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Volumn 25, Issue 3, 2011, Pages 275-291

Modeling of the structure and interactions of the B. anthracis antitoxin, MoxX: Deletion mutant studies highlight its modular structure and repressor function

Author keywords

Antitoxin DNA complex; Deletion mutants; Docking; Molecular dynamics; Molecular modeling; MoxXT; Peptide design; Repressor; RHH motif; Toxin antitoxin complex

Indexed keywords

BACTERIA; BACTERIOLOGY; BINDING ENERGY; BIOINFORMATICS; DIMERS; DNA; MOLECULAR MODELING; PEPTIDES; STRUCTURAL DESIGN; TOXIC MATERIALS;

EID: 79955989586     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-011-9419-z     Document Type: Article
Times cited : (27)

References (44)
  • 1
    • 0029083946 scopus 로고
    • Programmed cell death in bacteria: Proteic plasmid stabilization systems
    • Jensen RB, Gerdes K (1995) Programmed cell death in bacteria: proteic plasmid stabilization systems. Mol Microbiol 17:205-210
    • (1995) Mol Microbiol , vol.17 , pp. 205-210
    • Jensen, R.B.1    Gerdes, K.2
  • 4
    • 0030008368 scopus 로고    scopus 로고
    • An E. coli chromosomal 'addiction module' regulated by guanosine 3′-5′-bispyrophosphate: A model for programmed bacterial cell death
    • Aizenman E, Engelberg-Kulka H, Glaser G (1996) An E. coli chromosomal 'addiction module' regulated by guanosine 3′-5′-bispyrophosphate: a model for programmed bacterial cell death. Proc Natl Acad Sci USA 93:6059-6063
    • (1996) Proc Natl Acad Sci USA , vol.93 , pp. 6059-6063
    • Aizenman, E.1    Engelberg-Kulka, H.2    Glaser, G.3
  • 5
    • 0034002551 scopus 로고    scopus 로고
    • A dose-response study of antibiotic resistance in Pseudomonas aeruginosa biofilms
    • DOI 10.1128/AAC.44.3.640-646.2000
    • Brooun A, Songhua L, Lewis K (2000) A dose-response study of antibiotic resistance in Pseudomonas aeruginosa biofilms. Antimicrob Agents Chemother 44:640-646 (Pubitemid 30117954)
    • (2000) Antimicrobial Agents and Chemotherapy , vol.44 , Issue.3 , pp. 640-646
    • Brooun, A.1    Liu, S.2    Lewis, K.3
  • 6
    • 34247101571 scopus 로고    scopus 로고
    • Identification and characterization of a novel toxin-antitoxin module from Bacillus anthracis
    • DOI 10.1016/j.febslet.2007.03.051, PII S0014579307003237
    • Agarwal S, Agarwal S, Bhatnagar R (2007) Identification and characterization of a novel toxin-antitoxin module from Bacillus anthracis. FEBS Lett 581:1727-1734 (Pubitemid 46602263)
    • (2007) FEBS Letters , vol.581 , Issue.9 , pp. 1727-1734
    • Agarwal, S.1    Agarwal, S.2    Bhatnagar, R.3
  • 7
    • 77951214558 scopus 로고    scopus 로고
    • PemK toxin of Bacillus anthracis is a ribonuclease: An insight into its active site, structure and function
    • Agarwal S, Mishra NK, Bhatnagar S, Bhatnagar R (2010) PemK toxin of Bacillus anthracis is a ribonuclease: an insight into its active site, structure and function. J Biol Chem 285:7254-7270
    • (2010) J Biol Chem , vol.285 , pp. 7254-7270
    • Agarwal, S.1    Mishra, N.K.2    Bhatnagar, S.3    Bhatnagar, R.4
  • 9
    • 34547564386 scopus 로고    scopus 로고
    • The solution structure of ParD, the antidote of the ParDE toxin-antitoxin module, provides the structural basis for DNA and toxin binding
    • DOI 10.1110/ps.062680707
    • Oberer M, Zangger K, Gruber K, Keller W (2007) The solution structure of ParD, the antidote of the ParDE toxin-antitoxin module, provides the structural basis for DNA and toxin binding. Protein Sci 16:1676-1688 (Pubitemid 47195694)
    • (2007) Protein Science , vol.16 , Issue.8 , pp. 1676-1688
    • Oberer, M.1    Zangger, K.2    Gruber, K.3    Keller, W.4
