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Volumn 20, Issue 7, 2011, Pages 1220-1230

Structural consequences of ATP hydrolysis on the ABC transporter NBD dimer: Molecular dynamics studies of HlyB

Author keywords

Conformational changes; Exporters; Molecular modeling; Nucleotide binding domains; Subtraction technique

Indexed keywords

ABC TRANSPORTER; ADENOSINE TRIPHOSPHATE; DIMER; HELIX LOOP HELIX PROTEIN; HEMOLYSIN; MONOMER; NUCLEOTIDE; PROTEIN HLYB; UNCLASSIFIED DRUG;

EID: 79959352522     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.650     Document Type: Article
Times cited : (44)

References (59)
  • 1
    • 0031943304 scopus 로고    scopus 로고
    • The Escherichia coli ATP-binding cassette (ABC) proteins
    • DOI 10.1046/j.1365-2958.1998.00764.x
    • Linton KJ, Higgins CF (1998) The Escherichia coli ATP-binding cassette (ABC) proteins. Mol Microbiol 28:5-13. (Pubitemid 28160109)
    • (1998) Molecular Microbiology , vol.28 , Issue.1 , pp. 5-13
    • Linton, K.J.1    Higgins, C.F.2
  • 2
    • 0022051849 scopus 로고
    • Nucleotide binding by membrane components of bacterial periplasmic binding protein-dependent transport systems
    • Higgins CF, Hiles ID, Whalley K, Jamieson DJ (1985) Nucleotide binding by membrane components of bacterial periplasmic binding protein-dependent transport systems. EMBO J 4:1033-1039.
    • (1985) EMBO J , vol.4 , pp. 1033-1039
    • Higgins, C.F.1    Hiles, I.D.2    Whalley, K.3    Jamieson, D.J.4
  • 5
    • 0035878128 scopus 로고    scopus 로고
    • Protein secretion and the pathogenesis of bacterial infections
    • DOI 10.1101/gad.896801
    • Lee VT, Schneewind O (2001) Protein secretion and the pathogenesis of bacterial infections. Genes Dev 15:1725-1752. (Pubitemid 32905631)
    • (2001) Genes and Development , vol.15 , Issue.14 , pp. 1725-1752
    • Lee, V.T.1    Schneewind, O.2
  • 6
    • 1842610700 scopus 로고    scopus 로고
    • The ABC transporter structure and mechanism: Perspectives on recent research
    • DOI 10.1007/s00018-003-3336-9
    • Jones PM, George AM (2004) The ABC transporter structure and mechanism: perspectives on recent research. Cell Mol Life Sci 61:682-699. (Pubitemid 38446412)
    • (2004) Cellular and Molecular Life Sciences , vol.61 , Issue.6 , pp. 682-699
    • Jones, P.M.1    George, A.M.2
  • 7
    • 33745835398 scopus 로고    scopus 로고
    • Transmembrane transport of endo- and xenobiotics by mammalian ATP-binding cassette multidrug resistance proteins
    • DOI 10.1152/physrev.00035.2005
    • Deeley RG, Westlake C, Cole SPC (2006) Transmembrane transport of endo- and xenobiotics by mammalian ATP-binding cassette multidrug resistance proteins. Physiol Rev 86:849-899. (Pubitemid 44033384)
    • (2006) Physiological Reviews , vol.86 , Issue.3 , pp. 849-899
    • Deeley, R.G.1    Westlake, C.2    Cole, S.P.C.3
  • 8
    • 0035014565 scopus 로고    scopus 로고
    • The ABC of ABCs: A phylogenetic and functional classification of ABC systems in living organisms
    • DOI 10.1016/S0923-2508(01)01194-9
    • Dassa E, Bouige P (2001) The ABC of ABCS: a phylogenetic and functional classification of ABC systems in living organisms. Res Microbiol 152:211-229. (Pubitemid 32436481)
    • (2001) Research in Microbiology , vol.152 , Issue.3-4 , pp. 211-229
    • Dassa, E.1    Bouige, P.2
  • 10
    • 21244454073 scopus 로고    scopus 로고
    • H662 is the linchpin of ATP hydrolysis in the nucleotide-binding domain of the ABC transporter HlyB
    • DOI 10.1038/sj.emboj.7600657
    • Zaitseva J, Jenewein S, Jumpertz T, Holland IB, Schmitt L (2005) H662 is the linchpin of ATP hydrolysis in the nucleotide-binding domain of the ABC transporter HlyB. EMBO J 24:1901-1910. (Pubitemid 40896162)
    • (2005) EMBO Journal , vol.24 , Issue.11 , pp. 1901-1910
    • Zaitseva, J.1    Jenewein, S.2    Jumpertz, T.3    Holland, I.B.4    Schmitt, L.5
  • 11
    • 34548853133 scopus 로고    scopus 로고
    • Structure and mechanism of ABC transporter proteins
    • DOI 10.1016/j.sbi.2007.07.003, PII S0959440X07001029
    • Hollenstein K, Dawson RJP, Locher KP (2007) Structure and mechanism of ABC transporter proteins. Curr Opin Struct Biol 17:412-418. (Pubitemid 47451766)
    • (2007) Current Opinion in Structural Biology , vol.17 , Issue.4 , pp. 412-418
    • Hollenstein, K.1    Dawson, R.J.2    Locher, K.P.3
  • 12
    • 70349335633 scopus 로고    scopus 로고
    • ABC transporters: A riddle wrapped in a mystery inside an enigma
    • Jones PM, O'Mara ML, George AM (2009) ABC transporters: a riddle wrapped in a mystery inside an enigma. Trends Biochem Sci 34:520-531.
