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Volumn 374, Issue 1, 2007, Pages 250-266

Allosteric Communication in Dihydrofolate Reductase: Signaling Network and Pathways for Closed to Occluded Transition and Back

Author keywords

allosteric transition; Brownian dynamics; DHFR; self organized polymer model; signaling network

Indexed keywords

DIHYDROFOLATE REDUCTASE;

EID: 35348942279     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2007.08.047     Document Type: Article
Times cited : (64)

References (57)
  • 2
    • 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. The dynamic energy landscape of dihydrofolate reductase catalysis. Science 313 (2006) 1638-1642
    • (2006) Science , vol.313 , pp. 1638-1642
    • Boehr, D.D.1    McElheny, D.2    Dyson, H.J.3    Wright, P.E.4
  • 3
    • 0000413202 scopus 로고
    • Mechanism of enzyme catalysis
    • Hammes G.G. Mechanism of enzyme catalysis. Nature 204 (1964) 342-343
    • (1964) Nature , vol.204 , pp. 342-343
    • Hammes, G.G.1
  • 5
    • 16344371778 scopus 로고    scopus 로고
    • RNA and protein folding: common themes and variations
    • Thirumalai D., and Hyeon C. RNA and protein folding: common themes and variations. Biochemistry 44 (2005) 4957-4970
    • (2005) Biochemistry , vol.44 , pp. 4957-4970
    • Thirumalai, D.1    Hyeon, C.2
  • 7
    • 0037188007 scopus 로고    scopus 로고
    • Nuclear quantum effects and enzyme dynamics in dihydrofolate reductase catalysis
    • Agarwal P.K., Billeter S.R., and Hammes-Schiffer S. Nuclear quantum effects and enzyme dynamics in dihydrofolate reductase catalysis. J. Phys. Chem. B 106 (2002) 3283-3293
    • (2002) J. Phys. Chem. B , vol.106 , pp. 3283-3293
    • Agarwal, P.K.1    Billeter, S.R.2    Hammes-Schiffer, S.3
  • 8
    • 4344669913 scopus 로고    scopus 로고
    • Analysis of electrostatics and correlated motions for hydride transfer in dihydrofolate reductase
    • Wong K., Watney J., and Hammes-Schiffer S. Analysis of electrostatics and correlated motions for hydride transfer in dihydrofolate reductase. J. Phys. Chem. B 108 (2004) 12231-12241
    • (2004) J. Phys. Chem. B , vol.108 , pp. 12231-12241
    • Wong, K.1    Watney, J.2    Hammes-Schiffer, S.3
  • 9
    • 18744380681 scopus 로고    scopus 로고
    • Impact of distal mutations on the network of coupled motions correlated to hydride transfer in dihydrofolate reductase
    • Wong K.F., Selzer T., Benkovic S.J., and Hammes-Schiffer S. Impact of distal mutations on the network of coupled motions correlated to hydride transfer in dihydrofolate reductase. Proc. Natl. Acad. Sci. USA 102 (2005) 6807-6812
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 6807-6812
    • Wong, K.F.1    Selzer, T.2    Benkovic, S.J.3    Hammes-Schiffer, S.4
  • 10
    • 0037159205 scopus 로고    scopus 로고
    • Coupling interactions of distal residues enhance dihydrofolate reductase catalysis: mutational effects on hydride transfer rates
    • Rajagopalan P.T.R., Lutz S., and Benkovic S.J. Coupling interactions of distal residues enhance dihydrofolate reductase catalysis: mutational effects on hydride transfer rates. Biochemistry 41 (2002) 12618-12628
    • (2002) Biochemistry , vol.41 , pp. 12618-12628
    • Rajagopalan, P.T.R.1    Lutz, S.2    Benkovic, S.J.3
  • 12
    • 0033955055 scopus 로고    scopus 로고
    • Protein dynamics in enzymatic catalysis: exploration of dihydrofolate reductase
    • Radkiewicz J.L., and Brooks III C.L. Protein dynamics in enzymatic catalysis: exploration of dihydrofolate reductase. J. Am. Chem. Soc. 122 (2000) 225-231
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 225-231
    • Radkiewicz, J.L.1    Brooks III, C.L.2
  • 13
    • 0038810233 scopus 로고    scopus 로고
    • Correlated motion and the effect of distal mutations in dihydrofolate reductase
