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Volumn 27, Issue 6, 2009, Pages 723-734

Corrigendum to "Homology modeling of human transketolase: Description of critical sites useful for drug design and study of the cofactor binding mode" [J. Mol. Graph. Model. 27 (2009) 723-734] (DOI:10.1016/j.jmgm.2008.11.005);Homology modeling of human Transketolase: Description of critical sites useful for drug design and study of the cofactor binding mode

Author keywords

Binding free energy; Drug design; Homology modeling; Molecular dynamics; Transketolase

Indexed keywords

AMINO ACIDS; BINDING ENERGY; BINDING SITES; CATALYST ACTIVITY; CRYSTAL STRUCTURE; DIMERS; FREE ENERGY; MOLECULAR DYNAMICS; YEAST;

EID: 58849102080     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2009.02.002     Document Type: Erratum
Times cited : (15)

References (63)
  • 3
    • 0021112650 scopus 로고
    • The catalytic mechanism of Transketolase. Thiamin pyrophosphate-derived transition states for Transketolase and pyruvate dehydrogenase are not identical
    • Shreve D.S., Holloway M.P., Haggerty III J.C., and Sable H.Z. The catalytic mechanism of Transketolase. Thiamin pyrophosphate-derived transition states for Transketolase and pyruvate dehydrogenase are not identical. J. Biol. Chem. 258 (1993) 12405-12408
    • (1993) J. Biol. Chem. , vol.258 , pp. 12405-12408
    • Shreve, D.S.1    Holloway, M.P.2    Haggerty III, J.C.3    Sable, H.Z.4
  • 4
    • 0027018557 scopus 로고
    • Thiamin pyrophosphate binding mechanism and the function of the aminopyrimidine part
    • Spec No
    • Schellenberger A. Thiamin pyrophosphate binding mechanism and the function of the aminopyrimidine part. J. Nutr. Sci. Vitaminol. (1992) 392-396 Spec No
    • (1992) J. Nutr. Sci. Vitaminol. , pp. 392-396
    • Schellenberger, A.1
  • 6
    • 0027196884 scopus 로고
    • Crystal structure of Transketolase in complex with thiamine thiazolone diphosphate, an analogue of the reaction intermediate, at 2.3 Å resolution
    • Nilsson U., Lindqvist Y., Kluger Ro., and Schneider G. Crystal structure of Transketolase in complex with thiamine thiazolone diphosphate, an analogue of the reaction intermediate, at 2.3 Å resolution. FEBS Lett. 326 (1993) 145-148
    • (1993) FEBS Lett. , vol.326 , pp. 145-148
    • Nilsson, U.1    Lindqvist, Y.2    Kluger, Ro.3    Schneider, G.4
  • 8
    • 0026762799 scopus 로고
    • Three-dimensional structure of Transketolase, a thiamine diphosphate dependent enzyme, at 2.5 Å resolution
    • Lindqvist Y., Schneider G., Ermler U., and Sündstrom M. Three-dimensional structure of Transketolase, a thiamine diphosphate dependent enzyme, at 2.5 Å resolution. EMBO J. 11 (1992) 2373-2379
    • (1992) EMBO J. , vol.11 , pp. 2373-2379
    • Lindqvist, Y.1    Schneider, G.2    Ermler, U.3    Sündstrom, M.4
  • 9
    • 0028305456 scopus 로고
    • Refined structure of transketolase from Saccharomyces cerevisiae at 20 Å resolution
    • Nikkola M., Lindqvist Y., and Schneider G. Refined structure of transketolase from Saccharomyces cerevisiae at 20 Å resolution. J. Mol. Biol. 238 (1994) 387-404
    • (1994) J. Mol. Biol. , vol.238 , pp. 387-404
    • Nikkola, M.1    Lindqvist, Y.2    Schneider, G.3
  • 10
    • 58849145718 scopus 로고    scopus 로고
    • M.N. Isupov, M.P. Rupprecht, K.S. Wilson, Z. Dauter, J.A. Littlechild, Crystal Structure of Escherichia coli Transketolase, in press.
