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Volumn 9, Issue , 2015, Pages 1897-1912

Modeling, molecular dynamics, and docking assessment of transcription factor rho: A potential drug target in brucella melitensis 16M

Author keywords

ADMET analysis; Brucellosis; Rho proteins; SMD simulations; Therapeutics; Transcription inhibitors

Indexed keywords

PROTEIN INHIBITOR; TRANSCRIPTION TERMINATION FACTOR RHO; UNCLASSIFIED DRUG; ZINC 2493454; ZINC 72319544; ANTIINFECTIVE AGENT; RHO FACTOR;

EID: 84929166650     PISSN: 11778881     EISSN: 11778881     Source Type: Journal    
DOI: 10.2147/DDDT.S77020     Document Type: Article
Times cited : (49)

References (57)
  • 1
    • 65849408332 scopus 로고    scopus 로고
    • RhoBTB3: A Rho GTPase-family ATPase required for endosome to Golgi transport
    • Espinosa EJ, Calero M, Sridevi K, Pfeffer SR. RhoBTB3: a Rho GTPase-family ATPase required for endosome to Golgi transport. Cell. 2009;137(5):938–948.
    • (2009) Cell , vol.137 , Issue.5 , pp. 938-948
    • Espinosa, E.J.1    Calero, M.2    Sridevi, K.3    Pfeffer, S.R.4
  • 2
    • 33646849728 scopus 로고    scopus 로고
    • Rho-dependent transcription termination: More questions than answers
    • Banerjee S, Chalissery J, Bandey I, Sen R. Rho-dependent transcription termination: more questions than answers. J Microbiol. 2006;44(1):11–22.
    • (2006) J Microbiol , vol.44 , Issue.1 , pp. 11-22
    • Banerjee, S.1    Chalissery, J.2    Bandey, I.3    Sen, R.4
  • 4
    • 0021739701 scopus 로고
    • Binding of Rho factor to Escherichia coli RNA polymerase mediated by nusA protein
    • Schmidt MC, Chamberlin MJ. Binding of Rho factor to Escherichia coli RNA polymerase mediated by nusA protein. J Biol Chem. 1984;259(24):15000–15002.
    • (1984) J Biol Chem , vol.259 , Issue.24 , pp. 15000-15002
    • Schmidt, M.C.1    Chamberlin, M.J.2
  • 5
    • 0032904686 scopus 로고    scopus 로고
    • Autogenous regulation of transcription termination factor Rho and the requirement for Nus factors in Bacillus subtilis
    • Ingham CJ, Dennis J, Furneaux PA. Autogenous regulation of transcription termination factor Rho and the requirement for Nus factors in Bacillus subtilis. Mol Microbiol. 1999;31(2):651–663.
    • (1999) Mol Microbiol , vol.31 , Issue.2 , pp. 651-663
    • Ingham, C.J.1    Dennis, J.2    Furneaux, P.A.3
  • 6
    • 0038702662 scopus 로고    scopus 로고
    • Hijacking Rho GTPases by protein toxins and apoptosis: Molecular strategies of pathogenic bacteria
    • Fiorentini C, Falzano L, Travaglione S, Fabbri A. Hijacking Rho GTPases by protein toxins and apoptosis: molecular strategies of pathogenic bacteria. Cell Death Differ. 2003;10(2):147–152.
    • (2003) Cell Death Differ , vol.10 , Issue.2 , pp. 147-152
    • Fiorentini, C.1    Falzano, L.2    Travaglione, S.3    Fabbri, A.4
  • 7
    • 84904721645 scopus 로고    scopus 로고
    • Identification of genes required for the survival of B. Fragilis using massive parallel sequencing of a saturated transposon mutant library
    • Veeranagouda Y, Husain F, Tenorio EL, Wexler HM. Identification of genes required for the survival of B. fragilis using massive parallel sequencing of a saturated transposon mutant library. BMC Genomics. 2014;15:429.
    • (2014) BMC Genomics , vol.15 , pp. 429
    • Veeranagouda, Y.1    Husain, F.2    Tenorio, E.L.3    Wexler, H.M.4
  • 8
    • 33750477997 scopus 로고    scopus 로고
    • Structural insights into RNA-dependent ring closure and ATPase activation by the Rho termination factor
    • Skordalakes E, Berger JM. Structural insights into RNA-dependent ring closure and ATPase activation by the Rho termination factor. Cell. 2006;127(3):553–564.
