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Volumn 53, Issue 1, 2003, Pages 88-100

Understanding the acylation mechanisms of active-site serine penicillin-recognizing proteins: A molecular dynamics simulation study

Author keywords

lactamases; Acylation mechanism; Hybrid QM MM potentials; Molecular dynamics; Penicillin binding proteins

Indexed keywords

BETA LACTAM ANTIBIOTIC; BETA LACTAMASE; PENICILLIN BINDING PROTEIN;

EID: 0042320537     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10450     Document Type: Article
Times cited : (35)

References (58)
  • 1
    • 0013787826 scopus 로고
    • Penicillin: Its basic site of action as an inhibitor of a peptide cross-linking reaction in cell wall mucopeptide synthesis
    • Wise EM Jr, Park JT. Penicillin: its basic site of action as an inhibitor of a peptide cross-linking reaction in cell wall mucopeptide synthesis. Proc Natl Acad Sci USA 1965;54:75-81.
    • (1965) Proc Natl Acad Sci USA , vol.54 , pp. 75-81
    • Wise E.M., Jr.1    Park, J.T.2
  • 2
    • 0013808622 scopus 로고
    • Mechanism of action of penicillins: A proposal based on their structural similarity to acyl-D-alanyl-Dalanine
    • Tipper DJ, Strominger JL. Mechanism of action of penicillins: A proposal based on their structural similarity to acyl-D-alanyl-Dalanine. Proc Natl Acad Sci USA 1965;54:1133-1141.
    • (1965) Proc Natl Acad Sci USA , vol.54 , pp. 1133-1141
    • Tipper, D.J.1    Strominger, J.L.2
  • 3
    • 0026760182 scopus 로고
    • The crisis in antibiotic resistance
    • Neu HC. The crisis in antibiotic resistance. Science 1992;257:1064-1073.
    • (1992) Science , vol.257 , pp. 1064-1073
    • Neu, H.C.1
  • 4
    • 0034680167 scopus 로고    scopus 로고
    • Molecular mechanisms that confer antibacterial drug resistance
    • Walsh C. Molecular mechanisms that confer antibacterial drug resistance. Nature 2000;406:775-781.
    • (2000) Nature , vol.406 , pp. 775-781
    • Walsh, C.1
  • 5
    • 0023204095 scopus 로고
    • Bacterial resistance to β-lactam antibiotics: Crystal structure of β-lactamase from Staphylococcus aureus PC1 at 2.5 A resolution
    • Herzberg O, Moult J. Bacterial resistance to β-lactam antibiotics: crystal structure of β-lactamase from Staphylococcus aureus PC1 at 2.5 A resolution. Science 1987;236:694-701.
    • (1987) Science , vol.236 , pp. 694-701
    • Herzberg, O.1    Moult, J.2
  • 7
    • 0027446117 scopus 로고
    • Deletion analysis of the essentiality of penicillin-binding proteins 1A, 2B and 2X of Streptococcus pneumoniae
    • Kell CM, Sharma UK, Dowson CG, Town C, Balganesh TS, Spratt BG. Deletion analysis of the essentiality of penicillin-binding proteins 1A, 2B and 2X of Streptococcus pneumoniae. FEMS Microbiol Lett 1993;106:171-175.
    • (1993) FEMS Microbiol Lett , vol.106 , pp. 171-175
    • Kell, C.M.1    Sharma, U.K.2    Dowson, C.G.3    Town, C.4    Balganesh, T.S.5    Spratt, B.G.6
  • 8
    • 0030003591 scopus 로고    scopus 로고
    • Penicillin-binding proteins 2b and 2x of Streptococcus pneumoniae are primary resistance determinants for different classes of β-lactam antibiotics
    • Grebe T, Hakenbeck R. Penicillin-binding proteins 2b and 2x of Streptococcus pneumoniae are primary resistance determinants for different classes of β-lactam antibiotics. Antimicrob Agents Chemother 1996;40:829-834.
