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Volumn 53, Issue 7, 2014, Pages 1134-1145

Side chain conformational averaging in human dihydrofolate reductase

Author keywords

[No Author keywords available]

Indexed keywords

CATALYTIC INTERMEDIATES; COMPREHENSIVE ANALYSIS; CONFORMATIONAL CHANGE; DIHYDROFOLATE REDUCTASE; MAGNETIC RESONANCE RELAXATION; NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATES; SEQUENCE IDENTITY; THREE-DIMENSIONAL STRUCTURE;

EID: 84896832020     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi4015314     Document Type: Article
Times cited : (9)

References (48)
  • 1
    • 0028049327 scopus 로고
    • Dynamics of a flexible loop in dihydrofolate reductase from Escherichia coli and its implication for catalysis
    • Falzone, C. J., Wright, P. E., and Benkovic, S. J. (1994) Dynamics of a flexible loop in dihydrofolate reductase from Escherichia coli and its implication for catalysis Biochemistry 33, 439-442
    • (1994) Biochemistry , vol.33 , pp. 439-442
    • Falzone, C.J.1    Wright, P.E.2    Benkovic, S.J.3
  • 2
    • 0029102089 scopus 로고
    • Dynamics of the dihydrofolate reductase folate complex: Catalytic sites and regions known to undergo conformational change exhibit diverse dynamical features
    • Epstein, D. M., Benkovic, S. J., and Wright, P. E. (1995) Dynamics of the dihydrofolate reductase folate complex: Catalytic sites and regions known to undergo conformational change exhibit diverse dynamical features Biochemistry 34, 11037-11048
    • (1995) Biochemistry , vol.34 , pp. 11037-11048
    • Epstein, D.M.1    Benkovic, S.J.2    Wright, P.E.3
  • 3
    • 0035928796 scopus 로고    scopus 로고
    • Backbone dynamics in dihydrofolate reductase complexes: Role of loop flexibility in the catalytic mechanism
    • Osborne, M. J., Schnell, J., Benkovic, S. J., Dyson, H. J., and Wright, P. E. (2001) Backbone dynamics in dihydrofolate reductase complexes: Role of loop flexibility in the catalytic mechanism Biochemistry 40, 9846-9859
    • (2001) Biochemistry , vol.40 , pp. 9846-9859
    • Osborne, M.J.1    Schnell, J.2    Benkovic, S.J.3    Dyson, H.J.4    Wright, P.E.5
  • 4
    • 0345832242 scopus 로고    scopus 로고
    • Effect of cofactor binding and loop conformation on side chain methyl dynamics in dihydrofolate reductase
    • Schnell, J. R., Dyson, H. J., and Wright, P. E. (2004) Effect of cofactor binding and loop conformation on side chain methyl dynamics in dihydrofolate reductase Biochemistry 43, 374-383
    • (2004) Biochemistry , vol.43 , pp. 374-383
    • Schnell, J.R.1    Dyson, H.J.2    Wright, P.E.3
  • 5
  • 7
    • 11144328151 scopus 로고    scopus 로고
    • Conformational changes in the active site loops of dihydrofolate reductase during the catalytic cycle
    • Venkitakrishnan, R. P., Zaborowski, E., McElheny, D., Benkovic, S. J., Dyson, H. J., and Wright, P. E. (2004) Conformational changes in the active site loops of dihydrofolate reductase during the catalytic cycle Biochemistry 43, 16046-16055
    • (2004) Biochemistry , vol.43 , pp. 16046-16055
    • Venkitakrishnan, R.P.1    Zaborowski, E.2    McElheny, D.3    Benkovic, S.J.4    Dyson, H.J.5    Wright, P.E.6
  • 8
    • 33748781457 scopus 로고    scopus 로고
    • The dynamic energy landscape of dihydrofolate reductase catalysis
    • Boehr, D. D., McElheny, D., Dyson, H. J., and Wright, P. E. (2006) The dynamic energy landscape of dihydrofolate reductase catalysis Science 313, 1638-1642
    • (2006) Science , vol.313 , pp. 1638-1642
    • Boehr, D.D.1    McElheny, D.2    Dyson, H.J.3    Wright, P.E.4
  • 9
    • 33748619206 scopus 로고    scopus 로고
    • An NMR perspective on enzyme dynamics