    • (2006) Cell , vol.127 , Issue.3 , pp. 553-564
    • Skordalakes, E.1    Berger, J.M.2
  • 9
    • 0036791011 scopus 로고    scopus 로고
    • The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts
    • Paulsen IT, Seshadri R, Nelson KE, et al. The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts. Proc Natl Acad Sci U S A. 2002;99(20):13148–13153.
    • (2002) Proc Natl Acad Sci U S A , vol.99 , Issue.20 , pp. 13148-13153
    • Paulsen, I.T.1    Seshadri, R.2    Nelson, K.E.3
  • 11
    • 35648977694 scopus 로고    scopus 로고
    • The challenge of protein structure determination-lessons from structural genomics
    • Slabinski L, Jaroszewski L, Rodrigues AP, et al. The challenge of protein structure determination-lessons from structural genomics. Protein Sci. 2007;16(11):2472–2482.
    • (2007) Protein Sci , vol.16 , Issue.11 , pp. 2472-2482
    • Slabinski, L.1    Jaroszewski, L.2    Rodrigues, A.P.3
  • 12
    • 0026356891 scopus 로고
    • Predicting coiled coils from protein sequences
    • Lupas A, Van Dyke M, Stock J. Predicting coiled coils from protein sequences. Science. 1991;252(5009):1162–1164.
    • (1991) Science , vol.252 , Issue.5009 , pp. 1162-1164
    • Lupas, A.1    Van Dyke, M.2    Stock, J.3
  • 14
    • 0035910270 scopus 로고    scopus 로고
    • Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes
    • Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol. 2001;305(3):567–580.
    • (2001) J Mol Biol , vol.305 , Issue.3 , pp. 567-580
    • Krogh, A.1    Larsson, B.2    Von Heijne, G.3    Sonnhammer, E.L.4
  • 15
    • 46749146815 scopus 로고    scopus 로고
    • Prediction of signal peptides in protein sequences by neural networks
    • Plewczynski D, Slabinski L, Ginalski K, Rychlewski L. Prediction of signal peptides in protein sequences by neural networks. Acta Biochim Pol. 2008;55(2):261–267.
    • (2008) Acta Biochim Pol , vol.55 , Issue.2 , pp. 261-267
    • Plewczynski, D.1    Slabinski, L.2    Ginalski, K.3    Rychlewski, L.4
  • 16
    • 0028501914 scopus 로고
    • Non-globular domains in protein sequences: Automated segmentation using complexity measures
    • Wootton JC. Non-globular domains in protein sequences: automated segmentation using complexity measures. Comput Chem. 1994;18(3):269–285.
    • (1994) Comput Chem , vol.18 , Issue.3 , pp. 269-285
    • Wootton, J.C.1
  • 17
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol. 1999;292(2):195–202.
    • (1999) J Mol Biol , vol.292 , Issue.2 , pp. 195-202
    • Jones, D.T.1
  • 18
    • 39449105071 scopus 로고    scopus 로고
    • Cell-PLoc: A package of Web servers for predicting subcellular localization of proteins in various organisms
    • Chou KC, Shen HB. Cell-PLoc: a package of Web servers for predicting subcellular localization of proteins in various organisms. Nat Protoc. 2008;3(2):153–162.
    • (2008) Nat Protoc , vol.3 , Issue.2 , pp. 153-162
    • Chou, K.C.1    Shen, H.B.2
  • 19
    • 77954199597 scopus 로고    scopus 로고
    • PSORTb 3.0: Improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes
    • Yu NY, Wagner JR, Laird MR, et al. PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics. 2010;26(13):1608–1615.
    • (2010) Bioinformatics , vol.26 , Issue.13 , pp. 1608-1615
    • Yu, N.Y.1    Wagner, J.R.2    Laird, M.R.3
  • 20
    • 80053345905 scopus 로고    scopus 로고
    • SignalP 4.0: Discriminating signal peptides from transmembrane regions
    • Petersen TN, Brunak S, von Heijne G, Nielsen H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods. 2011;8(10):785–786.
    • (2011) Nat Methods , vol.8 , Issue.10 , pp. 785-786
    • Petersen, T.N.1    Brunak, S.2    Von Heijne, G.3    Nielsen, H.4
  • 21
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Altschul SF, Madden TL, Schaffer AA, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25(17):3389–3402.