    • (1996) Antimicrob Agents Chemother , vol.40 , pp. 829-834
    • Grebe, T.1    Hakenbeck, R.2
  • 9
    • 0029988098 scopus 로고    scopus 로고
    • X-ray structure of Streptococcus pneumoniae PBP2x, a primary penicillin target enzyme
    • Parès S, Mouz N, Pétillot Y, Hakenbeck R, Dideberg O. X-ray structure of Streptococcus pneumoniae PBP2x, a primary penicillin target enzyme. Nature Struct Biol 1996;3:284-289.
    • (1996) Nature Struct Biol , vol.3 , pp. 284-289
    • Parès, S.1    Mouz, N.2    Pétillot, Y.3    Hakenbeck, R.4    Dideberg, O.5
  • 10
    • 0034595512 scopus 로고    scopus 로고
    • The crystal structure of the penicillin-binding protein 2x from Streptococcus pneurnoniae and its acyl-enzyme form: Implication in drug resistance
    • Gordon E, Mouz N, Duée E, Dideberg O. The crystal structure of the penicillin-binding protein 2x from Streptococcus pneurnoniae and its acyl-enzyme form: implication in drug resistance. J Mol Biol 2000;299:477-485.
    • (2000) J Mol Biol , vol.299 , pp. 477-485
    • Gordon, E.1    Mouz, N.2    Duée, E.3    Dideberg, O.4
  • 12
    • 0027275788 scopus 로고
    • Crystal structure of Escherichia coli TEM-1 β-lactamase at 1.8 Å resolution
    • Jelsch C, Mourey L, Masson JM, Samama JP. Crystal structure of Escherichia coli TEM-1 β-lactamase at 1.8 Å resolution. Proteins 1993;16:364-383.
    • (1993) Proteins , vol.16 , pp. 364-383
    • Jelsch, C.1    Mourey, L.2    Masson, J.M.3    Samama, J.P.4
  • 13
    • 0033609444 scopus 로고    scopus 로고
    • X-ray structure of the Asn276Asp variant of the Escherichia coli TEM-1 β-lactamase: Direct observation of electrostatic modulation in resistance to inactivation by clavulanic acid
    • Swaren P, Golemi D, Cabantous S, Bulychev A, Maveyraud L, Mobashery S, Samama JP. X-ray structure of the Asn276Asp variant of the Escherichia coli TEM-1 β-lactamase: direct observation of electrostatic modulation in resistance to inactivation by clavulanic acid. Biochemistry 1999;38:9570-9576.
    • (1999) Biochemistry , vol.38 , pp. 9570-9576
    • Swaren, P.1    Golemi, D.2    Cabantous, S.3    Bulychev, A.4    Maveyraud, L.5    Mobashery, S.6    Samama, J.P.7
  • 15
    • 0029644936 scopus 로고
    • Electro-static analysis of TEM-1 β-lactamase: Effect of substrate binding, steep potential gradients and consequences of site-directed mutations
    • Swaren P, Maveyraud L, Guillet V, Masson JM, Mourey L, Samama JP. Electro-static analysis of TEM-1 β-lactamase: effect of substrate binding, steep potential gradients and consequences of site-directed mutations. Structure 1995;3:603-613.
    • (1995) Structure , vol.3 , pp. 603-613
    • Swaren, P.1    Maveyraud, L.2    Guillet, V.3    Masson, J.M.4    Mourey, L.5    Samama, J.P.6
  • 16
    • 0036533471 scopus 로고    scopus 로고
    • Noncovalent interaction energies in covalent complexes: TEM-1 β-lactamase and β-lactams
    • Wang X, Minasov G, Shoichet BK. Noncovalent interaction energies in covalent complexes: TEM-1 β-lactamase and β-lactams. Proteins 2002;47:86-96.
