- Demir, M. & Russelburg, L. P.; Lin, W.-J.; Trasviña-Arenas, C. H.; Huang, B.; Yuen, P. K.; Horvath, M. P.; David, S. S. (2023). Structural Snapshots of Base Excision by the Cancer-Associated Variant MutY N146S Reveal a Retaining Mechanism. Nucleic Acids.
- Russelburg LP, O'Shea Murray VL, Demir M, Knutsen KR, Sehgal SL, Cao S, David SS, Horvath MP. Structural Basis for Finding OG Lesions and Avoiding Undamaged G by the DNA Glycosylase MutY. ACS Chem Biol. 2020;15(1):93-102. Epub 2019/12/13. doi: 10.1021/acschembio.9b00639. PubMed PMID: 31829624. Published, 01/2020.
- Yuen PK & Green SA, Ashby J, Lay KT, Santra A, Chen X, Horvath MP, David SS. (2018). Targeting Base Excision Repair Glycosylases with DNA containing Transition State Mimics prepared via Click Chemistry. [Website/Blog]. Published, 12/2018.
- Shyam R, Gorusupudi A, Nelson K, Horvath MP & Bernstein PS (2017). RPE65 has an additional function as the lutein tomeso-zeaxanthin isomerase in the vertebrate eye. Proceedings of the National Academy of Sciences of the United States of America. Vol. 114, 10882-10887. Published, 10/01/2017.
- Shyam R & Gorusupudi A, Nelson K, Horvath MP, Bernstein PS. (2017). RPE65 has an additional function as the lutein to meso-zeaxanthin isomerase in the vertebrate eye. Proc Natl Acad Sci USA. Vol. 114(41), 10882-7. Published, 09/2017.
- Structure of the lutein-binding domain of human StARD3 at 1.74 Å resolution and model of a complex with lutein (2016). Acta Crystallogr F Struct Biol Commun 72: 609–618. Published, 03/01/2016.
- Classifying neuronal subclasses of the cerebellum through constellation pharmacology (2016). J. Neurophysiol. 115: 1031–1042. Published, 02/01/2016.
- Structure and stereochemistry of the base excision repair glycosylase MutY reveal a mechanism similar to retaining glycosidases (2016). Nucleic Acids Res. 44: 801–810. Published, 01/01/2016.
- Convergent Evolution of Head Crests in Two Domesticated Columbids Is Associated with Different Missense Mutations in EphB2. Mol Biol Evol, 32, 2657-2664. Published, 10/2015.
- Prey-Capture Strategies of Fish-Hunting Cone Snails: Behavior, Neurobiology and Evolution. Brain Behav Evol, 86, 58-74. Published, 09/2015.
- Olivera, B.M., Safavi-Hemami, H., Horvath, M.P. and Teichert, R.W. (2015) In Baker, B. J. (ed.), Marine Biomedicine: From Beach to Bedside. CRC Press, Boca Raton, FL (USA), pp. 461-495. Published, 06/2015.
- Teichert, R.W., Olivera, B.M., McIntosh, J.M., Bulaj, G. and Horvath, M.P. (2015) In King, G. F. (ed.), Venoms to Drugs: Venom as a Source for the Development of Human Therapeutics. The Royal Society of Chemistry, Cambridge, UK, pp. 163-203. Published, 04/2015.
- R.W. Teichert, B.M. Olivera, J.M. McIntosh, G. Bulaj and M.P. Horvath, The molecular diversity of conoidean venom peptides and their targets: From basic research to therapeutic applications. In Venoms to Drugs, King, G. F., Ed. RCS publishing: Cambridge UK, 2015. Published, 01/01/2015.
- R.J. Platt, K.J. Curtice, V.D. Twede, M. Watkins, P. Gruszczynski, G. Bulaj, M.P. Horvath and B.M. Olivera, From molecular phylogeny towards differentiating pharmacology for NMDA receptor subtypes, Toxicon, 2014, 81, 67-79. Published, 04/01/2014.
