메뉴 건너뛰기




Volumn 49, Issue 13, 2010, Pages 2860-2868

Molecular dynamics simulations of β-ketoacyl-, β-hydroxyaeyl-, and trans-2-enoyl-acyl carrier proteins of escherichia coli

Author keywords

[No Author keywords available]

Indexed keywords

ACYL CARRIER PROTEINS; ACYL CHAIN; ACYL-ACP; BINDING MODES; HYDROPHOBIC BINDING; HYDROPHOBIC POCKETS; MD SIMULATION; MOLECULAR DYNAMICS SIMULATIONS; POLAR FUNCTIONAL GROUPS; POLAR GROUPS; SYNTHASE ENZYMES; SYNTHASES;

EID: 77950387315     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi901713r     Document Type: Article
Times cited : (10)

References (46)
  • 1
    • 22244466130 scopus 로고    scopus 로고
    • The structural biology of type II fatty acid biosynthesis
    • White, S. W., Zheng, J., Zhang, Y. M., and Rock, C. O. (2005) The structural biology of type II fatty acid biosynthesis. Annu. Rev. Biochem. 74, 791-831.
    • (2005) Annu. Rev. Biochem. , vol.74 , pp. 791-831
    • White, S.W.1    Zheng, J.2    Zhang, Y.M.3    Rock, C.O.4
  • 2
    • 2342455737 scopus 로고    scopus 로고
    • Product diversity and regulation of type II fatty acid synthases
    • Lu, Y. J., Zhang, Y. M., and Rock, C. O. (2004) Product diversity and regulation of type II fatty acid synthases. Biochem. Cell Biol. 82, 145-155.
    • (2004) Biochem. Cell Biol. , vol.82 , pp. 145-155
    • Lu, Y.J.1    Zhang, Y.M.2    Rock, C.O.3
  • 3
    • 39149115737 scopus 로고    scopus 로고
    • Membrane lipid homeostasis in bacteria
    • Zhang,Y. M., and Rock, C. O. (2008) Membrane lipid homeostasis in bacteria. Nat. Rev. Microbiol. 6, 222-233.
    • (2008) Nat. Rev. Microbiol. , vol.6 , pp. 222-233
    • Zhang, Y.M.1    Rock, C.O.2
  • 4
    • 35748965549 scopus 로고    scopus 로고
    • Antibacterial targets in fatty acid biosynthesis
    • Wright, H. T., and Reynolds, K. A. (2007) Antibacterial targets in fatty acid biosynthesis. Curr. Opin. Microbiol. 10, 447-453.
    • (2007) Curr. Opin. Microbiol. , vol.10 , pp. 447-453
    • Wright, H.T.1    Reynolds, K.A.2
  • 5
    • 38849098884 scopus 로고    scopus 로고
    • Acyl carrier protein: Structurefunction relationships in a conserved multifunctional protein family
    • Byers, D. M., and Gong, H. (2007) Acyl carrier protein: structurefunction relationships in a conserved multifunctional protein family. Biochem. Cell Biol. 85, 649-662.
    • (2007) Biochem. Cell Biol. , vol.85 , pp. 649-662
    • Byers, D.M.1    Gong, H.2
  • 6
    • 0036277954 scopus 로고    scopus 로고
    • X-ray crystallographic studies on butyryl-ACP reveal flexibility of the structure around a putative acyl chain binding site
    • Roujeinikova, A., Baldock, C., Simon, W. J., Gilroy, J., Baker, P. J., Stuitje, A. R., Rice, D. W., Slabas, A. R., and Rafferty, J. B. (2002) X-ray crystallographic studies on butyryl-ACP reveal flexibility of the structure around a putative acyl chain binding site. Structure 10, 825-835. (Pubitemid 34628711)
    • (2002) Structure , vol.10 , pp. 825-835
    • Roujeinikova, A.1    Baldock, C.2    Simon, W.J.3    Gilroy, J.4    Baker, P.J.5    Stuitje, A.R.6    Rice, D.W.7    Slabas, A.R.8    Rafferty, J.B.9
  • 7
    • 33751512907 scopus 로고    scopus 로고
    • Structural studies of fatty acyl-(acyl carrier protein) thioesters reveal a hydrophobic binding cavity that can expand to fit longer substrates
    • Roujeinikova, A., Simon, W. J., Gilroy, J., Rice, D. W., Rafferty, J. B., and Slabas, A. R. (2007) Structural studies of fatty acyl-(acyl carrier protein) thioesters reveal a hydrophobic binding cavity that can expand to fit longer substrates. J. Mol. Biol. 365, 135-145.
