Structural Biology
Section Leader
Young-In Chi, Ph.D.
Assistant Professor

The Hormel Institute - Young-In Chi

 

Structural biology is a branch of biomedical science concerned with molecular structures of biological macromolecules, such as proteins and nucleic acids. Given that their biological functions are tightly coupled to their molecular structures, elucidating atomic details of their structures is crucial to understanding the molecular mechanisms underlying their physiological functions. Biomolecules are too small to be seen even with the most-advanced electron microscope. Special techniques need to be employed. We particularly harness X-ray crystallography as a main experimental tool to elucidate threedimensional structures. This technique involves various disciplines of modern biomedical research, such as molecular biology, nucleic acid/protein chemistry, biophysics, and various computations. We also perform eukaryotic cell-based functional studies to complement the structural studies. Our long-term goal is to elucidate how biomolecules work and identify new avenues for developing therapeutics.

 

Our research focuses on elucidating atomic details of key molecular interactions involved in diseases, especially diabetes and cancer. In particular, we focus on transcriptional regulators involved in diabetes and protein functional modulators involved in tumor progression and metastasis. We apply structural biology to better understand their normal function and dysfunction in the disease state as well as discover or design structure-based functional modulators.

HNF1. (Hepatocyte Nuclear Factor1.) and HNF4. are the master regulators of pancreatic .-cell development and function, and their mutations are the most common monogenic causes of diabetes referred to as MODY. Over the years, we have determined the crystal structures of the functional complexes made by HNF1. and HNF4.. These structures provided valuable information on the molecular basis of targetgene recognition, ligand-mediated activation, and functional disruption by disease-causing mutations. These structures, however, provided partial answers as to how their full transcriptional activities arise and how these proteins are involved in additional protein-protein interactions and physiological functions. We set out to identify previously unknown functional binding partners of HNF1. and HNF4. in .-cells and study these interactions. physiological implications . especially on insulin secretion that is impaired in MODY patients . and perform structural studies of the complexes and functional characterization of MODY mutations. We previously published findings on the mediator component of the main transcriptional machinery, MED25, as the functional binding partner of HNF4. and its implication to .-cell function. We are following up on additional binding partners and their physiological implications, such as novel transcriptional corepressors AES and EBP1 for HNF1. and HNF4., respectively. These studies will advance the understanding of the transcription regulatory network in .-cells and provide a new avenue for diabetes prevention/treatment by discovering novel, more-effective target sites for designing and further improving partial agonists selectively against them.

Another diabetes-related project is the structural basis of Glucose-6-phosphatase (G6pase) gene regulation, especially by the transcription factors Foxo1 and Creb. G6pase is a key regulating enzyme for gluconeogenesis in the liver and an attractive target for diabetes treatment. We finished the Foxo1/DNA complex structure and have submitted the manuscript for publication in which we identified a new Foxo1 binding site and novel binding modes on G6pase promoter.

“Our research currently is focused on elucidating the atomic
details of key molecular interactions involved in human
diseases, especially diabetes and cancer.”
Dr. Young-In Chi”

We also have embarked on new cancer research projects. Dub3 is an ubiquitin hydrolase (de-ubiquitinase) and key protein that relays extrinsic signals to regulate epithelial-mesenchymal transition (EMT) and metastasis in breast cancer. It can serve as a druggable target for treating triple negative/basallike breast cancers. We started determining the crystal structure of the Dub3 catalytic domain alone and/or its complex ubiquitin, its substrate. We have made sufficient progress and are improving the crystals as well as finishing the structure determination. Once complete, we will start computer-assisted docking analysis of chemical library compounds to discover/design specific inhibitors of Dub3 to improve the prognosis of these hard-to-treat breast cancers. Candidate compounds will be tested in vitro and in vivo for their ability to suppress the de-ubiquitinase activity of Dub3. These findings will validate the effectiveness of Dub3 target strategy and could lead to new therapeutic interventions.

Another study is on the leukemic fusion protein AML1-ETO that occurs frequently in acute myeloid leukemia (AML) and has received much attention over the past decade. We want to understand the critical roles of the EZH1/ AML1-ETO and HIF1a/AML1-ETO axes in acute myeloid leukemia cell formation and growth. This multifaceted project is in collaboration with The Hormel Institute.s Dr. Shujun Liu as we work on crystal structure determination of the complexes and virtual screening of compounds for potential functional modulator discovery.

Thirdly, hexokinase II (HK2), which catalyzes the first committed step in glucose metabolism, is expressed exclusively in prostate cancer cells, particularly elevated in lethal castration-resistant prostate cancer (CRPC) harboring PTEN/p53 deletions. HK2 has emerged as an attractive target for incurable CRPC. Together with Dr. Yibin Deng of The Hormel Institute, we have assembled a multidisciplinary research team targeting this protein from different angles. One way to inhibit HK2.s oncogenic activity is to suppress its gene expression. It recently was reported that HK2 expression is regulated by untranslated RNAs.

The Hormel Institute - Young-In Chi Lab

(Left to right) Puja Singh, Young-In Chi
Crystal specimens of a Not pictured: Shu-Ping Tung

We seek to elucidate the molecular mechanism of HK2 gene regulation by RNA local structures at the untranslated region, in particular its association with the translation initiation factors, such as eIF4a. These studies. successful outcomes, including the complex.s crystal structure, will help identify novel, anti-prostate cancer therapeutic compounds.

Additional cancer-related projects with therapeutic values include FABP/inhibitor complexes, novel protein kinases/inhibitor complexes, and small RNA molecules for drug delivery. Our lab will continue this work and expand target molecules to include more cancer-related proteins leading to additional preliminary data for sustaining grant applications. Crystal structure determination, functional studies, and drug discovery will provide a critical basis for human physiology, dysfunction in the disease state, and a better strategy for therapeutic intervention.