    • Rod T.H., Radkiewicz J.L., and Brooks III C.L. Correlated motion and the effect of distal mutations in dihydrofolate reductase. Proc. Natl. Acad. Sci. USA 100 (2003) 6980-6985
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 6980-6985
    • Rod, T.H.1    Radkiewicz, J.L.2    Brooks III, C.L.3
  • 14
    • 0346936519 scopus 로고    scopus 로고
    • Barriers to hydride transfer in wild-type and mutant dihydrofolate reductase from E. coli
    • Thorpe I.F., and Brooks III C.L. Barriers to hydride transfer in wild-type and mutant dihydrofolate reductase from E. coli. J. Phys. Chem. B 107 (2003) 14042-14051
    • (2003) J. Phys. Chem. B , vol.107 , pp. 14042-14051
    • Thorpe, I.F.1    Brooks III, C.L.2
  • 15
    • 6344294816 scopus 로고    scopus 로고
    • The coupling of structural fluctuations to hydride transfer in dihydrofolate reductase
    • Thorpe I.F., and Brooks III C.L. The coupling of structural fluctuations to hydride transfer in dihydrofolate reductase. Proteins: Struct., Funct., Bioinf. 57 (2004) 444-457
    • (2004) Proteins: Struct., Funct., Bioinf. , vol.57 , pp. 444-457
    • Thorpe, I.F.1    Brooks III, C.L.2
  • 16
    • 0344391945 scopus 로고    scopus 로고
    • Reaction-path energetics and kinetics of the hydride transfer reaction catalyzed by dihydrofolate reductase
    • Garcia-Viloca M., Truhlar D., and Gao J. Reaction-path energetics and kinetics of the hydride transfer reaction catalyzed by dihydrofolate reductase. Biochemistry 42 (2003) 13558-13575
    • (2003) Biochemistry , vol.42 , pp. 13558-13575
    • Garcia-Viloca, M.1    Truhlar, D.2    Gao, J.3
  • 17
    • 33646935697 scopus 로고    scopus 로고
    • Dynamical contributions to enzyme catalysis: critical tests of a popular hypothesis
    • Olsson M., Parson W., and Warshel A. Dynamical contributions to enzyme catalysis: critical tests of a popular hypothesis. Chem. Rev. 106 (2006) 1737-1756
    • (2006) Chem. Rev. , vol.106 , pp. 1737-1756
    • Olsson, M.1    Parson, W.2    Warshel, A.3
  • 18
    • 0031443372 scopus 로고    scopus 로고
    • Evidence for a functional role of the dynamics of glycine-121 of Escherichia coli dihydrofolate reductase obtained from kinetic analysis of a site-directed mutant
    • Cameron C.E., and Benkovic S.J. Evidence for a functional role of the dynamics of glycine-121 of Escherichia coli dihydrofolate reductase obtained from kinetic analysis of a site-directed mutant. Biochemistry 36 (1997) 15792-15800
    • (1997) Biochemistry , vol.36 , pp. 15792-15800
    • Cameron, C.E.1    Benkovic, S.J.2
  • 19
    • 33750441144 scopus 로고    scopus 로고
    • Coordinated effects of distal mutations on environmentally coupled tunneling in dihydrofolate reductase
    • Wang L., Goodey N.M., Benkovic S.J., and Kohen A. Coordinated effects of distal mutations on environmentally coupled tunneling in dihydrofolate reductase. Proc. Natl. Acad. Sci. USA 103 (2006) 15753-15758
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 15753-15758
    • Wang, L.1    Goodey, N.M.2    Benkovic, S.J.3    Kohen, A.4
  • 20
    • 0033619679 scopus 로고    scopus 로고
    • Characterization of rates of ring-flipping in trimethoprim in its ternary complexes with Lactobacillus casei dihydrofolate reductase and coenzyme analogues
    • Polshakov V.I., Birdsall B., and Feeney J. Characterization of rates of ring-flipping in trimethoprim in its ternary complexes with Lactobacillus casei dihydrofolate reductase and coenzyme analogues. Biochemistry 38 (1999) 15962-15969
    • (1999) Biochemistry , vol.38 , pp. 15962-15969
    • Polshakov, V.I.1    Birdsall, B.2    Feeney, J.3
  • 21
    • 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. Backbone dynamics in dihydrofolate reductase complexes: role of loop flexibility in the catalytic mechanism. Biochemistry 40 (2001) 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
  • 23
