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Volumn 405, Issue 3, 2011, Pages 819-830

Concerted dynamics link allosteric sites in the PBX homeodomain

Author keywords

conformational selection; CPMG; molecular recognition; NMR; protein folding

Indexed keywords

DNA; HOMEODOMAIN PROTEIN; HOX PROTEIN; TRANSCRIPTION FACTOR PBX1;

EID: 78650901441     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2010.11.016     Document Type: Article
Times cited : (26)

References (49)
  • 2
    • 0037428441 scopus 로고    scopus 로고
    • Lock and key binding of the HOX YPWM peptide to the PBX homeodomain
    • Sprules T., Green N., Featherstone M., and Gehring K. Lock and key binding of the HOX YPWM peptide to the PBX homeodomain J. Biol. Chem. 278 2003 1053 1058
    • (2003) J. Biol. Chem. , vol.278 , pp. 1053-1058
    • Sprules, T.1    Green, N.2    Featherstone, M.3    Gehring, K.4
  • 3
    • 0033582545 scopus 로고    scopus 로고
    • Structure of a HoxB1-Pbx1 heterodimer bound to DNA: Role of the hexapeptide and a fourth homeodomain helix in complex formation
    • Piper D.E., Batchelor A.H., Chang C.P., Cleary M.L., and Wolberger C. Structure of a HoxB1-Pbx1 heterodimer bound to DNA: role of the hexapeptide and a fourth homeodomain helix in complex formation Cell 96 1999 587 597
    • (1999) Cell , vol.96 , pp. 587-597
    • Piper, D.E.1    Batchelor, A.H.2    Chang, C.P.3    Cleary, M.L.4    Wolberger, C.5
  • 4
    • 0026321622 scopus 로고
    • DNA binding specificity of homeodomains
    • Laughon A. DNA binding specificity of homeodomains Biochemistry 30 1991 11357 11367
    • (1991) Biochemistry , vol.30 , pp. 11357-11367
    • Laughon, A.1
  • 5
    • 0029898760 scopus 로고    scopus 로고
    • Extra specificity from extradenticle: The partnership between HOX and PBX/EXD homeodomain proteins
    • Mann R.S., and Chan S.K. Extra specificity from extradenticle: the partnership between HOX and PBX/EXD homeodomain proteins Trends Genet. 12 1996 258 262
    • (1996) Trends Genet. , vol.12 , pp. 258-262
    • Mann, R.S.1    Chan, S.K.2
  • 6
    • 0027966927 scopus 로고
    • The DNA binding specificity of Ultrabithorax is modulated by cooperative interactions with extradenticle, another homeoprotein
    • Chan S.K., Jaffe L., Capovilla M., Botas J., and Mann R.S. The DNA binding specificity of Ultrabithorax is modulated by cooperative interactions with extradenticle, another homeoprotein Cell 78 1994 603 615
    • (1994) Cell , vol.78 , pp. 603-615
    • Chan, S.K.1    Jaffe, L.2    Capovilla, M.3    Botas, J.4    Mann, R.S.5
  • 7
    • 0029925624 scopus 로고    scopus 로고
    • An extradenticle-induced conformational change in a HOX protein overcomes an inhibitory function of the conserved hexapeptide motif
    • Chan S.K., Popperl H., Krumlauf R., and Mann R.S. An extradenticle- induced conformational change in a HOX protein overcomes an inhibitory function of the conserved hexapeptide motif EMBO J. 15 1996 2476 2487
    • (1996) EMBO J. , vol.15 , pp. 2476-2487
    • Chan, S.K.1    Popperl, H.2    Krumlauf, R.3    Mann, R.S.4
  • 8
    • 0030986189 scopus 로고    scopus 로고
    • Switching the in vivo specificity of a minimal Hox-responsive element
    • Chan S.K., Ryoo H.D., Gould A., Krumlauf R., and Mann R.S. Switching the in vivo specificity of a minimal Hox-responsive element Development 124 1997 2007 2014
