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David Bain, Associate Professor

Ph.D. Johns Hopkins University

Associate Professor of Molecular Biophysics
Department of Pharmaceutical Sciences
Director of Pharmaceutical Sciences Graduate Program

Mail Stop C238
Pharmacy and Pharmaceutical Sciences Building, Room 4117
Tel: (303)-724-6118
Fax: (303)-724-7266


The long-term goal of our research is to determine the molecular mechanisms responsible for higher eukaryotic gene regulation. We are specifically interested in quantitatively relating the physical and chemical principles that account for protein interactions at a promoter with the biological phenomenon of transcriptional activation. Our approach to solving this problem is to couple an experimental dissection of the microscopic energetic interactions (e.g. protein-protein, protein-ligand, protein-DNA) with a computational synthesis of the overall macroscopic behavior. We use tools such as analytical ultracentrifugation and quantitative footprinting to study the various macromolecular interactions. Statistical thermodynamics is used to model and fit the data.

We are analyzing the human progesterone receptor (PR) and its interactions at PR-regulated promoters as a model system. PR is a member of the nuclear receptor superfamily of ligand-activated transcription factors. The receptor exists naturally as two functionally distinct isoforms, PR-A and PR-B. The two isoforms are identical except for an additional 164 amino acids at the N-terminus of the B-receptor. Both isoforms contain a centrally located DNA-binding domain (DBD) and a C-terminal hormone binding domain (HBD). Transcriptional activation functions are located N-terminal to the DBD (AF-1) and within the HBD (AF-2). Residues unique to the B-isoform contain a context-dependent activation function, AF-3. The presence of the B-unique sequence (BUS) causes the two isoforms to maintain a number of distinct functional properties including differential transcriptional activation, differential activation by ligands, regulation of different subsets of genes, and tissue-specific functional roles. The molecular origins of these differences are largely unknown. In order to quantitatively describe and predict PR function, we ask: What are the accessible states of the system (structural states, energetic states, functional states) and, What are the rules of transition that connect the states? We then attempt to integrate these results into mathematical models receptor of function.

Connaghan-Jones, KD & Bain, DL (2009) “Using Thermodynamics to Understand Progesterone Receptor Function: Method and Theory”. Methods in Enzymol, 455, 41-70.

Connaghan-Jones, KD, Heneghan, AF, Miura, MT & Bain, DL (2008) “Thermodynamic Dissection of Progesterone Receptor Assembly at the Mouse Mammary Tumor Virus Promoter: Monomer Binding and Strong Cooperativity Dominate the Assembly Reaction.” J. Mol. Biol., 377, 1144-1160.

Connaghan-Jones, KD, Heneghan, AF, Miura, MT, & Bain, DL (2007) “Thermodynamic Analysis of Progesterone Receptor-Promoter Interactions Reveals a Molecular Model for Isoform-Specific Function.” Proc. Natl. Acad. Sci. USA, 104, 2187-2192.

Connaghan-Jones, KD, Heneghan, AF, Miura MT & Bain, DL (2006) “Hydrodynamic Analysis of the Human Progesterone Receptor A-Isoform Reveals that Self-Association Occurs in the Micromolar Range.” Biochemistry, in press.

Bain, DL, Heneghan, AF, Connaghan-Jones, KD & Miura, MT (2006) “Nuclear Receptor Structure: Implications for Function.” Ann. Rev. Physiol., 69, in press.

Heneghan, AF, Connaghan-Jones, KD, Miura, MT & Bain, DL (2006) “Cooperative DNA Binding by the B-Isoform of Human Progesterone Receptor: Thermodynamic Analysis Reveals Strongly Favorable and Unfavorable Contributions to Assembly”. Biochemistry, 45, 3285-3296.

Heneghan, AF, Berton, N, Miura, MT, & Bain, DL (2005) “Self-Assembly Energetics of an Intact, Full-length Nuclear Receptor: The B-Isoform of Human Progesterone Receptor Dimerizes in the Micromolar Range”. Biochemistry, 44, 9528-9537.

Martin, S.L., Branciforte, D., Keller, D. & Bain, D.L. (2003) “Trimeric Structure for an Essential Protein in L1 Retrotransposition”. Proc. Natl. Acad. Sci. USA, 100, 13815-13820.

McManaman, J.L. & Bain, D.L. "Structural and Conformational Analysis of the XD to XO Conversion of Xanthine Oxidoreductase." (2002) J. Biol. Chem. 277, 21261-21268.

Latest Publications in PubMed