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Faculty Profile

Syun-Ru Yeh, Ph.D.

Dr. Syun-Ru Yeh

Professional Interests

We are interested in structure, function, dynamics and folding of oxygen utilizing hemeproteins in general. Hemeproteins constitute one of the most important classes of biomolecules. Despite intense effort, it remains unclear as to how each hemeprotein tailors its function by modulating the environment of the heme prosthetic group. Our research goal is to investigate biological processes associated with physiologically important hemeproteins (such as indoleamine 2, 3-dioxygenase (IDO), tryptophan dioxygenase (TDO), nitric oxide synthase (NOS), cytochrome oxidase, cytochrome bc1 and globins), by using a complementary set of spectroscopic techniques (such as optical absorption, fluorescence, circular dichroism, UV/VIS resonance Raman scattering, FTIR, EPR, MS and X-ray crystallography), combined with computational methodologies (MD and QM/MM). In the past decade, we have also devoted a significant effort in developing faster and more efficient solution mixing technologies that can be used to study biological and chemical reactions in a sub-millisecond time window.

Indoleamine 2,3-dioxygenase (IDO) and tryptophan 2,3-dioxygenase (TDO). IDO and TDO are the only two heme-containing enzymes that catalyze the oxidative cleavage of tryptophan (Trp) to N-formyl kynurenine, the initial and rate-limiting step of the kynurenine pathway. Trp is the scarcest essential amino acid in mammals. The majority of our dietary Trp (~95%) is metabolized along the kynurenine pathway in the liver by TDO, which ultimately leads to the biosynthesis of NAD. A small amount of the Trp (~1%) is used to synthesize the neurotransmitter serotonin. Consequently, TDO plays a critical role in determining the relative Trp flux in the serotonergic and kynurenic pathways. In contrast to the hepatic TDO, IDO is ubiquitously distributed in all tissues other than liver. Instead of regulating homeostatic serum Trp concentrations like TDO, IDO plays an important immunomodulatory role that is mediated through effects of tryptophan catabolism on T cells. IDO has recently been identified as an important anti-cancer drug target, owing to its role in allowing cancer cells to escape from immune surveillance.  Our long term goal is: (1) to elucidate the dioxygenase reaction mechanism of IDO and TDO, a major gap in our current knowledge of heme oxygen chemistry, and (2) to develop pharmaceutically suitable IDO-selective inhibitors for the control of cancer, microbial pathogens, and various IDO-related pathological conditions.

Bacterial Hemoglobins (Hbs). The recent discoveries of Hbs in unicellular organisms add a new twist to our common perception of Hbs as an oxygen carrier. The objective of this research is to study the structural and functional properties of the Hbs from three human pathogens, M. tuberculosis (trHbN and trHbO), C. jejuni (trCtb and Cgb) and E. coli (Hmp), as compared to the classical mammalian globins. Mounting evidence suggests that the main function of trHbN, Cgb and Hmp is to perform oxygen chemistry, thereby protecting the bacteria against host attack by detoxifying reactive oxygen and nitrogen species, whereas that of trHbO and trCtb is to transport or sense oxygen, thereby regulating oxygen flux into and within the bacteria.  The long term goal of this research is to combine experimental and computational methodologies to decipher the structure and function relationships of these two intriguing groups of Hbs.

Development of Microfluidic Silicon Mixers and Freeze-Quenching Devices. The studies of fast biological reactions in general have been limited by ~1 millisecond deadtime of the commercially available stopped-flow or continuous-flow instrumentation. For freeze-quenching applications the deadtime can be even up to ~10-50 millisecond. The novel microfluidic silicon solution  mixers that we developed has a deadtime down to ~ 20 microsecond. They can be used in either a continuous-flow or freeze-quenching mode. For freeze-quenching applications, we have designed a double-wheel based freezing device that can be easily coupled with the microfluidic silicon mixers to trap reaction intermediates with a deadtime time down to 50 microsecond, which is ~200 times faster than that of commercially available freeze-quenching systems. The continuous-flow and freeze-quenching devices have been tested and successfully applied for the studies of several important biological reactions in a time window that was not accessible in the past.


