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Structure (78)
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Yang, L.-W., & Bahar, I. (2005). Coupling between Catalytic Site and Collective Dynamics: A Requirement for Mechanochemical Activity of Enzymes. Structure, 13(6), 893–904.

Authors 2
  1. Lee-Wei Yang (first)
  2. Ivet Bahar (additional)
References 74 Referenced 234
  1. 10.1021/bi0495228 / Biochemistry / Protein dynamics and enzymatic catalysis: investigating the peptidyl-prolyl cis-trans isomerization activity of cyclophilin A by Agarwal (2004)
  2. 10.1073/pnas.96.19.10637 / Proc. Natl. Acad. Sci. USA / Detoxification of environmental mutagens and carcinogens: structure-based mechanism and evolution of liver epoxide hydrolase by Argiriadi (1999)
  3. 10.1016/S0006-3495(01)76033-X / Biophys. J. / Anisotropy of fluctuation dynamics of proteins with an elastic network model by Atilgan (2001)
  4. 10.1016/S1359-0278(97)00024-2 / Fold. Des. / Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential by Bahar (1997)
  5. 10.1103/PhysRevLett.80.2733 / Phys. Rev. Lett. / Vibrational dynamics of folded proteins: significance of slow and fast motions in relation to function and stability by Bahar (1998)
  6. 10.1006/jmbi.1998.2371 / J. Mol. Biol. / Collective motions in HIV-1 reverse transcriptase: examination of flexibility and enzyme function by Bahar (1999)
  7. 10.1038/279773a0 / Nature / Sequence, structure and activity of phosphoglycerate kinase: a possible hinge-bending enzyme by Banks (1979)
  8. 10.1016/S0022-2836(02)01036-7 / J. Mol. Biol. / Analysis of catalytic residues in enzyme active sites by Bartlett (2002)
  9. 10.1016/S0022-2836(02)01036-7 / J. Mol. Biol. / Analysis of catalytic residues in enzyme active sites by Bartlett (2002)
  10. 10.1126/science.1085515 / Science / A perspective on enzyme catalysis by Benkovic (2003)
  11. 10.1093/nar/28.1.235 / Nucleic Acids Res. / The Protein Data Bank by Berman (2000)
  12. 10.1016/0022-2836(92)90472-V / J. Mol. Biol. / Inhibition of beta-lactamase by clavulanate. Trapped intermediates in cryocrystallographic studies by Chen (1992)
  13. 10.1093/bioinformatics/bth912 / Bioinformatics / Mining frequent patterns in protein structures: a study of protease families by Chen (2004)
  14. 10.1098/rstb.2004.1506 / Philos. Trans. R. Soc. Lond. B Biol. Sci. / Characteristics of nearly dry enzymes in organic solvents: implications for biocatalysis in the absence of water by Clark (2004)
  15. 10.1093/protein/11.10.891 / Protein Eng. / Hinge-bending motions in annexins: molecular dynamics and essential dynamics of apo-annexin V and of calcium bound annexin V and I by Cregut (1998)
  16. 10.1146/annurev.biophys.32.110601.142445 / Annu. Rev. Biophys. Biomol. Struct. / The role of dynamics in enzyme activity by Daniel (2002)
  17. 10.1021/ja027704o / J. Am. Chem. Soc. / Insights into the acylation mechanism of class A beta-lactamases from molecular dynamics simulations of the TEM-1 enzyme complexed with benzylpenicillin by Diaz (2003)
  18. 10.1126/science.1066176 / Science / Enzyme dynamics during catalysis by Eisenmesser (2002)
  19. 10.1046/j.1432-1327.1998.2570309.x / Eur. J. Biochem. / Crystal structure of subtilisin DY, a random mutant of subtilis in Carlsberg by Eschenburg (1998)
  20. 10.1074/jbc.274.43.30849 / J. Biol. Chem. / Glycine insertion in the hinge region of lactose repressor protein alters DNA binding by Falcon (1999)
