Structural biology of ion channels and transporters: The Gaudet lab uses a combination of structural, biophysical and biochemical approaches to study signaling and transport through biological membranes. Particular systems of interest are ABC transporters and thermosensing TRP ion changes.
Northwest Building, Room 311.13
52 Oxford St
Cambridge, MA 02138
Lab Size: Between 5 and 10
Structural biology of signaling and transport across biological membranes
My lab is broadly interested in the mechanisms of signaling and transport across cellular membranes. Our research encompasses several protein families: Nramp transporters that use a proton gradient to facilitate the entry of divalent ions (iron and manganese in particular) into cells; non-classical cadherins involved in cellular adhesion and signaling; ABC transporters that use ATP to fuel substrate transport; and TRP channels important to sensing temperature and painful stimuli. We use a variety of cell-based and in vitro biochemical assays, x-ray crystallography, and computational techniques (molecular dynamics simulations and bioinformatics analyses) to discover how these important proteins function in cells. Below are brief descriptions that illustrate our approaches and goals for specific projects.
Metals like iron and manganese are essential to physiological processes such as oxygen transport and energy metabolism. Nramps (Natural Resistance-Associated Macrophage Proteins) are transition metal transporters found in all kingdoms of life. They are the primary manganese importers in bacteria, and important metal uptake systems in plants, fungi and animals as well. In humans, Nramp1 is part of the immune system’s metal withdrawal to counter microbial pathogens, while Nramp2 is responsible for dietary and cellular uptake of non-heme iron. Nramps are thus crucial for adequate supply of these metals while avoiding toxicity from over-accumulation. The goal of this project is to determine at atomic resolution the molecular mechanism of metal-ion transport by the Nramp family of proteins, including conformational change mechanisms, metal selectivity, and the role of protons and pH in regulating transport.
As the brain develops, neurons play a complex game of Twister to keep their neuronal processes from getting tangled up and improperly wired. For example, dendrites exhibit self-avoidance – avoid contact with other dendrites from the same neuron. In higher animals, the clustered protocadherins (cPCDHs) mediate this self-avoidance. Each cell has a random but unique set to distinguish it from neighboring cells. The cPCDHs create a biological ‘AND’ gate: a cell recognizes itself if and only if all expressed isoforms form homophilic interactions. Mutations in these proteins are linked to neurodegenerative diseases and schizophrenia.
We use structural, biochemical methods and cell-based assays to understand how cPCDHs form supramolecular inter-cellular signaling assemblies. We also use various sequence- and structure-based bioinformatics approaches to study cadherin diversity and evolution. We aim to understand how the diversity of sequences and structures in the cadherin superfamily contributes to their diverse signaling and adhesion functions mediated in the animal kingdom.
TRP ion channels
We are particularly interested in TRP (Transient Receptor Potential) ion channels involved in temperature sensing and other sensory processes. For example, several temperature-sensing TRP channels, including TRPV1 and TRPM8, are expressed in nociceptor neurons, and therefore responsible for pain sensations in response to noxious stimuli. The biophysical and biochemical mechanisms of pain and heat sensing are therefore not only of academic interest, but also of medical and pharmacological interest. We have determined the structures of several TRPV channel cytosolic domains. We are also using patch-clamp electrophysiology and other functional assays to understand the role of ligand interactions with the cytosolic domains in TRP channel function.
Nicoludis JM, Green AG, Walujkar S, May EJ, Sotomayor M, Marks DS, Gaudet R. Interaction specificity of clustered protocadherins inferred from sequence covariation and structural analysis. Proc Natl Acad Sci U S A. 2019 Aug 20. pii: 201821063. doi: 10.1073/pnas.1821063116. PubMed PMID: 31431536.
Bozzi AT, Zimanyi CM, Nicoludis JM, Lee BK, Zhang CH, Gaudet R. Structures in multiple conformations reveal distinct transition metal and proton pathways in an Nramp transporter. Elife. 2019 Feb 4;8. pii: e41124. doi: 10.7554/eLife.41124. PubMed PMID: 30714568; PubMed Central PMCID: PMC6398981.
Woll KA, Skinner KA, Gianti E, Bhanu NV, Garcia BA, Carnevale V, Eckenhoff RG, Gaudet R. Sites Contributing to TRPA1 Activation by the Anesthetic Propofol Identified by Photoaffinity Labeling. Biophys J. 2017 Nov 21;113(10):2168-2172. doi: 10.1016/j.bpj.2017.08.040. Epub 2017 Sep 19. PubMed PMID: 28935134; PubMed Central PMCID: PMC5700380.
Grossmann N, Vakkasoglu AS, Hulpke S, Abele R, Gaudet R, Tampé R. Mechanistic determinants of the directionality and energetics of active export by a heterodimeric ABC transporter. Nat Commun. 2014 Nov 7;5:5419. doi: 10.1038/ncomms6419. PubMed PMID: 25377891; PubMed Central PMCID: PMC4242082.