    • (1997) Development , vol.124 , pp. 2007-2014
    • Chan, S.K.1    Ryoo, H.D.2    Gould, A.3    Krumlauf, R.4    Mann, R.S.5
  • 9
    • 0029054140 scopus 로고
    • Both Pbx1 and E2A-Pbx1 bind the DNA motif ATCAATCAA cooperatively with the products of multiple murine Hox genes, some of which are themselves oncogenes
    • Lu Q., Knoepfler P.S., Scheele J., Wright D.D., and Kamps M.P. Both Pbx1 and E2A-Pbx1 bind the DNA motif ATCAATCAA cooperatively with the products of multiple murine Hox genes, some of which are themselves oncogenes Mol. Cell. Biol. 15 1995 3786 3795
    • (1995) Mol. Cell. Biol. , vol.15 , pp. 3786-3795
    • Lu, Q.1    Knoepfler, P.S.2    Scheele, J.3    Wright, D.D.4    Kamps, M.P.5
  • 10
    • 0029008293 scopus 로고
    • Cooperative interactions between HOX and PBX proteins mediated by a conserved peptide motif
    • Phelan M.L., Rambaldi I., and Featherstone M.S. Cooperative interactions between HOX and PBX proteins mediated by a conserved peptide motif Mol. Cell. Biol. 15 1995 3989 3997
    • (1995) Mol. Cell. Biol. , vol.15 , pp. 3989-3997
    • Phelan, M.L.1    Rambaldi, I.2    Featherstone, M.S.3
  • 11
    • 0029055810 scopus 로고
    • Segmental expression of Hoxb-1 is controlled by a highly conserved autoregulatory loop dependent upon EXD/PBX
    • Popperl H., Bienz M., Studer M., Chan S.K., Aparicio S., and Brenner S. Segmental expression of Hoxb-1 is controlled by a highly conserved autoregulatory loop dependent upon EXD/PBX Cell 81 1995 1031 1042
    • (1995) Cell , vol.81 , pp. 1031-1042
    • Popperl, H.1    Bienz, M.2    Studer, M.3    Chan, S.K.4    Aparicio, S.5    Brenner, S.6
  • 12
    • 0030929326 scopus 로고    scopus 로고
    • The Abd-B-like Hox homeodomain proteins can be subdivided by the ability to form complexes with Pbx1a on a novel DNA target
    • Shen W.F., Rozenfeld S., Lawrence H.J., and Largman C. The Abd-B-like Hox homeodomain proteins can be subdivided by the ability to form complexes with Pbx1a on a novel DNA target J. Biol. Chem. 272 1997 8198 8206
    • (1997) J. Biol. Chem. , vol.272 , pp. 8198-8206
    • Shen, W.F.1    Rozenfeld, S.2    Lawrence, H.J.3    Largman, C.4
  • 13
    • 0028169993 scopus 로고
    • Extradenticle raises the DNA binding specificity of homeotic selector gene products
    • van Dijk M.A., and Murre C. Extradenticle raises the DNA binding specificity of homeotic selector gene products Cell 78 1994 617 624
    • (1994) Cell , vol.78 , pp. 617-624
    • Van Dijk, M.A.1    Murre, C.2
  • 14
    • 0029160039 scopus 로고
    • Hox gene products modulate the DNA binding activity of Pbx1 and Pbx2
    • van Dijk M.A., Peltenburg L.T., and Murre C. Hox gene products modulate the DNA binding activity of Pbx1 and Pbx2 Mech. Dev. 52 1995 99 108
    • (1995) Mech. Dev. , vol.52 , pp. 99-108
    • Van Dijk, M.A.1    Peltenburg, L.T.2    Murre, C.3
  • 15
    • 0029917042 scopus 로고    scopus 로고
    • Functional dissection of the mouse Hox-a5 gene
    • Zhao J.J.G., Lazzarini R.A., and Pick L. Functional dissection of the mouse Hox-a5 gene EMBO J. 15 1996 1313 1322
    • (1996) EMBO J. , vol.15 , pp. 1313-1322
    • Zhao, J.J.G.1    Lazzarini, R.A.2    Pick, L.3
  • 16
    • 0028947525 scopus 로고
    • Pbx proteins display hexapeptide-dependent cooperative DNA binding with a subset of Hox proteins
