메뉴 건너뛰기




Volumn 434, Issue 3, 2011, Pages 427-434

Crystal structure of unliganded TRAP: Implications for dynamic allostery

Author keywords

Conformation; Dynamic allostery; Protein dynamics

Indexed keywords

BACTERIAL PROTEIN; MESSENGER RNA; REGULATOR PROTEIN; TRP RNA BINDING ATTENUATION PROTEIN; TRYPTOPHAN; UNCLASSIFIED DRUG;

EID: 79952168694     PISSN: 02646021     EISSN: 14708728     Source Type: Journal    
DOI: 10.1042/BJ20101813     Document Type: Article
Times cited : (14)

References (43)
  • 1
    • 78651189765 scopus 로고
    • On the nature of allosteric transitions: A plausible model
    • Monod, J., Wyman, J. and Changeux, J.-P. (1965) On the nature of allosteric transitions: a plausible model. J. Mol. Biol. 12, 88-118
    • (1965) J. Mol. Biol. , vol.12 , pp. 88-118
    • Monod, J.1    Wyman, J.2    Changeux, J.-P.3
  • 2
    • 0013863816 scopus 로고
    • Comparison of experimental binding data and theoretical models in proteins containing subunits
    • Koshland, D. E., Némethy, G. and Filmer, D. (1966) Comparison of experimental binding data and theoretical models in proteins containing subunits. Biochemistry 5, 365-385
    • (1966) Biochemistry , vol.5 , pp. 365-385
    • Koshland, D.E.1    Némethy, G.2    Filmer, D.3
  • 3
    • 77952391486 scopus 로고
    • Fluctuation in quarternary structure of proteins and cooperative ligand binding I: Generalizations of Monod-Wyman-Changeux model of allosteric enzymes
    • Kotani, M. (1968) Fluctuation in quarternary structure of proteins and cooperative ligand binding I: generalizations of Monod-Wyman-Changeux model of allosteric enzymes. Prog. Theor. Phys. Suppl. E68, 233-241
    • (1968) Prog. Theor. Phys. Suppl. , vol.E68 , pp. 233-241
    • Kotani, M.1
  • 4
    • 0021658956 scopus 로고
    • Allostery without conformational change. A plausible model
    • Cooper, A. and Dryden, D. T. (1984) Allostery without conformational change. A plausible model. Eur. Biophys. J. 11, 103-109
    • (1984) Eur. Biophys. J. , vol.11 , pp. 103-109
    • Cooper, A.1    Dryden, D.T.2
  • 5
    • 48249141040 scopus 로고    scopus 로고
    • Allostery and cooperativity revisited
    • Cui, Q. and Karplus, M. (2008) Allostery and cooperativity revisited. Protein Sci. 17, 1295-1307
    • (2008) Protein Sci. , vol.17 , pp. 1295-1307
    • Cui, Q.1    Karplus, M.2
  • 6
    • 33748442882 scopus 로고    scopus 로고
    • Coupling of global and local vibrational modes in dynamic allostery of proteins
    • Hawkins, R. J. and McLeish, T. C. (2006) Coupling of global and local vibrational modes in dynamic allostery of proteins. Biophys. J. 91, 2055-2062
    • (2006) Biophys. J. , vol.91 , pp. 2055-2062
    • Hawkins, R.J.1    McLeish, T.C.2
  • 7
    • 27744469829 scopus 로고    scopus 로고
    • Scoring functions: The first 100 years
    • Tame, J. R. H. (2005) Scoring functions: the first 100 years. J. Comput. Aided Mol. Des. 19, 445-451
    • (2005) J. Comput. Aided Mol. Des. , vol.19 , pp. 445-451
    • Tame, J.R.H.1
  • 8
    • 41149104308 scopus 로고    scopus 로고
    • Allostery: Absence of a change in shape does not imply that allostery is not at play
    • Tsai, C. J., del Sol, A. and Nussinov, R. (2008) Allostery: absence of a change in shape does not imply that allostery is not at play. J. Mol. Biol. 378, 1-11
    • (2008) J. Mol. Biol. , vol.378 , pp. 1-11
    • Tsai, C.J.1    Del Sol, A.2    Nussinov, R.3
  • 9
    • 34447503697 scopus 로고    scopus 로고
    • Conformational entropy in molecular recognition by proteins
    • DOI 10.1038/nature05959, PII NATURE05959