    • Boehr, D. D., Dyson, H. J., and Wright, P. E. (2006) An NMR perspective on enzyme dynamics Chem. Rev. 106, 3055-3079
    • (2006) Chem. Rev. , vol.106 , pp. 3055-3079
    • Boehr, D.D.1    Dyson, H.J.2    Wright, P.E.3
  • 10
    • 50849111095 scopus 로고    scopus 로고
    • Conformational relaxation following hydride transfer plays a limiting role in dihydrofolate reductase catalysis
    • Boehr, D. D., Dyson, H. J., and Wright, P. E. (2008) Conformational relaxation following hydride transfer plays a limiting role in dihydrofolate reductase catalysis Biochemistry 47, 9227-9233
    • (2008) Biochemistry , vol.47 , pp. 9227-9233
    • Boehr, D.D.1    Dyson, H.J.2    Wright, P.E.3
  • 11
    • 76549109225 scopus 로고    scopus 로고
    • Millisecond timescale fluctuations in dihydrofolate reductase are exquisitely sensitive to the bound ligands
    • Boehr, D. D., McElheny, D., Dyson, H. J., and Wright, P. E. (2010) Millisecond timescale fluctuations in dihydrofolate reductase are exquisitely sensitive to the bound ligands Proc. Natl. Acad. Sci. U.S.A. 107, 1373-1378
    • (2010) Proc. Natl. Acad. Sci. U.S.A. , vol.107 , pp. 1373-1378
    • Boehr, D.D.1    McElheny, D.2    Dyson, H.J.3    Wright, P.E.4
  • 12
    • 84878224305 scopus 로고    scopus 로고
    • Side-chain conformational heterogeneity of intermediates in the Escherichia coli dihydrofolate reductase catalytic cycle
    • Tuttle, L. M., Dyson, H. J., and Wright, P. E. (2013) Side-chain conformational heterogeneity of intermediates in the Escherichia coli dihydrofolate reductase catalytic cycle Biochemistry 52, 3464-3477
    • (2013) Biochemistry , vol.52 , pp. 3464-3477
    • Tuttle, L.M.1    Dyson, H.J.2    Wright, P.E.3
  • 14
    • 0025325955 scopus 로고
    • Unusual transient- and steady-state kinetic behavior is predicted by the kinetic scheme operational for recombinant human dihydrofolate reductase
    • Appleman, J. R., Beard, W. A., Delcamp, T. J., Prendergast, N. J., Freisheim, J. H., and Blakley, R. L. (1990) Unusual transient- and steady-state kinetic behavior is predicted by the kinetic scheme operational for recombinant human dihydrofolate reductase J. Biol. Chem. 265, 2740-2748
    • (1990) J. Biol. Chem. , vol.265 , pp. 2740-2748
    • Appleman, J.R.1    Beard, W.A.2    Delcamp, T.J.3    Prendergast, N.J.4    Freisheim, J.H.5    Blakley, R.L.6
  • 16
    • 0031015737 scopus 로고    scopus 로고
    • Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: Crystallographic evidence
    • Sawaya, M. R. and Kraut, J. (1997) Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: Crystallographic evidence Biochemistry 36, 586-603
    • (1997) Biochemistry , vol.36 , pp. 586-603
    • Sawaya, M.R.1    Kraut, J.2
  • 17
    • 80855143648 scopus 로고    scopus 로고
    • Identification of endogenous ligands bound to bacterially expressed human and E coli dihydrofolate reductase by 2D NMR
    • Bhabha, G., Tuttle, L., Martinez-Yamout, M. A., and Wright, P. E. (2011) Identification of endogenous ligands bound to bacterially expressed human and E. coli dihydrofolate reductase by 2D NMR FEBS Lett. 585, 3528-3532
    • (2011) FEBS Lett. , vol.585 , pp. 3528-3532
    • Bhabha, G.1    Tuttle, L.2    Martinez-Yamout, M.A.3    Wright, P.E.4
  • 22
    • 77949411905 scopus 로고    scopus 로고
    • Comprehensive and cost-effective NMR spectroscopy of methyl groups in large proteins
    • Otten, R., Chu, B., Krewulak, K. D., Vogel, H. J., and Mulder, F. A. A. (2010) Comprehensive and cost-effective NMR spectroscopy of methyl groups in large proteins J. Am. Chem. Soc. 132, 2952-2960
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 2952-2960