My research explores how macromolecules work, especially how molecular interactions establish the emergent properties of specificity, allostery, and catalysis. I apply x-ray crystallography to describe the structures of proteins at atomic level detail. Hypotheses suggested by these structures are tested with biochemical approaches. Four collaborative projects will be summarized in this Research Statement. The first two are funded through NSF (Horvath - PI) and NIH (Horvath - Key Senior Personnel). Students in the Horvath lab are actively pursuing preliminary data to support funding applications for the third project focused on structure determination of a membrane protein involved in chronic pain. Also, I have recently taken steps to launch a fourth project applying machine learning to explore structure and function of insect odorant receptors.
The Horvath lab currently comprises three graduate students, five undergraduate researchers, two post-baccalaureates, and a research technician. We are located in ASB 440 and occupy approximately 500 square feet, plus some equipment and a cold room on the third floor of ASB.
Structure and mechanism of the DNA repair enzyme MutY
MutY and its mammalian homolog MUTYH find OG:A mispairs and initiate base excision repair at these lesions by removing the adenine (A) base. In collaboration with Dr. Sheila David (Chemistry UC Davis), we solved the structure of this enzyme complexed with DNA containing a transition state analog. The transition state is an unstable intermediate encountered in a chemical reaction. Enzymes accelerate chemical reactions by stabilizing the TS, and our crystal structure revealed a close approach of negatively charged Asp 144, indicating strong electrostatic stabilization of the positively charged oxacarbenium ion transition state. The structure also showed the location of a water molecule that likely serves as nucleophile to complete the hydrolytic reaction. This work uncovered a previously unrecognized relationship between DNA glycosylases and glycosidases such as hen egg white lysozyme which also hydrolyze bonds to sugar moieties with retention of stereochemistry. The article published in 2016 provided preliminary data for the NSF funding application which was awarded and renewed in 2019. An application for a second renewal has been submitted November 2021.
As part of this project, Graduate student Peyton Russleburg in my lab has been further exploring the source of cross-strand base specificity. MutY operates on OG:A lesions and pays particular attention to the OG base, which remains intact in the MutY-generated product. OG arises in DNA through oxidative damage of G bases and is promutagenic because of its ability to template insertion of A during replication. A second round of replication would potentially create a GC to TA transversion mutation, but MutY prevents this event by locating OG:A and removing the A base. MutY is very efficient acting on OG:A substrates and avoiding G:A substrates, a remarkable example of substrate specificity given that these differ by only two atoms, one of which is a hydrogen. Peyton solved the structure of MutY complexed to DNA with OG replaced by G and noted that Ser 308 adopts a new rotamer so as to break two hydrogen bonds previously observed in the structure of OG DNA-MutY. Peyton replaced Ser 308 and its nearest neighbors Phe 307 and His 309 to demonstrate that the three residues (FSH in single-letter code) impart OG versus G discrimination. Replacing two or more of these residues led to higher mutation rates in bacteria cultures and an enzyme that treated OG:A and G:A similarly. This work was published in 2020 in the journal ACS Chemical Biology with cover art created by Peyton. Peyton recently defended December 2021 and is finalizing her PhD thesis which will be the basis for two more manuscripts to be submitted this spring. She is pursuing a postdoctoral appointment in academia or in biotechnology.
Vincent Mays was recruited to the MutY project in 2021 and will be defending his thesis proposal spring 2022. During his rotation project and soon after joining the lab, Vincent made the exciting discovery that MutY acts on RNA-DNA substrates with important implications for development of a base pair editing tool. This result is the cornerstone for one subaim in the NSF renewal application. A number of undergraduate students have contributed to the MutY project. Notable among these is Sonia Sehgal who began as an ACCESS student her freshman year, earned the Biology Research Scholars award summer 2019, and was further recognized with the competitive and prestigious Beckman Foundation Fellowship award in her senior year. Sonia’s current work explores the potential impact of common medicines on MutY function. She is now a first-year medical student at Univ of Utah but still finds time to come to do experiments!
