Francesco Tombola

Picture of Francesco Tombola
Professor, Physiology & Biophysics
School of Medicine
Associate Dean for Graduate and Postdoctoral Studies
School of Medicine
Ph.D., University of Padua, Molecular & Cellular Biology
Phone: (949) 824-9137
Fax: (949) 824-8540
University of California, Irvine
D349 Medical Sciences I
Mail Code: 4560
Irvine, CA 92697
Research Interests
Mechanisms of electrical and mechanical sensing in excitable cells: ion channels and receptor enzymes
Research Abstract
We are interested in the molecular mechanisms by which excitable cells detect physical cues at their plasma membrane and then convert these cues into intracellular signals. Our approach is to combine fluorescence microscopy, electrophysiology, synthetic chemistry, biochemistry and molecular biology to make dynamic measurements in live cells of the following events: 1) the protein motions of ion channels that underlie signal detection, 2) the molecular events that couple the sensing process to the movement of the “gates” of ion-conducting effectors, 3) the intracellular events that mediate the transduction process of physical stimuli.

As a paradigm of “electrical sensing”, we study proteins containing voltage-sensing domains (VSDs). These domains are made of four transmembrane segments and confer voltage sensitivity to channels that generate the action potential in nerves and muscles, as well as channels that modulate the production of reactive oxygen species by the NADPH oxidase, and voltage-dependent enzymes that dephosphorylate phosphoinositide lipids. We are currently studying the voltage-gated proton channel Hv1, which contains two proton-conducting VSDs interacting via a cytoplasmic coiled-coil domain. The excessive activity of this channel has been implicated in cancer development and in brain damage during ischemic stroke. Hv1 inhibitors could find applications as anticancer drugs or neuroprotective agents. We have recently developed small-molecule inhibitors of the channel, which we are using to explore the mechanisms of permeation and gating.

As a paradigm of “mechanical sensing”, we study the Piezo proteins, which are calcium-permeable cation channels activated by membrane stretch. Piezo channels play important roles in mechanosensory pain and touch sensing, as well as in erythrocyte volume regulation, epithelial crowding, cell migration, and detection of blood flow. In collaboration with the Flanagan laboratory at UCI, we have found that the Piezo1 channel is expressed by human neural stem/progenitor cells (hNSPCs) where it is responsible for calcium influx triggered by traction forces. Piezo1-mediated calcium transients depend on the stiffness of the substrate supporting the cells, with stiffer substrates eliciting larger and more frequent transients. We also found strong evidence that Piezo1 activity directs mechanosensitive lineage specification of hNSPCs and are currently studying the mechanism underlying this phenomenon.
Zhao, C., Webster, P.D., De Angeli, A., Tombola, F. (2023) Mechanically-primed voltage-gated proton channels from angiosperm plants. Nature Commun. 14:7515.
Noh, S., Tombola, F., Burke, P. (2023) Nanowire biosensors with olfactory proteins: towards a genuine electronic nose with single molecule sensitivity and high selectivity. Nanotechnology 34: 465502.
Zhao, C., Hong, L., Riahi, S., Lim, V.T., Tobias, D.J., Tombola, F. (2021) Hv1 inhibition by HIF reveals a new druggable pocket in a voltage-sensing domain. J. Gen. Physiol. 153 (9): e202012833.

Zhao, C., Hong, L., Galpin, J.D., Riahi, S., Lim, V.T., Webster, P.D., Tobias, D.J., Ahern, C.A., Tombola, F. (2021) Development of HIFs: arginine-mimic inhibitors of Hv1 with improved VSD-ligand interactions. J. Gen. Physiol. 153 (9): e202012832.

Zhao, C., Tombola, F. (2021) Voltage-gated proton channels from fungi highlight role of peripheral regions in channel activation. Commun. Biol. 4: 261.

Lim, V.T., Freites, J.A., Tombola, F., Tobias, D.J. (2021) Thermodynamics and Mechanism of the Membrane Permeation of Hv1 Channel Blockers. J. Membr. Biol. 254: 5-16.

Lim, V.T., Geragotelis, A.D., Lim, N.M., Freites, J.A., Tombola, F., Mobley, D., Tobias, D. (2020) Insights on small molecule binding to the Hv1 proton channel from free energy calculations with molecular dynamics simulations. Sci. Rep. 10: 13587.