    • (2009) Trends Biochem Sci , vol.34 , pp. 520-531
    • Jones, P.M.1    O'Mara, M.L.2    George, A.M.3
  • 13
    • 33748644877 scopus 로고    scopus 로고
    • Structure of a bacterial multidrug ABC transporter
    • DOI 10.1038/nature05155, PII NATURE05155
    • Dawson RJP, Locher KP (2006) Structure of a bacterial multidrug ABC transporter. Nature 443:180-185. (Pubitemid 44387602)
    • (2006) Nature , vol.443 , Issue.7108 , pp. 180-185
    • Dawson, R.J.P.1    Locher, K.P.2
  • 14
    • 36549018568 scopus 로고    scopus 로고
    • Crystal structure of a catalytic intermediate of the maltose transporter
    • DOI 10.1038/nature06264
    • Oldham ML, Khare D, Quiocho FA, Davidson AL, Chen J (2007) Crystal structure of a catalytic intermediate of the maltose transporter. Nature 450:515-521. (Pubitemid 350190241)
    • (2007) Nature , vol.450 , Issue.7169 , pp. 515-521
    • Oldham, M.L.1    Khare, D.2    Quiocho, F.A.3    Davidson, A.L.4    Chen, J.5
  • 15
    • 37649004412 scopus 로고    scopus 로고
    • Flexibility in the ABC transporter MsbA: Alternating access with a twist
    • Ward A, Reyes CL, Yu J, Roth CB, Chang G (2007) Flexibility in the ABC transporter MsbA: Alternating access with a twist. Proc Natl Acad Sci USA 104:19005-19010.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 19005-19010
    • Ward, A.1    Reyes, C.L.2    Yu, J.3    Roth, C.B.4    Chang, G.5
  • 16
    • 47249084799 scopus 로고    scopus 로고
    • The high-affinity E. coli methionine ABC transporter: Structure and allosteric regulation
    • DOI 10.1126/science.1157987
    • Kadaba NS, Kaiser JT, Johnson E, Lee A, Rees DC (2008) The high-affinity E. coli methionine ABC transporter: structure and allosteric regulation. Science 321:250-253. (Pubitemid 351989096)
    • (2008) Science , vol.321 , Issue.5886 , pp. 250-253
    • Kadaba, N.S.1    Kaiser, J.T.2    Johnson, E.3    Lee, A.4    Rees, D.C.5
  • 18
    • 60549097035 scopus 로고    scopus 로고
    • Alternating access in maltose transporter mediated by rigid-body rotations
    • Khare D, Oldham ML, Orelle C, Davidson AL, Chen J (2009) Alternating access in maltose transporter mediated by rigid-body rotations. Mol Cell 33:528-536.
    • (2009) Mol Cell , vol.33 , pp. 528-536
    • Khare, D.1    Oldham, M.L.2    Orelle, C.3    Davidson, A.L.4    Chen, J.5
  • 19
    • 70349785109 scopus 로고    scopus 로고
    • Conformational cycle of the ABC transporter MsbA in liposomes: Detailed analysis using double electron-electron resonance spectroscopy
    • Zou P, Bortolus M, McHaourab HS (2009) Conformational cycle of the ABC transporter MsbA in liposomes: detailed analysis using double electron-electron resonance spectroscopy. J Mol Biol 393:586-597.
