메뉴 건너뛰기




Volumn 69, Issue 2, 2007, Pages 340-348

Simulated annealing exploration of an active-site tyrosine in TEM-1β-lactamase suggests the existence of alternate conformations

Author keywords

Molecular modelling; Rotameric analysis; Structure validation; Structure function relationship

Indexed keywords

BETA LACTAMASE TEM 1; CEPHALOSPORIN; PENICILLIN G; TYROSINE;

EID: 34548804945     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21485     Document Type: Article
Times cited : (21)

References (41)
  • 1
    • 0031029659 scopus 로고    scopus 로고
    • Evolution and dissemination of β-lactamases accelerated by generations of β-lactam antibiotics
    • Medeiros AA. Evolution and dissemination of β-lactamases accelerated by generations of β-lactam antibiotics. Clin Infect Dis 1997;24(Suppl 1):S19-S45.
    • (1997) Clin Infect Dis , vol.24 , Issue.SUPPL. 1
    • Medeiros, A.A.1
  • 2
    • 23444440823 scopus 로고
    • Inactivation of antibiotics and the dissemination of resistance genes
    • Davies J. Inactivation of antibiotics and the dissemination of resistance genes. Science 1994;264:375-382.
    • (1994) Science , vol.264 , pp. 375-382
    • Davies, J.1
  • 3
    • 0013850042 scopus 로고
    • Penicillinase synthesis controlled by infectious R factors in Enterobacteriaceae
    • Datta N, Kontomichalou P. Penicillinase synthesis controlled by infectious R factors in Enterobacteriaceae. Nature 1965;208:239-241.
    • (1965) Nature , vol.208 , pp. 239-241
    • Datta, N.1    Kontomichalou, P.2
  • 4
    • 2442549622 scopus 로고    scopus 로고
    • Predicting the evolution of antibiotic resistance genes
    • Hall BG. Predicting the evolution of antibiotic resistance genes. Nat Rev Microbiol 2004;2:430-435.
    • (2004) Nat Rev Microbiol , vol.2 , pp. 430-435
    • Hall, B.G.1
  • 5
    • 0035122917 scopus 로고    scopus 로고
    • Predicting the emergence of antibiotic resistance by directed evolution and structural analysis
    • Orencia MC, Yoon JS, Ness JE, Stemmer WP, Stevens RC. Predicting the emergence of antibiotic resistance by directed evolution and structural analysis. Nat Struct Biol 2001;8:238-242.
    • (2001) Nat Struct Biol , vol.8 , pp. 238-242
    • Orencia, M.C.1    Yoon, J.S.2    Ness, J.E.3    Stemmer, W.P.4    Stevens, R.C.5
  • 7
    • 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
  • 8
    • 25144503869 scopus 로고    scopus 로고
    • Structure of the wild-type TEM-1 β-lactamase at 1.55 Å and the mutant enzyme Ser70Ala at 2.1 Å suggest the mode of noncovalent catalysis for the mutant enzyme
    • Stec B, Holtz KM, Wojciechowski CL, Kantrowitz ER. Structure of the wild-type TEM-1 β-lactamase at 1.55 Å and the mutant enzyme Ser70Ala at 2.1 Å suggest the mode of noncovalent catalysis for the mutant enzyme. Acta Crystallogr D Biol Crystallogr 2005;61:1072-1079.
    • (2005) Acta Crystallogr D Biol Crystallogr , vol.61 , pp. 1072-1079
    • Stec, B.1    Holtz, K.M.2    Wojciechowski, C.L.3    Kantrowitz, E.R.4
  • 9
    • 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
    • Swarén 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
    • Swarén, P.1    Golemi, D.2    Cabantous, S.3    Bulychev, A.4    Maveyraud, L.5    Mobashery, S.6    Samama, J.P.7
  • 11
    • 0037200056 scopus 로고    scopus 로고
    • The structural bases of antibiotic resistance in the clinically derived mutant β-lactamases TEM-30, TEM-32, and TEM-34
    • Wang X, Minasov G, Shoichet BK. The structural bases of antibiotic resistance in the clinically derived mutant β-lactamases TEM-30, TEM-32, and TEM-34. J Biol Chem 2002;277:32149-32156.