    • Chang C.P., Shen W.F., Rozenfeld S., Lawrence H.J., Largman C., and Cleary M.L. Pbx proteins display hexapeptide-dependent cooperative DNA binding with a subset of Hox proteins Genes Dev. 9 1995 663 674
    • (1995) Genes Dev. , vol.9 , pp. 663-674
    • Chang, C.P.1    Shen, W.F.2    Rozenfeld, S.3    Lawrence, H.J.4    Largman, C.5    Cleary, M.L.6
  • 17
    • 1842339865 scopus 로고    scopus 로고
    • Analysis of TALE superclass homeobox genes (MEIS, PBC, KNOX, Iroquois, TGIF) reveals a novel domain conserved between plants and animals
    • Burglin T.R. Analysis of TALE superclass homeobox genes (MEIS, PBC, KNOX, Iroquois, TGIF) reveals a novel domain conserved between plants and animals Nucleic Acids Res. 25 1997 4173 4180
    • (1997) Nucleic Acids Res. , vol.25 , pp. 4173-4180
    • Burglin, T.R.1
  • 18
    • 0029118224 scopus 로고
    • The pentapeptide motif of Hox proteins is required for cooperative DNA-binding with Pbx1, physically contacts Pbx1 and enhances DNA-binding by Pbx1
    • Knoepfler P.S., and Kamps M.P. The pentapeptide motif of Hox proteins is required for cooperative DNA-binding with Pbx1, physically contacts Pbx1 and enhances DNA-binding by Pbx1 Mol. Cell. Biol. 15 1995 5811 5819
    • (1995) Mol. Cell. Biol. , vol.15 , pp. 5811-5819
    • Knoepfler, P.S.1    Kamps, M.P.2
  • 19
    • 0029966661 scopus 로고    scopus 로고
    • Structural determinants within Pbx1 that mediate cooperative DNA binding with pentapeptide-containing Hox proteins: Proposal for a model of a Pbx1-Hox-DNA complex
    • Lu Q., and Kamps M.P. Structural determinants within Pbx1 that mediate cooperative DNA binding with pentapeptide-containing Hox proteins: proposal for a model of a Pbx1-Hox-DNA complex Mol. Cell. Biol. 16 1996 1632 1640
    • (1996) Mol. Cell. Biol. , vol.16 , pp. 1632-1640
    • Lu, Q.1    Kamps, M.P.2
  • 20
    • 0030894303 scopus 로고    scopus 로고
    • Specific residues in the Pbx homeodomain differentially modulate the DNA-binding activity of Hox and Engrailed proteins
    • Peltenburg L.T.C., and Murre C. Specific residues in the Pbx homeodomain differentially modulate the DNA-binding activity of Hox and Engrailed proteins Development 124 1997 1089 1098
    • (1997) Development , vol.124 , pp. 1089-1098
    • Peltenburg, L.T.C.1    Murre, C.2
  • 21
    • 0034663970 scopus 로고    scopus 로고
    • Conformational changes in the PBX homeodomain and C-terminal extension upon binding DNA and HOX-derived YPWM peptides
    • Sprules T., Green N., Featherstone M., and Gehring K. Conformational changes in the PBX homeodomain and C-terminal extension upon binding DNA and HOX-derived YPWM peptides Biochemistry 39 2000 9943 9950
    • (2000) Biochemistry , vol.39 , pp. 9943-9950
    • Sprules, T.1    Green, N.2    Featherstone, M.3    Gehring, K.4
  • 22
    • 0032557549 scopus 로고    scopus 로고
    • A conserved C-terminal domain in PBX increases DNA binding by the PBX homeodomain and is not a primary site of contact for the YPWM motif of HOXA1
    • Green N.C., Rambaldi I., Teakles J., and Featherstone M.S. A conserved C-terminal domain in PBX increases DNA binding by the PBX homeodomain and is not a primary site of contact for the YPWM motif of HOXA1 J. Biol. Chem. 273 1998 13273 13279
    • (1998) J. Biol. Chem. , vol.273 , pp. 13273-13279
    • Green, N.C.1    Rambaldi, I.2    Teakles, J.3    Featherstone, M.S.4