  21. 10.1098/rspa.1976.0146 / Proc. R. Soc. Lond. A / Statistical thermodynamics of random networks by Flory (1976)
  22. 10.1073/pnas.95.9.4795 / Proc. Natl. Acad. Sci. USA / Dynamics and functions of proteins: the search of general concepts by Frauenfelder (1998)
  23. 10.1073/pnas.96.18.10118 / Proc. Natl. Acad. Sci. USA / The propagation of binding interactions to remote sites in proteins: analysis of the binding of the monoclonal antibody D1.3 to lysozyme by Freire (1999)
  24. 10.1073/pnas.80.12.3696 / Proc. Natl. Acad. Sci. USA / Dynamics of a small globular protein in terms of low-frequency vibrational modes by Go (1983)
  25. {'key': '10.1016/j.str.2005.03.015_bib25', 'first-page': '11940', 'article-title': 'Using a neural network and spatial clustering to predict the location of active sites in enzymes', 'volume': '37', 'author': 'Gutteridge', 'year': '2003', 'journal-title': 'Biochemistry'} / Biochemistry / Using a neural network and spatial clustering to predict the location of active sites in enzymes by Gutteridge (2003)
  26. 10.1103/PhysRevLett.79.3090 / Phys. Rev. Lett. / Gaussian dynamics of folded proteins by Haliloglu (1997)
  27. 10.1093/emboj/cdf575 / EMBO J. / Hinge-mediated dimerization of SMC protein is essential for its dynamic interaction with DNA by Hirano (2002)
  28. 10.1006/jmbi.1998.2089 / J. Mol. Biol. / Structures of native and complexed complement factor D: implications of the atypical His57 conformation and self-inhibitory loop in the regulation of specific serine protease activity by Jing (1998)
  29. 10.1146/annurev.bi.52.070183.001403 / Annu. Rev. Biochem. / Dynamics of proteins: elements and functions by Karplus (1983)
  30. 10.1021/bi9821364 / Biochemistry / Lowering the entropic barrier for binding conformationally flexible inhibitors to enzymes by Khan (1998)
  31. 10.1016/S0959-440X(99)80023-2 / Curr. Opin. Struct. Biol. / Investigating protein dynamics in collective coordinate space by Kitao (1999)
  32. 10.1038/20981 / Nature / Enzyme dynamics and hydrogen tunnelling in a thermophilic alcohol dehydrogenase by Kohen (1999)
  33. 10.1016/S0006-3495(02)75203-X / Biophys. J. / Dynamics of proteins in crystals: comparison of experiment with simple models by Kundu (2002)
  34. 10.1016/0022-2836(85)90230-X / J. Mol. Biol. / Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme by Levitt (1985)
  35. 10.1126/science.282.5392.1324 / Science / Structure of human methionine aminopeptidase-2 complexed with fumagillin by Liu (1998)
  36. 10.1021/bi972059x / Biochemistry / Hydrophilic peptides derived from the transframe region of Gag-Pol inhibit the HIV-1 protease by Louis (1998)
  37. 10.1073/pnas.95.9.4831 / Proc. Natl. Acad. Sci. USA / Structure of the catalytic domain of avian sarcoma virus integrase with a bound HIV-1 integrase-targeted inhibitor by Lubkowski (1998)
  38. 10.1073/pnas.0405502101 / Proc. Natl. Acad. Sci. USA / Anticorrelated motions as a driving force in enzyme catalysis: the dehydrogenase reaction by Luo (2004)
  39. 10.1073/pnas.95.15.8502 / Proc. Natl. Acad. Sci. USA / The allosteric mechanism of the chaperonin GroEL: a dynamic analysis by Ma (1998)
  40. 10.1073/pnas.96.20.11000 / Proc. Natl. Acad. Sci. USA / Structure-assisted design of mechanism-based irreversible inhibitors of human rhinovirus 3C protease with potent antiviral activity against multiple rhinovirus serotypes by Matthews (1999)