    • (1997) Nucleic Acids Res , vol.25 , Issue.17 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schaffer, A.A.3
  • 23
    • 0037559627 scopus 로고    scopus 로고
    • Structure of the Rho transcription terminator: Mechanism of mRNA recognition and helicase loading
    • Skordalakes E, Berger JM. Structure of the Rho transcription terminator: mechanism of mRNA recognition and helicase loading. Cell. 2003;114(1):135–146.
    • (2003) Cell , vol.114 , Issue.1 , pp. 135-146
    • Skordalakes, E.1    Berger, J.M.2
  • 24
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol. 1993;234(3):779–815.
    • (1993) J Mol Biol , vol.234 , Issue.3 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 25
    • 0033810049 scopus 로고    scopus 로고
    • Modeling of loops in protein structures
    • Fiser A, Do RK, Sali A. Modeling of loops in protein structures. Protein Sci. 2000;9(9):1753–1773.
    • (2000) Protein Sci , vol.9 , Issue.9 , pp. 1753-1773
    • Fiser, A.1    Do, R.K.2    Sali, A.3
  • 26
    • 0000243829 scopus 로고
    • PROCHECK: A program to check the stereochemical quality of protein structures
    • Laskowski RA, MacArthur MW, Moss DS, Thornton JM. PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr. 1993;26(Pt 2):283–291.
    • (1993) J Appl Crystallogr , vol.26 , pp. 283-291
    • Laskowski, R.A.1    Macarthur, M.W.2    Moss, D.S.3    Thornton, J.M.4
  • 27
    • 0027180507 scopus 로고
    • Verification of protein structures: Patterns of nonbonded atomic interactions
    • Colovos C, Yeates T. Verification of protein structures: patterns of nonbonded atomic interactions. Protein Sci. 1993;2(9):1511–1519.
    • (1993) Protein Sci , vol.2 , Issue.9 , pp. 1511-1519
    • Colovos, C.1    Yeates, T.2
  • 28
    • 0026610767 scopus 로고
    • Assessment of protein models with three-dimensional profiles
    • Lüthy R, Bowie JU, Eisenberg D. Assessment of protein models with three-dimensional profiles. Nature. 1992;356(6364):83–85.
    • (1992) Nature , vol.356 , Issue.6364 , pp. 83-85
    • Lüthy, R.1    Bowie, J.U.2    Eisenberg, D.3
  • 29
    • 34547566446 scopus 로고    scopus 로고
    • ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins
    • Wiederstein M, Sippl MJ. ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res. 2007;35(Web Server issue):W407–W410.
    • (2007) Nucleic Acids Res , vol.35 , Issue.Web Server issue , pp. W407-W410
    • Wiederstein, M.1    Sippl, M.J.2
  • 30
    • 3242881211 scopus 로고    scopus 로고
    • SuperPose: A simple server for sophisticated structural superposition
    • Maiti R, Van Domselaar GH, Zhang H, Wishart DS. SuperPose: a simple server for sophisticated structural superposition. Nucleic Acids Res. 2004;32(Web Server issue):W590–W594.
    • (2004) Nucleic Acids Res , vol.32 , Issue.Web Server issue , pp. W590-W594
    • Maiti, R.1    Van Domselaar, G.H.2    Zhang, H.3    Wishart, D.S.4
  • 32
    • 84930989053 scopus 로고    scopus 로고
    • Structural comparison, substrate specificity, and inhibitor binding of AGPase small subunit from monocot and dicot: Present insight and future potential
    • Sarma K, Sen P, Barooah M, Choudhury MD, Roychoudhury S, Modi MK. Structural comparison, substrate specificity, and inhibitor binding of AGPase small subunit from monocot and dicot: present insight and future potential. Biomed Res Int. 2014;2014:583606.
    • (2014) Biomed Res Int , pp. 2014
    • Sarma, K.1    Sen, P.2    Barooah, M.3    Choudhury, M.D.4    Roychoudhury, S.5    Modi, M.K.6
  • 33
    • 33747818007 scopus 로고    scopus 로고
    • CASTp: Computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues
    • Dundas J, Ouyang Z, Tseng J, Binkowski A, Turpaz Y, Liang J. CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucleic Acids Res. 2006;34(Web Server issue):W116–W118.
    • (2006) Nucleic Acids Res , vol.34 , Issue.Web Server issue , pp. W116-W118
    • Dundas, J.1    Ouyang, Z.2    Tseng, J.3    Binkowski, A.4    Turpaz, Y.5    Liang, J.6
  • 34
    • 13844312649 scopus 로고    scopus 로고
    • ZINC – a free database of commercially available compounds for virtual screening
    • Irwin JJ, Shoichet BK. ZINC – a free database of commercially available compounds for virtual screening. J Chem Inf Model. 2005;45(1):177–182.
