Vladimir Yarov-Yarovoy, Ph.D.
Associate Professor
4131 Tupper Hall
Davis Campus
530-752-5298
e-mail

For more information visit the Laboratory Website »

My research interests and expertise encompass neuroscience, protein structure, computational biology, and evolution. Main focus of my research group is on structure and function studies of voltage-gated ion channels, computational design and chemical synthesis of subtype-specific modulators of voltage-gated ion channels, development of computational methods for membrane protein structure prediction and design, and analysis of evolution of human voltage-gated ion channels.

Function and modulation of neuronal sodium channels are critical for the neuromodulation of electrical excitability and synaptic transmission in neurons - the basis for many aspects of signal transduction, learning, memory and physiological regulation. Mutations in neuronal voltage-gated sodium channel genes are responsible for various human neurological disorders. Furthermore, human neuronal voltage-gated sodium channels are primary targets of therapeutic drugs used as local anesthetics and for treatment of neurological and cardiac disorders. My first project is focusing on studying of neuronal voltage-gated sodium channels structure, function, and modulation in order to design new therapeutically useful drugs for treatment of pain and epilepsy. Serious, chronic pain affects at least 116 million Americans each year and epilepsy affects nearly 3 million Americans and 50 million people Worldwide. However, the treatment of chronic pain and epilepsy remains a major unmet medical need because the use of currently available drugs is limited due to incomplete efficacy and/or significant side effects. Considerable efforts by pharmaceutical industry toward identifying selective inhibitors of one or more of Nav channel subtypes did not generate any genuinely subtype selective blockers and none are currently advancing through clinical trials. My laboratory uses an innovative approach to design novel subtype selective Nav channel blocking drugs with high efficacy and minimum side effects. Novel drugs will be tested using methods of electrophysiology, biochemistry, and molecular biology. This project will provide key structural information on the molecular basis of neuronal voltage-gated sodium channels function and its interaction with therapeutically useful subtype-specific modulators. Understanding of function and modulation of the neuronal voltage-gated sodium channels on structural level will give us profound insights into the fundamental mechanisms underlying neuromodulation and signal transduction

Over the past decade, there has been significant progress in determining membrane protein structures in general and ion channel structures in particular using x-ray crystallography methods. However, it is still very difficult to obtain high-resolution structural information about these proteins. My second project is focusing on further development of the Rosetta-Membrane computational method for high-resolution membrane protein structure prediction and design. I developed the original Rosetta-Membrane method for membrane protein structure prediction in collaboration with David Baker's group at the University of Washington and applied it for modeling of membrane proteins in general and ion channels in particular. I now propose to further improve accuracy of the Rosetta-Membrane method and expand its capabilities to design membrane proteins with new functions.

Evolution of ion channels from bacteria to human took several billion years and while there are basic features that are common to bacterial and human ion channels, such as pore-forming and/or voltage-sensing domains, there are abundance of unique features in every human ion channel family that are absent in bacterial ion channels and have been designed through evolutionary time to accomplish highly specific functions. My third project is focusing on exploring evolution of human voltage-gated ion channels using available prokaryotic and eukaryotic genomes and high-resolution ion channels structures. Human ion channel family is ranking third in a number of family members after the G protein coupled receptors and the protein kinases. To identify the mechanisms by which historical mutations generated distinct human ion channel functions, it is essential to compare proteins through evolutionary time. Moreover, reconstruction of key intermediate ancestors of ion channels by computational structural design can further advance our understanding of evolution of human ion channel function. Previously, I used bioinformatics based analysis of available high-resolution membrane proteins structures to derive parameters of membrane environment-specific scoring function used in the Rosetta-Membrane method. I now propose to analyze evolution of human voltage-gated sodium channels using phylogenetic trees and multiple sequence alignments of homologous sequences and correlate it with available structural and functional data. I will use the Rosetta-Membrane method to predict structures of human ion channels for which high-resolution structures are not available. Mapping of evolutionary information onto human voltage-gated sodium channel structures will give us significant new insights into evolution of their structure and function.

See: An updated list of current publications on PubMed, Google Scholar »

Yarov-Yarovoy V, DeCaen PG (2019) The Sodium Channel Voltage Sensor Slides to Rest. Trends Pharmacol Sci. pii: S0165-6147(19) 30195-6. doi: 10.1016/j.tips.2019.08.009.