    • Frederick, K. K., Marlow, M. S., Valentine, K. G. and Wand, A. J. (2007) Conformational entropy in molecular recognition by proteins. Nature 448, 325-329 (Pubitemid 47080342)
    • (2007) Nature , vol.448 , Issue.7151 , pp. 325-329
    • Frederick, K.K.1    Marlow, M.S.2    Valentine, K.G.3    Wand, A.J.4
  • 10
    • 33645834303 scopus 로고    scopus 로고
    • New tools provide new insights in NMR studies of protein dynamics
    • Mittermaier, A. and Kay, L. E. (2006) New tools provide new insights in NMR studies of protein dynamics. Science 312, 224-228
    • (2006) Science , vol.312 , pp. 224-228
    • Mittermaier, A.1    Kay, L.E.2
  • 12
    • 33646364809 scopus 로고    scopus 로고
    • Rounding up: Engineering 12-membered rings from the cyclic 11-mer TRAP
    • Heddle, J. G., Yokoyama, T., Yamashita, I., Park, S.-Y. and Tame, J. R. H. (2006) Rounding up: engineering 12-membered rings from the cyclic 11-mer TRAP. Structure 14, 925-933
    • (2006) Structure , vol.14 , pp. 925-933
    • Heddle, J.G.1    Yokoyama, T.2    Yamashita, I.3    Park, S.-Y.4    Tame, J.R.H.5
  • 15
    • 0033022150 scopus 로고    scopus 로고
    • Regulatory features of the trp operon and the crystal structure of the trp RNA-binding attenuation protein from Bacillus stearothermophilus
    • Chen, X., Antson, A. A., Yang, M., Li, P., Baumann, C., Dodson, E. J., Dodson, G. G. and Gollnick, P. (1999) Regulatory features of the trp operon and the crystal structure of the trp RNA-binding attenuation protein from Bacillus stearothermophilus. J. Mol. Biol. 289, 1003-1016
    • (1999) J. Mol. Biol. , vol.289 , pp. 1003-1016
    • Chen, X.1    Antson, A.A.2    Yang, M.3    Li, P.4    Baumann, C.5    Dodson, E.J.6    Dodson, G.G.7    Gollnick, P.8
  • 16
    • 0033575897 scopus 로고    scopus 로고
    • Structure of the trp RNA-binding attenuation protein, TRAP, bound to RNA
    • Antson, A. A., Dodson, E. J., Dodson, G., Greaves, R. B., Chen, X. and Gollnick, P. (1999) Structure of the trp RNA-binding attenuation protein, TRAP, bound to RNA. Nature 401, 235-242
    • (1999) Nature , vol.401 , pp. 235-242
    • Antson, A.A.1    Dodson, E.J.2    Dodson, G.3    Greaves, R.B.4    Chen, X.5    Gollnick, P.6
  • 17
    • 1842421817 scopus 로고    scopus 로고
    • The interaction of RNA with TRAP: The role of triplet repeats and separating spacer nucleotides
    • Hopcroft, N. H., Manfredo, A., Wendt, A. L., Brzozowski, A. M., Gollnick, P. and Antson, A. A. (2004) The interaction of RNA with TRAP: the role of triplet repeats and separating spacer nucleotides. J. Mol. Biol. 338, 43-53
    • (2004) J. Mol. Biol. , vol.338 , pp. 43-53
    • Hopcroft, N.H.1    Manfredo, A.2    Wendt, A.L.3    Brzozowski, A.M.4    Gollnick, P.5    Antson, A.A.6
  • 18
    • 0036005615 scopus 로고    scopus 로고
    • Specificity of TRAP-RNA interactions: Crystal structures of two complexes with different RNA sequences
    • Hopcroft, N. H., Wendt, A. L., Gollnick, P. and Antson, A. A. (2002) Specificity of TRAP-RNA interactions: crystal structures of two complexes with different RNA sequences. Acta Crystallogr. Sect. D Biol. Crystallogr. 58, 615-621
    • (2002) Acta Crystallogr. Sect. D Biol. Crystallogr. , vol.58 , pp. 615-621
    • Hopcroft, N.H.1    Wendt, A.L.2    Gollnick, P.3    Antson, A.A.4
  • 19
    • 29144475324 scopus 로고    scopus 로고
    • Complexity in regulation of tryptophan biosynthesis in Bacillus subtilis
    • Gollnick, P., Babitzke, P., Antson, A. and Yanofsky, C. (2005) Complexity in regulation of tryptophan biosynthesis in Bacillus subtilis. Annu. Rev. Genet. 39, 47-68
