Structure of the ancient TRPY1 channel from Saccharomyces cerevisiae reveals mechanisms of modulation by lipids and calcium

Tofayel Ahmed; Collin R Nisler; Edwin C Fluck 3rd; Sanket Walujkar; Marcos Sotomayor; Vera Y Moiseenkova-Bell

doi:10.1016/j.str.2021.08.003

Structure of the ancient TRPY1 channel from Saccharomyces cerevisiae reveals mechanisms of modulation by lipids and calcium

Structure. 2022 Jan 6;30(1):139-155.e5. doi: 10.1016/j.str.2021.08.003. Epub 2021 Aug 27.

Authors

Tofayel Ahmed¹, Collin R Nisler², Edwin C Fluck 3rd³, Sanket Walujkar⁴, Marcos Sotomayor⁵, Vera Y Moiseenkova-Bell⁶

Affiliations

¹ Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
² Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA; Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.
³ Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
⁴ Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Chemical Physics Graduate Program, The Ohio State University, Columbus, OH 43210, USA.
⁵ Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA; Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Chemical Physics Graduate Program, The Ohio State University, Columbus, OH 43210, USA.
⁶ Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address: vmb@pennmedicine.upenn.edu.

Abstract

Transient receptor potential (TRP) channels emerged in fungi as mechanosensitive osmoregulators. The Saccharomyces cerevisiae vacuolar TRP yeast 1 (TRPY1) is the most studied TRP channel from fungi, but the structure and details of channel modulation remain elusive. Here, we describe the full-length cryoelectron microscopy structure of TRPY1 at 3.1 Å resolution in a closed state. The structure, despite containing an evolutionarily conserved and archetypical transmembrane domain, reveals distinctive structural folds for the cytosolic N and C termini, compared with other eukaryotic TRP channels. We identify an inhibitory phosphatidylinositol 3-phosphate (PI(3)P) lipid-binding site, along with two Ca²⁺-binding sites: a cytosolic site, implicated in channel activation and a vacuolar lumen site, implicated in inhibition. These findings, together with data from microsecond-long molecular dynamics simulations and a model of a TRPY1 open state, provide insights into the basis of TRPY1 channel modulation by lipids and Ca²⁺, and the molecular evolution of TRP channels.

Keywords: calcium; cryo electron microscopy (cryo-EM); ion channel; membrane protein; molecular dynamics simulation; transient receptor potential (TRP) channel.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Binding Sites
Calcium / metabolism*
Cryoelectron Microscopy
Cytosol / metabolism
Models, Molecular
Molecular Dynamics Simulation
Phosphatidylinositol Phosphates / chemistry
Phosphatidylinositol Phosphates / pharmacology*
Protein Conformation
Protein Domains
Protein Multimerization
Saccharomyces cerevisiae / chemistry
Saccharomyces cerevisiae / metabolism*
Saccharomyces cerevisiae Proteins / chemistry*
Saccharomyces cerevisiae Proteins / metabolism*
TRPC Cation Channels / chemistry*
TRPC Cation Channels / metabolism*

Substances

Phosphatidylinositol Phosphates
Saccharomyces cerevisiae Proteins
TRPC Cation Channels
Yvc1 protein, S cerevisiae
phosphatidylinositol 3-phosphate
Calcium

Abstract

Publication types

MeSH terms

Substances

Grants and funding