  • 23
    • 44949262025 scopus 로고    scopus 로고
    • 15N relaxation dispersion experiment for the measurement of millisecond time-scale dynamics in proteins
    • 15N relaxation dispersion experiment for the measurement of millisecond time-scale dynamics in proteins J. Phys. Chem. B 112 2008 5898 5904
    • (2008) J. Phys. Chem. B , vol.112 , pp. 5898-5904
    • Hansen, D.F.1    Vallurupalli, P.2    Kay, L.E.3
  • 24
    • 0034919305 scopus 로고    scopus 로고
    • Nuclear magnetic resonance methods for quantifying microsecond-to- millisecond motions in biological macromolecules
    • Palmer A.G. III, Kroenke C.D., and Loria J.P. Nuclear magnetic resonance methods for quantifying microsecond-to-millisecond motions in biological macromolecules Methods Enzymol. 339 2001 204 238
    • (2001) Methods Enzymol. , vol.339 , pp. 204-238
    • Palmer Iii, A.G.1    Kroenke, C.D.2    Loria, J.P.3
  • 25
    • 36849127400 scopus 로고
    • Nuclear magnetic resonance study of protolysis of trimethylammonium ion in aqueous solution-order of reaction with respect to solvent
    • Luz Z., and Meiboom S. Nuclear magnetic resonance study of protolysis of trimethylammonium ion in aqueous solution-order of reaction with respect to solvent J. Chem. Phys. 39 1963 366
    • (1963) J. Chem. Phys. , vol.39 , pp. 366
    • Luz, Z.1    Meiboom, S.2
  • 26
    • 0034728579 scopus 로고    scopus 로고
    • The static magnetic field dependence of chemical exchange line broadening defines the NMR chemical shift time scale
    • Millet O., Loria J.P., Kroenke C.D., Pons M., and Palmer A.G. The static magnetic field dependence of chemical exchange line broadening defines the NMR chemical shift time scale J. Am. Chem. Soc. 122 2000 2867 2877
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 2867-2877
    • Millet, O.1    Loria, J.P.2    Kroenke, C.D.3    Pons, M.4    Palmer, A.G.5
  • 27
    • 77951680126 scopus 로고    scopus 로고
    • Analyzing protein folding cooperativity by differential scanning calorimetry and NMR spectroscopy
    • Farber P., Darmawan H., Sprules T., and Mittermaier A. Analyzing protein folding cooperativity by differential scanning calorimetry and NMR spectroscopy J. Am. Chem. Soc. 132 2010 6214 6222
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 6214-6222
    • Farber, P.1    Darmawan, H.2    Sprules, T.3    Mittermaier, A.4
  • 29
    • 70350340728 scopus 로고    scopus 로고
    • The role of dynamic conformational ensembles in biomolecular recognition
    • Boehr D.D., Nussinov R., and Wright P.E. The role of dynamic conformational ensembles in biomolecular recognition Nat. Chem. Biol. 5 2009 789 796
    • (2009) Nat. Chem. Biol. , vol.5 , pp. 789-796
    • Boehr, D.D.1    Nussinov, R.2    Wright, P.E.3
  • 30
    • 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
  • 31
    • 0033621104 scopus 로고    scopus 로고
    • Folding and binding cascades: Shifts in energy landscapes
    • Tsai C.J., Ma B.Y., and Nussinov R. Folding and binding cascades: shifts in energy landscapes Proc. Natl Acad. Sci. USA 96 1999 9970 9972
    • (1999) Proc. Natl Acad. Sci. USA , vol.96 , pp. 9970-9972
    • Tsai, C.J.1    Ma, B.Y.2    Nussinov, R.3
  • 32
    • 0027943261 scopus 로고
    • Conformational isomerism and the diversity of antibodies