    • 0040193886 scopus 로고
    • Simulations of quantum mechanical corrections for rate constants of hydride-transfer reactions in enzymes and solutions
    • Hwang J.K., Chu Z.T., Yadav A., and Warshel A. Simulations of quantum mechanical corrections for rate constants of hydride-transfer reactions in enzymes and solutions. J. Phys. Chem. 95 (1991) 8445-8448
    • (1991) J. Phys. Chem. , vol.95 , pp. 8445-8448
    • Hwang, J.K.1    Chu, Z.T.2    Yadav, A.3    Warshel, A.4
  • 24
    • 0035707451 scopus 로고    scopus 로고
    • Dynamics of biochemical and biophysical reactions: insight from computer simulations
    • Warshel A., and Parson W. Dynamics of biochemical and biophysical reactions: insight from computer simulations. Q. Rev. Biophys. 34 (2001) 563-679
    • (2001) Q. Rev. Biophys. , vol.34 , pp. 563-679
    • Warshel, A.1    Parson, W.2
  • 25
    • 0035940264 scopus 로고    scopus 로고
    • Energetics and dynamics of enzymatic reactions
    • Villa J., and Warshel A. Energetics and dynamics of enzymatic reactions. J. Phys. Chem. B 105 (2001) 7887-7907
    • (2001) J. Phys. Chem. B , vol.105 , pp. 7887-7907
    • Villa, J.1    Warshel, A.2
  • 26
    • 34249104188 scopus 로고    scopus 로고
    • The catalytic effect of dihydrofolate reductase and its mutants is determined by reorganization energies
    • Liu H., and Warshel A. The catalytic effect of dihydrofolate reductase and its mutants is determined by reorganization energies. Biochemistry 46 (2007) 6011-6025
    • (2007) Biochemistry , vol.46 , pp. 6011-6025
    • Liu, H.1    Warshel, A.2
  • 27
    • 0031808658 scopus 로고    scopus 로고
    • Stretching exercises-flexibility in dihydrofolate reductase catalysis
    • Miller G.P., and Benkovic S.J. Stretching exercises-flexibility in dihydrofolate reductase catalysis. Chem. Biol. 5 (1998) R105-R113
    • (1998) Chem. Biol. , vol.5
    • Miller, G.P.1    Benkovic, S.J.2
  • 29
    • 0017785773 scopus 로고
    • Dihydrofolate reductase: x-ray structure of the binary complex with methotrexate
    • Matthews D., Alden R., Bolin J., Freer S., Hamlin R., Xuong N., et al. Dihydrofolate reductase: x-ray structure of the binary complex with methotrexate. Science 197 (1977) 452-455
    • (1977) Science , vol.197 , pp. 452-455
    • Matthews, D.1    Alden, R.2    Bolin, J.3    Freer, S.4    Hamlin, R.5    Xuong, N.6
  • 30
    • 0031015737 scopus 로고    scopus 로고
    • Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: crystallographic evidence
    • Sawaya M., and Kraut J. Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: crystallographic evidence. Biochemistry 36 (1997) 586-603
    • (1997) Biochemistry , vol.36 , pp. 586-603
    • Sawaya, M.1    Kraut, J.2
  • 31
    • 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. Conformational changes in the active site loops of dihydrofolate reductase during the catalytic cycle. Biochemistry 43 (2004) 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
  • 32
    • 0033536602 scopus 로고    scopus 로고
    • Evolutionarily conserved pathways of energetic connectivity in protein families
    • Lockless S., and Ranganathan R. Evolutionarily conserved pathways of energetic connectivity in protein families. Science 286 (1999) 295-299
    • (1999) Science , vol.286 , pp. 295-299
    • Lockless, S.1    Ranganathan, R.2
  • 33
    • 31344432159 scopus 로고    scopus 로고
    • Determination of network of residues that regulate allostery in protein families using sequence analysis
    • Dima R.I., and Thirumalai D. Determination of network of residues that regulate allostery in protein families using sequence analysis. Protein Sci. 15 (2006) 258-268
    • (2006) Protein Sci. , vol.15 , pp. 258-268
    • Dima, R.I.1    Thirumalai, D.2
  • 34
    • 0037219686 scopus 로고    scopus 로고
    • Evolutionarily conserved networks of residues mediate allosteric communication in proteins