  • 10
    • 0028177303 scopus 로고
    • DNA recognition by β-sheets in the Arc repressor-operator crystal structure
    • Raumann BE, Rould MA, Pabo CO, Sauer RT (1994) DNA recognition by β-sheets in the Arc repressor-operator crystal structure. Nature 367:754-757
    • (1994) Nature , vol.367 , pp. 754-757
    • Raumann, B.E.1    Rould, M.A.2    Pabo, C.O.3    Sauer, R.T.4
  • 12
    • 0026641755 scopus 로고
    • Crystal structure of the met repressor-operator complex at 2.8 Å resolution reveals DNA recognition by β-strands
    • Somers WS, Philips SE (1992) Crystal structure of the met repressor-operator complex at 2.8 Å resolution reveals DNA recognition by β-strands. Nature 359:387-393
    • (1992) Nature , vol.359 , pp. 387-393
    • Somers, W.S.1    Philips, S.E.2
  • 14
    • 0037738520 scopus 로고    scopus 로고
    • Crystal structure of the MazE/MazF complex: Molecular bases of antidote-toxin recognition
    • DOI 10.1016/S1097-2765(03)00097-2
    • Kamada K, Hanoaka F, Burley SK (2003) Crystal structure of MazE/MazF complex: molecular bases of antidote-toxin recognition. Mol Cell 11:875-884 (Pubitemid 36569246)
    • (2003) Molecular Cell , vol.11 , Issue.4 , pp. 875-884
    • Kamada, K.1    Hanaoka, F.2    Burley, S.K.3
  • 16
    • 44649143795 scopus 로고    scopus 로고
    • Structural mechanism of transcripitional autorepression of the E. coli RelB/RelE antitoxin/toxin module
    • Li GY, Zhang Y, Inouye M, Ikura M (2008) Structural mechanism of transcripitional autorepression of the E. coli RelB/RelE antitoxin/toxin module. J Mol Biol 380:107-119
    • (2008) J Mol Biol , vol.380 , pp. 107-119
    • Li, G.Y.1    Zhang, Y.2    Inouye, M.3    Ikura, M.4
  • 18
    • 33846011436 scopus 로고    scopus 로고
    • Structure of FitAB from Neisseria gonorrhoeae bound to DNA reveals a tetramer of toxin-antitoxin heterodimers containing pin domains and ribbon-helix-helix motifs
    • DOI 10.1074/jbc.M605198200
    • Mattison K, Wilbur JS, So M, Brennan RG (2006) Structure of FitAB from Neisseria gonorrhoeae bound to DNA reveals a tetramer of toxin-antitoxin heterodimers containing pin domains and ribbon-helix-helix motifs. J Biol Chem 281:37942-37951 (Pubitemid 46042098)
    • (2006) Journal of Biological Chemistry , vol.281 , Issue.49 , pp. 37942-37951
    • Mattison, K.1    Wilbur, J.S.2    So, M.3    Brennan, R.G.4
  • 19
    • 33846680128 scopus 로고    scopus 로고
    • Toxin-antitoxin regulation: Bimodal interaction of YefM-YoeB with paired DNA palindromes exerts transcriptional autorepression
    • DOI 10.1093/nar/gkl1028
    • Kedzierska B, Lian L, Hayes F (2007) Toxin-antitoxin regulation: bimodal interaction of YefM-YoeB with paired DNA palindromes exerts transcriptional autorepression. Nucleic Acids Res 35:325-339 (Pubitemid 46189857)
    • (2007) Nucleic Acids Research , vol.35 , Issue.1 , pp. 325-339
    • Kedzierska, B.1    Lian, L.-Y.2    Hayes, F.3
  • 21
    • 0027190754 scopus 로고
    • Evaluation of secondary structure of proteins from UV circular dichroism spectra using an unsupervised learning neural network
    • Andrade MA (1993) Evaluation of secondary structure of proteins from UV circular dichroism spectra using an unsupervised learning neural network. Protein Eng 6:383-390
    • (1993) Protein Eng , vol.6 , pp. 383-390
    • Andrade, M.A.1
  • 22
    • 0033810049 scopus 로고    scopus 로고
    • Modeling of loops in protein structure
    • Fiser A, Do RK, Sali A (2000) Modeling of loops in protein structure. Protein Sci 9:1753-1773
    • (2000) Protein Sci , vol.9 , pp. 1753-1773
    • Fiser, A.1    Do, R.K.2    Sali, A.3
  • 25
    • 63849246525 scopus 로고    scopus 로고