    • (2002) J Biol Chem , vol.277 , pp. 32149-32156
    • Wang, X.1    Minasov, G.2    Shoichet, B.K.3
  • 12
    • 0036295508 scopus 로고    scopus 로고
    • Evolution of an antibiotic resistance enzyme constrained by stability and activity trade-offs
    • Wang X, Minasov G, Shoichet BK. Evolution of an antibiotic resistance enzyme constrained by stability and activity trade-offs. J Mol Biol 2002;320:85-95.
    • (2002) J Mol Biol , vol.320 , pp. 85-95
    • Wang, X.1    Minasov, G.2    Shoichet, B.K.3
  • 14
    • 1242294467 scopus 로고    scopus 로고
    • Allosteric inhibition through core disruption
    • Horn JR, Shoichet BK. Allosteric inhibition through core disruption. J Mol Biol 2004;336:1283-1291.
    • (2004) J Mol Biol , vol.336 , pp. 1283-1291
    • Horn, J.R.1    Shoichet, B.K.2
  • 16
    • 0032581949 scopus 로고    scopus 로고
    • Structural basis for clinical longevity of carbapenem antibiotics in the face of challenge by the common class A β-lactamases from the antibiotic-resistant bacteria
    • Maveyraud L, Mourey L, Kotra LP, Pedelacq JD, Guillet V, Mobashery S, Samama JP. Structural basis for clinical longevity of carbapenem antibiotics in the face of challenge by the common class A β-lactamases from the antibiotic-resistant bacteria. J Am Chem Soc 1998;120:9748-9752.
    • (1998) J Am Chem Soc , vol.120 , pp. 9748-9752
    • Maveyraud, L.1    Mourey, L.2    Kotra, L.P.3    Pedelacq, J.D.4    Guillet, V.5    Mobashery, S.6    Samama, J.P.7
  • 17
    • 0034625157 scopus 로고    scopus 로고
    • Structure-based design guides the improved efficacy of deacylation transition state analogue inhibitors of TEM-1 β-lactamase
    • Ness S, Martin R, Kindler AM, Paetzel M, Gold M, Jensen SE, Jones JB, Strynadka NC. Structure-based design guides the improved efficacy of deacylation transition state analogue inhibitors of TEM-1 β-lactamase. Biochemistry 2000;39:5312-5321.
    • (2000) Biochemistry , vol.39 , pp. 5312-5321
    • Ness, S.1    Martin, R.2    Kindler, A.M.3    Paetzel, M.4    Gold, M.5    Jensen, S.E.6    Jones, J.B.7    Strynadka, N.C.8
  • 19
    • 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
  • 20
    • 0032562183 scopus 로고    scopus 로고
    • Crystal structure of an acylation transition-state analog of the TEM-1 β-lactamase. Mechanistic implications for class A β-lactamases
    • Maveyraud L, Pratt RF, Samama JP. Crystal structure of an acylation transition-state analog of the TEM-1 β-lactamase. Mechanistic implications for class A β-lactamases. Biochemistry 1998;37:2622-2628.
    • (1998) Biochemistry , vol.37 , pp. 2622-2628
    • Maveyraud, L.1    Pratt, R.F.2    Samama, J.P.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 XJ, 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.J.2    Shoichet, B.K.3
  • 22
    • 8544219754 scopus 로고    scopus 로고
    • Site-saturation mutagenesis of Tyr-105 reveals its importance in substrate stabilization and discrimination in TEM-1 β-lactamase
    • Doucet N, De Wals PY, Pelletier JN. Site-saturation mutagenesis of Tyr-105 reveals its importance in substrate stabilization and discrimination in TEM-1 β-lactamase. J Biol Chem 2004;279:46295-46303.
    • (2004) J Biol Chem , vol.279 , pp. 46295-46303
    • Doucet, N.1    De Wals, P.Y.2    Pelletier, J.N.3
  • 23
    • 0034663722 scopus 로고    scopus 로고
    • Lovell SC, Word JM, Richardson JS, Richardson DC. The penultimate rotamer library. Proteins 2000;40:389-408.