    • Otten, R.1    Chu, B.2    Krewulak, K.D.3    Vogel, H.J.4    Mulder, F.A.A.5
  • 24
    • 0034809982 scopus 로고    scopus 로고
    • Probing slow time scale dynamics at methyl-containing side chains in proteins by relaxation dispersion NMR measurements: Application to methionine residues in a cavity mutant of T4 lysozyme
    • Skrynnikov, N. R., Mulder, F. A. A., Hon, B., Dahlquist, F. W., and Kay, L. E. (2001) Probing slow time scale dynamics at methyl-containing side chains in proteins by relaxation dispersion NMR measurements: Application to methionine residues in a cavity mutant of T4 lysozyme J. Am. Chem. Soc. 123, 4556-4566
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 4556-4566
    • Skrynnikov, N.R.1    Mulder, F.A.A.2    Hon, B.3    Dahlquist, F.W.4    Kay, L.E.5
  • 26
    • 84880137185 scopus 로고    scopus 로고
    • Fast and accurate fitting of relaxation dispersion data using the flexible software package GLOVE
    • Sugase, K., Konuma, T., Lansing, J. C., and Wright, P. E. (2013) Fast and accurate fitting of relaxation dispersion data using the flexible software package GLOVE J. Biomol. NMR 56, 275-283
    • (2013) J. Biomol. NMR , vol.56 , pp. 275-283
    • Sugase, K.1    Konuma, T.2    Lansing, J.C.3    Wright, P.E.4
  • 27
    • 0027636003 scopus 로고
    • CC couplings between backbone carbonyl and methyl carbons in isotopically enriched proteins
    • CC couplings between backbone carbonyl and methyl carbons in isotopically enriched proteins J. Biomol. NMR 3, 487-493
    • (1993) J. Biomol. NMR , vol.3 , pp. 487-493
    • Grzesiek, S.1    Vuister, G.W.2    Bax, A.3
  • 31
    • 0034715485 scopus 로고    scopus 로고
    • Static and dynamic effects on vicinal scalar J couplings in proteins and peptides: A MD/DFT analysis
    • Case, D. A., Scheurer, C., and Brüschweiler, R. (2000) Static and dynamic effects on vicinal scalar J couplings in proteins and peptides: A MD/DFT analysis J. Am. Chem. Soc. 122, 10390-10397
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 10390-10397
    • Case, D.A.1    Scheurer, C.2    Brüschweiler, R.3
  • 32
    • 50249158519 scopus 로고    scopus 로고
    • 13C shifts on dihedral angle: Application to conformational analysis
    • 13C shifts on dihedral angle: Application to conformational analysis J. Am. Chem. Soc. 130, 11097-11105
    • (2008) J. Am. Chem. Soc. , vol.130 , pp. 11097-11105
    • London, R.E.1    Wingad, B.D.2    Mueller, G.A.3
  • 33
    • 70349558318 scopus 로고    scopus 로고
    • 13C NMR chemical shifts
    • 13C NMR chemical shifts ChemBioChem 10, 1477-1479
    • (2009) ChemBioChem , vol.10 , pp. 1477-1479
    • Mulder, F.A.A.1
  • 34
    • 24044459801 scopus 로고
    • Carbon-13 magnetic resonance. II. Chemical shift data for the alkanes
    • Grant, D. M. and Paul, E. G. (1964) Carbon-13 magnetic resonance. II. Chemical shift data for the alkanes J. Am. Chem. Soc. 86, 2984-2990
    • (1964) J. Am. Chem. Soc. , vol.86 , pp. 2984-2990
    • Grant, D.M.1    Paul, E.G.2
  • 35
    • 0001687029 scopus 로고
    • 13C-NMR spectra of 3,5,7,9,11,13,15-heptamethylheptadecane stereoisomers and their implications for the conformational characteristics of polypropylene
    • 13C-NMR spectra of 3,5,7,9,11,13,15-heptamethylheptadecane stereoisomers and their implications for the conformational characteristics of polypropylene Macromolecules 11, 565-567
    • (1978) Macromolecules , vol.11 , pp. 565-567
    • Tonelli, A.E.1
  • 36
    • 79958079887 scopus 로고    scopus 로고
    • A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions
    • Shapovalov, M. V. and Dunbrack, R. L., Jr. (2011) A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions Structure 19, 844-858