    • (2002) Proteins , vol.47 , pp. 86-96
    • Wang, X.1    Minasov, G.2    Shoichet, B.K.3
  • 17
    • 0028802117 scopus 로고
    • Contribution of mutant analysis to the understanding of enzyme catalysis: The case of class A β-lactamases
    • Matagne A, Frère JM. Contribution of mutant analysis to the understanding of enzyme catalysis: the case of class A β-lactamases. Biochim Biophys Acta 1995;1246:109-127.
    • (1995) Biochim Biophys Acta , vol.1246 , pp. 109-127
    • Matagne, A.1    Frère, J.M.2
  • 18
    • 0032032930 scopus 로고    scopus 로고
    • Catalytic properties of class A β-lactamases: Efficiency and diversity
    • Matagne A, Lamotte-Brasseur J, Frère J-M. Catalytic properties of class A β-lactamases: efficiency and diversity. Biochem J 1998;330:581-598.
    • (1998) Biochem J , vol.330 , pp. 581-598
    • Matagne, A.1    Lamotte-Brasseur, J.2    Frère, J.-M.3
  • 19
    • 0025801845 scopus 로고
    • Site-directed mutants, at position 166, of RTEM-1 β-lactamase that form a stable acylenzyme intermediate with penicillin
    • Adachi H, Ohta T, Matsuzawa H. Site-directed mutants, at position 166, of RTEM-1 β-lactamase that form a stable acylenzyme intermediate with penicillin. J Biol Chem 1991;266:3186-3191.
    • (1991) J Biol Chem , vol.266 , pp. 3186-3191
    • Adachi, H.1    Ohta, T.2    Matsuzawa, H.3
  • 21
    • 0037094114 scopus 로고    scopus 로고
    • An ultrahigh resolution structure of TEM-1 β-lactamase suggests a role for Glu166 as the general base in acylation
    • Minasov G, Wang X, Shoichet BK. An ultrahigh resolution structure of TEM-1 β-lactamase suggests a role for Glu166 as the general base in acylation. J Am Chem Soc 2002; 124:5333-5340.
    • (2002) J Am Chem Soc , vol.124 , pp. 5333-5340
    • Minasov, G.1    Wang, X.2    Shoichet, B.K.3
  • 22
    • 0036882101 scopus 로고    scopus 로고
    • α, MM and QM studies of mechanisms of β-lactamases and penicillin-binding proteins: Acylation step
    • α, MM and QM studies of mechanisms of β-lactamases and penicillin-binding proteins: acylation step. J Comput Chem 2002;23:1559-1576.
    • (2002) J Comput Chem , vol.23 , pp. 1559-1576
    • Massova, I.1    Kollman, P.A.2
  • 23
    • 0036227417 scopus 로고    scopus 로고
    • Increase of the deacylation rate of PBP2x from Streptococcus pneumoniae by single point mutations mimicking the class A β-lactamases
    • Chesnel L, Zapun A, Mouz N, Dideberg O, Vernet T. Increase of the deacylation rate of PBP2x from Streptococcus pneumoniae by single point mutations mimicking the class A β-lactamases. Eur J Biochem 2002;269:1678-1683.
    • (2002) Eur J Biochem , vol.269 , pp. 1678-1683
    • Chesnel, L.1    Zapun, A.2    Mouz, N.3    Dideberg, O.4    Vernet, T.5
  • 24
    • 0025647444 scopus 로고
    • Site-directed mutagenesis of β-lactamase I. Single and double mutants of Glu166 and Lys73
    • Gibson RM, Christensen H, Waley SG. Site-directed mutagenesis of β-lactamase I. Single and double mutants of Glu166 and Lys73. Biochem J 1990;272:613-619.
