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Volumn 44, Issue 34, 2005, Pages 11307-11314

What are the roles of substrate-assisted catalysis and proximity effects in peptide bond formation by the ribosome?

Author keywords

[No Author keywords available]

Indexed keywords

CATALYSIS; CHEMICAL BONDS; COMPUTER SIMULATION; ELECTROSTATICS; ENTROPY; ENZYMES; REACTION KINETICS; SUBSTRATES;

EID: 23944472625     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi0509806     Document Type: Article
Times cited : (113)

References (38)
  • 3
    • 0034637111 scopus 로고    scopus 로고
    • The complete atomic structure of the large ribosomal subunit at 2.4 angstrom resolution
    • Ban, N., Nissen, P., Hansen, J., Moore, P. B., and Steitz, T. A. (2000) The complete atomic structure of the large ribosomal subunit at 2.4 angstrom resolution, Science 289, 905-920.
    • (2000) Science , vol.289 , pp. 905-920
    • Ban, N.1    Nissen, P.2    Hansen, J.3    Moore, P.B.4    Steitz, T.A.5
  • 6
    • 11244281701 scopus 로고    scopus 로고
    • Ribosome mechanism is a puzzler
    • Borman, S. (2004) Ribosome mechanism is a puzzler, Chem. Eng. News 82, 29-30.
    • (2004) Chem. Eng. News , vol.82 , pp. 29-30
    • Borman, S.1
  • 7
    • 0034637161 scopus 로고    scopus 로고
    • The structural basis of ribosome activity in peptide bond synthesis
    • Nissen, P., Hansen, J., Ban, N., Moore, P. B., and Steitz, T. A. (2000) The structural basis of ribosome activity in peptide bond synthesis, Science 289, 920-930.
    • (2000) Science , vol.289 , pp. 920-930
    • Nissen, P.1    Hansen, J.2    Ban, N.3    Moore, P.B.4    Steitz, T.A.5
  • 8
    • 0036671344 scopus 로고    scopus 로고
    • Important contribution to catalysis of peptide bond formation by a single ionizing group within the ribosome
    • Katunin, V. I., Muth, G. W., Strobel, S. A., Wintermeyer, W., and Rodnina, M. V. (2002) Important contribution to catalysis of peptide bond formation by a single ionizing group within the ribosome, Mol. Cell 10, 339-346.
    • (2002) Mol. Cell , vol.10 , pp. 339-346
    • Katunin, V.I.1    Muth, G.W.2    Strobel, S.A.3    Wintermeyer, W.4    Rodnina, M.V.5
  • 10
    • 3042695182 scopus 로고    scopus 로고
    • Peptide bond formation is all about proximity
    • Gregory, S. T., and Dahlberg, A. E. (2004) Peptide bond formation is all about proximity, Nat. Struct. Mol. Biol. 11, 586-587.
    • (2004) Nat. Struct. Mol. Biol. , vol.11 , pp. 586-587
    • Gregory, S.T.1    Dahlberg, A.E.2
  • 12
    • 0037321497 scopus 로고    scopus 로고
    • After the ribosome structures: How does peptidyl transferase work?
    • Moore, P. B., and Steitz, T. A. (2003) After the ribosome structures: How does peptidyl transferase work? RNA 9, 155-159.
    • (2003) RNA , vol.9 , pp. 155-159
    • Moore, P.B.1    Steitz, T.A.2
  • 16
    • 84961983443 scopus 로고    scopus 로고
    • Theoretical modeling of enzyme catalytic power: Analysis of "cratic" and electrostatic factors in catechol O-methyltransferase
    • Roca, M., Marti, S., Andres, J., Moliner, V., Tunon, M., Bertran, J., and Williams, A. H. (2003) Theoretical modeling of enzyme catalytic power: Analysis of "cratic" and electrostatic factors in catechol O-methyltransferase, J. Am. Chem. Soc. 125, 7726-7737.
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 7726-7737
    • Roca, M.1    Marti, S.2    Andres, J.3    Moliner, V.4    Tunon, M.5    Bertran, J.6    Williams, A.H.7
  • 17
    • 0034663824 scopus 로고    scopus 로고