    • (2011) Structure , vol.19 , pp. 844-858
    • Shapovalov, M.V.1    Dunbrack Jr., R.L.2
  • 37
    • 0035544152 scopus 로고    scopus 로고
    • 13C′ chemical shifts in proteins using a density functional database
    • 13C′ chemical shifts in proteins using a density functional database J. Biomol. NMR 21, 321-333
    • (2001) J. Biomol. NMR , vol.21 , pp. 321-333
    • Xu, X.P.1    Case, D.A.2
  • 39
    • 0023668190 scopus 로고
    • Construction and evaluation of the kinetic scheme associated with dihydrofolate reductase from Escherichia coli
    • Fierke, C. A., Johnson, K. A., and Benkovic, S. J. (1987) Construction and evaluation of the kinetic scheme associated with dihydrofolate reductase from Escherichia coli Biochemistry 26, 4085-4092
    • (1987) Biochemistry , vol.26 , pp. 4085-4092
    • Fierke, C.A.1    Johnson, K.A.2    Benkovic, S.J.3
  • 40
    • 77953101437 scopus 로고    scopus 로고
    • Determination of isoleucine side-chain conformations in ground and excited states of proteins from chemical shifts
    • Hansen, D. F., Neudecker, P., and Kay, L. E. (2010) Determination of isoleucine side-chain conformations in ground and excited states of proteins from chemical shifts J. Am. Chem. Soc. 132, 7589-7591
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 7589-7591
    • Hansen, D.F.1    Neudecker, P.2    Kay, L.E.3
  • 41
    • 74849091641 scopus 로고    scopus 로고
    • Determination of Leu side-chain conformations in excited protein states by NMR relaxation dispersion
    • Hansen, D. F., Neudecker, P., Vallurupalli, P., Mulder, F. A. A., and Kay, L. E. (2010) Determination of Leu side-chain conformations in excited protein states by NMR relaxation dispersion J. Am. Chem. Soc. 132, 42-43
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 42-43
    • Hansen, D.F.1    Neudecker, P.2    Vallurupalli, P.3    Mulder, F.A.A.4    Kay, L.E.5
  • 42
    • 79957767719 scopus 로고    scopus 로고
    • 13C chemical shifts: Application to the 360 kDa half-proteasome
    • 13C chemical shifts: Application to the 360 kDa half-proteasome J. Am. Chem. Soc. 133, 8272-8281
    • (2011) J. Am. Chem. Soc. , vol.133 , pp. 8272-8281
    • Hansen, D.F.1    Kay, L.E.2
  • 44
    • 0037402111 scopus 로고    scopus 로고
    • Functional role for Tyr 31 in the catalytic cycle of chicken dihydrofolate reductase
    • Shrimpton, P., Mullaney, A., and Allemann, R. K. (2003) Functional role for Tyr 31 in the catalytic cycle of chicken dihydrofolate reductase Proteins 51, 216-223
    • (2003) Proteins , vol.51 , pp. 216-223
    • Shrimpton, P.1    Mullaney, A.2    Allemann, R.K.3
  • 46
    • 0028037407 scopus 로고
    • Nonadditivity of mutational effects at the folate binding site of Escherichia coli dihydrofolate reductase
    • Huang, Z., Wagner, C. R., and Benkovic, S. J. (1994) Nonadditivity of mutational effects at the folate binding site of Escherichia coli dihydrofolate reductase Biochemistry 33, 11576-11585
    • (1994) Biochemistry , vol.33 , pp. 11576-11585
    • Huang, Z.1    Wagner, C.R.2    Benkovic, S.J.3
  • 47
    • 0025037428 scopus 로고
    • Crystal structures of recombinant human dihydrofolate reductase complexed with folate and 5-deazafolate
    • Davies, J. F., II, Delcamp, T. J., Prendergast, N. J., Ashford, V. A., Freisheim, J. H., and Kraut, J. (1990) Crystal structures of recombinant human dihydrofolate reductase complexed with folate and 5-deazafolate Biochemistry 29, 9467-9479
    • (1990) Biochemistry , vol.29 , pp. 9467-9479
    • Davies, J.F.I.I.1    Delcamp, T.J.2    Prendergast, N.J.3    Ashford, V.A.4    Freisheim, J.H.5    Kraut, J.6


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