Geragotelis, A.D., Wood, M.L., Göddeke, H., Hong, L., Webster, P.D., Wong, E.K., Freites, J.A., Tombola, F., Tobias, D.J. (2020) Voltage-dependent structural models of the human Hv1 proton channel from long-timescale molecular dynamics simulations. Proc. Nat. Acad. Sci. USA 117(24) 13490-13498.

Kautz, R., Phan, L., Arulmoli, J., Chatterjee, A., Kerr, J.P., Naeim, M., Long, J., Allevato, A., Leal-Cruz, J.E., Le, L., Derakhshan, P., Tombola, F., Flanagan, L.A., Gorodetsky, A.A. (2020) Growth and Spatial Control of Murine Neural Stem Cells on Reflectin Films. ACS Biomater. Sci. Eng. 6(3): 1311-1320.

Ellefsen, K.L., Holt, J.R., Chang, A.C., Nourse, J.L., Arulmoli, J., Mekhdjian, A.H., Abuwarda, H., Tombola, F., Flanagan, L.A., Dunn, A.R., Parker, I., Pathak, M.M. (2019) Myosin-II mediated traction forces evoke localized Piezo1-dependent Ca2+ flickers. Commun. Biol. 2: 298.

Wood, M.L., Freites, J.A., Tombola, F., Tobias, D.J. (2017) Atomistic modeling of ion conduction through the voltage-sensing domain of the Shaker K+ ion channel. J. Phys. Chem. B. 121(15):3804-3812.

Pathak, M.M., Tran, T., Hong, L., Joós, B., Morris, C.E., Tombola, F. (2016) The Hv1 proton channel responds to mechanical stimuli. J. Gen. Physiol. 148(5): 405-418.

Hong, L., Tombola, F. (2016) Allostery: A lipid two-step. Nat. Chem. Biol. 12(4):202-3.

Phan, L., Kautz, R., Arulmoli, J., Kim, I.H., Le, D.T., Shenk, M.A., Pathak, M.M., Flanagan, L.A., Tombola, F., Gorodetsky, A.A. (2016) Reflectin as a material for neural stem cell growth. ACS Appl. Mater. Interfaces. 8(1):278-84.

Hong, L., Singh, V., Wulff, H., Tombola, F. (2015) Interrogation of the intersubunit interface of the open Hv1 proton channel with a probe of allosteric coupling. Sci. Rep. Sep 14; 5:14077.

Arulmoli, J., Pathak, M.M., McDonnell, L.P., Nourse, J.L., Tombola, F., Earthman, J.C., Flanagan, L.A. (2015) Static stretch affects neural stem cell differentiation in an extracellular matrix-dependent manner. Sci. Rep. Feb 17; 5:8499.

Pathak, M.M., Nourse, J.L., Tran, T., Hwe, J., Arulmoli, J., Le, D-T.T., Bernardis, E., Flanagan, L.A., Tombola, F. (2014) Stretch-activated ion channel Piezo1 directs lineage choice in human neural stem cells. Proc. Nat. Acad. Sci. USA 111(45):16148-53.

Kim, I.H., Hevezi, P., Varga, C., Pathak, M.M., Hong, L., Ta, D., Tran, C.T., Zlotnik, A., Soltesz, I., Tombola, F. (2014) Evidence for functional diversity between the voltage-gated proton channel Hv1 and its closest related protein HVRP1. PLoS ONE Aug 28; 9(8):e105926.

Hong, L., Kim, I.H., Tombola, F. (2014) Molecular determinants of Hv1 proton channel inhibition by guanidine derivatives. Proc. Nat. Acad. Sci. USA 111(27):9971-6.

Nourse, J.L., Prieto, J.L., Dickson, A.R., Lu, J., Pathak, M.M., Tombola, F., Demetriou, M., Lee, A.P., Flanagan, L.A. (2014) Membrane biophysics define neuron and astrocyte progenitors in the neural lineage. Stem Cells 32(3):706-16.

Hong, L., Pathak, M.M., Kim, I.H., Ta, D., Tombola, F. (2013) Voltage-sensing domain of voltage-gated proton channel Hv1 shares mechanism of block with pore domains. Neuron 77(2): 274-286.