    • (2005) J Chem Inf Model , vol.45 , Issue.1 , pp. 177-182
    • Irwin, J.J.1    Shoichet, B.K.2
  • 36
    • 70349932423 scopus 로고    scopus 로고
    • AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
    • Morris GM, Huey R, Lindstrom W, et al. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem. 2009;30(16):2785–2791.
    • (2009) J Comput Chem , vol.30 , Issue.16 , pp. 2785-2791
    • Morris, G.M.1    Huey, R.2    Lindstrom, W.3
  • 37
    • 76149120388 scopus 로고    scopus 로고
    • AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
    • Trott O, Olson AJ. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem. 2010;31(2):455–461.
    • (2010) J Comput Chem , vol.31 , Issue.2 , pp. 455-461
    • Trott, O.1    Olson, A.J.2
  • 38
    • 80054911951 scopus 로고    scopus 로고
    • LigPlot+: Multiple ligand-protein interaction diagrams for drug discovery
    • Laskowski RA, Swindells MB. LigPlot+: multiple ligand-protein interaction diagrams for drug discovery. J Chem Inf Model. 2011;51(10):2778–2786.
    • (2011) J Chem Inf Model , vol.51 , Issue.10 , pp. 2778-2786
    • Laskowski, R.A.1    Swindells, M.B.2
  • 39
    • 84863168282 scopus 로고    scopus 로고
    • Applications of genetically modified tools to safety assessment in drug development
    • Kay HY, Wu H, Lee SI, Kim SG. Applications of genetically modified tools to safety assessment in drug development. Toxicol Res. 2010;26(1):1–8.
    • (2010) Toxicol Res , vol.26 , Issue.1 , pp. 1-8
    • Kay, H.Y.1    Wu, H.2    Lee, S.I.3    Kim, S.G.4
  • 40
    • 65249170905 scopus 로고    scopus 로고
    • OSIRIS, an entirely in-house developed drug discovery informatics system
    • Sander T, Freyss J, von Korff M, Reich JR, Rufener C. OSIRIS, an entirely in-house developed drug discovery informatics system. J Chem Inf Model. 2009;49(2):232−246.
    • (2009) J Chem Inf Model , vol.49 , Issue.2 , pp. 232-246
    • Sander, T.1    Freyss, J.2    Von Korff, M.3    Reich, J.R.4    Rufener, C.5
  • 42
    • 8344276781 scopus 로고    scopus 로고
    • NAMD: A parallel, object-oriented molecular dynamics program
    • Nelson MT, Humphrey W, Gursoy A, et al. NAMD: a parallel, object-oriented molecular dynamics program. Int J Supercomput Appl. 1996;10(4):251–268.
    • (1996) Int J Supercomput Appl , vol.10 , Issue.4 , pp. 251-268
    • Nelson, M.T.1    Humphrey, W.2    Gursoy, A.3
  • 43
  • 44
    • 84890447773 scopus 로고    scopus 로고
    • Polarizable force field for peptides and proteins based on the classical Drude oscillator
    • Lopes PE, Huang J, Shim J, et al. Polarizable force field for peptides and proteins based on the classical Drude oscillator. J Chem Theory Comput. 2013;9(12):5430–5449.
    • (2013) J Chem Theory Comput , vol.9 , Issue.12 , pp. 5430-5449
    • Lopes, P.E.1    Huang, J.2    Shim, J.3
  • 46
    • 36449007836 scopus 로고
    • Constant pressure molecular dynamics simulation: The Langevin piston method
    • Feller S, Zhang Y, Pastor R, Brooks B. Constant pressure molecular dynamics simulation: the Langevin piston method. J Chem Phys. 1995;103:4613–4621.
    • (1995) J Chem Phys , vol.103 , pp. 4613-4621
    • Feller, S.1    Zhang, Y.2    Pastor, R.3    Brooks, B.4
  • 47
    • 4444221565 scopus 로고    scopus 로고
    • UCSF Chimera – a visualization system for exploratory research and analysis
    • Pettersen EF, Goddard TD, Huang CC, et al. UCSF Chimera – a visualization system for exploratory research and analysis. J Comput Chem. 2004;25(13):1605–1612.