Biochemistry of macular carotenoids
Primates have adapted to daytime hunting and gathering by recruiting pigment molecules to the retinal epithelium. In collaboration with Dr. Paul Bernstein (Moran Eye Center, Ophthalmology, University of Utah Medical School), we have sought to understand the biochemistry of lutein, zeaxanthin, and meso-zeaxanthin. This work is funded through an NIH grant. Students in my lab have determined high-resolution structures for the proteins GSTP1 and StARD3 that bind to these xanthophylls. Additionally, we have applied molecular docking to generate realistic carotenoid-bound models. This molecular modeling has led to a protein kissing hypothesis whereby the large, highly hydrophobic ligands leave the binding site in one partner protein and enter the active site of another in a directional manner. While lutein and zeaxanthin are commonly found in our diet, meso-zeaxanthin is rarely available except in the skin of certain fish. My molecular modeling experiments support the hypothesis that RPE65 is the isomerase that converts zeaxanthin to meso-zeaxanthin in chickens and humans. Intriguingly, RPE65 from mouse lacks this isomerase activity. My research technician, Markell Kolendrianos, applied bioinformatics to identify 5 residues that differ in chicken and mouse RPE65 and which also co-evolve with specific residues in other xanthophyll-binding proteins. With this preliminary data in hand, I wrote aim 1 for the funding renewal proposal which recently scored in the top 10%, guaranteeing continuation of support.
Membrane protein structural biology
Chronic neuropathic pain is difficult to treat with no known cure. Michael McIntosh (Psychiatry, Univ of Utah) has discovered derivatives of a natural product found in the venom of the cone snail C. regius that alleviate and prevent establishment of the chronic pain state in animals. The target of these pain-preventing compounds is the alpha9 nicotinic acetylcholine receptor (a9R). In 2017, I traveled to UT Southwestern in Dallas Texas for a 6-month sabbatical with Dr. Ryan Hibbs (Neurobiology, Biophysics) to learn how to purify and determine the structure for this non-opioid receptor pain target. I returned for another 6-month term in 2021 after learning others had discovered accessory proteins that establish functional expression for a9R in mammalian cell culture. We obtained a 14-Å resolution view of the receptor through single-particle cryo-electron microscopy. My research technician Markell Kolendrianos and MS graduate student Keelah Barger are continuing the pursuit of preliminary data to support funding applications, which so far have not been awarded (see attached summary statements).
Machine learning to discover protein function for insect odorant receptors
Odorant receptors (OR)s in insects assemble as trans-membrane heterotetramers with odorant binding sites in each receptor subunit and one (or more) co-receptor (ORCO) subunit. The project aims to develop structure-aware, generalizable, and interpretable machine learning models for understanding protein function, especially the interactions of ORs with hydrophobic odorant chemicals. The working hypothesis is that ML will learn and enrich protein structure representations for better prediction of protein function. With no formal background in computer science, I am building a team comprising Dr. Bei Wang Phillips (Computational Science), Dr. Yi Zhao (Computational Engineering) and Dr. Neil Vickers (Co-director, School of Biological Sciences) to develop a competitive proposal with the Molecular Foundations in Biotechnology program at NSF.
- X-ray Diffraction
- Structural Biology
- Odorant Receptors
- Membrane Structure or Function
- Machine Learning
- DNA-protein interactions
- Chronic Pain
- Biorecognition of Macromolecules
- Biochemistry, Proteins
- Biochemistry, Nucleic Acids
- Tara Tazehabadi, MP Horvath Bioinformatics Detecting Functional Interactions Important for DNA Repair Enzyme MUTYH. Undergraduate Research Symposium, University of Utah, Salt Lake City, USA . Poster, Presented, 08/2022.
- Harini Srinivasan, MP Horvath Molecular Drug Docking and Biochemical Performance of Adenine Specific Glycosylase Enzyme MutY in the Presence of 8-Oxo-7,8-Dihydroguanine (OG) Nucleotide. Undergraduate Research Symposium, University of Utah, Salt Lake City, USA . Poster, Presented, 04/2022.
- Mary Fairbanks, MP Horvath Examining Impact of FDA Approved Drugs on DNA Repair Enzymes. Undergraduate Research Symposium, University of Utah, Salt Lake City, USA . Poster, Presented, 04/2022.
- Exploring the Role of Biological Probes on MUTYH. Beckman Foundation Virtual Research Symposium, California, USA. Poster, Presented, 08/2021.