Wood, M.L., Schow, E.V., Freites, J.A., White, S.H., Tombola, F., Tobias, D.J. (2012) Water wires in atomistic models of the Hv1 proton channel. Biochim. Biophys. Acta 1818(2): 286-93.

Tombola, F., Ulbrich, M.H., Kohout, S.C., Isacoff, E.Y. (2010) The opening of the two pores of the Hv1 voltage-gated proton channel is tuned by cooperativity. Nat. Struct. Mol. Biol. 17(1) 44-50.

Tombola, F., Ulbrich, M.H. Isacoff, E.Y. (2009) Architecture and gating of Hv1 proton channels. J. Physiol. 587, 5325–5329.

Tombola, F., Ulbrich, M.H., Isacoff, E.Y. (2008) The voltage-gated proton channel Hv1 has two pores, each controlled by one voltage sensor. Neuron 58(4):546-56.

Pathak, M.M., Yarov-Yarovoy, V., Agarwal, G., Roux, B., Barth, P., Kohout, S., Tombola, F., Isacoff, E.Y. (2007) Closing in on the resting state of the Shaker K(+) channel. Neuron 56(1):124-40.

Ruggiero, P., Rossi, G., Tombola, F., Pancotto, L., Lauretti, L., Del Giudice, G., Zoratti, M. (2007) Red wine and green tea reduce H. pylori- or VacA-induced gastritis in a mouse model. World J. Gastroenterol. 13(3):349-54.

Tombola, F., Pathak, M.M., Gorostiza, P., Isacoff, E.Y. (2007) The twisted ion-permeation pathway of a resting voltage-sensing domain. Nature 445(7127):546-9.

Tombola, F., Pathak, M.M., Isacoff, E.Y. (2006) How does voltage open an ion channel? Annu. Rev. Cell Dev. Biol. 22:23-52.

Ruggiero, P., Tombola, F., Rossi, G., Pancotto, L., Lauretti, L., Del Giudice, G., Zoratti, M. (2006) Polyphenols reduce gastritis induced by Helicobacter pylori infection or VacA toxin administration in mice. Antimicrob Agents Chemother. 50(7):2550-2.

Gorostiza, P., Tombola, F., Verdaguer, A., Smith, S.B., Bustamante, C., Isacoff, E.Y. (2005) Molecular handles for the mechanical manipulation of single-membrane proteins in living cells. IEEE Trans. Nanobioscience 4(4):269-76.

Tombola, F., Pathak, M.M., Isacoff, E.Y. (2005a) How far will you go to sense voltage? Neuron 48(5):719-25.

Tombola, F., Pathak, M.M., Isacoff, E.Y. (2005b) Voltage-sensing arginines in a potassium channel permeate and occlude cation-selective pores. Neuron 48(3):379-88.

Campello, S., De Marchi, U., Szabò, I., Tombola, F., Martinou, J.C., Zoratti, M. (2005) The properties of the mitochondrial megachannel in mitoplasts from human colon carcinoma cells are not influenced by Bax. FEBS Lett. 579(17):3695-700.

Pathak, M., Kurtz, L., Tombola, F., Isacoff, E. (2005) The cooperative voltage sensor motion that gates a potassium channel. J. Gen. Physiol. 2005 125(1):57-69.

De Marchi, U., Campello, S., Szabò, I., Tombola, F., Martinou, J.C., Zoratti, M. (2004) Bax does not directly participate in the Ca(2+)-induced permeability transition of isolated mitochondria. J. Biol. Chem. 279(36):37415-22.

Tombola, F., Campello, S., De Luca, L., Ruggiero, P., Del Giudice, G., Papini, E., Zoratti, M. (2003) Plant polyphenols inhibit VacA, a toxin secreted by the gastric pathogen Helicobacter pylori. FEBS Lett. 543(1-3):184-9.

Campello, S., Tombola, F., Cabrini, G., Zoratti, M. (2002) The vacuolating toxin of Helicobacter pylori mimicks the CFTR-mediated chloride conductance. FEBS Lett. 532(1-2):237-40.

Moschioni, M., Tombola, F., de Bernard, M., Coelho, A., Zitzer, A., Zoratti, M., Montecucco, C. (2002) The Vibrio cholerae haemolysin anion channel is required for cell vacuolation and death. Cell Microbiol. 4(7):397-409.