    • (2005) Annu. Rev. Genet. , vol.39 , pp. 47-68
    • Gollnick, P.1    Babitzke, P.2    Antson, A.3    Yanofsky, C.4
  • 21
    • 33746906309 scopus 로고    scopus 로고
    • Thermodynamics of tryptophan-mediated activation of the trp RNA-binding attenuation protein
    • DOI 10.1021/bi0526074
    • McElroy, C. A., Manfredo, A., Gollnick, P. and Foster, M. P. (2006) Thermodynamics of tryptophan-mediated activation of the trp RNA-binding attenuation protein. Biochemistry 45, 7844-7853 (Pubitemid 44185501)
    • (2006) Biochemistry , vol.45 , Issue.25 , pp. 7844-7853
    • McElroy, C.A.1    Manfredo, A.2    Gollnick, P.3    Foster, M.P.4
  • 22
    • 0036416144 scopus 로고    scopus 로고
    • TROSY-NMR studies of the 91kDa TRAP protein reveal allosteric control of a gene regulatory protein by ligand-altered flexibility
    • McElroy, C., Manfredo, A., Wendt, A., Gollnick, P. and Foster, M. (2002) TROSY-NMR studies of the 91kDa TRAP protein reveal allosteric control of a gene regulatory protein by ligand-altered flexibility. J. Mol. Biol. 323, 463-473
    • (2002) J. Mol. Biol. , vol.323 , pp. 463-473
    • McElroy, C.1    Manfredo, A.2    Wendt, A.3    Gollnick, P.4    Foster, M.5
  • 23
    • 44349096354 scopus 로고    scopus 로고
    • Insights into activation and RNA binding of trp RNA-binding attenuation protein (TRAP) through all-atom simulations
    • DOI 10.1002/prot.21878
    • Murtola, T., Vattulainen, I. and Falck, E. (2008) Insights into activation and RNA binding of trpRNA-binding attenuation protein (TRAP) through all-atom simulations. Proteins: Struct., Funct., Bioinf. 71, 1995-2011 (Pubitemid 351732951)
    • (2008) Proteins: Structure, Function and Genetics , vol.71 , Issue.4 , pp. 1995-2011
    • Murtola, T.1    Vattulainen, I.2    Falck, E.3
  • 25
    • 39549117361 scopus 로고    scopus 로고
    • Intersubunit linker length as a modifier of protein stability: Crystal structures and thermostability of mutant TRAP
    • Watanabe, M., Mishima, Y., Yamashita, I., Park, S.-Y., Tame, J. R. H. and Heddle, J. G. (2008) Intersubunit linker length as a modifier of protein stability: crystal structures and thermostability of mutant TRAP. Protein Sci. 17, 518-526
    • (2008) Protein Sci. , vol.17 , pp. 518-526
    • Watanabe, M.1    Mishima, Y.2    Yamashita, I.3    Park, S.-Y.4    Tame, J.R.H.5    Heddle, J.G.6
  • 27
    • 0031059866 scopus 로고    scopus 로고
    • Processing of X-ray diffraction data collected in oscillation mode
    • Carter, Jr, C. W., ed., Academic Press
    • Otwinowski, Z. and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode. In Methods in Enzymology (Carter, Jr, C. W., ed.), pp. 307-326, Academic Press
    • (1997) Methods in Enzymology , pp. 307-326
    • Otwinowski, Z.1    Minor, W.2
  • 28
    • 0028103275 scopus 로고
    • The CCP4 suite: Programs for protein crystallography
    • The Collaborative Computational Project 4
    • The Collaborative Computational Project 4 (1994) The CCP4 suite: programs for protein crystallography Acta Crystallogr. Sect. D Biol. Crystallogr. 50, 760-763
    • (1994) Acta Crystallogr. Sect. D Biol. Crystallogr. , vol.50 , pp. 760-763
  • 34
    • 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. (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283-291
    • (1993) J. Appl. Crystallogr. , vol.26 , pp. 283-291
    • Laskowski, R.A.1    MacArthur, M.W.2    Moss, D.S.3    Thornton, J.M.4
  • 35
    • 79952174977 scopus 로고    scopus 로고
    • Reference deleted
    • Reference deleted
  • 36
    • 34250166166 scopus 로고    scopus 로고