    • (2009) J Mol Biol , vol.393 , pp. 586-597
    • Zou, P.1    Bortolus, M.2    McHaourab, H.S.3
  • 20
    • 33750038243 scopus 로고    scopus 로고
    • Characterization of the LSGGQ and H motifs from the Escherichia coli lipid A transporter MsbA
    • DOI 10.1021/bi060830a
    • Buchaklian AH, Klug CS (2006) Characterization of the LSGGQ and H motifs from the Escherichia coli lipid A transporter MsbA. Biochemistry 45:12539-12546. (Pubitemid 44583696)
    • (2006) Biochemistry , vol.45 , Issue.41 , pp. 12539-12546
    • Buchaklian, A.H.1    Klug, C.S.2
  • 22
    • 58149359858 scopus 로고    scopus 로고
    • Dimer opening of the nucleotide binding domains of ABC transporters after ATP hydrolysis
    • Wen P-C, Tajkhorshid E (2008) Dimer opening of the nucleotide binding domains of ABC transporters after ATP hydrolysis. Biophys J 95:5100-5110.
    • (2008) Biophys J , vol.95 , pp. 5100-5110
    • Wen, P.-C.1    Tajkhorshid, E.2
  • 23
    • 66149139241 scopus 로고    scopus 로고
    • Opening of the ADPbound active site in the ABC transporter ATPase dimer: Evidence for a constant contact, alternating sites model for the catalytic cycle
    • Jones PM, George AM (2009) Opening of the ADPbound active site in the ABC transporter ATPase dimer: evidence for a constant contact, alternating sites model for the catalytic cycle. Proteins 75:387-396.
    • (2009) Proteins , vol.75 , pp. 387-396
    • Jones, P.M.1    George, A.M.2
  • 24
    • 79955741987 scopus 로고    scopus 로고
    • Conformational changes induced by ATP-hydrolysis in an ABC transporter: A molecular dynamics study of the Sav1866 exporter
    • Oliveira ASF, Baptista AM, Soares CM (2011) Conformational changes induced by ATP-hydrolysis in an ABC transporter: A molecular dynamics study of the Sav1866 exporter. Proteins 79:1977-1990.
    • (2011) Proteins , vol.79 , pp. 1977-1990
    • Oliveira, A.S.F.1    Baptista, A.M.2    Soares, C.M.3
  • 25
    • 77951539821 scopus 로고    scopus 로고
    • Insights into the molecular mechanism of an ABC transporter: Conformational changes in the NBD dimer of MJ0796
    • Oliveira ASF, Baptista AM, Soares CM (2010) Insights into the molecular mechanism of an ABC transporter: conformational changes in the NBD dimer of MJ0796. J Phys Chem B 114:5486-5496.
    • (2010) J Phys Chem B , vol.114 , pp. 5486-5496
    • Oliveira, A.S.F.1    Baptista, A.M.2    Soares, C.M.3
  • 28
    • 36849067873 scopus 로고    scopus 로고
    • Catalytic cycle of ATP hydrolysis by P-glycoprotein: Evidence for formation of the E•S reaction intermediate with ATP-c-S, a nonhydrolyzable analogue of ATP
    • DOI 10.1021/bi701385t
    • Sauna ZE, Kim I-W, Nandigama K, Kopp S, Chiba P, Ambudkar SV (2007) Catalytic cycle of ATP hydrolysis by P-glycoprotein: evidence for formation of the E•S reaction intermediate with ATP-c-S, a nonhydrolyzable analogue of ATP. Biochemistry 46:13787-13799. (Pubitemid 350223906)
    • (2007) Biochemistry , vol.46 , Issue.48 , pp. 13787-13799
    • Sauna, Z.E.1    Kim, I.-W.2    Nandigama, K.3    Kopp, S.4    Chiba, P.5    Ambudkar, S.V.6
  • 30
    • 34547943910 scopus 로고    scopus 로고
    • Nucleotide-dependent allostery within the ABC transporter ATP-binding cassette: A computational study of the MJ0796 dimer
    • DOI 10.1074/jbc.M700809200
    • Jones PM, George AM (2007) Nucleotide-dependent allostery within the ABC transporter ATP-binding cassette: a computational study of the MJ0796 dimer. J Biol Chem 282:22793-22803. (Pubitemid 47267351)
    • (2007) Journal of Biological Chemistry , vol.282 , Issue.31 , pp. 22793-22803
    • Jones, P.M.1    George, A.M.2
  • 31
    • 18844428872 scopus 로고    scopus 로고
    • Type 1 protein secretion in bacteria, the ABC-transporter dependent pathway
    • DOI 10.1080/09687860500042013