  41. 10.1038/262325a0 / Nature / Hinge-bending mode in lysozyme by McCammon (1976)
  42. 10.1073/pnas.112222299 / Proc. Natl. Acad. Sci. USA / Domain movements in human fatty acid synthase by quantized elastic deformational model by Ming (2002)
  43. 10.1073/pnas.082148899 / Proc. Natl. Acad. Sci. USA / How to describe protein motion without amino acid sequence and atomic coordinates by Ming (2002)
  44. 10.1074/jbc.272.10.6539 / J. Biol. Chem. / Structure of recombinant human CPP32 in complex with the tetrapeptide acetyl-Asp-Val-Ala-Asp fluoromethyl ketone by Mittl (1997)
  45. 10.1074/jbc.274.10.6031 / J. Biol. Chem. / Structure of the complex between the antibiotic cerulenin and its target, beta-ketoacyl-acyl carrier protein synthase by Moche (1999)
  46. 10.1006/jmbi.1997.1364 / J. Mol. Biol. / The structures of human glutathione transferase P1–1 in complex with glutathione and various inhibitors at high resolution by Oakley (1997)
  47. 10.1016/S0014-5793(03)00866-4 / FEBS Lett. / Interdomain dynamics and ligand binding: molecular dynamics simulations of glutamine binding protein by Pang (2003)
  48. 10.1093/nar/gkh028 / Nucleic Acids Res. / The catalytic site atlas: a resource of catalytic sites and residues identified in enzymes using structural data by Porter (2004)
  49. 10.1021/bi971129x / Biochemistry / Catalytic domain structure of vampire bat plasminogen activator: a molecular paradigm for proteolysis without activation cleavage by Renatus (1997)
  50. 10.1016/S0301-4622(03)00096-6 / Biophys. Chem. / The ‘glass transition’ in protein dynamics: what it is, why it occurs, and how to exploit it by Ringe (2004)
  51. 10.1021/jm980403y / J. Med. Chem. / Structural basis for inhibition of the Hsp90 molecular chaperone by the antitumor antibiotics radicicol and geldanamycin by Roe (1999)
  52. 10.1021/bi9719915 / Biochemistry / Three-dimensional structure of Escherichia coli dihydrodipicolinate reductase in complex with NADH and the inhibitor 2,6-pyridinedicarboxylate by Scapin (1997)
  53. 10.1021/bi982946f / Biochemistry / Sugar ring distortion in the glycosyl-enzyme intermediate of a family G/11 xylanase by Sidhu (1999)
  54. 10.1016/S0969-2126(01)00687-6 / Structure / Inter-domain interactions in hinge-bending transitions by Sinha (2001)
  55. 10.1002/pro.5560070303 / Protein Sci. / Structures of murine carbonic anhydrase IV and human carbonic anhydrase II complexed with brinzolamide: molecular basis of isozyme-drug discrimination by Stams (1998)
  56. 10.1002/pro.5560060506 / Protein Sci. / Three-dimensional structures of glycolate oxidase with bound active-site inhibitors by Stenberg (1997)
  57. 10.1093/protein/14.1.1 / Protein Eng. / Conformational change of proteins arising from normal mode calculations by Tama (2001)
  58. 10.1002/1097-0134(20001001)41:1<1::AID-PROT10>3.0.CO;2-P / Proteins / Building-block approach for determining low-frequency normal modes of macromolecules by Tama (2000)
  59. 10.1002/prot.10183 / Proteins / Inhibitor binding alters the directions of domain motions in HIV-1 reverse transcriptase by Temiz (2002)
  60. 10.1103/PhysRevLett.77.1905 / Phys. Rev. Lett. / Large amplitude elastic motions in proteins from a single-parameter, atomic analysis by Tirion (1996)