    • The rate of TRAP binding to RNA is crucial for transcription attenuation control of the B. subtilis trp operon
    • Barbolina, M. V., Kristoforov, R., Manfredo, A., Chen, Y. and Gollnick, P. (2007) The rate of TRAP binding to RNA is crucial for transcription attenuation control of the B. subtilis trp operon. J. Mol. Biol. 370, 925-938
    • (2007) J. Mol. Biol. , vol.370 , pp. 925-938
    • Barbolina, M.V.1    Kristoforov, R.2    Manfredo, A.3    Chen, Y.4    Gollnick, P.5
  • 37
    • 17544365656 scopus 로고    scopus 로고
    • Kinetic and thermodynamic analysis of the interaction between TRAP (trp RNA-binding attenuation protein) of Bacillus subtilis and trp leader RNA
    • Baumann, C., Otridge, J. and Gollnick, P. (1996) Kinetic and thermodynamic analysis of the interaction between TRAP (trp RNA-binding attenuation protein) of Bacillus subtilis and trp leader RNA. J. Biol. Chem. 271, 12269-12274
    • (1996) J. Biol. Chem. , vol.271 , pp. 12269-12274
    • Baumann, C.1    Otridge, J.2    Gollnick, P.3
  • 38
    • 0037023767 scopus 로고    scopus 로고
    • Creating hetero-11-mers composed of wild-type and mutant subunits to study RNA binding to TRAP
    • Li, P. T., Scott, D. J. and Gollnick, P. (2002) Creating hetero-11-mers composed of wild-type and mutant subunits to study RNA binding to TRAP. J. Biol. Chem. 277, 11838-11844
    • (2002) J. Biol. Chem. , vol.277 , pp. 11838-11844
    • Li, P.T.1    Scott, D.J.2    Gollnick, P.3
  • 39
    • 0034635443 scopus 로고    scopus 로고
    • Effects of mutations in the L-tryptophan binding pocket of the Trp RNA-binding attenuation protein of Bacillus subtilis
    • Yakhnin, A. V., Trimble, J. J., Chiaro, C. R. and Babitzke, P. (2000) Effects of mutations in the L-tryptophan binding pocket of the Trp RNA-binding attenuation protein of Bacillus subtilis. J. Biol. Chem. 275, 4519-4524
    • (2000) J. Biol. Chem. , vol.275 , pp. 4519-4524
    • Yakhnin, A.V.1    Trimble, J.J.2    Chiaro, C.R.3    Babitzke, P.4
  • 40
    • 0032860710 scopus 로고    scopus 로고
    • Probing the TRAP-RNA interaction with nucleoside analogs
    • DOI 10.1017/S1355838299991057
    • Elliott, M. B., Gottlieb, P. A. and Gollnick, P. (1999) Probing the TRAP-RNA interaction with nucleoside analogs. RNA 5, 1277-1289 (Pubitemid 29489810)
    • (1999) RNA , vol.5 , Issue.10 , pp. 1277-1289
    • Elliott, M.B.1    Gottlieb, P.A.2    Gollnick, P.3
  • 41
    • 0030821725 scopus 로고    scopus 로고
    • Regulation of tryptophan biosynthesis: Trp-ing the TRAP or how Bacillus subtilis reinvented the wheel
    • Babitzke, P. (1997) Regulation of tryptophan biosynthesis: Trp-ing the TRAP or how Bacillus subtilis reinvented the wheel. Mol. Microbiol. 26, 1-9
    • (1997) Mol. Microbiol. , vol.26 , pp. 1-9
    • Babitzke, P.1
  • 42
    • 1842610529 scopus 로고    scopus 로고
    • Regulation of transcription attenuation and translation initiation by allosteric control of an RNA-binding protein: The Bacillus subtilis TRAP protein
    • Babitzke, P. (2004) Regulation of transcription attenuation and translation initiation by allosteric control of an RNA-binding protein: the Bacillus subtilis TRAP protein. Curr. Opin. Microbiol. 7, 132-139
    • (2004) Curr. Opin. Microbiol. , vol.7 , pp. 132-139
    • Babitzke, P.1
  • 43
    • 0028217753 scopus 로고
    • Regulation of the Bacillus subtilis trp operon by an RNA-binding protein
    • Gollnick, P. (1994) Regulation of the Bacillus subtilis trp operon by an RNA-binding protein. Mol. Microbiol. 11, 991-997
    • (1994) Mol. Microbiol. , vol.11 , pp. 991-997
    • Gollnick, P.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.