    • (1990) Biochem J , vol.272 , pp. 613-619
    • Gibson, R.M.1    Christensen, H.2    Waley, S.G.3
  • 27
    • 0034476988 scopus 로고    scopus 로고
    • Insights into class D β-lactamases are revealed by the crystal structure of the OXA10 enzyme from Pseudomonas aeruginosa
    • Maveyraud L, Golemi D, Kotra LP, Tranier S, Vakulenko S, Mobashery S, Samama J-P. Insights into class D β-lactamases are revealed by the crystal structure of the OXA10 enzyme from Pseudomonas aeruginosa. Structure 2000;8:1289-1298.
    • (2000) Structure , vol.8 , pp. 1289-1298
    • Maveyraud, L.1    Golemi, D.2    Kotra, L.P.3    Tranier, S.4    Vakulenko, S.5    Mobashery, S.6    Samama, J.-P.7
  • 28
    • 0035807996 scopus 로고    scopus 로고
    • Critical involvement of a carbamylated lysine in catalytic function of class D β-lactamases
    • Golemi D, Maveyraud L, Vakulenko S, Samama J-P, Mobashery S. Critical involvement of a carbamylated lysine in catalytic function of class D β-lactamases. Proc Natl Acad Sci USA 2001;98: 14280-14285.
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 14280-14285
    • Golemi, D.1    Maveyraud, L.2    Vakulenko, S.3    Samama, J.-P.4    Mobashery, S.5
  • 29
    • 0034175153 scopus 로고    scopus 로고
    • A quantum mechanics/molecular mechanics study of the acylation reaction of TEM-1 β-lactamase and penicillanate
    • Pitarch J, Pascual-Ahuir J-L, Silla E, Tuñón I. A quantum mechanics/molecular mechanics study of the acylation reaction of TEM-1 β-lactamase and penicillanate. J Chem Soc Perkin Trans 2000;2:761-767.
    • (2000) J Chem Soc Perkin Trans , vol.2 , pp. 761-767
    • Pitarch, J.1    Pascual-Ahuir, J.-L.2    Silla, E.3    Tuñón, I.4
  • 30
    • 0037181086 scopus 로고    scopus 로고
    • Role of protein flexibility in enzymatic catalysis: Quantum mechanical-molecular mechanical study of the deacylation reaction in class A β-lactamases
    • Castillo R, Silla E, Tuñón I. Role of protein flexibility in enzymatic catalysis: Quantum mechanical-molecular mechanical study of the deacylation reaction in class A β-lactamases. J Am Chem Soc 2002;124:1809-1816.
    • (2002) J Am Chem Soc , vol.124 , pp. 1809-1816
    • Castillo, R.1    Silla, E.2    Tuñón, I.3
  • 31
    • 0029896566 scopus 로고    scopus 로고
    • Modeling study on a hydrolytic mechanism of class A β-lactamases
    • Ishiguro M, Imajo S. Modeling study on a hydrolytic mechanism of class A β-lactamases. J Med Chem 1996;39:2207-2218.
    • (1996) J Med Chem , vol.39 , pp. 2207-2218
    • Ishiguro, M.1    Imajo, S.2
  • 32
    • 0035892151 scopus 로고    scopus 로고
    • Acylation of class A β-lactamases by penicillins: A theoretical examination of the role of Serine 130 and the β-lactam carboxylate group
    • Dfaz N, Suárez D, Sordo TL, Merz KM Jr. Acylation of class A β-lactamases by penicillins: A theoretical examination of the role of Serine 130 and the β-lactam carboxylate group. J Phys Chem B 2001;105:11302-11313.
    • (2001) J Phys Chem B , vol.105 , pp. 11302-11313
    • Dfaz, N.1    Suárez, D.2    Sordo, T.L.3    Merz K.M., Jr.4
  • 33
    • 0003103514 scopus 로고    scopus 로고
    • Serine peptidase catalytic machinery: Cooperative one-step mechanism
    • Dive G, Dehareng D. Serine peptidase catalytic machinery: cooperative one-step mechanism. Int J Quant Chem 1999;73:161-174.
