Molecular Mechanisms and Structural Biology of Hemeproteins

We are interested in understanding how proteins, in particular hemeproteins, work within their cellular environment in health and disease. The three-dimensional structures of hemeproteins are designed by nature to perform a variety of biological functions raging from delivering electrons, transporting oxygen, sensing small gas molecules, to oxidizing inert organic substances. These biological activities are typically finely tuned by translational / post-translational regulations and/or by intermolecular interactions with small cellular metabolites or macromolecules in response to environmental stimuli. Our current research is focused on the comprehension of structure-and-function relationships of a group of human hemeproteins called dioxygenases, including tryptophan dioxygenase (TDO) and two isoforms of indoleamine 2,3-dioxygenase (IDO1 and IDO2), at the molecular level.

The three dioxygenases catalyze the first and rate-limiting step of the Kynurenine pathway, the major metabolic pathway of tryptophan (Trp), by degrading it to N-formyl Kynurenine. Through controlling the Trp metabolism, these enzymes downregulate autoimmunity by depleting Trp, the least abundant essential amino acid required for immune cell growth, and by producing immunosuppressive Trp metabolites. The malfunction and/or dysregulation of the dioxygenases leads to a wide variety of disorders, such as inflammatory diseases, cardiovascular diseases, diabetes, mental disorders, and cancer.

Comprehending the functional and regulatory mechanisms of these enzymes in healthy and disease states can thus identify novel opportunities for targeted therapies.

To achieve our research goals, we employ diverse and complementary approaches spanning from spectroscopy, crystallography, high throughput screening, medicinal chemistry, protein engineering to computational biology. We develop novel techniques, such as spectroscopy-guided X-ray crystallography and serial crystallography, to understand the evolution of protein allostery, the choreography of biochemical pathways and enzyme catalysis.

Selected References

  • Ishigami I, Russi S, Cohen A, Yeh SR, Rousseau DL. “Temperature-dependent structural transition following X-ray-induced metal center reduction in oxidized cytochrome c oxidase.” J Biol Chem. 298, 101799, 2022.
  • Guo L, Schurink B, Roos E, Nossent EJ, Duitman JW, Vlaar AP, van der Valk P, Vaz FM, Yeh SR, Geeraerts Z, Dijkhuis A, van Vught L, Bugiani M, Lutter R, “Indoleamine 2,3-dioxygenase IDO-1 and IDO-2 activity and severe course of COVID-19.” J Pathol. 256, 256-261, 2022.
  • Pham KN, Lewis-Ballester A, Yeh SR. “Conformational Plasticity in Human Heme-Based Dioxygenases.” J Am Chem Soc. 143, 1836-1845, 2021.
  • Liu Y, Kim SM, Wang Y, Karkashon S, Lewis-Ballester A, Yeh SR, Correia MA. “Characterization of the structural determinants of the ubiquitin-dependent proteasomal degradation of human hepatic tryptophan 2,3-dioxygenase.” Biochem J. 478, 1999-2017, 2021.
  • Pham KN, Lewis-Ballester A, Yeh SR. “Structural Basis of Inhibitor Selectivity in Human Indoleamine 2,3-Dioxygenase 1 and Tryptophan Dioxygenase.” J Am Chem Soc. 141, 18771-18779, 2019.
  • Ishigami I, Lewis-Ballester A, Echelmeier A, Brehm G, Zatsepin NA, Grant TD, Coe JD, Lisova S, Nelson G, Zhang S, Dobson ZF, Boutet S, Sierra RG, Batyuk A, Fromme P, Fromme R, Spence JCH, Ros A, Yeh SR, Rousseau DL. “Snapshot of an oxygen intermediate in the catalytic reaction of cytochrome c oxidase.” Proc Natl Acad Sci U S A. 116, 3572-3577, 2019.
  • Winters M, DuHadaway JB, Pham KN, Lewis-Ballester A, Badir S, Wai J, Sheikh E, Yeh SR, Prendergast GC, Muller AJ, Malachowski WP. “Diaryl hydroxylamines as pan or dual inhibitors of indoleamine 2,3-dioxygenase-1, indoleamine 2,3-dioxygenase-2 and tryptophan dioxygenase.” Eur J Med Chem. 162, 455-464, 2019.
  • Pham KN, Yeh SR. “Mapping the Binding Trajectory of a Suicide Inhibitor in Human Indoleamine 2,3-Dioxygenase 1.” J Am Chem Soc. 140, 14538-14541, 2018.
  • Lewis-Ballester A, Karkashon S, Batabyal D, Poulos TL, Yeh SR. “Inhibition Mechanisms of Human Indoleamine 2,3 Dioxygenase 1.” J Am Chem Soc. 140, 8518-8525, 2018.
  • Lewis-Ballester A, Pham KN, Batabyal D, Karkashon S, Bonanno JB, Poulos TL, Yeh SR. “Structural insights into substrate and inhibitor binding sites in human indoleamine 2,3-dioxygenase 1.” Nat Commun. 8, 1693, 2017.
  • Lewis-Ballester A, Forouhar F, Kim SM, Lew S, Wang Y, Karkashon S, Seetharaman J, Batabyal D, Chiang BY, Hussain M, Correia MA, Yeh SR*, Tong L.* “Molecular basis for catalysis and substrate-mediated cellular stabilization of human tryptophan 2,3-dioxygenase.” Sci Rep. 6, 35169, 2016.
  • Kaluka D, Batabyal D, Chiang BY, Poulos TL, Yeh SR. “Spectroscopic and mutagenesis studies of human PGRMC1.” Biochemistry. 54, 1638-47, 2015.