    • Suel G., Lockless S., Wall M., and Ranganathan R. Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nat. Struct. Biol. 10 (2003) 59-68
    • (2003) Nat. Struct. Biol. , vol.10 , pp. 59-68
    • Suel, G.1    Lockless, S.2    Wall, M.3    Ranganathan, R.4
  • 36
    • 0347719392 scopus 로고    scopus 로고
    • Local complexity of amino acid interactions in a protein core
    • Jain R., and Ranganathan R. Local complexity of amino acid interactions in a protein core. Proc. Natl. Acad. Sci. USA 101 (2002) 111-116
    • (2002) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 111-116
    • Jain, R.1    Ranganathan, R.2
  • 37
    • 1642304065 scopus 로고    scopus 로고
    • Structural determinants of allosteric ligand activation in rxr heterodimers
    • Shulman A., Larson C., Mangelsdorf D., and Ranganathan R. Structural determinants of allosteric ligand activation in rxr heterodimers. Cell 116 (2004) 417-429
    • (2004) Cell , vol.116 , pp. 417-429
    • Shulman, A.1    Larson, C.2    Mangelsdorf, D.3    Ranganathan, R.4
  • 38
    • 33846820159 scopus 로고    scopus 로고
    • Mechanical unfolding of RNA: from hairpins to structures with internal multiloops
    • Hyeon C., and Thirumalai D. Mechanical unfolding of RNA: from hairpins to structures with internal multiloops. Biophys. J. 192 (2007) 731-743
    • (2007) Biophys. J. , vol.192 , pp. 731-743
    • Hyeon, C.1    Thirumalai, D.2
  • 39
    • 33751086423 scopus 로고    scopus 로고
    • Visualization of transient encounter complexes in protein-protein association
    • Tang C., Iwahara J., and Clore G. Visualization of transient encounter complexes in protein-protein association. Nature 444 (2006) 383-386
    • (2006) Nature , vol.444 , pp. 383-386
    • Tang, C.1    Iwahara, J.2    Clore, G.3
  • 41
    • 0027968068 scopus 로고
    • Clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson J., Higgins D., and Gibson T. Clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 (1994) 4673-4680
    • (1994) Nucleic Acids Res. , vol.22 , pp. 4673-4680
    • Thompson, J.1    Higgins, D.2    Gibson, T.3
  • 42
    • 0000521616 scopus 로고    scopus 로고
    • Superparamagnetic clustering of data
    • Blatt M., Wiseman S., and Domany E. Superparamagnetic clustering of data. Phys. Rev. Lett. 76 (1996) 3251-3254
    • (1996) Phys. Rev. Lett. , vol.76 , pp. 3251-3254
    • Blatt, M.1    Wiseman, S.2    Domany, E.3
  • 43
    • 0000269043 scopus 로고    scopus 로고
    • Superparamagnetic clustering of data-the definitive solution of an ill-posed problem
    • Domany E. Superparamagnetic clustering of data-the definitive solution of an ill-posed problem. Physica A (Amsterdam) 263 (1999) 158-169
    • (1999) Physica A (Amsterdam) , vol.263 , pp. 158-169
    • Domany, E.1
  • 44
    • 0037438479 scopus 로고    scopus 로고
    • Annealing. function of GroEL: structural and bioinformatic analysis
    • Stan G., Thirumalai D., Lorimer G.H., and Brooks B.R. Annealing. function of GroEL: structural and bioinformatic analysis. Biophys. Chem. 100 (2003) 453-467
    • (2003) Biophys. Chem. , vol.100 , pp. 453-467
    • Stan, G.1    Thirumalai, D.2    Lorimer, G.H.3    Brooks, B.R.4
  • 45
    • 0022546047 scopus 로고
    • Functional role of aspartic acid-27 in dihydrofolate reductase revealed by mutagenesis
    • Howell E., Villafranca J., Warren M., Oatley S., and Kraut J. Functional role of aspartic acid-27 in dihydrofolate reductase revealed by mutagenesis. Science 231 (1986) 1123-1128
    • (1986) Science , vol.231 , pp. 1123-1128
    • Howell, E.1    Villafranca, J.2    Warren, M.3    Oatley, S.4    Kraut, J.5
  • 46
    • 33748354485 scopus 로고    scopus 로고
    • The role of enzyme dynamics and tunnelling in catalysing hydride transfer: studies of distal mutants of dihydrofolate reductase
