Research Interests:

Molecular basis of mutations found in inherited human diseases

The complete human genome sequence and modern genetic tools allow us to facilitate the identification of all genes that contribute to human diseases (www.ncbi.nlm.nih.gov/Omim). Random nucleotide mismatch, insertion or deletion during DNA replications can lead to many different types of mutations such as frame shift, nonsense (truncation) or missense (point) mutations. Among these, missense mutations and the encoded single amino acid substitutions are more instructive as site-specific measures of protein function.

We are utilizing the method of X-ray crystallography to understand the molecular basis of these point mutations found in the culprit gene products, especially transciption factors and mediators, from their three-dimensional structures. Transcription factors are central players in all developmental processes and also in adult homeostasis. Because transcription factors orchestrate the manufacture of proteins that make up living tissues and regulate all of the body’s functions, any genetic defects in them can lead to serious illnesses such as developmental defects, metabolic disorders and malignant tumors.  Because the structure dictates protein’s functions, these structures of the proteins and complexes will shed lights on how these mutations cause the loss of protein functions at the molecular level, and aid us to design agonists or antagonists once we identified key residues for their functions.

The projects in progress include a transcription factor HNF1a (Hepatocyte Nuclear Factor1a) whose mutations are the most common Mendelian cause of diabetes mellitus, and another transcription factor LMX1B (LIM-homeodomain factor1B) whose mutations are responsible for Nail-patella syndrome, and a putative transcription factor AIRE (Auto Immune Regulator) whose mutations cause onset of various multi-organ autoimmune diseases. More projects will be considered and the accumulated findings and knowledge will be added to the resources available in the public domain.

 Structural studies on the mechanisms of cAMP-dependent gene regulation

Many physiological events in a living cell require signal transduction pathways and inducible gene expressions as final readouts. These orchestrated cellular communications involve various protein-protein, protein-DNA, and protein-ligand interactions.

The cyclic AMP-responsive gene regulations represent a good model for ligand-induced signal transduction and gene activation. Upon ligand binding to a Gprotein-coupled receptor, cAMP is produced and initiates a cascade of signal transduction results in the activations of a set of transcription factors known as the cyclic AMP-responsive element binding (CREB) protein family. These transcription factors control the expression of a large number of genes in response to various signaling pathways leading to physiological functions such as memory, circadian rhythm and metabolic pathways. Activation by CREB can occur classically upon phosphorylation at an essential regulatory site (Ser133 in CREB) and the subsequent interaction with the ubiquitous coactivator CREB-binding protein (CBP), or through interaction with a recently identified tissue-specific coactivator ACT (activator of CREM in testis) in a phosphorylation-independent manner. These interactions would further trigger the formation of the transcription initiation complex by recruiting the basal components of the transcriptional machinery.

Our laboratory utilizes a tool of X-ray crystallography to visualize the molecular details of the complexes with CREB, DNA, coregulators and other mediators regulating the cAMP-responsive gene expressions. These efforts will aid us to understand the mechanisms that relay the signal to the main players of the transcriptional machinery, and the mechanisms by which selectivity is achieved in the identification of target genes, as well as the routes adopted to ensure tissue-specific activation upon physiological changes and needs.

Selected Recent Publications:

Chi, Y.-I., Frantz, J.D., Oh, B.C., Hansen, L., Dhe-Paganon, S. and Shoelson, S.E. Diabetes mutations delineate an atypical POU domain in HNF-1alpha Mol Cell. 10:1129-37, 2002