- Payton Utzman, MP Horvath A Structural Analysis of the LC MutY Metagenome. Undergraduate Research Symposium, University of Utah. Poster, Presented, 05/2020.
- Mary Fairbanks, MP Horvath The role of calcium on MutY. ACCESS Women in Science and Mathematics Symposium, University of Utah. Poster, Presented, 04/2020.
- Sonia Ling Sehgal, MP Horvath (August 2019) Improving Expression in Lost City MutY DNA Repair Enzymes. Undergraduate Research Scholars, SBS 2019 Science Retreat & Gordon Lark Symposium, University of Utah, Salt Lake City, USA. Poster, Presented, 08/2019.
- Karina Cedeno, MP Horvath (April 2019) Alpha-9 nicotinic acetylcholine receptor, a non-opioid target for treatment of chronic neuropathic pain. Undergraduate Research Symposium, University of Utah, Salt Lake City, USA. Poster, Presented, 04/2019.
- Malika Kadirova, MP Horvath Structure determination for lutein-complexed proteins in the human eye. Undergraduate Research Symposium, University of Utah, Salt Lake City, USA. Poster, Presented, 04/2018.
- Mechanism and evolution of the DNA repair enzyme MutY. Understanding Biology Through Structure Symposium, Santa Fe, New Mexico, 13-16 May 2017. Poster, Presented, 05/13/2017.
- Cecily T. Bader, Sieburth LE and MP Horvath The response of Arabidopsis mutant bps 1-2 on salt media. Undergraduate Research Symposium, University of Utah, Salt Lake City, USA. Poster, Presented, 04/2017.
- Kacey A. Davis and MP Horvath Predatory Marine Snail Toxins: a Study of Protein Folds. Utah Conference for Undergraduate Research (UCUR), Utah Valley University, American Fork, Utah, USA. Poster, Presented, 02/2016.
- Alexander M. Cao and M.P. Horvath (April 2015) Refolding of protein domains derived from the NMDA receptor, National Conference for Undergraduate Research, Eastern Washington University, Spokane Washington, USA. Poster, Presented, 08/2015.
- Alexander M. Cao and M.P. Horvath (March 2015) Refolding of protein domains derived from the NMDA receptor, University of Utah Undergraduate Symposium, Salt Lake City Utah, USA. Poster, Presented, 06/2015.
- Alyssa I. Fredbo and M.P. Horvath (April 2015) Bacterial expression of predatory cone snail toxins to identify potential novel therapeutic drugs, National Conference for Undergraduate Research, Eastern Washington University, Spokane Washington, USA. Poster, Presented, 06/2015.
- Sara Lee, Gabe Zharov & MP Horvath. Modifying StARD3 protein for tagless expression in bacteria. High School Poster Session. Poster, Presented, 07/31/2014.
- MP Horvath, B Li, H Sharifzadeh and PS Bernstein (June 2014) Electron density difference maps calculated for an ocular carotenoid-binding protein GSTP1. (June 2014) Northwest crystallography workshop, Oregon State University, Corvallis Oregon, USA. Poster, Presented, 06/20/2014.
- Challenges in Crystallography. Informal seminar discussion presented at the University of Oregon, Department of Biochemistry, Biophysics & Molecular Biology. Contributed Talk, Presented, 06/19/2014.
- Bianca E. Rich and M.P. Horvath (April 2014) Toward crystallizing proteins from NMDA receptor in complex with toxins from marine snails, National Conference for Undergraduate Research, University of Kentucky, Lexington Kentucky, USA. Poster, Presented, 04/03/2014.
- Sara L. Mann and M.P. Horvath (April 2014) Purification and characterization of aryl alcohol dehydrogenase, a detoxification enzyme found in the gut of woodrats that eat a poison diet, University of Utah Undergraduate Symposium, Salt Lake City Utah, USA . Poster, Presented, 04/01/2014.
Research Equipment and Testing Expertise
- FSEC fluorescence detection size exclusion chromatography. Allows for analysis of protein expression and receptor assembly in crude extracts without labor intensive purification. Contact: Martin Horvath , 801-891-3477 , School of Biological Sciences.
- French, functional.
- Swedish, fluent.