    • Foote J., and Milstein C. Conformational isomerism and the diversity of antibodies Proc. Natl Acad. Sci. USA 91 1994 10370 10374
    • (1994) Proc. Natl Acad. Sci. USA , vol.91 , pp. 10370-10374
    • Foote, J.1    Milstein, C.2
  • 33
    • 0033056708 scopus 로고    scopus 로고
    • Folding funnels, binding funnels, and protein function
    • Tsai C.J., Kumar S., Ma B.Y., 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.J.1    Kumar, S.2    Ma, B.Y.3    Nussinov, R.4
  • 34
    • 0026493924 scopus 로고
    • Crystallographic evidence of a large ligand-induced hinge-twist motion between the 2 domains of the maltodextrin binding-protein involved in active-transport and chemotaxis
    • Sharff A.J., Rodseth L.E., Spurlino J.C., and Quiocho F.A. Crystallographic evidence of a large ligand-induced hinge-twist motion between the 2 domains of the maltodextrin binding-protein involved in active-transport and chemotaxis Biochemistry 31 1992 10657 10663
    • (1992) Biochemistry , vol.31 , pp. 10657-10663
    • Sharff, A.J.1    Rodseth, L.E.2    Spurlino, J.C.3    Quiocho, F.A.4
  • 35
    • 35548976322 scopus 로고    scopus 로고
    • Open-to-closed transition in apo maltose-binding protein observed by paramagnetic NMR
    • Tang C., Schwieters C.D., and Clore G.M. Open-to-closed transition in apo maltose-binding protein observed by paramagnetic NMR Nature 449 2007 1078 1082
    • (2007) Nature , vol.449 , pp. 1078-1082
    • Tang, C.1    Schwieters, C.D.2    Clore, G.M.3
  • 36
    • 0034710950 scopus 로고    scopus 로고
    • Binding sites in Escherichia coli dihydrofolate reductase communicate by modulating the conformational ensemble
    • Pan H., Lee J.C., and Hilser V.J. Binding sites in Escherichia coli dihydrofolate reductase communicate by modulating the conformational ensemble Proc. Natl Acad. Sci. USA 97 2000 12020 12025
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 12020-12025
    • Pan, H.1    Lee, J.C.2    Hilser, V.J.3
  • 37
    • 0346220393 scopus 로고    scopus 로고
    • The role of dynamics in allosteric regulation
    • Kern D., and Zuiderweg E.R.P. The role of dynamics in allosteric regulation Curr. Opin. Struct. Biol. 13 2003 748 757
    • (2003) Curr. Opin. Struct. Biol. , vol.13 , pp. 748-757
    • Kern, D.1    Zuiderweg, E.R.P.2
  • 38
    • 0035937443 scopus 로고    scopus 로고
    • Two-state allosteric behavior in a single-domain signaling protein
    • Volkman B.F., Lipson D., Wemmer D.E., and Kern D. Two-state allosteric behavior in a single-domain signaling protein Science 291 2001 2429 2433
    • (2001) Science , vol.291 , pp. 2429-2433
    • Volkman, B.F.1    Lipson, D.2    Wemmer, D.E.3    Kern, D.4
  • 40
    • 0034671172 scopus 로고    scopus 로고
    • Modeling the cAMP-induced allosteric transition using the crystal structure of CAP-cAMP at 2.1 Å resolution
    • Passner J.M., Schultz S.C., and Steitz T.A. Modeling the cAMP-induced allosteric transition using the crystal structure of CAP-cAMP at 2.1 Å resolution J. Mol. Biol. 304 2000 847 859
    • (2000) J. Mol. Biol. , vol.304 , pp. 847-859
    • Passner, J.M.1    Schultz, S.C.2    Steitz, T.A.3
  • 41
    • 70450191983 scopus 로고    scopus 로고
    • Dynamic activation of an allosteric regulatory protein
    • Tzeng S.R., and Kalodimos C.G. Dynamic activation of an allosteric regulatory protein Nature 462 2009 U139 U368
    • (2009) Nature , vol.462