    • (2007) J. Mol. Biol. , vol.365 , pp. 135-145
    • Roujeinikova, A.1    Simon, W.J.2    Gilroy, J.3    Rice, D.W.4    Rafferty, J.B.5    Slabas, A.R.6
  • 8
    • 33645968397 scopus 로고    scopus 로고
    • Solution structures of spinach acyl carrier protein with decanoate and stearate
    • Zornetzer, G. A., Fox, B. G., and Markley, J. L. (2006) Solution structures of spinach acyl carrier protein with decanoate and stearate. Biochemistry 45, 5217-5227.
    • (2006) Biochemistry , vol.45 , pp. 5217-5227
    • Zornetzer, G.A.1    Fox, B.G.2    Markley, J.L.3
  • 9
    • 0022410208 scopus 로고
    • Acyl-acyl carrier protein as a source of fatty acids for bacterial bioluminescence
    • Byers, D. M., and Meighen, E. A. (1985) Acyl-acyl carrier protein as a source of fatty acids for bacterial bioluminescence. Proc. Natl. Acad. Sci. U. S. A. 82, 6085-6089.
    • (1985) Proc. Natl. Acad. Sci. U. S. A. , vol.82 , pp. 6085-6089
    • Byers, D.M.1    Meighen, E.A.2
  • 10
    • 0023654454 scopus 로고
    • Biosynthesis of lipid A precursors in Escherichia coli. A cytoplasmic acyltransferase that converts UDP-N-acetylglucosamine to UDP-3-O-(R-3- hydroxymyristoyl)-N-acetylglucosamine
    • Anderson, M. S., and Raetz, C. R. (1987) Biosynthesis of lipid A precursors in Escherichia coli. A cytoplasmic acyltransferase that converts UDP-N-acetylglucosamine to UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine. J. Biol. Chem. 262, 5159-5169.
    • (1987) J. Biol. Chem. , vol.262 , pp. 5159-5169
    • Anderson, M.S.1    Raetz, C.R.2
  • 11
    • 0029817781 scopus 로고    scopus 로고
    • Generation of cell-to-cell signals in quorum sensing: Acyl homoserine lactone synthase activity of a purified Vibrio fischeri LuxI protein
    • Schaefer, A. L., Val, D. L., Hanzelka, B. L., Cronan, J. E., Jr., and Greenberg, E. P. (1996) Generation of cell-to-cell signals in quorum sensing: acyl homoserine lactone synthase activity of a purified Vibrio fischeri LuxI protein. Proc. Natl. Acad. Sci. U. S. A. 93, 9505-9509.
    • (1996) Proc. Natl. Acad. Sci. U. S. A. , vol.93 , pp. 9505-9509
    • Schaefer, A.L.1    Val, D.L.2    Hanzelka, B.L.3    Cronan Jr., J.E.4    Greenberg, E.P.5
  • 13
    • 0346101746 scopus 로고    scopus 로고
    • Key residues responsible for acyl carrier protein and beta-ketoacyl-acyl carrier protein reductase (FabG) interaction
    • Zhang,Y. M., Wu, B., Zheng, J., and Rock, C. O. (2003) Key residues responsible for acyl carrier protein and beta-ketoacyl-acyl carrier protein reductase (FabG) interaction. J. Biol. Chem. 278, 52935-52943.