    • M.N. Isupov, M.P. Rupprecht, K.S. Wilson, Z. Dauter, J.A. Littlechild, Crystal Structure of Escherichia coli Transketolase, in press.
  • 12
    • 0030853640 scopus 로고    scopus 로고
    • Aspartate 155 of human Transketolase is essential for thiamine diphosphate-magnesium binding, and cofactor binding is required for dimer formation
    • Wang J.J., Martin P.R., and Singleton C.K. Aspartate 155 of human Transketolase is essential for thiamine diphosphate-magnesium binding, and cofactor binding is required for dimer formation. Biochim. Biophys. Acta 1341 (1997) 165-172
    • (1997) Biochim. Biophys. Acta , vol.1341 , pp. 165-172
    • Wang, J.J.1    Martin, P.R.2    Singleton, C.K.3
  • 13
    • 16644364379 scopus 로고    scopus 로고
    • Identification of novel small-molecule inhibitors for human Transketolase by high-throughput screening with fluorescent intensity (FLINT) assay
    • Du M.X., Sim J., Fang L., Yin Z., Koh S., Stratton J., Pons J., Wang J.J., and Carte B. Identification of novel small-molecule inhibitors for human Transketolase by high-throughput screening with fluorescent intensity (FLINT) assay. J. Biomol. Screen. 9 (2003) 427-433
    • (2003) J. Biomol. Screen. , vol.9 , pp. 427-433
    • Du, M.X.1    Sim, J.2    Fang, L.3    Yin, Z.4    Koh, S.5    Stratton, J.6    Pons, J.7    Wang, J.J.8    Carte, B.9
  • 14
    • 0032527731 scopus 로고    scopus 로고
    • Critical role of arg433 in rat Transketolase activity as probed by site-directed mutagenesis
    • Soh Y., Song B.J., Jeng J., and Kallarakal A.T. Critical role of arg433 in rat Transketolase activity as probed by site-directed mutagenesis. Biochem. J. 333 (1998) 367-372
    • (1998) Biochem. J. , vol.333 , pp. 367-372
    • Soh, Y.1    Song, B.J.2    Jeng, J.3    Kallarakal, A.T.4
  • 18
    • 33750045454 scopus 로고    scopus 로고
    • Structure modeling, ligand binding, and binding affinity calculation (LR-MM-PBSA) of human heparanase for inhibition and drug design
    • Zhou Z., Bates M., and Madura J.D. Structure modeling, ligand binding, and binding affinity calculation (LR-MM-PBSA) of human heparanase for inhibition and drug design. Proteins 65 (2006) 580-592
    • (2006) Proteins , vol.65 , pp. 580-592
    • Zhou, Z.1    Bates, M.2    Madura, J.D.3
  • 20
    • 35448959252 scopus 로고    scopus 로고
    • Homology modeling and examination of the effect of the D92E mutation on the N5H1 nonstructural protein NS1 effector domain
    • Li M., and Wang B. Homology modeling and examination of the effect of the D92E mutation on the N5H1 nonstructural protein NS1 effector domain. J. Mol. Model. 13 (2007) 1237-1244
    • (2007) J. Mol. Model. , vol.13 , pp. 1237-1244
    • Li, M.1    Wang, B.2
  • 22
    • 0032537590 scopus 로고    scopus 로고
    • Sixty years of thiamin diphosphate biochemistry
    • Schellenberger A. Sixty years of thiamin diphosphate biochemistry. Biochim. Biophys. Acta 1385 (1998) 177-186
    • (1998) Biochim. Biophys. Acta , vol.1385 , pp. 177-186
    • Schellenberger, A.1
  • 23
    • 58849125422 scopus 로고    scopus 로고
    • N. Eswar, M.A. Mari-Renom, B. Webb, M.S. Madhusudhan, D. Eramian, M. Shen, U. Pieper, S. Sali, Comparative protein structure modeling with MODELLER, Curr. Protoc. Bioinformatics, 2006, Chapter 5, Unit 5.6.