    • Holland IB, Schmitt L, Young J (2005) Type 1 protein secretion in bacteria, the ABC-transporter dependent pathway (review). Mol Membr Biol 22:29-39. (Pubitemid 40692152)
    • (2005) Molecular Membrane Biology , vol.22 , Issue.1-2 , pp. 29-39
    • Holland, I.B.1    Schmitt, L.2    Young, J.3
  • 32
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogenbonded and geometrical features
    • Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogenbonded and geometrical features. Biopolymers 22:2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 33
    • 0036342413 scopus 로고    scopus 로고
    • ATP binding to the motor domain from an ABC transporter drives formation of a nucleotide sandwich dimer
    • DOI 10.1016/S1097-2765(02)00576-2
    • Smith PC, Karpowich N, Millen L, Moody JE, Rosen J, Thomas PJ, Hunt JF (2002) ATP binding to the motor domain from an ABC transporter drives formation of a nucleotide sandwich dimer. Mol Cell 10:139-149. (Pubitemid 34876568)
    • (2002) Molecular Cell , vol.10 , Issue.1 , pp. 139-149
    • Smith, P.C.1    Karpowich, N.2    Millen, L.3    Moody, J.E.4    Rosen, J.5    Thomas, P.J.6    Hunt, J.F.7
  • 35
    • 68949107624 scopus 로고    scopus 로고
    • Secondary structure propensities in peptide folding simulations: A systematic comparison of molecular mechanics interaction schemes
    • Matthes D, de Groot BL (2009) Secondary structure propensities in peptide folding simulations: a systematic comparison of molecular mechanics interaction schemes. Biophys J 97:599-608.
    • (2009) Biophys J , vol.97 , pp. 599-608
    • Matthes, D.1    De Groot, B.L.2
  • 36
    • 77955135754 scopus 로고    scopus 로고
    • Scrutinizing molecular mechanics force fields on the submicrosecond timescale with NMR data
    • Lange OF, van der Spoel D, de Groot BL (2010) Scrutinizing molecular mechanics force fields on the submicrosecond timescale with NMR data. Biophys J 99:647-655.
    • (2010) Biophys J , vol.99 , pp. 647-655
    • Lange, O.F.1    Van Der Spoel, D.2    De Groot, B.L.3
  • 37
    • 33746537716 scopus 로고    scopus 로고
    • A structural analysis of asymmetry required for catalytic activity of an ABC-ATPase domain dimer
    • DOI 10.1038/sj.emboj.7601208, PII 7601208
    • Zaitseva J, Oswald C, Jumpertz T, Jenewein S, Wiedenmann A, Holland IB, Schmitt L (2006) A structural analysis of asymmetry required for catalytic activity of an ABC-ATPase domain dimer. EMBO J 25:3432-3443. (Pubitemid 44141799)
    • (2006) EMBO Journal , vol.25 , Issue.14 , pp. 3432-3443
    • Zaitseva, J.1    Oswald, C.2    Jumpertz, T.3    Jenewein, S.4    Wiedenmann, A.5    Holland, I.B.6    Schmitt, L.7
  • 38
    • 0034941969 scopus 로고    scopus 로고
    • Crystal structures of the MJ1267 ATP binding cassette reveal an induced-fit effect at the ATPase active site of an ABC transporter
    • DOI 10.1016/S0969-2126(01)00617-7, PII S0969212601006177
    • Karpowich N, Martsinkevich O, Millen L, Yuan YR, Dai PL, MacVey K, Thomas PJ, Hunt JF (2001) Crystal structures of the MJ1267 ATP binding cassette reveal an induced-fit effect at the ATPase active site of an ABC transporter. Structure 9:571-586. (Pubitemid 32695582)
    • (2001) Structure , vol.9 , Issue.7 , pp. 571-586
    • Karpowich, N.1    Martsinkevich, O.2    Millen, L.3    Yuan, Y.-R.4    Dai, P.L.5    MacVey, K.6    Thomas, P.J.7    Hunt, J.F.8
  • 39
    • 0035943735 scopus 로고    scopus 로고
    • The crystal structure of the MJ0796 ATP-binding cassette. Implications for the structural consequences of ATP hydrolysis in the active site of an ABC transporter
    • Yuan YR, Blecker S, Martsinkevich O, Millen L, Thomas PJ, Hunt JF (2001) The crystal structure of the MJ0796 ATP-binding cassette. Implications for the structural consequences of ATP hydrolysis in the active site of an ABC transporter. J Biol Chem 276:32313-32321.