    • (1999) Int J Quant Chem , vol.73 , pp. 161-174
    • Dive, G.1    Dehareng, D.2
  • 34
    • 0028260708 scopus 로고
    • Ab initio molecular orbital calculations on neutral hydrolysis and methanolysis of azetidinones, including catalysis by water. Relationship to the mechanism of action of β-lactam antibiotics
    • Wolfe S, Kim C-K, Yang K. Ab initio molecular orbital calculations on neutral hydrolysis and methanolysis of azetidinones, including catalysis by water. relationship to the mechanism of action of β-lactam antibiotics. Can J Chem 1994;72:1033-1043.
    • (1994) Can J Chem , vol.72 , pp. 1033-1043
    • Wolfe, S.1    Kim, C.-K.2    Yang, K.3
  • 35
    • 0034724334 scopus 로고    scopus 로고
    • Protonation of β-lactam nitrogen is the trigger event in the catalytic of class A β-lactamases
    • Atanasov BP, Mustafi D, Makinen MW, Protonation of β-lactam nitrogen is the trigger event in the catalytic of class A β-lactamases. Proc Natl Acad Sci USA 2000;97:3160-3165.
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 3160-3165
    • Atanasov, B.P.1    Mustafi, D.2    Makinen, M.W.3
  • 37
    • 0029738864 scopus 로고    scopus 로고
    • Crystal structure of 6α-(Hydroxymethyl)penicillanate complexed to TEM-1 β-lactamase from Escherichia coli: Evidence on the mechanism of action of a novel inhibitor designed by a computer-aided process
    • Maveyraud L, Massova I, Birck C, Miyashita K, Samama J-P, Mobashery S. Crystal structure of 6α-(Hydroxymethyl)penicillanate complexed to TEM-1 β-lactamase from Escherichia coli: evidence on the mechanism of action of a novel inhibitor designed by a computer-aided process. J Am Chem Soc 1996;118:7435-7440.
    • (1996) J Am Chem Soc , vol.118 , pp. 7435-7440
    • Maveyraud, L.1    Massova, I.2    Birck, C.3    Miyashita, K.4    Samama, J.-P.5    Mobashery, S.6
  • 38
    • 0033618429 scopus 로고    scopus 로고
    • The crystal structure of a penicilloyl-serine transferase of intermediate penicillin sensitivity
    • Fonzé E, Vermeire M, Nguyen-Distèche M, Brasseur R, Charlier P. The crystal structure of a penicilloyl-serine transferase of intermediate penicillin sensitivity. J Biol Chem 1999;274:21853-21860.
    • (1999) J Biol Chem , vol.274 , pp. 21853-21860
    • Fonzé, E.1    Vermeire, M.2    Nguyen-Distèche, M.3    Brasseur, R.4    Charlier, P.5
  • 39
    • 0028305457 scopus 로고
    • Prediction of pH-dependent properties of proteins
    • Antosiewicz J, Mc Cammon JA, Gilson MK. Prediction of pH-dependent properties of proteins. J Mol Biol 1994;238:415-436.
    • (1994) J Mol Biol , vol.238 , pp. 415-436
    • Antosiewicz, J.1    Mc Cammon, J.A.2    Gilson, M.K.3
  • 45
    • 84986468608 scopus 로고
    • An approach to computing electrostatic charges for molecules
    • Singh UC, Kollman PA. An approach to computing electrostatic charges for molecules. J Comp Chem 1984;5:129-145.
    • (1984) J Comp Chem , vol.5 , pp. 129-145
    • Singh, U.C.1    Kollman, P.A.2
  • 46
    • 84986492477 scopus 로고
    • Atomic charges derived from semiempirical methods
    • Besler BH, Merz KM Jr, Kollman PA. Atomic charges derived from semiempirical methods. J Comp Chem 1990;11:431-439.