Selected Publications

Structure and Function Relationship of IDO TDO and NOS

“Catalytic intermediates of inducible nitric oxide synthase stabilized by the W188H mutation.”Sabat J, Egawa T, Lu C, Stuehr DJ, Gerfen GJ, Rousseau DL, Yeh SR. J Biol Chem. 288, 6095-106, 2012.

“Ferryl derivatives of human indoleamine 2,3-dioxygenase” Lu C, Yeh SR. J Biol Chem. 286, 21220-30, 2011.

“Molecular basis for the substrate stereoselectivity in tryptophan dioxygenase.” Capece L, Lewis-Ballester A, Marti MA, Estrin DA, Yeh SR., Biochemistry, 50, 10910-8, 2011.

“Spectroscopic Studies of Ligand and Substrate Binding to Human Indoleamine 2,3-Dioxygenase.” Lu C, Lin Y, Yeh SR. Biochemistry, 49, 5028-34, 2010.

"Evidence for a ferryl intermediate in a heme-based dioxygenase." Lewis-Ballester A, Batabyal D, Egawa T, Lu C, Lin Y, Marti MA, Capece L, Estrin DA, Yeh SR. Proc Natl Acad Sci U S A. 106, 17371-6, 2009.

"Inhibitory substrate binding site of human indoleamine 2,3-dioxygenase." Lu C, Lin Y, Yeh SR. J Am Chem Soc.131, 12866-7, 2009.

"Substrate-protein interaction in human tryptophan dioxygenase: the critical role of H76." Batabyal D, Yeh SR. J Am Chem Soc. 131, 3260-70, 2009

Structure and Function Relationship of Globins

“An Unconventional Hexacoordinated Flavohemoglobin from Mycobacterium tuberculosis.” Gupta S, Pawaria S, Lu C, Hade MD, Singh C, Yeh SR, Dikshit KL. J Biol Chem. 287, 16435-46, 2012.

“Novel Flavohemoglobins of Mycobacteria” Gupta S, Pawaria S, Lu C, Yeh SR, Dikshit KL. IUBMB Life, 63, 337-45, 2011.

“Role of the distal hydrogen-bonding network in regulating oxygen affinity in the truncated hemoglobin III from Campylobacter jejuni.”  Arroyo M. P, Lu C, Boechi L, Marti MA, Shepherd M, Wilson JL, Poole RK, Luque FJ, Yeh SR, Estrin DA. Biochemistry, 50, 3946-56, 2011.

"Role of Copper Ion in Regulating Ligand Binding in a Myoglobin-Based Cytochrome c Oxidase Model." Lu C, Zhao X, Lu Y, Rousseau DL, Yeh SR. J Am Chem Soc. 132, 1598-605, 2010.

“The single-domain globin from the pathogenic bacterium campylobacter jejuni: Novel D-helix conformation, proximal hydrogen bonding that influences ligand binding, and peroxidase-like redox properties.” Shepherd M, Barynin V, Lu C, Bernhardt PV, Wu G, Yeh SR, Egawa T, Sedelnikova SE, Rice DW, Wilson JL, Poole RK. J Biol Chem. 285, 12747-54, 2010.

Development of Microfluidic Silicon Mixers and Freeze-Quenching Devices

"Design and evaluation of a passive alcove-based microfluidic mixer." Egawa T, Durand JL, Hayden EY, Rousseau DL, Yeh SR. Anal Chem. 81, 1622-7, 2009.

"Ultrafast microfluidic mixer and freeze-quenching device." Lin Y, Gerfen GJ, Rousseau DL, Yeh SR. Anal Chem. 75, 5381-6, 2003.



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