  61. 10.1016/j.chembiol.2004.06.007 / Chem. Biol. / Protein motions promote catalysis by Tousignant (2004)
  62. 10.1074/jbc.M311191200 / J. Biol. Chem. / ACE2 X-ray structures reveal a large hinge-bending motion important for inhibitor binding and catalysis by Towler (2004)
  63. 10.1021/bi00137a012 / Biochemistry / Crystal structure of an actinidin-E-64 complex by Varughese (1992)
  64. 10.1073/pnas.95.7.3472 / Proc. Natl. Acad. Sci. USA / Structure and mechanism of a proline-specific aminopeptidase from Escherichia coli by Wilce (1998)
  65. 10.1074/jbc.273.10.5771 / J. Biol. Chem. / Engineering of cyclodextrin product specificity and pH optima of the thermostable cyclodextrin glycosyltransferase from Thermoanaerobacterium thermosulfurigenes EM1 by Wind (1998)
  66. 10.1038/nsmb821 / Nat. Struct. Mol. Biol. / Linkage between dynamics and catalysis in a thermophilic-mesophilic enzyme pair by Wolf-watz (2004)
  67. 10.1006/jmbi.2001.4536 / J. Mol. Biol. / The importance of hinge sequence for loop function and catalytic activity in the reaction catalyzed by triosephosphate isomerase by Xiang (2001)
  68. 10.1016/j.jmb.2003.08.027 / J. Mol. Biol. / Allosteric changes in protein structure computed by a simple mechanical model: hemoglobin T <-> R2 transition by Xu (2003)
  69. 10.1006/jmbi.1996.0865 / J. Mol. Biol. / Structure-based identification of a ricin inhibitor by Yan (1997)
  70. {'author': 'Yang', 'key': '10.1016/j.str.2005.03.015_bib70'} by Yang
  71. Yang, L.W., Liu, X., Jursa, C.J., Holliman, M., Rader, A.J., Karimi, H., and Bahar, I. (2005b). iGNM: a database of protein functional motions based on a Gaussian Network Model. Bioinformatics 266, in press. (10.1093/bioinformatics/bti469)
  72. 10.1002/prot.340170304 / Proteins / Crystal structure of the complex of human alpha-thrombin and nonhydrolyzable bifunctional inhibitors, hirutonin-2 and hirutonin-6 by Zdanov (1993)
  73. 10.1016/S0006-3495(03)75090-5 / Biophys. J. / Molecular dynamics simulations of peptides and proteins with amplified collective motions by Zhang (2003)
  74. 10.1016/S0041-0101(97)00169-4 / Toxicon / Structure of a snake venom phospholipase A2 modified by p-bromo-phenacyl-bromide by Zhao (1998)
Dates
Type When
Created 20 years, 2 months ago (June 9, 2005, 1:05 p.m.)
Deposited 1 year, 6 months ago (Feb. 10, 2024, 11:53 a.m.)
Indexed 2 days, 16 hours ago (Aug. 30, 2025, 12:29 p.m.)
Issued 20 years, 3 months ago (June 1, 2005)
Published 20 years, 3 months ago (June 1, 2005)
Published Print 20 years, 3 months ago (June 1, 2005)
Funders 2
  1. National Science Foundation 10.13039/100000001

    Region: Americas

    gov (National government)

    Labels4
    1. U.S. National Science Foundation
    2. NSF
    3. US NSF
    4. USA NSF
    Awards1
    1. 0225636
  2. National Institutes of Health 10.13039/100000002

    Region: Americas

    gov (National government)

    Labels3
    1. Institutos Nacionales de la Salud
    2. US National Institutes of Health
    3. NIH
    Awards1
    1. 1R01LM007994-01A1

@article{Yang_2005, title={Coupling between Catalytic Site and Collective Dynamics: A Requirement for Mechanochemical Activity of Enzymes}, volume={13}, ISSN={0969-2126}, url={http://dx.doi.org/10.1016/j.str.2005.03.015}, DOI={10.1016/j.str.2005.03.015}, number={6}, journal={Structure}, publisher={Elsevier BV}, author={Yang, Lee-Wei and Bahar, Ivet}, year={2005}, month=jun, pages={893–904} }