    • Lovell SC, Word JM, Richardson JS, Richardson DC. The penultimate rotamer library. Proteins 2000;40:389-408.
  • 24
    • 0027208112 scopus 로고
    • Rotamers: To be or not to be? An analysis of amino acid side-chain conformations in globular proteins
    • Schrauber H, Eisenhaber F, Argos P. Rotamers: to be or not to be? An analysis of amino acid side-chain conformations in globular proteins. J Mol Biol 1993;230:592-612.
    • (1993) J Mol Biol , vol.230 , pp. 592-612
    • Schrauber, H.1    Eisenhaber, F.2    Argos, P.3
  • 25
    • 0029760859 scopus 로고    scopus 로고
    • Structure-based design of a potent transition state analogue for TEM-1 β-lactamase
    • Strynadka NCJ, Martin R, Jensen SE, Gold M, Jones JB. Structure-based design of a potent transition state analogue for TEM-1 β-lactamase. Nat Struct Biol 1996;3:688-695.
    • (1996) Nat Struct Biol , vol.3 , pp. 688-695
    • Strynadka, N.C.J.1    Martin, R.2    Jensen, S.E.3    Gold, M.4    Jones, J.B.5
  • 26
    • 0029949210 scopus 로고    scopus 로고
    • A potent new mode of β-lactamase inhibition revealed by the 1.7 Å X-ray crystallography structure of the TEM-1-BLIP complex
    • Strynadka NC, Jensen SE, Alzari PM, James MN. A potent new mode of β-lactamase inhibition revealed by the 1.7 Å X-ray crystallography structure of the TEM-1-BLIP complex. Nat Struct Biol 1996;3:290-297.
    • (1996) Nat Struct Biol , vol.3 , pp. 290-297
    • Strynadka, N.C.1    Jensen, S.E.2    Alzari, P.M.3    James, M.N.4
  • 27
    • 33749007969 scopus 로고    scopus 로고
    • Backbone dynamics of TEM-1 determined by NMR: Evidence for a highly ordered protein
    • Savard PY, Gagne SM. Backbone dynamics of TEM-1 determined by NMR: evidence for a highly ordered protein. Biochemistry 2006;45:11414-11424.
    • (2006) Biochemistry , vol.45 , pp. 11414-11424
    • Savard, P.Y.1    Gagne, S.M.2
  • 28
    • 0031427720 scopus 로고    scopus 로고
    • Molecular modeling of the conformational complexity of (+)-anti-B[a]PDE-adducted DNA using simulated annealing
    • Kozack RE, Loechler EL. Molecular modeling of the conformational complexity of (+)-anti-B[a]PDE-adducted DNA using simulated annealing. Carcinogenesis 1997;18:1585-1593.
    • (1997) Carcinogenesis , vol.18 , pp. 1585-1593
    • Kozack, R.E.1    Loechler, E.L.2
  • 29
    • 1242338103 scopus 로고    scopus 로고
    • Conformational sampling for the impatient
    • Tai K. Conformational sampling for the impatient. Biophys Chem 2004;107:213-220.
    • (2004) Biophys Chem , vol.107 , pp. 213-220
    • Tai, K.1
  • 30
    • 0024519351 scopus 로고
    • Treatment of electrostatic effects in macromolecular modeling
    • Harvey SC. Treatment of electrostatic effects in macromolecular modeling. Proteins 1989;5:78-92.
    • (1989) Proteins , vol.5 , pp. 78-92
    • Harvey, S.C.1
  • 31
    • 0036284090 scopus 로고    scopus 로고
    • VEGA: A versatile program to convert, handle and visualize molecular structure on Windows-based PCs
    • Pedretti A, Villa L, Vistoli G. VEGA: a versatile program to convert, handle and visualize molecular structure on Windows-based PCs. J Mol Graph Model 2002;21:47-49.
    • (2002) J Mol Graph Model , vol.21 , pp. 47-49
    • Pedretti, A.1    Villa, L.2    Vistoli, G.3
  • 32
    • 4043162793 scopus 로고    scopus 로고
    • An open platform to develop chemo-bio-informatics applications, using plug-in architecture and script programming
    • Pedretti A, Villa L, Vistoli G. VEGA. An open platform to develop chemo-bio-informatics applications, using plug-in architecture and script programming. J Comput Aided Mol Des 2004;18:167-173.
