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department of molecular biosciences, evanston, il 60208

 
 
 
 
 

   
Research

Research in the Radhakrishnan lab focuses on the molecular mechanisms of eukaryotic transcription regulation with an emphasis on how transcription factors select and assemble on DNA targets, how they recruit coregulator complexes with chromatin-modifying activities, and how the latter complexes are themselves assembled and regulated. We are asking these questions in the context of (i) so-called orphan or ligand-independent nuclear receptors that promote normal development in organisms as diverse as fly and human, (ii) a cohort of related, yet functionally distinct, histone deacetylase-associated chromatin-modifying complexes that fundamentally impact on cellular physiology in all eukaryotes, and (iii) cyclic AMP signaling mediated by the prototypical and signal-inducible factor CREB and its coactivators. We use a broad range of biochemical, biophysical and computational approaches including solution NMR spectroscopy, x-ray crystallography, electron microscopy and molecular dynamics simulations to answer these questions.

Current projects in the lab focus on the structure, molecular evolution and dynamics (aka internal motions) of the Ftz-F1/NR5A sub-family of nuclear receptors. We are asking how the Ftz-F1 factor in Drosophila cooperates with the homeotic protein Ftz to specifically and synergistically bind DNA and how the ligand-binding domain of Ftz-F1 has evolved to activate transcription via ligand-dependent (in mouse and human) and ligand-independent (in fly) mechanisms and the role of internal motions in dictating protein allostery by facilitating communication between the ligand-binding pocket and the coactivator-binding site. Separately, we are asking how the evolutionarily-conserved, histone deacetylase (HDAC)-containing Sin3L/Rpd3L complex is assembled, what the precise molecular role(s) of the conserved subunits, which harbor domains of poorly characterized structure and function, are, including whether they regulate HDAC activity and how the complex engages chromatin and DNA-bound factors. Finally, we are developing the next iteration of a popular web application called MONSTER that can mine experimentally-determined structures for stabilizing interactions in macromolecular complexes. New enhancements include a JavaScript-based user interface, a database for storing and mining results, a stability predictor for mutants, and an automated tool for generating evolutionary conservation profiles.

 
 

 

SELECTED PUBLICATIONS

Clark, M.D., Kumar, G.S., Marcum, R., Luo, Q., Zhang, Y., and Radhakrishnan, I. (2015). Molecular basis for the mechanism of constitutive CBP/p300 coactivator recruitment by CRTC1-MAML2 and its implications in cAMP signaling. Biochemistry 54, 5439-5446.

Clark, M.D., Marcum, R., Graveline, R., Chan, C.W., Xie, R. Chen, Z., Ding, Y., Zhang, Y., Mondragón, A., David, G., and Radhakrishnan, I. (2015). Structural insights into the assembly of the histone deacetylase-associated Sin3L/Rpd3L corepressor complex. Proc. Natl. Acad. Sci. USA 112, E3669-E3678.

Xie, T., Zmyslowski, M., Zhang, Y., and Radhakrishnan, I. (2015). Multi-specificity of MRG domains. Structure 23, 1049-1057.

Luo, Q., Viste, K., Zaa, J.C., Kumar, G.S., Tsai, W.W., Talai, A., Mayo, K.E., Montminy, M., and Radhakrishnan, I. (2012). Mechanism of CREB recognition and coactivation by the CREB-regulated transcriptional coactivator CRTC2. Proc. Natl. Acad. Sci. USA 109, 20865-20870.

Kumar, G.S., Chang, W., Xie, T., Patel, A., Zhang, Y., Wang, G.G., David, G., and Radhakrishnan, I. (2012). Sequence requirements for combinatorial recognition of histone H3 by the MRG15 and Pf1 subunits of the Rpd3S/Sin3S corepressor complex. J. Mol. Biol. 422, 519-531.

Xie, T., Graveline, R., Kumar, G.S., Zhang, Y., Krishnan, A., David, G. and Radhakrishnan, I. (2012). Structural basis for molecular interactions involving MRG domains: Implications in chromatin biology. Structure 20, 151-160.

Xie, T., He, Y., Korkeamaki, H., Zhang, Y., Imhoff, R., Lohi, O., and Radhakrishnan, I. (2011). Structure of the 30 kDa Sin3-associated protein (SAP30) in complex with the mammalian Sin3A corepressor and its role in nucleic acid binding. J. Biol. Chem. 286, 27814-27824.

Kumar, G.S., Xie, T., Zhang, Y., and Radhakrishnan, I. (2011). Solution structure of the mSin3A PAH2-Pf1 SID1 Complex: a Mad1/Mxd1-like interaction disrupted by MRG15 in the mammalian Rpd3S/Sin3S complex. J. Mol. Biol. 408, 987-1000.

He, Y., Imhoff, R., Sahu, A., and Radhakrishnan, I. (2009). Solution structure of a novel zinc finger motif in the SAP30 polypeptide of the Sin3 corepressor complex and its potential role in nucleic acid recognition. Nucleic Acids Res. 37, 2142-2152.

Sahu, S.C., Swanson, K.A., Kang, R.S., Huang, K., Brubaker, K., Ratcliff, K., & Radhakrishnan, I. (2008). Conserved themes in target recognition by the PAH1 and PAH2 domains of the Sin3 transcriptional corepressor. J. Mol. Biol. 375, 1444-1456.

Little, T.H., Zhang, Y., Matulis, C.K., Weck, J., Zhang, Z., Ramachandran, A., Mayo, K.E. and Radhakrishnan, I. (2005). Sequence-specific DNA recognition by Steroidogenic Factor 1: A helix at the carboxy-terminus of the DNA binding domain is necessary for complex stability. Mol. Endocrinol. 20, 831-843.

Swanson, K.A., Knoepfler, P.S., Huang, K., Kang, R.S., Cowley, S.M., Laherty, C.D., Eisenman, R.N., and Radhakrishnan, I. (2004). HBP1 and Mad1 repressors bind the Sin3 corepressor PAH2 domain with opposite helical orientations. Nat. Struct. Mol. Biol. 11, 738-746.

Swanson, K.A., Kang, R.S., Stamenova, S.D., Hicke, L., and Radhakrishnan, I. (2003). Solution structure of Vps27 UIM-ubiquitin complex important for endosomal sorting and receptor downregulation. EMBO J. 22, 4597-4606.

Kang, R.S., Daniels, C.M., Francis, S.A., Shih, S.C., Salerno, W.J., Hicke, L., and Radhakrishnan, I. (2003). Solution structure of a CUE-ubiquitin complex reveals a conserved mode of ubiquitin binding. Cell 113, 621-630.

Brubaker, K., Cowley, S.M., Huang, K., Loo, L., Yochum, G.S., Ayer, D.E., Eisenman, R.N., and Radhakrishnan, I. (2000). Solution structure of the interacting domains of the Mad-Sin3 complex: Implications for recruitment of a chromatin-modifying repression complex. Cell 103, 655-665.

Radhakrishnan, I., Pérez-Alvarado, G.C., Parker, D., Dyson, H.J., Montminy, M.R., and Wright, P.E. (1997). Solution structure of the KIX binding domain of CBP bound to the transactivation domain of CREB: A model for activator:coactivator interactions. Cell 91, 741-752.

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