    • Wang L., Goodey N.M., Benkovic S.J., and Kohen A. The role of enzyme dynamics and tunnelling in catalysing hydride transfer: studies of distal mutants of dihydrofolate reductase. Philos. Trans. R. Soc. London, Ser. B 361 (2006) 1307-1315
    • (2006) Philos. Trans. R. Soc. London, Ser. B , vol.361 , pp. 1307-1315
    • Wang, L.1    Goodey, N.M.2    Benkovic, S.J.3    Kohen, A.4
  • 47
    • 33644784083 scopus 로고    scopus 로고
    • Freezing a single distal motion in dihydrofolate reductase
    • Sergi A., Watney J., Wong K., and Hammes-Schiffer S. Freezing a single distal motion in dihydrofolate reductase. J. Phys. Chem. B 110 (2006) 2435-2441
    • (2006) J. Phys. Chem. B , vol.110 , pp. 2435-2441
    • Sergi, A.1    Watney, J.2    Wong, K.3    Hammes-Schiffer, S.4
  • 48
    • 0033056708 scopus 로고    scopus 로고
    • Folding funnels, binding funnels, and protein function
    • Tsai C., Kumar S., Ma B., and Nussinov R. Folding funnels, binding funnels, and protein function. Protein Sci. 8 (1999) 1181-1190
    • (1999) Protein Sci. , vol.8 , pp. 1181-1190
    • Tsai, C.1    Kumar, S.2    Ma, B.3    Nussinov, R.4
  • 49
    • 0001858251 scopus 로고
    • Application of a theory of enzyme specificity to protein synthesis
    • Koshland D.E. Application of a theory of enzyme specificity to protein synthesis. Proc. Natl. Acad. Sci. USA 44 (1958) 98-104
    • (1958) Proc. Natl. Acad. Sci. USA , vol.44 , pp. 98-104
    • Koshland, D.E.1
  • 50
    • 20344370764 scopus 로고    scopus 로고
    • Allosteric mechanism of signal transduction
    • Changeux J., and Edlestein S. Allosteric mechanism of signal transduction. Science 308 (2005) 1424-1428
    • (2005) Science , vol.308 , pp. 1424-1428
    • Changeux, J.1    Edlestein, S.2
  • 51
    • 34547456661 scopus 로고    scopus 로고
    • Origin of the temperature dependence of isotope effects in enzymatic reactions: the case of dihydrofolate reductase
    • Liu H., and Warshel A. Origin of the temperature dependence of isotope effects in enzymatic reactions: the case of dihydrofolate reductase. J. Phys. Chem. B 111 (2007) 7852-7861
    • (2007) J. Phys. Chem. B , vol.111 , pp. 7852-7861
    • Liu, H.1    Warshel, A.2
  • 52
    • 33846193288 scopus 로고    scopus 로고
    • Pathways and kinetic barriers in mechanical unfolding and refolding of RNA and proteins
    • Hyeon C., Dima R.I., and Thirumalai D. Pathways and kinetic barriers in mechanical unfolding and refolding of RNA and proteins. Structure 14 (2006) 1633-1645
    • (2006) Structure , vol.14 , pp. 1633-1645
    • Hyeon, C.1    Dima, R.I.2    Thirumalai, D.3
  • 54
    • 0034710876 scopus 로고    scopus 로고
    • Coupled two-way clustering analysis of gene microarray data
    • Getz G., Levine E., and Domany E. Coupled two-way clustering analysis of gene microarray data. Proc. Natl. Acad. Sci. USA 97 (2000) 12079-12084
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 12079-12084
    • Getz, G.1    Levine, E.2    Domany, E.3
  • 55
    • 33847770916 scopus 로고    scopus 로고
    • Internal strain regulates the nucleotide binding site of the kinesin leading head
    • Hyeon C., and Onuchic J.N. Internal strain regulates the nucleotide binding site of the kinesin leading head. Proc. Natl. Acad. Sci. USA 104 (2007) 2175
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 2175
    • Hyeon, C.1    Onuchic, J.N.2
  • 57
    • 0030624384 scopus 로고    scopus 로고
    • Protein folding kinetics: timescales, pathways and energy landscapes in terms of sequence-dependent properties
    • Veitshans T., Klimov D., and Thirumalai D. Protein folding kinetics: timescales, pathways and energy landscapes in terms of sequence-dependent properties. Fold Des. 2 (1997) 1-22
    • (1997) Fold Des. , vol.2 , pp. 1-22
    • Veitshans, T.1    Klimov, D.2    Thirumalai, D.3


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