    • N. Eswar, M.A. Mari-Renom, B. Webb, M.S. Madhusudhan, D. Eramian, M. Shen, U. Pieper, S. Sali, Comparative protein structure modeling with MODELLER, Curr. Protoc. Bioinformatics, 2006, Chapter 5, Unit 5.6.
  • 24
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • Sali A., and Blundell T.L. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234 (1993) 779-815
    • (1993) J. Mol. Biol. , vol.234 , 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 R.K., and Sali A. Modeling of loops in protein structures. Protein Sci. 9 (2000) 1753-1773
    • (2000) Protein Sci. , vol.9 , pp. 1753-1773
    • Fiser, A.1    Do, R.K.2    Sali, A.3
  • 26
    • 0027515306 scopus 로고
    • Yeast TKL1 gene encodes a Transketolase that is required for efficient glycolysis and biosynthesis of aromatic amino acids
    • Sundström M., Lindqvist Y., Schneider G., Hellman U., and Ronne H. Yeast TKL1 gene encodes a Transketolase that is required for efficient glycolysis and biosynthesis of aromatic amino acids. J. Biol. Chem. 268 (1993) 24346-24352
    • (1993) J. Biol. Chem. , vol.268 , pp. 24346-24352
    • Sundström, M.1    Lindqvist, Y.2    Schneider, G.3    Hellman, U.4    Ronne, H.5
  • 27
    • 3242887525 scopus 로고    scopus 로고
    • STRIDE: a web server for secondary structure assigment from known atomic coordinates of proteins
    • Heinig M., and Frishman D. STRIDE: a web server for secondary structure assigment from known atomic coordinates of proteins. Nucleic Acids Res. 32 (2004) W500-W502
    • (2004) Nucleic Acids Res. , vol.32
    • Heinig, M.1    Frishman, D.2
  • 28
    • 58849151887 scopus 로고    scopus 로고
    • D.A. Case, D.A. Pearlman, J.W. Caldwell, T.E. Cheathan III, J. Wang, W.S. Ross, C.L. Simmerling, T.D. Darden, K.M. Merz, R.V. Stanton, A.L.Cheng, J.J. Vincent, M. Crowley, V. Tsui, H. Gohlke, R.J. Radmer, Y. Duan, J. Pitera, I. Massova, G.L. Seibel, U.C. Sligh, P.K. Weiner, P.A. Kollman, AMBER 7, Univ. California, San Francisco, 2002.
    • D.A. Case, D.A. Pearlman, J.W. Caldwell, T.E. Cheathan III, J. Wang, W.S. Ross, C.L. Simmerling, T.D. Darden, K.M. Merz, R.V. Stanton, A.L.Cheng, J.J. Vincent, M. Crowley, V. Tsui, H. Gohlke, R.J. Radmer, Y. Duan, J. Pitera, I. Massova, G.L. Seibel, U.C. Sligh, P.K. Weiner, P.A. Kollman, AMBER 7, Univ. California, San Francisco, 2002.