    • Temperature effects on the catalytic efficiency, rate enhancement, and transition state affinity of cytidine deaminase, and the thermodynamic consequences for catalysis of removing a substrate "anchor"
    • Snider, M. J., Gaunitz, S., Ridgeway, C., Short, S. A., and Wolfenden, R. (2000) Temperature effects on the catalytic efficiency, rate enhancement, and transition state affinity of cytidine deaminase, and the thermodynamic consequences for catalysis of removing a substrate "anchor", Biochemistry 39, 9746-9753.
    • (2000) Biochemistry , vol.39 , pp. 9746-9753
    • Snider, M.J.1    Gaunitz, S.2    Ridgeway, C.3    Short, S.A.4    Wolfenden, R.5
  • 18
    • 0035707451 scopus 로고    scopus 로고
    • Dynamics of biochemical and biophysical reactions: Insight from computer simluations
    • Warshel, A., and Parson, W. W. (2001) Dynamics of biochemical and biophysical reactions: Insight from computer simluations, Q. Rev. Biophys. 34, 563-670.
    • (2001) Q. Rev. Biophys. , vol.34 , pp. 563-670
    • Warshel, A.1    Parson, W.W.2
  • 21
    • 0034616816 scopus 로고    scopus 로고
    • Ab initio evaluation of the potential surface for general base-catalyzed methanolysis of formamide: A reference solution reaction for studies of serine proteases
    • Strajbl, M., Florian, J., and Warshel, A. (2000) Ab initio evaluation of the potential surface for general base-catalyzed methanolysis of formamide: A reference solution reaction for studies of serine proteases, J. Am. Chem. Soc. 122, 5354-5366.
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 5354-5366
    • Strajbl, M.1    Florian, J.2    Warshel, A.3
  • 22
    • 0031187388 scopus 로고    scopus 로고
    • Langevin dipoles model for ab initio calculations of chemical processes in solution: Parametrization and application to hydration free energies of neutral and ionic solutes and conformational analysis in aqueous solution
    • Florian, J., and Warshel, A. (1997) Langevin dipoles model for ab initio calculations of chemical processes in solution: Parametrization and application to hydration free energies of neutral and ionic solutes and conformational analysis in aqueous solution, J. Phys. Chem. B 101, 5583-5595.
    • (1997) J. Phys. Chem. B , vol.101 , pp. 5583-5595
    • Florian, J.1    Warshel, A.2
  • 23
    • 0036473751 scopus 로고    scopus 로고
    • Fast solvent screening via quantum chemistry: COSMO-RS approach
    • Eckert, F., and Klamt, A. (2002) Fast solvent screening via quantum chemistry: COSMO-RS approach, AlChE J. 48, 369-385.
    • (2002) AlChE J. , vol.48 , pp. 369-385
    • Eckert, F.1    Klamt, A.2
  • 25
    • 4243810035 scopus 로고
    • Simulation of enzyme reactions using valence bond force fields and other hybrid quantum/classical approaches
    • Aqvist, J., and Warshel, A. (1993) Simulation of enzyme reactions using valence bond force fields and other hybrid quantum/classical approaches, Chem. Rev. 93, 2523-2544.
    • (1993) Chem. Rev. , vol.93 , pp. 2523-2544
    • Aqvist, J.1    Warshel, A.2
  • 26
    • 0032233055 scopus 로고    scopus 로고
    • Computer simulations with explicit solvent: Recent progress in the thermodynamic decomposition of free energies and in modeling electrostatic effects
    • Levy, R. M., and Gallicchio, E. (1998) Computer simulations with explicit solvent: Recent progress in the thermodynamic decomposition of free energies and in modeling electrostatic effects, Anna. Rev. Phys. Chem. 49, 531-567.
    • (1998) Anna. Rev. Phys. Chem. , vol.49 , pp. 531-567
    • Levy, R.M.1    Gallicchio, E.2
  • 27