Ng LCT, Vien TN, Yarov-Yarovoy V, DeCaen PG (2019) Opening TRPP2 (PKD2L1) requires the transfer of gating charges. Proc Natl Acad Sci USA 116(31): 15540-15549. doi: 10.1073/pnas.1902917116.

Dong Y, Yin Y, Vu S, Yang F, Yarov-Yarovoy V, Tian Y, Zheng J (2019) A distinct structural mechanism underlies TRPV1 activation by piperine. Biochem Biophys Res Commun. 516(2): 365-372. doi: 10.1016/j.bbrc.2019.06.039.

Yin Y, Dong Y, Vu S, Yang F, Yarov-Yarovoy V, Tian Y, Zheng J (2019) Structural mechanisms underlying activation of TRPV1 channels by pungent compounds in gingers. Br J Pharmacol. 176: 3364-3377. doi: 10.1111/bph.14766.

Kimball IH, Nguyen PT, Olivera BM, Sack JT, Yarov-Yarovoy V (2019) Molecular Determinants of μ-Conotoxin KIIIA interaction with the Voltage-Gated Sodium Channel Nav1.7. bioRxiv. doi: https://doi.org/10.1101/654889.

Rudell JB, Maselli RA, Yarov-Yarovoy V, Ferns MJ (2019) Pathogenic effects of agrin V1727F mutation are isoform-specific and decrease its expression and affinity for HSPGs and LRP4. Hum Mol Genet. 28(16): 2648-2658. doi: 10.1093/hmg/ddz081.

Heeney DD, Yarov-Yarovoy V, Marco ML (2019) Sensitivity to the two peptide bacteriocin plantaricin EF is dependent on CorC, a membrane-bound, magnesium/cobalt efflux protein. Microbiologyopen. 2019 Mar 19:e827. doi: 10.1002/mbo3.827. [Epub ahead of print].

Noskov SY, Yarov-Yarovoy V (2019) Editorial. Neurosci Lett. 700: 1-2. doi: 10.1016/j.neulet.2019.02.040.

Wulff H, Christophersen P, Colussi P, Chandy KG, Yarov-Yarovoy V (2019) Antibodies and venom peptides: new therapeutic modalities for ion channels. Nature Reviews Drug Discovery 18(5): 339-357. doi: 10.1038/s41573-019-0013-8.

Nguyen PT, DeMarco KR, Vorobyov I, Clancy CE, Yarov-Yarovoy V (2019) Structural Basis of Antiarrhythmic Drug Interactions with the Human Cardiac Sodium Channel. Proc Natl Acad Sci USA 116(8): 2945-2954. doi: 10.1073/pnas.1817446116.

Yang F, Xiao X, Lee BH, Vu S, Yang W, Yarov-Yarovoy V, Zheng J (2018) The conformational wave in capsaicin activation of Transient Receptor Potential Vanilloid 1 ion channel. Nat Commun. 9: 2879. doi: 10.1038/s41467-018-05339-6.

Brown BM, Shim H, Zhang M, Yarov-Yarovoy V, Wulff H (2017) Structural Determinants for the Selectivity of the Positive KCa3.1 Gating Modulator 5-Methylnaphtho[2,1-d]oxazol-2-amine (SKA-121). Molecular Pharmacology 92, 469-480. doi: 10.1124/mol.117.109421.

Tanaka BS, Nguyen PT, Zhou EY, Yang Y, Yarov-Yarovoy V, Dib-Hajj SD, Waxman SG (2017) Gain-of-function mutation of a voltage-gated sodium channel Nav1.7 associated with peripheral pain and impaired limb development. J Biol Chem. 292, 9262-9272. doi: 10.1074/jbc.M117.778779.

Tang C, Zhou X, Nguyen PT, Zhang Y, Hu Z, Zhang C, Yarov-Yarovoy V, DeCaen PG, Liang S, Liu Z (2017) A novel tarantula toxin stabilizes the deactivated voltage sensor of bacterial sodium channel. FASEB J. 31, 3167-3178. doi: 10.1096/fj.201600882R.