  • 29
    • 0035471015 scopus 로고    scopus 로고
    • Functional flexibility of the Transketolase molecule
    • Kochetov G.A. Functional flexibility of the Transketolase molecule. Biochemistry 66 (2001) 1077-1085
    • (2001) Biochemistry , vol.66 , pp. 1077-1085
    • Kochetov, G.A.1
  • 32
    • 33846823909 scopus 로고
    • Particle mesh Ewald: an W log(N) method for Ewald sums in large systems
    • Darden T., York D., and Pedersen L. Particle mesh Ewald: an W log(N) method for Ewald sums in large systems. J. Chem. Phys. 98 (1993) 10089-10092
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 37
    • 33646940952 scopus 로고
    • Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
    • Ryckaert J.P., Ciccotti G., and Berendsen H.J. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Chem. 23 (1977) 327-341
    • (1977) J. Comput. Chem. , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.3
  • 38
    • 0026612756 scopus 로고
    • a values of ionizable groups in bacteriorhodopsin
    • a values of ionizable groups in bacteriorhodopsin. J. Mol. Biol. 224 (1992) 473-486
    • (1992) J. Mol. Biol. , vol.224 , pp. 473-486
    • Bashford, D.1    Gerwent, K.2
  • 39
    • 32844457567 scopus 로고
    • Accurate calculations of hydration free energies using macroscopic solvents
    • Sitkoff D., Sharp K., and Honing B. Accurate calculations of hydration free energies using macroscopic solvents. J. Phys. Chem. 98 (1994) 1978-1988
    • (1994) J. Phys. Chem. , vol.98 , pp. 1978-1988
    • Sitkoff, D.1    Sharp, K.2    Honing, B.3
  • 40
    • 14244273182 scopus 로고    scopus 로고
    • Theory and applications of the generalized born solvation model in macromolecular simulations
    • Tsui V., and Case D.A. Theory and applications of the generalized born solvation model in macromolecular simulations. Nucleic Acids Sci. 56 (2001) 275-291
    • (2001) Nucleic Acids Sci. , vol.56 , pp. 275-291
    • Tsui, V.1    Case, D.A.2
  • 41
    • 0033654297 scopus 로고    scopus 로고
    • Generalized Born models of macromolecular solvation effects
    • Onufriev A., Bashford D., and Case D.A. Generalized Born models of macromolecular solvation effects. Annu. Rev. Phys. Chem. 51 (2000) 129-152
    • (2000) Annu. Rev. Phys. Chem. , vol.51 , pp. 129-152
    • Onufriev, A.1    Bashford, D.2    Case, D.A.3
  • 42
    • 20544433165 scopus 로고
    • VDW volumes and radii
    • Bondi A. VDW volumes and radii. J. Phys. Chem. 68 (1964) 441-451
    • (1964) J. Phys. Chem. , vol.68 , pp. 441-451
    • Bondi, A.1
  • 43
    • 0000408363 scopus 로고    scopus 로고
    • Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO)
    • Weiser J., Shemkin P.S., and Still W.C. Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO). J. Comput. Chem. 20 (1999) 217-230
    • (1999) J. Comput. Chem. , vol.20 , pp. 217-230
    • Weiser, J.1    Shemkin, P.S.2    Still, W.C.3
  • 44
    • 0000243829 scopus 로고
    • PROCHECK: a program to check the stereochemical quality of protein structures
    • Laskowski R.A., MacArthur M.W., Moss D.S., and Thornton J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst. 26 (1993) 283-291
    • (1993) J. Appl. Cryst. , vol.26 , pp. 283-291
    • Laskowski, R.A.1    MacArthur, M.W.2    Moss, D.S.3    Thornton, J.M.4
  • 45
    • 0030767485 scopus 로고    scopus 로고
    • VERIFY3D: assessment of protein models with three-dimensional profiles
    • Eisenberg D., Luthy R., and Bowie J.U. VERIFY3D: assessment of protein models with three-dimensional profiles. Methods Enzymol. 277 (1997) 396-404
    • (1997) Methods Enzymol. , vol.277 , pp. 396-404
    • Eisenberg, D.1    Luthy, R.2    Bowie, J.U.3
  • 46
    • 34547566446 scopus 로고    scopus 로고
