Liu, Q.3    Clement-Mella, C.4    Mikol, V.5
  • 42
    • 0029864507 scopus 로고    scopus 로고
    • Chemical trapping of ternary complexes of human immunodeficiency virus type 1 integrase, divalent metal, and DNA substrates containing an abasic site
    • Mazumder A., Neamati N., Pilon A.A., Sunder S., Pommier Y. Chemical trapping of ternary complexes of human immunodeficiency virus type 1 integrase, divalent metal, and DNA substrates containing an abasic site. J Biol Chem. 271:1996;27330-27338.
    • (1996) J Biol Chem , vol.271 , pp. 27330-27338
    • Mazumder, A.1    Neamati, N.2    Pilon, A.A.3    Sunder, S.4    Pommier, Y.5
  • 43
    • 84986486656 scopus 로고
    • A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation
    • Nicholls A., Honig B. A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation. J Comput Chem. 12:1991;435-445.
    • (1991) J Comput Chem , vol.12 , pp. 435-445
    • Nicholls, A.1    Honig, B.2
  • 46
    • 33646940952 scopus 로고
    • Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of N-alkenes
    • Ryckaert J.P., Ciccitti G., Berendsen H.J.C. Numerical integration of the Cartesian equations of motion of a system with constraints. molecular dynamics of N-alkenes J Comput Phys. 23:1977;327-341.
    • (1977) J Comput Phys , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccitti, G.2    Berendsen, H.J.C.3
  • 47
    • 0027179416 scopus 로고
    • Identification of amino acids in HIV-2 integrase involved in site-specific hydrolysis and alcoholysis of viral DNA termini
    • van Gent D.C., Groeneger A.A.M.O., Plasterk R.H.A. Identification of amino acids in HIV-2 integrase involved in site-specific hydrolysis and alcoholysis of viral DNA termini. Nucleic Acids Res. 21:1993;3373-3377.
    • (1993) Nucleic Acids Res , vol.21 , pp. 3373-3377
    • Van Gent, D.C.1    Groeneger, A.A.M.O.2    Plasterk, R.H.A.3
  • 48
    • 0027210608 scopus 로고
    • Identification of the catalytic end DNA-binding region of the human immunodeficiency virus type 1 integrase protein
    • Vink C., Groeneger A.A.M.O., Plasterk R.H.A. Identification of the catalytic end DNA-binding region of the human immunodeficiency virus type 1 integrase protein. Nucleic Acids Res. 21:1993;1419-1425.
    • (1993) Nucleic Acids Res , vol.21 , pp. 1419-1425
    • Vink, C.1    Groeneger, A.A.M.O.2    Plasterk, R.H.A.3
  • 49
    • 0025398721 scopus 로고
    • What if: Molecular modeling and drug design program
    • Vriend G. What if. molecular modeling and drug design program J Mol Graphics. 8:1990;52-56.
    • (1990) J Mol Graphics , vol.8 , pp. 52-56
    • Vriend, G.1
  • 51
    • 0030478950 scopus 로고    scopus 로고
    • Zinc folds the N-terminal domain of HIV-1 integrase, promotes multimerization, and enhances catalytic activity
    • Zheng R., Jenkins T.M., Cragie R. Zinc folds the N-terminal domain of HIV-1 integrase, promotes multimerization, and enhances catalytic activity. Proc Natl Acad Sci USA. 93:1996;13659-13664.
    • (1996) Proc Natl Acad Sci USA , vol.93 , pp. 13659-13664
    • Zheng, R.1    Jenkins, T.M.2    Cragie, R.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.