    • (2003) J. Biol. Chem. , vol.278 , pp. 52935-52943
    • Zhang, Y.M.1    Wu, B.2    Zheng, J.3    Rock, C.O.4
  • 14
    • 0023813070 scopus 로고
    • Three-dimensional structure of acyl carrier protein determined by NMR pseudoenergy and distance geometry calculations
    • Holak, T. A., Kearsley, S. K., Kim, Y., and Prestegard, J. H. (1988) Three-dimensional structure of acyl carrier protein determined by NMR pseudoenergy and distance geometry calculations. Biochemistry 27, 6135-6142.
    • (1988) Biochemistry , vol.27 , pp. 6135-6142
    • Holak, T.A.1    Kearsley, S.K.2    Kim, Y.3    Prestegard, J.H.4
  • 15
    • 0034662753 scopus 로고    scopus 로고
    • Crystal structures of substrate binding to Bacillus subtilis holo-(acyl carrier protein) synthase reveal a novel trimeric arrangement of molecules resulting in three active sites
    • Parris, K. D., Lin, L., Tam, A., Mathew, R., Hixon, J., Stahl, M., Fritz, C. C., Seehra, J., and Somers, W. S. (2000) Crystal structures of substrate binding to Bacillus subtilis holo-(acyl carrier protein) synthase reveal a novel trimeric arrangement of molecules resulting in three active sites. Structure 8, 883-895.
    • (2000) Structure , vol.8 , pp. 883-895
    • Parris, K.D.1    Lin, L.2    Tam, A.3    Mathew, R.4    Hixon, J.5    Stahl, M.6    Fritz, C.C.7    Seehra, J.8    Somers, W.S.9
  • 17
    • 57749116302 scopus 로고    scopus 로고
    • Molecular Dynamics simulations of the apo-, holo-, and acyl-forms of Escherichia coli acyl carrier protein
    • Chan, D. I., Stockner, T., Tieleman, D. P., and Vogel, H. J. (2008) Molecular Dynamics simulations of the apo-, holo-, and acyl-forms of Escherichia coli acyl carrier protein. J. Biol. Chem. 283, 33620-33629.
    • (2008) J. Biol. Chem. , vol.283 , pp. 33620-33629
    • Chan, D.I.1    Stockner, T.2    Tieleman, D.P.3    Vogel, H.J.4
  • 19
    • 69249111810 scopus 로고    scopus 로고
    • Structural insights into the acyl intermediates of the Plasmodium falciparum fatty acid synthesis pathway
    • Upadhyay, S. K., Misra, A., Srivastava, R., Surolia, N., Surolia, A., and Sundd, M. (2009) Structural insights into the acyl intermediates of the Plasmodium falciparum fatty acid synthesis pathway. J. Biol. Chem. 284, 22390-22400.
    • (2009) J. Biol. Chem. , vol.284 , pp. 22390-22400
    • Upadhyay, S.K.1    Misra, A.2    Srivastava, R.3    Surolia, N.4    Surolia, A.5    Sundd, M.6
  • 21
    • 2942715138 scopus 로고    scopus 로고
    • Molecular dynamics simulation of a polyunsaturated lipid bilayer susceptible to lipid peroxidation
    • Bachar, M., Brunelle, P., Tieleman, D. P., and Rauk, A. (2004) Molecular dynamics simulation of a polyunsaturated lipid bilayer susceptible to lipid peroxidation. J. Phys. Chem. B 108, 7170-7179.
    • (2004) J. Phys. Chem. B , vol.108 , pp. 7170-7179
    • Bachar, M.1    Brunelle, P.2    Tieleman, D.P.3    Rauk, A.4
  • 22
    • 0036975364 scopus 로고    scopus 로고
    • Molecular dynamics simulations of photoactive yellow protein (PYP) in three states of its photocycle: A comparison with X-ray and NMR data and analysis of the effects of Glu46 deprotonation and mutation
    • Antes, I., Thiel, W., and van Gunsteren, W. F. (2002) Molecular dynamics simulations of photoactive yellow protein (PYP) in three states of its photocycle: a comparison with X-ray and NMR data and analysis of the effects of Glu46 deprotonation and mutation. Eur. Biophys. J. 31, 504-520.