    • ProSA-Web: interactive web service for the recognition of errors in three-dimensional structures of proteins
    • Wiederstein M., and Sippl M.J. ProSA-Web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res. 35 (2007) 407-410
    • (2007) Nucleic Acids Res. , vol.35 , pp. 407-410
    • Wiederstein, M.1    Sippl, M.J.2
  • 47
    • 0034213559 scopus 로고    scopus 로고
    • Conservation of polar residues as hot spots at protein interfaces
    • Hu Z., Ma B., Wolfson H., and Nussinov R. Conservation of polar residues as hot spots at protein interfaces. Proteins 39 (2000) 331-334
    • (2000) Proteins , vol.39 , pp. 331-334
    • Hu, Z.1    Ma, B.2    Wolfson, H.3    Nussinov, R.4
  • 48
    • 0019332362 scopus 로고
    • The active site of Transketolase. Two arginine residues are essential for activity
    • Kremer A.B., Egan R.M., and Sable H.Z. The active site of Transketolase. Two arginine residues are essential for activity. J. Biol. Chem. 255 (1980) 2405-2410
    • (1980) J. Biol. Chem. , vol.255 , pp. 2405-2410
    • Kremer, A.B.1    Egan, R.M.2    Sable, H.Z.3
  • 49
    • 33845360094 scopus 로고    scopus 로고
    • Arginine mimetic structures in biologically active antagonists and inhibitors
    • Masic P.L. Arginine mimetic structures in biologically active antagonists and inhibitors. Curr. Med. Chem. 13 (2006) 3627-3648
    • (2006) Curr. Med. Chem. , vol.13 , pp. 3627-3648
    • Masic, P.L.1
  • 50
    • 0037378406 scopus 로고    scopus 로고
    • Thyroxine-derivatives of lipopeptides: bifunctional dimerization inhibitors of human immunodeficiency virus-1 protease
    • Dumond J., Boggetto N., Schramm H.J., Schramm W., Takahashi M., and Reboud-Ravaux M. Thyroxine-derivatives of lipopeptides: bifunctional dimerization inhibitors of human immunodeficiency virus-1 protease. Biochem. Pharmacol. 65 (2003) 1097-1102
    • (2003) Biochem. Pharmacol. , vol.65 , pp. 1097-1102
    • Dumond, J.1    Boggetto, N.2    Schramm, H.J.3    Schramm, W.4    Takahashi, M.5    Reboud-Ravaux, M.6
  • 52
    • 0031029945 scopus 로고    scopus 로고
    • Examination of substrate binding in thiamin diphosphate-dependent Transketolase by protein crystallography and site-directed mutagenesis
    • Nilsson U., Meshalkina C., Cindqvist Y., and Schneider G. Examination of substrate binding in thiamin diphosphate-dependent Transketolase by protein crystallography and site-directed mutagenesis. J. Biol. Chem. 272 (1997) 1864-1869
    • (1997) J. Biol. Chem. , vol.272 , pp. 1864-1869
    • Nilsson, U.1    Meshalkina, C.2    Cindqvist, Y.3    Schneider, G.4
  • 53
    • 0037170794 scopus 로고    scopus 로고
    • Biphenyls as potential mimetics of α-Helix
    • Jacoby E. Biphenyls as potential mimetics of α-Helix. Bioorg. Med. Chem. Lett. 12 (2002) 891-893
    • (2002) Bioorg. Med. Chem. Lett. , vol.12 , pp. 891-893
    • Jacoby, E.1
  • 54
    • 0043245780 scopus 로고    scopus 로고
    • Insights into protein-protein binding by binding free energy calculation and free energy decomposition for Ras-Raf and Ras-RalGDS complexes
    • Gohlke H., Kiel Ch., and Case D.A. Insights into protein-protein binding by binding free energy calculation and free energy decomposition for Ras-Raf and Ras-RalGDS complexes. Mol. Biol. 330 (2003) 891-913
    • (2003) Mol. Biol. , vol.330 , pp. 891-913
    • Gohlke, H.1    Kiel, Ch.2    Case, D.A.3
  • 55
    • 0027459038 scopus 로고
    • Cloning of human Transketolase cDNAs and comparison of the nucleotide sequence of the coding region in Wernicke-Korsakoff and non-Wernicke-Korsakoff individuals