    • 0033581989 scopus 로고    scopus 로고
    • Calculations of hydration entropies of hydrophobic, polar, and ionic solutes in the framework of the Langevin dipoles solvation model, J
    • Florian, J., and Warshel, A. (1999) Calculations of hydration entropies of hydrophobic, polar, and ionic solutes in the framework of the Langevin dipoles solvation model, J. Phys. Chem. B 103, 10282-10288.
    • (1999) Phys. Chem. B , vol.103 , pp. 10282-10288
    • Florian, J.1    Warshel, A.2
  • 28
    • 0342321950 scopus 로고    scopus 로고
    • Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease
    • Sham, Y. Y., Chu, Z. T., Tao, H., and Warshel, A. (2000) Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease, Proteins: Struct., Funct., Genet. 39, 393-407.
    • (2000) Proteins: Struct., Funct., Genet. , vol.39 , pp. 393-407
    • Sham, Y.Y.1    Chu, Z.T.2    Tao, H.3    Warshel, A.4
  • 29
    • 0032538627 scopus 로고    scopus 로고
    • Electrostatic origin of the catalytic power of enzymes and the role of preorganized active sites
    • Warshel, A. (1998) Electrostatic origin of the catalytic power of enzymes and the role of preorganized active sites, J. Biol. Chem. 273, 27035-27038.
    • (1998) J. Biol. Chem. , vol.273 , pp. 27035-27038
    • Warshel, A.1
  • 30
    • 0041429611 scopus 로고    scopus 로고
    • Apparent NAC effect in chorismate mutase reflects electrostatic transition state stabilization
    • Strajbl, M., Shurki, A., Kato, M., and Warshel, A. (2003) Apparent NAC effect in chorismate mutase reflects electrostatic transition state stabilization, J. Am. Chem. Soc. 125, 10228-10237.
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 10228-10237
    • Strajbl, M.1    Shurki, A.2    Kato, M.3    Warshel, A.4
  • 32
    • 0000354626 scopus 로고
    • Investigation of the free energy functions for electron transfer reactions
    • King, G., and Warshel, A. (1990) Investigation of the free energy functions for electron transfer reactions, J. Chem. Phys. 93, 8682-8692.
    • (1990) J. Chem. Phys. , vol.93 , pp. 8682-8692
    • King, G.1    Warshel, A.2
  • 33
    • 0000115003 scopus 로고
    • A local reaction field method for fast evaluation of long-range electrostatic interactions in molecular simulations
    • Lee, F. S., and Warshel, A. (1992) A local reaction field method for fast evaluation of long-range electrostatic interactions in molecular simulations, J. Chem. Phys. 97, 3100-3107.
    • (1992) J. Chem. Phys. , vol.97 , pp. 3100-3107
    • Lee, F.S.1    Warshel, A.2
  • 35
    • 0041561440 scopus 로고    scopus 로고
    • University of Southern California, Los Angeles
    • Florian, J., and Warshel, A. (1999) ChemSol, University of Southern California, Los Angeles.
    • (1999) ChemSol
    • Florian, J.1    Warshel, A.2
  • 37
    • 0028464366 scopus 로고
    • Why have mutagenesis studies not located the general base in ras p21
    • Schweins, T., Langen, R., and Warshel, A. (1994) Why Have Mutagenesis Studies Not Located the General Base in ras p21, Nat. Struct Biol. 1, 476-484.
    • (1994) Nat. Struct Biol. , vol.1 , pp. 476-484
    • Schweins, T.1    Langen, R.2    Warshel, A.3
  • 38
    • 0033957143 scopus 로고    scopus 로고
    • Substrate-assisted catalysis: Molecular basis and biological significance
    • Dall'Acqua, W., and Carter, P. (2000) Substrate-assisted catalysis: Molecular basis and biological significance, Protein Sci. 9, 1-9.
    • (2000) Protein Sci. , vol.9 , pp. 1-9
    • Dall'Acqua, W.1    Carter, P.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.