    • (2002) Eur. Biophys. J. , vol.31 , pp. 504-520
    • Antes, I.1    Thiel, W.2    Van Gunsteren, W.F.3
  • 23
    • 0037569250 scopus 로고    scopus 로고
    • A consistent potential energy parameter set for lipids: Dipalmitoylphosphatidylcholine as a benchmark of theGROMOS96 45A3 force field
    • Chandrasekhar, I., Kastenholz, M., Lins, R. D., Oostenbrink, C., Schuler, L. D., Tieleman, D. P., and van Gunsteren, W. F. (2003) A consistent potential energy parameter set for lipids: dipalmitoylphosphatidylcholine as a benchmark of theGROMOS96 45A3 force field. Eur. Biophys. J. 32, 67-77.
    • (2003) Eur. Biophys. J. , vol.32 , pp. 67-77
    • Chandrasekhar, I.1    Kastenholz, M.2    Lins, R.D.3    Oostenbrink, C.4    Schuler, L.D.5    Tieleman, D.P.6    Van Gunsteren, W.F.7
  • 24
    • 0029633168 scopus 로고
    • Gromacs - A message-passing parallel Molecular-Dynamics implementation
    • Berendsen, H. J. C., van der Spoel, D., and van Drunen, R. (1995) Gromacs - A message-passing parallel Molecular-Dynamics implementation. Comput. Phys. Commun. 91, 43-56.
    • (1995) Comput. Phys. Commun. , vol.91 , pp. 43-56
    • Berendsen, H.J.C.1    Van Der Spoel, D.2    Van Drunen, R.3
  • 25
    • 0035789518 scopus 로고    scopus 로고
    • GROMACS 3.0: A package for molecular simulation and trajectory analysis
    • Lindahl, E., Hess, B., and 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 , pp. 306-317
    • Lindahl, E.1    Hess, B.2    Van Der Spoel, D.3
  • 26
    • 0001585978 scopus 로고    scopus 로고
    • Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems
    • Feenstra, K. A., Hess, B., and Berendsen, H. J. C. (1999) Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems. J. Comput. Chem. 20, 786-798.
    • (1999) J. Comput. Chem. , vol.20 , pp. 786-798
    • Feenstra, K.A.1    Hess, B.2    Berendsen, H.J.C.3
  • 27
    • 0242292035 scopus 로고    scopus 로고
    • Brute-force molecular dynamics simulations of Villin headpiece: Comparison with NMR parameters
    • van der Spoel, D., and Lindahl, E. (2003) Brute-force molecular dynamics simulations of Villin headpiece: Comparison with NMR parameters. J. Phys. Chem. B 107, 11178-11187.
    • (2003) J. Phys. Chem. B , vol.107 , pp. 11178-11187
    • Van Der Spoel, D.1    Lindahl, E.2
  • 30
    • 7544226311 scopus 로고    scopus 로고
    • PRODRG: A tool for high-throughput crystallography of protein-ligand complexes
    • Schüttelkopf, A. W., and van Aalten, D. M. F. (2004) PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr. D Biol. Crystallogr. 60, 1355-1363.
    • (2004) Acta Crystallogr. D Biol. Crystallogr. , vol.60 , pp. 1355-1363
    • Schüttelkopf, A.W.1    Van Aalten, D.M.F.2
  • 31
    • 58149471085 scopus 로고    scopus 로고
    • Structural modification of acyl carrier protein by butyryl group
    • Wu, B. N., Zhang, Y. M., Rock, C. O., and Zheng, J. J. (2009) Structural modification of acyl carrier protein by butyryl group. Protein Sci. 18, 240-246.
    • (2009) Protein Sci. , vol.18 , pp. 240-246
    • Wu, B.N.1    Zhang, Y.M.2    Rock, C.O.3    Zheng, J.J.4
  • 32
    • 0036079707 scopus 로고    scopus 로고
    • Forty years of bacterial fatty acid synthesis
    • Rock, C. O., and Jackowski, S. (2002) Forty years of bacterial fatty acid synthesis. Biochem. Biophys. Res. Commun. 292, 1155-1166.