    • McCool B.A., Plonk S.G., Martins P.R., and Singleton C.K. Cloning of human Transketolase cDNAs and comparison of the nucleotide sequence of the coding region in Wernicke-Korsakoff and non-Wernicke-Korsakoff individuals. J. Biol. Chem. 268 (1993) 1397-1404
    • (1993) J. Biol. Chem. , vol.268 , pp. 1397-1404
    • McCool, B.A.1    Plonk, S.G.2    Martins, P.R.3    Singleton, C.K.4
  • 56
    • 18744394070 scopus 로고    scopus 로고
    • Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites
    • Laurie A.T., and Jackson R.M. Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites. Bioinformatics 21 (2005) 1908-1916
    • (2005) Bioinformatics , vol.21 , pp. 1908-1916
    • Laurie, A.T.1    Jackson, R.M.2
  • 57
    • 0037442584 scopus 로고    scopus 로고
    • Molecular dynamics simulations and thermodynamics analysis of DNA-drug complexes. Minor groove binding between 4′,6′-diamidino-2-phenylindole and DNA duplexes in solution
    • Spackova N., Cheatham T.E., Ryjacek F., Lankas F., van Meervelt L., Hobza P., and Sponer J. Molecular dynamics simulations and thermodynamics analysis of DNA-drug complexes. Minor groove binding between 4′,6′-diamidino-2-phenylindole and DNA duplexes in solution. J. Am. Chem. Soc. 125 (2003) 1759-1769
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 1759-1769
    • Spackova, N.1    Cheatham, T.E.2    Ryjacek, F.3    Lankas, F.4    van Meervelt, L.5    Hobza, P.6    Sponer, J.7
  • 58
    • 28144441347 scopus 로고    scopus 로고
    • Evaluating the molecular mechanics Poisson-Boltzmann surface area free energy method using a cogeneric series of ligands to p38 MAP kinase
    • Pearlman D.A. Evaluating the molecular mechanics Poisson-Boltzmann surface area free energy method using a cogeneric series of ligands to p38 MAP kinase. J. Med. Chem. 48 (2005) 7796-7806
    • (2005) J. Med. Chem. , vol.48 , pp. 7796-7806
    • Pearlman, D.A.1
  • 59
    • 25444447108 scopus 로고    scopus 로고
    • Scoring binding affinity of multiple ligands using implicit solvent and a single molecular dynamics trajectory: application to influenza neuraminidase
    • Bonnet P., and Bryce R.A. Scoring binding affinity of multiple ligands using implicit solvent and a single molecular dynamics trajectory: application to influenza neuraminidase. J. Mol. Graph. Model. 24 (2005) 147-156
    • (2005) J. Mol. Graph. Model. , vol.24 , pp. 147-156
    • Bonnet, P.1    Bryce, R.A.2
  • 60
    • 1842611470 scopus 로고    scopus 로고
    • Molecular dynamics and free energy analysis of neuraminidase-ligand interactions
    • Bonnet P., and Bryce R.A. Molecular dynamics and free energy analysis of neuraminidase-ligand interactions. Protein Sci. 13 (2004) 946-957
    • (2004) Protein Sci. , vol.13 , pp. 946-957
    • Bonnet, P.1    Bryce, R.A.2
  • 62
    • 0030157593 scopus 로고    scopus 로고
    • A structural and energetics analysis of the binding of a series of N-acetylneuraminic-acid-based inhibitors to influenza virus sialidase
    • Taylor N.R., and von Itzstein M. A structural and energetics analysis of the binding of a series of N-acetylneuraminic-acid-based inhibitors to influenza virus sialidase. J. Comput. Aided Mol. Des. 10 (1996) 233-246
    • (1996) J. Comput. Aided Mol. Des. , vol.10 , pp. 233-246
    • Taylor, N.R.1    von Itzstein, M.2
  • 63
    • 33846881144 scopus 로고    scopus 로고
    • Comparative evaluation of MMPBSA and XSCORE to compute binding free energy in XIAP-peptide complexes
    • Obiol-Pardo C., and Rubio-Martinez J. Comparative evaluation of MMPBSA and XSCORE to compute binding free energy in XIAP-peptide complexes. J. Chem. Inform. Model. 47 (2007) 134-142
    • (2007) J. Chem. Inform. Model. , vol.47 , pp. 134-142
    • Obiol-Pardo, C.1    Rubio-Martinez, J.2


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