    • PHYRE:Protein structure prediction on the web: A case study using the PHYRE server
    • Kelly LA, Sternberg MJE (2009) PHYRE:Protein structure prediction on the web: a case study using the PHYRE server. Nat Protoc 4:363-371
    • (2009) Nat Protoc , vol.4 , pp. 363-371
    • Kelly, L.A.1    Sternberg, M.J.E.2
  • 26
    • 16344373015 scopus 로고    scopus 로고
    • Protein homology detection by HMM-HMM comparison
    • Söding J (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics 21:951-960
    • (2005) Bioinformatics , vol.21 , pp. 951-960
    • Söding, J.1
  • 27
    • 0002051540 scopus 로고    scopus 로고
    • BIOEDIT, a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT
    • Hall TA (1999) BIOEDIT, a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95-98
    • (1999) Nucleic Acids Symp Ser , vol.41 , pp. 95-98
    • Hall, T.A.1
  • 28
    • 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 modeling. 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
  • 29
    • 0031473847 scopus 로고    scopus 로고
    • SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling
    • DOI 10.1002/elps.1150181505
    • Guex N, Peitsch MC (1997) SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 18:2714-2723 (Pubitemid 28059943)
    • (1997) Electrophoresis , vol.18 , Issue.15 , pp. 2714-2723
    • Guex, N.1    Peitsch, M.C.2
  • 30
    • 33747840389 scopus 로고    scopus 로고
    • GRAMM-X public web server for protein-protein docking
    • DOI 10.1093/nar/gkl206
    • Tovchigrechko A, Vakser IA (2006) GRAMM-X public web server for protein-protein docking. Nucleic Acids Res 34:W310-W314 (Pubitemid 44529784)
    • (2006) Nucleic Acids Research , vol.34 , Issue.WEB. SERV. ISS.
    • Tovchigrechko, A.1    Vakser, I.A.2
  • 31
    • 0029633186 scopus 로고
    • AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules
    • Pearlman DA, Case DA, Caldwell JW, Ross WS, Cheatham TE III, DeBolt S, Ferguson D, Seibel G, Kollman P (1995) AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comput Phys Commun 91:1-41
    • (1995) Comput Phys Commun , vol.91 , pp. 1-41
    • Pearlman, D.A.1    Case, D.A.2    Caldwell, J.W.3    Ross, W.S.4    Cheatham III, T.E.5    DeBolt, S.6    Ferguson, D.7    Seibel, G.8    Kollman, P.9
  • 32
    • 33846823909 scopus 로고
    • Particle Mesh-Ewald method: An N-log (N) method for ewald sums in large systems
    • Darden T, York D, Pederson L (1993) Particle Mesh-Ewald method: an N-log (N) method for ewald sums in large systems. J Chem Phys 98:10089-10092
    • (1993) J Chem Phys , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pederson, L.3
  • 33
    • 40449101942 scopus 로고    scopus 로고
    • Computational de novo peptide and protein design: Rigid templates versus flexible templates
    • DOI 10.1021/ie071286k
    • Fung HK, Welsh WJ, Floudas CA (2008) Computational de novo peptide and protein design: rigid templates versus flexible templates. Ind Engin Chem Res 47:993-1001 (Pubitemid 351345883)
    • (2008) Industrial and Engineering Chemistry Research , vol.47 , Issue.4 , pp. 993-1001
    • Fung, H.K.1    Welsh, W.J.2    Floudas, C.A.3
  • 34
    • 67849130555 scopus 로고    scopus 로고
    • PEP-FOLD: An online resource for de novo peptide structure prediction
    • Maupetit J, Derreumaux P, Tuffery P (2009) PEP-FOLD: an online resource for de novo peptide structure prediction. Nucleic Acids Res 37(suppl 2):W498-W503
    • (2009) Nucleic Acids Res , vol.37 , Issue.SUPPL. 2
    • Maupetit, J.1    Derreumaux, P.2    Tuffery, P.3
  • 35
    • 77953573815 scopus 로고    scopus 로고
    • Sub-angstrom modeling of complexes between flexible peptides and globular proteins