    • (1990) J Comp Chem , vol.11 , pp. 431-439
    • Besler, B.H.1    Merz K.M., Jr.2    Kollman, P.A.3
  • 48
    • 0000831054 scopus 로고    scopus 로고
    • The DYNAMO library for molecular simulations using hybrid quantum mechanical and molecular mechanical potentials
    • Field MJ, Albe M, Bret C, Proust-De Martin F, Thomas A. The DYNAMO library for molecular simulations using hybrid quantum mechanical and molecular mechanical potentials. J Comp Chem 2000;21:1088-1100.
    • (2000) J Comp Chem , vol.21 , pp. 1088-1100
    • Field, M.J.1    Albe, M.2    Bret, C.3    Proust-De Martin, F.4    Thomas, A.5
  • 50
    • 0029912748 scopus 로고    scopus 로고
    • Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
    • Jorgensen WL, Maxwell DS, Tirado-Rives J. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 1996;118: 11225-11236.
    • (1996) J Am Chem Soc , vol.118 , pp. 11225-11236
    • Jorgensen, W.L.1    Maxwell, D.S.2    Tirado-Rives, J.3
  • 52
    • 0036898699 scopus 로고    scopus 로고
    • Biochemistry and comparative genomics of SxxK super-family acyltransferases offer a clue to the mycobacterial paradox: Presence of penicillin-susceptible target proteins versus lack of efficiency of penicillin as therapeutic agent
    • Goffin C, Ghuysen JM. Biochemistry and comparative genomics of SxxK super-family acyltransferases offer a clue to the mycobacterial paradox: presence of penicillin-susceptible target proteins versus lack of efficiency of penicillin as therapeutic agent. Microbiol Mol Biol Rev 2002;66:702-738.
    • (2002) Microbiol Mol Biol Rev , vol.66 , pp. 702-738
    • Goffin, C.1    Ghuysen, J.M.2
  • 53
    • 0033516564 scopus 로고    scopus 로고
    • Mutations in the active site of penicillin-binding protein PBP2x from Streptococcus pneumoniae
    • Mouz M, Guilmi AM Di, Gordon E, Hakenbeck R, Dideberg O, and Vernet T. Mutations in the active site of penicillin-binding protein PBP2x from Streptococcus pneumoniae. J. Biol. Chem. 1999;274: 19175-19180.
    • (1999) J Biol Chem , vol.274 , pp. 19175-19180
    • Mouz, M.1    Di Guilmi, A.M.2    Gordon, E.3    Hakenbeck, R.4    Dideberg, O.5    Vernet, T.6
  • 55
    • 0035977042 scopus 로고    scopus 로고
    • Crystal structure of PBP2x from a highly penicillin-resistant Streptococcus pneumoniae clinical isolate: A mosaic framework containing 83 mutations
    • Dessen A, Mouz N, Gordon E, Hopkins J, and Dideberg O. Crystal structure of PBP2x from a highly penicillin-resistant Streptococcus pneumoniae clinical isolate: a mosaic framework containing 83 mutations. J Biol Chem, 2001;276:45106-45112.
    • (2001) J Biol Chem , vol.276 , pp. 45106-45112
    • Dessen, A.1    Mouz, N.2    Gordon, E.3    Hopkins, J.4    Dideberg, O.5
  • 57
    • 0025270942 scopus 로고
    • β-lactamases as fully efficient enzymes, determination of all the rate constants in the acyl-enzyme mechanism
    • Christensen H, Martin MT, and Waley SG. β-lactamases as fully efficient enzymes, determination of all the rate constants in the acyl-enzyme mechanism. Biochem J, 1990;266:853-861.
    • (1990) Biochem J , vol.266 , pp. 853-861
    • Christensen, H.1    Martin, M.T.2    Waley, S.G.3
  • 58
    • 0028304962 scopus 로고
    • Satisfying hydrogen bonding potential in proteins
    • McDonald IK and Thornton JM. Satisfying hydrogen bonding potential in proteins. J. Mol. Biol., 1994;238:777-793.
    • (1994) J Mol Biol , vol.238 , pp. 777-793
    • McDonald, I.K.1    Thornton, J.M.2


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