    • (2004) J Comput Chem , vol.25 , Issue.13 , pp. 1605-1612
    • Pettersen, E.F.1    Goddard, T.D.2    Huang, C.C.3
  • 48
    • 79958841703 scopus 로고    scopus 로고
    • SwissParam, a Fast Force Field Generation Tool For Small Organic Molecules
    • Zoete V, Cuendet MA, Grosdidier A, Michielin O. SwissParam, a Fast Force Field Generation Tool For Small Organic Molecules. J Comput Chem. 2011;32(11):2359–2368.
    • (2011) J Comput Chem , vol.32 , Issue.11 , pp. 2359-2368
    • Zoete, V.1    Cuendet, M.A.2    Grosdidier, A.3    Michielin, O.4
  • 49
    • 0030941120 scopus 로고    scopus 로고
    • How hormone receptor-DNA binding affects nucleosomal DNA: The role of symmetry
    • Bishop TC, Kosztin D, Schulten K. How hormone receptor-DNA binding affects nucleosomal DNA: the role of symmetry. Biophys J. 1997;72(5):2056–2067.
    • (1997) Biophys J , vol.72 , Issue.5 , pp. 2056-2067
    • Bishop, T.C.1    Kosztin, D.2    Schulten, K.3
  • 50
    • 0030805890 scopus 로고    scopus 로고
    • Binding of the estrogen receptor to DNA: The role of waters
    • Kosztin D, Bishop TC, Schulten K. Binding of the estrogen receptor to DNA: the role of waters. Biophys J. 1997;73(2):557–570.
    • (1997) Biophys J , vol.73 , Issue.2 , pp. 557-570
    • Kosztin, D.1    Bishop, T.C.2    Schulten, K.3
  • 51
    • 4243754128 scopus 로고    scopus 로고
    • Nonequilibrium equality for free energy differences
    • Jarzynski C. Nonequilibrium equality for free energy differences. Phys Rev Lett. 1997;78(14):2690–2693.
    • (1997) Phys Rev Lett , vol.78 , Issue.14 , pp. 2690-2693
    • Jarzynski, C.1
  • 52
    • 27344436659 scopus 로고    scopus 로고
    • Scalable molecular dynamics with NAMD
    • Phillips JC, Braun R, Wang W, et al. Scalable molecular dynamics with NAMD. J Comp Chem. 2005;26(16):1781–1802.
    • (2005) J Comp Chem , vol.26 , Issue.16 , pp. 1781-1802
    • Phillips, J.C.1    Braun, R.2    Wang, W.3
  • 53
    • 0030987036 scopus 로고    scopus 로고
    • Molecular dynamics study of unbinding of the avidin-biotin complex
    • Izrailev S, Stepaniants S, Balsera M, Oono Y, Schulten K. Molecular dynamics study of unbinding of the avidin-biotin complex. Biophys J. 1997;72(4):1568–1581.
    • (1997) Biophys J , vol.72 , Issue.4 , pp. 1568-1581
    • Izrailev, S.1    Stepaniants, S.2    Balsera, M.3    Oono, Y.4    Schulten, K.5
  • 54
    • 0030872242 scopus 로고    scopus 로고
    • Reconstructing potential energy functions from simulated force-induced unbinding processes
    • Balsera M, Stepaniants S, Izrailev S, Oono Y, Schulten K. Reconstructing potential energy functions from simulated force-induced unbinding processes. Biophys J. 1997;73(3):1281–1287.
    • (1997) Biophys J , vol.73 , Issue.3 , pp. 1281-1287
    • Balsera, M.1    Stepaniants, S.2    Izrailev, S.3    Oono, Y.4    Schulten, K.5
  • 55
    • 0031001349 scopus 로고    scopus 로고
    • Dynamic strength of molecular adhesion bonds
    • Evans E, Ritchie K. Dynamic strength of molecular adhesion bonds. Biophys J. 1997;72(4):1541–1555.
    • (1997) Biophys J , vol.72 , Issue.4 , pp. 1541-1555
    • Evans, E.1    Ritchie, K.2
  • 56
    • 84893482610 scopus 로고
    • A solution for the best rotation to relate two sets of vectors
    • Kabsch W. A solution for the best rotation to relate two sets of vectors. Acta Crystallogr A Found Adv. 1976;A32:922–923.
    • (1976) Acta Crystallogr a Found Adv , vol.A32 , pp. 922-923
    • Kabsch, W.1


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