Zhang P, Zawadzki RJ, Goswami M, Nguyen PT, Yarov-Yarovoy V, Burns ME, Pugh EN Jr. (2017) In vivo optophysiology reveals that G-protein activation triggers osmotic swelling and increased light scattering of rod photoreceptors. Proc Natl Acad Sci USA 114, E2937-E2946. doi: 10.1073/pnas.1620572114.

Nguyen HM, Singh V, Pressly B, Jenkins DP, Wulff H, Yarov-Yarovoy V (2017) Structural Insights into the Atomistic Mechanisms of Action of Small Molecule Inhibitors Targeting the KCa3.1 Channel Pore. Molecular Pharmacology 91, 392-402. doi: 10.1124/mol.116.108068.

Grandi E, Sanguinetti MC, Bartos DC, Bers DM, Chen-Izu Y, Chiamvimonvat N, Colecraft HM, Delisle BP, Heijman J, Navedo MF, Noskov S, Proenza C, Vandenberg JI, Yarov-Yarovoy V (2017) Potassium channels in the heart: structure, function and regulation. Journal of Physiology 595, 2209-2228. doi: 10.1113/JP272864.

Yang F, Vu S, Yarov-Yarovoy V, Zheng J (2016) Rational design and validation of a vanilloid-sensitive TRPV2 ion channel. Proc Natl Acad Sci U S A 113, E3657-66.

Tuluc P*, Yarov-Yarovoy V*, Benedetti B, Flucher BE (2016) Molecular Interactions in the Voltage Sensor Controlling Gating Properties of Cav Calcium Channels. Structure 24, 261-71.

Yang F, Vu S, Yarov-Yarovoy V, Zheng J (2016) Rational design and validation of a vanilloid-sensitive TRPV2 ion channel. Proc Natl Acad Sci U S A 113, E3657-66.

Becker EA, Yao AI, Seitzer PM, Kind T, Wang T, Eigenheer R, Shao KS, Yarov-Yarovoy V, Facciotti MT (2016) A Large and Phylogenetically Diverse Class of Type 1 Opsins Lacking a Canonical Retinal Binding Site. PLoS One 11, e0156543.

Kaur I, Yarov-Yarovoy V, Kirk LM, Plambeck KE, Barragan EV, Ontiveros ES, Díaz E (2016) Activity-Dependent Palmitoylation Controls SynDIG1 Stability, Localization, and Function. J Neurosci. 36, 7562-8.

  • University of Washington Royalty Research Fund Award, University of Washington
  • National Institutes of Health Research Career Development Award
  • Biophysical Society Graduate Student Award
  • Department of Anesthesiology and Pain Medicine: Scott Fishman
  • Department of Biochemistry and Molecular Medicine: Kit Lam, Justin Siegel, Lin Tian, and John Voss
  • Department of Biomedical Engineering: Marc Facciotti
  • Department of Cell Biology and Human Anatomy: Paul Fitzgerald
  • Department of Internal Medicine: Nipavan Chiamvimonvat
  • Department of Molecular and Cellular Biology: Jonathan Scholey
  • Department of Neurobiology, Physiology and Behavior: James Trimmer
  • Department of Pharmacology: Donald Bers, Colleen Clancy, Elva Diaz, and Heike Wulff
  • Department of Physiology and Membrane Biology: Pete Cala, Michel Ferns, Alla Fomina, Jon Sack, and Jie Zheng
  • City College of New York: Themis Lazaridis
  • Johns Hopkins University: Mark Donowitz and Jeff Gray
  • National Institutes of Health: Kenton Swartz
  • Royal Melbourne Institute of Technology (Australia): Toby Allen
  • Stanford University: Justin Du Bois
  • University of Calgary (Canada): Sergei Noskov
  • University of California Berkeley: Ehud Isacoff
  • University of California San Francisco: Bill DeGrado and Daniel Minor
  • University of Chicago: Benoit Roux
  • University of Copenhagen (Denmark): Stine Pedersen
  • University of Innsbruck (Austria): Bernhard Flucher and Joerg Striessnig
  • University of Utah: Baldomero Olivera
  • University of Washington: David Baker, William Catterall, and Allan Rettie
  • Vanderbilt University: Jens Meiler
  • Weizmann Institute of Science (Israel): Sarel Fleishman
  • Biophysical Society
  • Protein Society
  • National Institutes of Health
  • University of Washington