CBFβ allosterically regulates the Runx1 Runt domain via a dynamic conformational equilibrium (original) (raw)

• Kagoshima, H. et al. The Runt-domain identifies a new family of heteromeric DNA-binding transcriptional regulatory proteins. Trends Genet. 9, 338–341 (1993).
  Article CAS Google Scholar
• Tang, Y.Y. et al. Biophysical characterization of interactions between the core binding factor α and β subunits and DNA. FEBS Lett. 470, 167–172 (2000).
  Article CAS Google Scholar
• Bravo, J., Li, Z., Speck, N.A. & Warren, A.J. The leukemia-associated AML1 (Runx1)–CBF β complex functions as a DNA-induced molecular clamp. Nat. Struct. Biol. 8, 371–378 (2001).
  Article CAS Google Scholar
• Tahirov, T.H. et al. Structural analyses of DNA recognition by the AML1/Runx–1 Runt domain and its allosteric control by CBFβ. Cell 104, 755–767 (2001).
  Article CAS Google Scholar
• Backstrom, S. et al. The RUNX1 Runt domain at 1.25 Å resolution: a structural switch and specifically bound chloride ions modulate DNA binding. J. Mol. Biol. 322, 259–272 (2002).
  Article CAS Google Scholar
• Warren, A.J., Bravo, J., Williams, R.L. & Rabbitts, T.H. Structural basis for the heterodimeric interaction between the acute leukaemia-associated transcription factors AML1 and CBFβ. EMBO J. 19, 3004–3015 (2000).
  Article CAS Google Scholar
• Bartfeld, D. et al. DNA recognition by the RUNX1 transcription factor is mediated by an allosteric transition in the RUNT domain and by DNA bending. Structure 10, 1395–1407 (2002).
  Article CAS Google Scholar
• Case, D.A. Molecular dynamics and NMR spin relaxation in proteins. Acc. Chem. Res. 35, 325–331 (2002).
  Article CAS Google Scholar
• Akke, M. NMR methods for characterizing microsecond to millisecond dynamics in recognition and catalysis. Curr. Opin. Struct. Biol. 12, 642–647 (2002).
  Article CAS Google Scholar
• Wand, A.J. Dynamic activation of protein function: a view emerging from NMR spectroscopy. Nat. Struct. Biol. 8, 926–931 (2001).
  Article CAS Google Scholar
• Palmer, A.G. 3rd. NMR probes of molecular dynamics: overview and comparison with other techniques. Annu. Rev. Biophys. Biomol. Struct. 30, 129–155 (2001).
  Article CAS Google Scholar
• Ishima, R. & Torchia, D.A. Protein dynamics from NMR. Nat. Struct. Biol. 7, 740–743 (2000).
  Article CAS Google Scholar
• Kay, L.E. Protein dynamics from NMR. Biochem. Cell Biol. 76, 145–152 (1998).
  Article CAS Google Scholar
• Berardi, M.J. et al. The Ig fold of the core binding factor α Runt domain is a member of a family of structurally and functionally related Ig-fold DNA-binding domains. Structure 7, 1247–1256 (1999).
  Article CAS Google Scholar
• Yan, J. & Bushweller, J.H. An optimized PCR-based procedure for production of 13C/15N-labeled DNA. Biochem. Biophys. Res. Commun. 284, 295–300 (2001).
  Article CAS Google Scholar
• Nekludova, L. & Pabo, C.O. Distinctive DNA conformation with enlarged major groove is found in Zn-finger–DNA and other protein–DNA complexes. Proc. Natl. Acad. Sci. USA 91, 6948–6952 (1994).
  Article CAS Google Scholar
• Lipari, G. & Szabo, A. model-free approach to the interpretation of nuclear magnetic-resonance relaxation in macromolecules 1. Theory and range of validity. J. Am. Chem. Soc. 104, 4546–4559 (1982).
  Article CAS Google Scholar
• Lipari, G. & Szabo, A. Model-free approach to the interpretation of nuclear magnetic-resonance relaxation in macromolecules 2. Analysis of experimental results. J. Am. Chem. Soc. 104, 4559–4570 (1982).
  Article CAS Google Scholar
• Kneller, J.M., Lu, M. & Bracken, C. An effective method for the discrimination of motional anisotropy and chemical exchange. J. Am. Chem. Soc. 124, 1852–1853 (2002).
  Article CAS Google Scholar
• Li, Z. et al. Energetic contribution of residues in the Runx1 Runt domain to DNA binding. J. Biol. Chem. 278, 33088–33096 (2003).
  Article CAS Google Scholar
• Zhang, L. et al. Mutagenesis of the Runt domain defines two energetic hotspots for heterodimerization with the core binding factor β subunit. J. Biol. Chem. 278, 33097–33104 (2003).
  Article CAS Google Scholar
• Bartfeld, D. et al. DNA recognition by the RUNX1 transcription factor is mediated by an allosteric transition in the RUNT domain and by DNA bending. Structure 10, 1–20 (2002).
