Environmentally-regulated protein/protein interactions

Environmental cues regulate many biological processes, controlling pathways used by cells to respond to changing conditions.  Such regulation is often initiated by sensory protein domains that use internally-bound ligands to convert environmentally-triggered changes into altered protein/protein interactions.  Several families of these domains have evolved with remarkable diversity in the stimuli they sense and outputs that they control.  Combining biophysics, biochemistry and cell biology in our group – and critically collaborating with labs in related areas – we seek insights into the signaling mechanisms of proteins used by cells to sense and respond to the environment around them.  In doing so, we aim to decipher how proteins use common sensory mechanisms despite tremendous diversity in their functions and biological settings – for example, revealing how a cancer-related transcription factor in human cells senses natural metabolites similarly to a photosensory protein looking for blue light within marine bacteria.  Such studies lay the foundation for both understanding the natural regulation of these systems and artificially controlling them, leading to first-in-class anti-cancer drugs (Merck's belzutifan) and optogenetic tools for biotechnology.

Cleere, M.M. and Gardner, K.H. (2024) Optogenetic control of phosphate-responsive genes using single component fusion proteins in Saccharomyces cerevisiae.  Manuscript under review; available at bioRxiv (DOI: 10.1101/2024.08.02.605841).

Gagné, D., Azad, R., Aramini, J.M., Xu, X., Isiorho, E.A., Edupuganti, U.R., Williams, J., Marcelino, L.P., Akasaka, K. and Gardner, K.H.  (2024)  Use of high pressure NMR spectroscopy to rapidly identify proteins with internal ligand-binding voids.  Manuscript in revision; available at bioRxiv (DOI: 10.1101/2020.08.25.267195v2).

Xu, X., Closson, J.D., Marcelino, L.P., Favaro, D.C., Silvestrini, M.L., Solazzo, R., Chong, L.T., and Gardner, K.H. (2024) Identification of small molecule ligand binding sites on and in the ARNT PAS-B domain. J. Biol. Chem., 300, 107606.

Xiao, M.*, Dhungel, S.*, Azad, R.*, Favaro, D., Rajesh, R.P., Gardner, K.H.# and Kikani, C.K.#  (2024). Signal-regulated unmasking of nuclear localization motif in the PAS domain regulates the nuclear translocation of PASK.  J. Mol. Biol., 436: 168433.

Dikiy, I.*, Swingle, D.*, Toy, K., Edupuganti, U.R., Rivera-Cancel, G. and Gardner K.H. (2023) Conservation of function with diversification of higher-order structure within sensor histidine kinase.  J. Biol. Chem., 299: 104934.

Hart, J.E. and Gardner, K.H.  (2021)  Lighting the way: Recent progress on the structure and function of phototropin blue light receptors.  J. Biol. Chem., 296: 100594.

Xu, X., Dikiy, I., Evans, M.R., Marcelino, L.P. and Gardner, K.H.  (2021)  Fragile protein folds: Sequence and environmental factors affecting the equilibrium of two interconverting, stably folded protein conformations.  Magn. Reson., 2: 63-76.

Xu, X., Gagné, D., Aramini, J.M. and Gardner, K.H.  (2021)  Volume and compressibility differences between protein conformations revealed by high-pressure NMR.  Biophys J., 120: 924-935.

Dikiy, I., Edupuganti, U.R., Abzalimov, R.R., Borbat, P.B., Srivastava, M., Freed, J.H., and Gardner, K.H.  (2019)  Insights into histidine kinase activation mechanisms from the monomeric blue light sensor EL346. Proc Natl Acad Sci, 116: 4963-4972.

Glantz, S.T., Berlew, E.E., Jaber, Z., Schuster, B.S., Gardner, K.H. and Chow, B.Y.  (2018)  Directly light-regulated binding of RGS-LOV photoreceptors to anionic membrane phospholipids.  Proc Natl Acad Sci, 115: E7720-E7727.

Losi, A., Gardner, K.H. and Möglich, A.  (2018)  Blue-light receptors for optogenetics.  Chem Res, 118: 10659-10709.

Clark, L.*, Dikiy, I.*, Chapman, K., Rödström, K.E., Aramini, J., LeVine, M., Khelashvili, G., Rasmussen, S.G.F., Gardner, K.H. and Rosenbaum, D.M.  (2017)  Ligand modulation of sidechain dynamics in a wild-type human GPCR.  eLife, 6: e28505. (*:equal contributors).

Chen, W., Hill, H., Christie, A., Kim, M.S., Holloman, E., Pavía-Jiménez, A., Homayoun, F., Ma, Y., Patel, N., Yell, P., Hao, G., Yousuf, Q., Joyce, A., Pedrosa, I., Geiger, H., Zhang, H., Chang, J. Gardner, K.H., Bruick, R.K., Reeves, C., Hwang, T.H., Courtney, K., Frenkel, E., Sun, X., Zojwalla, N., Wong, T., Rizzi, J.P., Wallace, E.M., Josey, J.A., Xie, Y., Xie, X.-J., Kapur, P., McKay, R.M. and Brugarolas, J.  (2016)  Targeting renal cell carcinoma with a HIF-2 antagonist.  Nature, 539: 112-117

Motta-Mena, L.B., Reade, A., Mallory, M.J., Glantz, S., Weiner, O.D., Lynch, K.W. and Gardner, K.H.  (2014)  An optogenetic gene expression system with rapid activation and deactivation kinetics.  Nat Chem Biol, 10: 196-202.

Scheuermann, T.H., Li, Q., Ma, H.-W., Key, J., Zhang, L., Chen, R., Garcia, J.A., Naidoo, J., Longgood, J., Frantz, D.E., Tambar, U.K., Gardner, K.H.† and Bruick, R.K.†  (2013)  Allosteric inhibition of Hypoxia Inducible Factor 2 with small molecules.  Nat Chem Biol, 9: 271-276. (†: corresponding authors).

Nash, A.I.*, McNulty, R.*, Shillito, M.E., Swartz, T.E., Bogomolni, R.A., Luecke, H.† and Gardner, K.H.† (2011)  Structural basis of photosensitivity in a bacterial LOV-HTH DNA binding protein.  Proc Natl Acad Sci, 108: 9449-9454. (*: equal contributors, †: corresponding authors)

Harper, S.M., Neil, L.C. and Gardner, K.H.  (2003)  Structural basis of a phototropin light switch.  Science, 301: 1541-1544.

Amezcua, C.A., Harper, S.M., Rutter J. and Gardner, K.H.  (2002)  Structure and interactions of PAS kinase N-terminal PAS domain: Model for intramolecular kinase regulation.  Structure, 10: 1349-1361.