    • (2002) Biochem. Biophys. Res. Commun. , vol.292 , pp. 1155-1166
    • Rock, C.O.1    Jackowski, S.2
  • 33
    • 51149098989 scopus 로고    scopus 로고
    • The crystal structure of a mammalian fatty acid synthase
    • Maier, T., Leibundgut, M., and Ban, N. (2008) The crystal structure of a mammalian fatty acid synthase. Science 321, 1315-1322.
    • (2008) Science , vol.321 , pp. 1315-1322
    • Maier, T.1    Leibundgut, M.2    Ban, N.3
  • 34
    • 38049136859 scopus 로고    scopus 로고
    • A mammalian type i fatty acid synthase acyl carrier protein domain does not sequester acyl chains
    • Ploskon, E., Arthur, C. J., Evans, S. E., Williams, C., Crosby, J., Simpson, T. J., and Crump, M. P. (2008) A mammalian type I fatty acid synthase acyl carrier protein domain does not sequester acyl chains. J. Biol. Chem. 283, 518-528.
    • (2008) J. Biol. Chem. , vol.283 , pp. 518-528
    • Ploskon, E.1    Arthur, C.J.2    Evans, S.E.3    Williams, C.4    Crosby, J.5    Simpson, T.J.6    Crump, M.P.7
  • 35
    • 59649102440 scopus 로고    scopus 로고
    • Conformational flexibility of metazoan fatty acid synthase enables catalysis
    • Brignole, E. J., Smith, S., and Asturias, F. J. (2009) Conformational flexibility of metazoan fatty acid synthase enables catalysis. Nat. Struct. Mol. Biol. 16, 190-197.
    • (2009) Nat. Struct. Mol. Biol. , vol.16 , pp. 190-197
    • Brignole, E.J.1    Smith, S.2    Asturias, F.J.3
  • 36
    • 33744954170 scopus 로고    scopus 로고
    • Solution structures of conformationally equilibrium forms of holo-acyl carrier protein (PfACP) from Plasmodium falciparum provides insight into the mechanism of activation of ACPs
    • Sharma, A. K., Sharma, S. K., Surolia, A., Surolia, N., and Sarma, S. P. (2006) Solution structures of conformationally equilibrium forms of holo-acyl carrier protein (PfACP) from Plasmodium falciparum provides insight into the mechanism of activation of ACPs. Biochemistry 45, 6904-6916. (Pubitemid 43856675)
    • (2006) Biochemistry , vol.45 , pp. 6904-6916
    • Sharma, A.K.1    Sharma, S.K.2    Surolia, A.3    Surolia, N.4    Sarma, S.P.5
  • 37
    • 0037435617 scopus 로고    scopus 로고
    • Amino acid residues of Escherichia coli acyl carrier protein involved in heterologous protein interactions
    • Worsham, L. M., Earls, L., Jolly, C., Langston, K. G., Trent, M. S., and Ernst-Fonberg, M. L. (2003) Amino acid residues of Escherichia coli acyl carrier protein involved in heterologous protein interactions. Biochemistry 42, 167-176. (Pubitemid 36083863)
    • (2003) Biochemistry , vol.42 , pp. 167-176
    • Worsham, L.M.S.1    Earls, L.2    Jolly, C.3    Langston, K.G.4    Trent, M.S.5    Ernst-Fonberg, M.L.6
  • 39
    • 27744606438 scopus 로고    scopus 로고
    • A salt-bridge motif involved in ligand binding and large-scale domain motions of the maltose-binding protein
    • Stockner, T., Vogel, H. J., and Tieleman, D. P. (2005) A salt-bridge motif involved in ligand binding and large-scale domain motions of the maltose-binding protein. Biophys. J. 89, 3362-3371. (Pubitemid 41636092)
    • (2005) Biophysical Journal , vol.89 , pp. 3362-3371
    • Stockner, T.1    Vogel, H.J.2    Tieleman, D.P.3
  • 40
    • 58149114916 scopus 로고    scopus 로고
    • Mechanical features of Plasmodium falciparum acyl carrier protein in the delivery of substrates
    • Colizzi, F., Recanatini, M., and Cavalli, A. (2008) Mechanical features of Plasmodium falciparum acyl carrier protein in the delivery of substrates. J. Chem. Inf. Model. 48, 2289-2293.