  Article Google Scholar
• Backstrom, S. et al. The RUNX1 Runt domain at 1.25Å resolution: a structural switch and specifically bound chloride ions modulate DNA binding. J. Mol. Biol. 322, 259–272 (2002).
  Article CAS Google Scholar
• Volkman, B.F., Lipson, D., Wemmer, D.E. & Kern, D. Two-state allosteric behavior in a single-domain signaling protein. Science 291, 2429–2433 (2001).
  Article CAS Google Scholar
• Hammes, G.G. Multiple conformational changes in enzyme catalysis. Biochemistry 41, 8221–8228 (2002).
  Article CAS Google Scholar
• Howlett, G.J., Balckburn, M.N., Compton, J.G. & Schachman, H.K. Allosteric regulation of aspartate transcarbamoylase. Analysis of the structural and functional behavior in terms of a two-state model. Biochemistry 16, 5091–5100 (1977).
  Article CAS Google Scholar
• Hammes, G.G. & Wu, C.W. Kinetics of allosteric enzymes. Annu. Rev. Biophys. Bioeng. 3, 1–33 (1974).
  Article CAS Google Scholar
• Sakash, J.B. & Kantrowitz, E.R. The contribution of individual interchain interactions to the stabilization of the T and R states of Escherichia coli aspartate transcarbamoylase. J. Biol. Chem. 275, 28701–28707 (2000).
  Article CAS Google Scholar
• Chan, R.S. et al. The role of intersubunit interactions for the stabilization of the T state of Escherichia coli aspartate transcarbamoylase. J. Biol. Chem. 277, 49755–49760 (2002).
  Article CAS Google Scholar
• Lipscomb, W.N. Aspartate transcarbamylase from Escherichia coli: activity and regulation. Adv. Enzymol. Relat. Areas Mol. Biol. 68, 67–151 (1994).
  CAS PubMed Google Scholar
• Crute, B.E., Lewis, A.F., Wu, Z., Bushweller, J.H. & Speck, N.A. Biochemical and biophysical properties of the core-binding factor α2 (AML1) DNA-binding domain. J. Biol. Chem. 271, 26251–26260 (1996).
  Article CAS Google Scholar
• Farrow, N.A. et al. Backbone dynamics of a free and phosphopeptide-complexed Src homology 2 domain studied by 15N NMR relaxation. Biochemistry 33, 5984–6003 (1994).
  Article CAS Google Scholar
• Palmer, A.G. III, Rance, M. & Wright, P.E. Intramolecular motions of a zinc finger DNA-binding domain from Xfin characterized by proton-detected natural abundance 13C heteronuclear NMR spectroscopy. J. Am. Chem. Soc. 113, 4371–4380 (1991).
  Article CAS Google Scholar
• Nicholson, L.K. et al. Dynamics of methyl groups in proteins as studied by proton-detected 13C NMR spectroscopy. Application to the leucine residues of staphylococcal nuclease. Biochemistry 31, 5253–5263 (1992).
  Article CAS Google Scholar
• Pawley, N.H., Wang, C., Koide, S. & Nicholson, L.K. An improved method for distinguishing between anisotropic tumbling and chemical exchange in analysis of 15N relaxation parameters. J. Biomol. NMR 20, 149–165 (2001).
  Article CAS Google Scholar
• Kay, L.E., Torchia, D.A. & Bax, A. Backbone dynamics of proteins as studied by 15N inverse detected heteronuclear NMR spectroscopy: application to staphylococcal nuclease. Biochemistry 28, 8972–8979 (1989).
  Article CAS Google Scholar
• Lee, L.K., Rance, M., Chazin, W.J. & Palmer, A.G. 3rd. Rotational diffusion anisotropy of proteins from simultaneous analysis of 15N and 13C α nuclear spin relaxation. J. Biomol. NMR 9, 287–298 (1997).
  Article CAS Google Scholar
• Tjandra, N., Feller, S.E., Pastor, R.W. & Bax, A. Rotational diffusion anisotropy of human ubiquitin from N-15 NMR relaxation. J. Am. Chem. Soc. 117, 12562–12566 (1995).
  Article CAS Google Scholar
• Bruschweiler, R., Liao, X.B. & Wright, P.E. Long-range motional restrictions in a multidomain zinc-finger protein from anisotropic tumbling. Science 268, 886–889 (1995).
  Article CAS Google Scholar
• Mandel, A.M., Akke, M. & Palmer, A.G. 3rd. Backbone dynamics of Escherichia coli ribonuclease HI: correlations with structure and function in an active enzyme. J. Mol. Biol. 246, 144–163 (1995).
  Article CAS Google Scholar
• Pierce, M.M., Raman, C.S. & Nall, B.T. Isothermal titration calorimetry of protein-protein interactions. Methods 19, 213–221 (1999).
  Article CAS Google Scholar