    • Tzeng, S.R.1    Kalodimos, C.G.2
  • 42
    • 0034992645 scopus 로고    scopus 로고
    • A method for efficient isotopic labeling of recombinant proteins
    • Marley J., Lu M., and Bracken C. A method for efficient isotopic labeling of recombinant proteins J. Biomol. NMR 20 2001 71 75
    • (2001) J. Biomol. NMR , vol.20 , pp. 71-75
    • Marley, J.1    Lu, M.2    Bracken, C.3
  • 43
    • 0029166532 scopus 로고
    • Thermal denaturation methods in the study of protein folding
    • Academic Press, Inc. San Diego, CA
    • Freire E. Thermal denaturation methods in the study of protein folding Methods in Enzymology 259 1995 Academic Press, Inc. San Diego, CA 144 168
    • (1995) Methods in Enzymology , vol.259 , pp. 144-168
    • Freire, E.1
  • 44
    • 0037943192 scopus 로고    scopus 로고
    • A new set of peptide-based group heat capacities for use in protein stability calculations
    • Hackel N., Hinz H.J., and Hedwig G.R. A new set of peptide-based group heat capacities for use in protein stability calculations J. Mol. Biol. 291 1999 197 213
    • (1999) J. Mol. Biol. , vol.291 , pp. 197-213
    • Hackel, N.1    Hinz, H.J.2    Hedwig, G.R.3
  • 45
    • 0028845120 scopus 로고
    • Precise scanning calorimeter for studying thermal properties of biological molecules in dilute solution
    • Privalov G., Kavina V., Freire E., and Privalov P.L. Precise scanning calorimeter for studying thermal properties of biological molecules in dilute solution Anal. Biochem. 232 1995 79 85
    • (1995) Anal. Biochem. , vol.232 , pp. 79-85
    • Privalov, G.1    Kavina, V.2    Freire, E.3    Privalov, P.L.4
  • 46
    • 44949262025 scopus 로고    scopus 로고
    • An improved N-15 relaxation dispersion experiment for the measurement of millisecond time-scale dynamics in proteins
    • Hansen A.F., Vallurupalli P., and Kay L.E. An improved N-15 relaxation dispersion experiment for the measurement of millisecond time-scale dynamics in proteins J. Phys. Chem. B 112 2008 5898 5904
    • (2008) J. Phys. Chem. B , vol.112 , pp. 5898-5904
    • Hansen, A.F.1    Vallurupalli, P.2    Kay, L.E.3
  • 47
    • 67849119942 scopus 로고    scopus 로고
    • Binding mechanism of an SH3 domain studied by NMR and ITC
    • Demers J.P., and Mittermaier A. Binding mechanism of an SH3 domain studied by NMR and ITC J. Am. Chem. Soc. 131 2009 4355 4367
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 4355-4367
    • Demers, J.P.1    Mittermaier, A.2
  • 48
    • 33646130861 scopus 로고    scopus 로고
    • Accuracy of optimized chemical-exchange parameters derived by fitting CPMG R-2 dispersion profiles when R-2(0a)=R-2(0b)
    • Ishima R., and Torchia D.A. Accuracy of optimized chemical-exchange parameters derived by fitting CPMG R-2 dispersion profiles when R-2(0a)=R-2(0b) J. Biomol. NMR 34 2006 209 219
    • (2006) J. Biomol. NMR , vol.34 , pp. 209-219
    • Ishima, R.1    Torchia, D.A.2
  • 49
    • 84964203940 scopus 로고
    • Bootstrap methods for standard errors, confidence intervals and other measures of statistical accuracy
    • Efron B., and Tibshirani R. Bootstrap methods for standard errors, confidence intervals and other measures of statistical accuracy Stat. Sci. 1 1986 54 77
    • (1986) Stat. Sci. , vol.1 , pp. 54-77
    • Efron, B.1    Tibshirani, R.2


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