    • Raveh B, London N, Schueler-Furman O (2010) Sub-angstrom modeling of complexes between flexible peptides and globular proteins. Proteins 78:2029-2040
    • (2010) Proteins , vol.78 , pp. 2029-2040
    • Raveh, B.1    London, N.2    Schueler-Furman, O.3
  • 37
    • 67849110013 scopus 로고    scopus 로고
    • 3D-DART: A DNA structure modeling server
    • Van Dijk M, Bonvin AM (2009) 3D-DART: a DNA structure modeling server. Nucleic Acid Res 37:W235-W239
    • (2009) Nucleic Acid Res , vol.37
    • Van Dijk, M.1    Bonvin, A.M.2
  • 38
    • 84885949386 scopus 로고    scopus 로고
    • Improved disorder prediction by combination of orthogonal approaches
    • Schlessinger A, Punta M, Yachdav G, Kajan L, Rost B (2009) Improved disorder prediction by combination of orthogonal approaches. PLoS One 4:e4433
    • (2009) PLoS One , vol.4
    • Schlessinger, A.1    Punta, M.2    Yachdav, G.3    Kajan, L.4    Rost, B.5
  • 40
    • 17144395996 scopus 로고    scopus 로고
    • Structure of Pyrococcus horikoshii NikR: Nickel sensing and implications for the regulation of DNA recognition
    • DOI 10.1016/j.jmb.2005.03.017
    • Chivers PT, Tahirov TH (2005) Structure of Pyrococcus horikoshii NikR: nickel sensing and implications for the regulation of DNA recognition. J Mol Biol 348:597-607 (Pubitemid 40515672)
    • (2005) Journal of Molecular Biology , vol.348 , Issue.3 , pp. 597-607
    • Chivers, P.T.1    Tahirov, T.H.2
  • 41
    • 33746849786 scopus 로고    scopus 로고
    • Structural Basis of the Nickel Response in Helicobacter pylori: Crystal Structures of HpNikR in Apo and Nickel-bound States
    • DOI 10.1016/j.jmb.2006.06.058, PII S0022283606007996
    • Dian C, Schauer K, Kapp U, McSweeney SM, Labigne A, Terradot L (2006) Sructural basis of the nickel response in Helicobacter pylori: crystal structures of HpNikR in Apo and nickel bound states. J Mol Biol 361:715-730 (Pubitemid 44175384)
    • (2006) Journal of Molecular Biology , vol.361 , Issue.4 , pp. 715-730
    • Dian, C.1    Schauer, K.2    Kapp, U.3    McSweeney, S.M.4    Labigne, A.5    Terradot, L.6
  • 42
    • 1542472730 scopus 로고    scopus 로고
    • New connections in the prokaryotic toxin-antitoxin network: Relationship with the eukaryotic nonsense-mediated RNA decay system
    • Ananthraman V, Aravind L (2003) New connections in the prokaryotic toxin-antitoxin network: relationship with the eukaryotic nonsense-mediated RNA decay system. Genome Biol 4:R81
    • (2003) Genome Biol , vol.4
    • Ananthraman, V.1    Aravind, L.2
  • 43
    • 24944525711 scopus 로고    scopus 로고
    • Neisseria gonorrhoeae FitA interacts with FitB to bind DNA through its ribbon-helix-helix motif
    • DOI 10.1021/bi0511080
    • Wilbur JS, Chivers PT, Mattison K, Potter L, Brennan RG, So M (2005) Neisseria gonorrhoeae FitA interacts with FitB to bind DNA through its ribbon-helix-helix motif. Biochemistry 44:12515-12524 (Pubitemid 41324342)
    • (2005) Biochemistry , vol.44 , Issue.37 , pp. 12515-12524
    • Wilbur, J.S.1    Chivers, P.T.2    Mattison, K.3    Potter, L.4    Brennan, R.G.5    So, M.6
  • 44
    • 33645528243 scopus 로고    scopus 로고
    • Structures of omega repressors bound to direct and inverted DNA repeats explain modulation of transcription
    • Weihofen WA, Cicek A, Pratto F, Saenger W (2006) Structures of omega repressors bound to direct and inverted DNA repeats explain modulation of transcription. Nucleic Acids Res 34:1450-1458
    • (2006) Nucleic Acids Res , vol.34 , pp. 1450-1458
    • Weihofen, W.A.1    Cicek, A.2    Pratto, F.3    Saenger, W.4


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