    • (2001) J Biol Chem , vol.276 , pp. 32313-32321
    • Yuan, Y.R.1    Blecker, S.2    Martsinkevich, O.3    Millen, L.4    Thomas, P.J.5    Hunt, J.F.6
  • 40
    • 84913591509 scopus 로고
    • Improved strategy in analytic surface calculation for molecular systems: Handling of singularities and computational efficiency
    • Eisenhaber F, Argos P (1993) Improved strategy in analytic surface calculation for molecular systems: handling of singularities and computational efficiency. J Comput Chem 14:1272-1280.
    • (1993) J Comput Chem , vol.14 , pp. 1272-1280
    • Eisenhaber, F.1    Argos, P.2
  • 41
    • 0025197061 scopus 로고
    • pKa's of ionizable groups in proteins: Atomic detail from a continuum electrostatic model
    • Bashford D, Karplus M (1990) pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model. Biochemistry 29:10219-10225.
    • (1990) Biochemistry , vol.29 , pp. 10219-10225
    • Bashford, D.1    Karplus, M.2
  • 42
    • 0026612756 scopus 로고
    • Electrostatic calculations of the pKa values of ionizable groups in bacteriorhodopsin
    • Bashford D, Gerwert K (1992) Electrostatic calculations of the pKa values of ionizable groups in bacteriorhodopsin. J Mol Biol 224:473-486.
    • (1992) J Mol Biol , vol.224 , pp. 473-486
    • Bashford, D.1    Gerwert, K.2
  • 43
    • 0035120969 scopus 로고    scopus 로고
    • Some theoretical and computational aspects of the inclusion of proton isomerism in the protonation equilibrium of proteins
    • Baptista AM, Soares CM (2001) Some theoretical and computational aspects of the inclusion of proton isomerism in the protonation equilibrium of proteins. J Phys Chem B 105:293-309.
    • (2001) J Phys Chem B , vol.105 , pp. 293-309
    • Baptista, A.M.1    Soares, C.M.2
  • 44
    • 0036359052 scopus 로고    scopus 로고
    • Studies of the reduction and protonation behavior of tetraheme cytochromes using atomic detail
    • DOI 10.1007/s007750100287
    • Teixeira V, Soares C, Baptista A (2002) Studies of the reduction and protonation behavior of tetraheme cytochromes using atomic detail. J Biol Inorg Chem 7:200-216. (Pubitemid 41490233)
    • (2002) Journal of Biological Inorganic Chemistry , vol.7 , Issue.1-2 , pp. 200-216
    • Teixeira, V.H.1    Soares, C.M.2    Baptista, A.M.3
  • 48
    • 0035789518 scopus 로고    scopus 로고
    • GROMACS 3.0: A package for molecular simulation and trajectory analysis
    • DOI 10.1007/S008940100045
    • Lindahl E, Hess B, van der Spoel D (2001) GROMACS 3.0: a package for molecular simulation and trajectory analysis. J Mol Model 7:306-317. (Pubitemid 36153547)
    • (2001) Journal of Molecular Modeling , vol.7 , Issue.8 , pp. 306-317
    • Lindahl, E.1    Hess, B.2    Van Der Spoel, D.3
  • 51
    • 33846823909 scopus 로고
    • Particle mesh Ewald: An N•log(N) method for Ewald sums in large systems
    • Darden T, York D, Pedersen L (1993) Particle mesh Ewald: 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    Pedersen, L.3
  • 54
    • 84986440341 scopus 로고
    • Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models
    • Miyamoto S, Kollman PA (1992) Settle: an analytical version of the SHAKE and RATTLE algorithm for rigid water models. J Comput Chem 13:952-962.
    • (1992) J Comput Chem , vol.13 , pp. 952-962
    • Miyamoto, S.1    Kollman, P.A.2
  • 56
    • 7044239742 scopus 로고
    • Free energy calculations: Applications to chemical and biochemical phenomena
    • Kollman P (1993) Free energy calculations: applications to chemical and biochemical phenomena. Chem Rev 93:2395-2417.
    • (1993) Chem Rev , vol.93 , pp. 2395-2417
    • Kollman, P.1
  • 59
    • 28444483273 scopus 로고    scopus 로고
    • Reorganization and conformational changes in the reduction of tetraheme cytochromes
    • DOI 10.1529/biophysj.105.065144
    • Oliveira ASF, Teixeira VH, Baptista AM, Soares CM (2005) Reorganization and conformational changes in the reduction of tetraheme cytochromes. Biophys J 89:3919-3930. (Pubitemid 41725614)
    • (2005) Biophysical Journal , vol.89 , Issue.6 , pp. 3919-3930
    • Oliveira, A.S.F.1    Teixeira, V.H.2    Baptista, A.M.3    Soares, C.M.4


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