Szabo, I., Tombola, F., Martinucci, S., Zoratti, M. (2002) DNA interacts with Bacillus subtilis mechano-sensitive channels in native membrane patches. Cell Physiol. Biochem. 12(2-3):127-34.

Tombola, F., Pagliaccia, C., Campello, S., Telford, J.L., Montecucco, C., Papini, E., Zoratti, M. (2001) How the loop and middle regions influence the properties of Helicobacter pylori VacA channels. Biophys. J. 81(6):3204-15.

Morbiato, L., Tombola, F., Campello, S., Del Giudice, G., Rappuoli, R., Zoratti, M., Papini, E. (2001) Vacuolation induced by VacA toxin of Helicobacter pylori requires the intracellular accumulation of membrane permeant bases, Cl(-) and water. FEBS Lett. 508(3):479-83.

Tombola, F., Morbiato, L., Del Giudice, G., Rappuoli, R., Zoratti, M., Papini, E. (2001) The Helicobacter pylori VacA toxin is a urea permease that promotes urea diffusion across epithelia. J. Clin. Invest. 108(6):929-37.

Báthori, G., Parolini, I., Szabó, I., Tombola, F., Messina, A., Oliva, M., Sargiacomo, M., De Pinto, V., Zoratti, M. (2000) J. Bioenerg. Biomembr. 32(1):79-89.

Martinucci, S., Szabò, I., Tombola, F., Zoratti, M. (2000) Ca2+-reversible inhibition of the mitochondrial megachannel by ubiquinone analogues. FEBS Lett. 480(2-3):89-94.

Tombola, F., Del Giudice, G., Papini, E., Zoratti, M. (2000) Blockers of VacA provide insights into the structure of the pore. Biophys. J. 79(2):863-73.

Tombola, F., Oregna, F., Brutsche, S., Szabò, I., Del Giudice, G., Rappuoli, R., Montecucco, C., Papini, E., Zoratti, M. (1999) Inhibition of the vacuolating and anion channel activities of the VacA toxin of Helicobacter pylori. FEBS Lett. 460(2):221-5.

Szabò, I., Brutsche, S., Tombola, F., Moschioni, M., Satin, B., Telford, J.L., Rappuoli, R., Montecucco, C., Papini, E., Zoratti, M. (1999) Formation of anion-selective channels in the cell plasma membrane by the toxin VacA of Helicobacter pylori is required for its biological activity. EMBO J. 18(20):5517-27.

Bàthori, G., Parolini, I., Tombola, F., Szabò, I., Messina, A., Oliva, M., De Pinto, V., Lisanti, M., Sargiacomo, M., Zoratti, M. (1999) Porin is present in the plasma membrane where it is concentrated in caveolae and caveolae-related domains. J. Biol. Chem. 274(42):29607-12.

Tombola, F., Carlesso, C., Szabò, I., de Bernard, M., Reyrat, J.M., Telford, J.L., Rappuoli, R., Montecucco, C., Papini, E., Zoratti, M. (1999) Helicobacter pylori vacuolating toxin forms anion-selective channels in planar lipid bilayers: possible implications for the mechanism of cellular vacuolation. Biophys. J. 76(3):1401-9.

Szabò, I., Bàthori, G., Tombola, F., Coppola, A., Schmehl, I., Brini, M., Ghazi, A., De Pinto, V., Zoratti, M. (1998) Double-stranded DNA can be translocated across a planar membrane containing purified mitochondrial porin. FASEB J. 12(6):495-502.

Báthori, G., Szabó., I, Schmehl, I., Tombola, F., Messina, A., De Pinto, V., Zoratti, M. (1998) Novel aspects of the electrophysiology of mitochondrial porin. Biochem. Biophys. Res. Commun. 243(1):258-63.

Szabò, I., Bàthori, G., Tombola, F., Brini, M., Coppola, A., Zoratti, M. (1997) DNA translocation across planar bilayers containing Bacillus subtilis ion channels. J. Biol. Chem. 272(40):25275-82.
Professional Societies
American Association for the Advancement of Science, American Chemical Society, American Physiological Society, American Heart Association, Biophysical Society, Italian Scientists & Scholars of North America Foundation
Graduate Programs
Cellular and Molecular Biosciences
Interdepartmental Neuroscience Program
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