    • (2004) J Comput Aided Mol Des , vol.18 , pp. 167-173
    • Pedretti, A.1    Villa, L.2    Vistoli, G.3    VEGA4
  • 33
    • 0037441653 scopus 로고    scopus 로고
    • Lovell SC, Davis IW, Arendall WB, III, de Bakker PI, Word JM, Prisant MG, Richardson JS, Richardson DC. Structure validation by Cα geometry: φ, ψ and Cβ deviation. Proteins 2003;50:437-450.
    • Lovell SC, Davis IW, Arendall WB, III, de Bakker PI, Word JM, Prisant MG, Richardson JS, Richardson DC. Structure validation by Cα geometry: φ, ψ and Cβ deviation. Proteins 2003;50:437-450.
  • 34
    • 32544436601 scopus 로고    scopus 로고
    • Multiple alignment of protein structures and sequences for VMD
    • Eargle J, Wright D, Luthey-Schulten Z. Multiple alignment of protein structures and sequences for VMD. Bioinformatics 2006;22:504-506.
    • (2006) Bioinformatics , vol.22 , pp. 504-506
    • Eargle, J.1    Wright, D.2    Luthey-Schulten, Z.3
  • 36
    • 0036135747 scopus 로고    scopus 로고
    • Protein-ligand recognition using spherical harmonic molecular surfaces: Towards a fast and efficient filter for large virtual throughput screening
    • Cai W, Shao X, Maigret B. Protein-ligand recognition using spherical harmonic molecular surfaces: towards a fast and efficient filter for large virtual throughput screening. J Mol Graph Model 2002;20:313-328.
    • (2002) J Mol Graph Model , vol.20 , pp. 313-328
    • Cai, W.1    Shao, X.2    Maigret, B.3
  • 37
    • 0034875587 scopus 로고    scopus 로고
    • Evaluation of site-directed spin labeling for characterizing protein-ligand complexes using simulated restraints
    • Constantine KL. Evaluation of site-directed spin labeling for characterizing protein-ligand complexes using simulated restraints. Biophys J 2001;81:1275-1284.
    • (2001) Biophys J , vol.81 , pp. 1275-1284
    • Constantine, K.L.1
  • 38
    • 0037199417 scopus 로고    scopus 로고
    • NMR structure of lung surfactant peptide SP-B(11-25)
    • Kurutz JW, Lee KY. NMR structure of lung surfactant peptide SP-B(11-25). Biochemistry 2002;41:9627-9636.
    • (2002) Biochemistry , vol.41 , pp. 9627-9636
    • Kurutz, J.W.1    Lee, K.Y.2
  • 39
    • 31544478873 scopus 로고    scopus 로고
    • Protein-protein interactions: Modeling the hepatitis C virus ion channel p 7
    • Patargias G, Zitzmann N, Dwek R, Fischer WB. Protein-protein interactions: modeling the hepatitis C virus ion channel p 7. J Med Chem 2006;49:648-655.
    • (2006) J Med Chem , vol.49 , pp. 648-655
    • Patargias, G.1    Zitzmann, N.2    Dwek, R.3    Fischer, W.B.4
  • 40
    • 0037460169 scopus 로고    scopus 로고
    • Insights into the acylation mechanism of class A β-lactamases from molecular dynamics simulations of the TEM-1 enzyme complexed with benzylpenicillin
    • Díaz N, Sordo TL, Merz KM, Suárez D. Insights into the acylation mechanism of class A β-lactamases from molecular dynamics simulations of the TEM-1 enzyme complexed with benzylpenicillin. J Am Chem Soc 2003;125:672-684.
    • (2003) J Am Chem Soc , vol.125 , pp. 672-684
    • Díaz, N.1    Sordo, T.L.2    Merz, K.M.3    Suárez, D.4
  • 41
    • 13444302257 scopus 로고    scopus 로고
    • Molecular dynamics simulations of the TEM-1 β-lactamase complexed with cephalothin
    • Díaz N, Suárez D, Merz KM, Sordo TL. Molecular dynamics simulations of the TEM-1 β-lactamase complexed with cephalothin. J Med Chem 2005;48:780-791.
    • (2005) J Med Chem , vol.48 , pp. 780-791
    • Díaz, N.1    Suárez, D.2    Merz, K.M.3    Sordo, T.L.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.