    • (2008) J. Chem. Inf. Model. , vol.48 , pp. 2289-2293
    • Colizzi, F.1    Recanatini, M.2    Cavalli, A.3
  • 41
    • 0020351537 scopus 로고
    • Regulation of phospholipid synthesis in Escherichia coli. Composition of the acyl-acyl carrier protein pool in vivo
    • Rock, C. O., and Jackowski, S. (1982) Regulation of phospholipid synthesis in Escherichia coli. Composition of the acyl-acyl carrier protein pool in vivo. J. Biol. Chem. 257, 10759-10765.
    • (1982) J. Biol. Chem. , vol.257 , pp. 10759-10765
    • Rock, C.O.1    Jackowski, S.2
  • 42
    • 0037238269 scopus 로고    scopus 로고
    • The application of computational methods to explore the diversity and structure of bacterial fatty acid synthase
    • Zhang, Y. M., Marrakchi, H., White, S. W., and Rock, C. O. (2003) The application of computational methods to explore the diversity and structure of bacterial fatty acid synthase. J. Lipid Res. 44, 1-10. (Pubitemid 36114764)
    • (2003) Journal of Lipid Research , vol.44 , pp. 1-10
    • Zhang, Y.-M.1    Marrakchi, H.2    White, S.W.3    Rock, C.O.4
  • 43
    • 33947504254 scopus 로고    scopus 로고
    • Neutralization of acidic residues in helix II stabilizes the folded conformation of acyl carrier protein and variably alters its function with different enzymes
    • Gong, H. S., Murphy, A., McMaster, C. R., and Byers, D. M. (2007) Neutralization of acidic residues in helix II stabilizes the folded conformation of acyl carrier protein and variably alters its function with different enzymes. J. Biol. Chem. 282, 4494-4503.
    • (2007) J. Biol. Chem. , vol.282 , pp. 4494-4503
    • Gong, H.S.1    Murphy, A.2    McMaster, C.R.3    Byers, D.M.4
  • 44
    • 0030033704 scopus 로고    scopus 로고
    • Regulation of fatty acid elongation and initiation by acyl-acyl carrier protein in Escherichia coli
    • Heath, R. J., and Rock, C. O. (1996) Regulation of fatty acid elongation and initiation by acyl-acyl carrier protein in Escherichia coli. J. Biol. Chem. 271, 1833-1836.
    • (1996) J. Biol. Chem. , vol.271 , pp. 1833-1836
    • Heath, R.J.1    Rock, C.O.2
  • 45
    • 33745817391 scopus 로고    scopus 로고
    • Inhibiting bacterial fatty acid synthesis
    • Zhang, Y. M., White, S. W., and Rock, C. O. (2006) Inhibiting bacterial fatty acid synthesis. J. Biol. Chem. 281, 17541-17544.
    • (2006) J. Biol. Chem. , vol.281 , pp. 17541-17544
    • Zhang, Y.M.1    White, S.W.2    Rock, C.O.3
  • 46
    • 60049089356 scopus 로고    scopus 로고
    • Novel E. coli beta-ketoacyl-acyl carrier protein synthase III inhibitors as targeted antibiotics
    • Lee, J. Y., Jeong, K. W., Lee, J. U., Kang, D. I., and Kim, Y. (2009) Novel E. coli beta-ketoacyl-acyl carrier protein synthase III inhibitors as targeted antibiotics. Bioorg. Med. Chem. 17, 1506-1513.
    • (2009) Bioorg. Med. Chem. , vol.17 , pp. 1506-1513
    • Lee, J.Y.1    Jeong, K.W.2    Lee, J.U.3    Kang, D.I.4    Kim, Y.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.