1. ABOUT THE DATASET
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Title:
Simulation and experimental data from the publication - Smith et al., “Regulation of PIEZO1 channel force sensitivity by inter-blade handshaking”

Creator(s): Katie A Smith, Oleksandr Povstyan, Jian Shi, Eulashini Chuntharpursat-Bon, Jian Shi, David Beech, Antreas C Kalli

Organisations: University of Leeds.

Publication Year: 2025

Description:

A repository of simulation data from the publication “Regulation of PIEZO1 channel force sensitivity by inter-blade handshaking”. PIEZOs form trimeric calcium-permeable non-selective cationic channels that serve mechanical sensing needs across eukaryotic biology. Forces act on the channels by causing their curved blades to flatten and decompact, leading to an activated state, but it is unclear how this might be regulated to enable the channels to adapt to different contexts. To identify potential mechanisms, we performed coarse-grained and all-atom molecular dynamics simulations on human PIEZO1 channel. We observed an inter-blade handshake interaction mediated by basic amino acid residues in two flexible helices that coordinate with the regulated anionic lipid phosphatidylinositol 4,5-bisphosphate. In silico mutation of phosphatidylinositol 4,5-bisphosphate sites on the handshake short helix, referred to as SHM PIEZO1, destabilised the inter-blade handshake interaction. The interaction determined the resting configuration of the channel, blade curvature, compactness and ion pore structure. This dataset contains: -Dataset 1: Coarse-grained MD simulation data for the wildtype human PIEZO1 simulated in an endothelial membrane containing 5% PIP2. -Dataset 2: Coarse-grained MD simulation data for the wildtype human PIEZO1 simulated in an endothelial membrane containing 0% PIP2. -Dataset 3: Coarse-grained MD simulation data for the SHM PIEZO1 simulated in an endothelial membrane containing 5% PIP2. -Dataset 4: All-atom MD simulation data for the WT PIEZO1 simulated in an endothelial membrane containing 5% PIP2 without applied tension (+1 bar) and with applied tension (-30 bar). -Dataset 5: All-atom MD simulation data for the SHM PIEZO1 simulated in an endothelial membrane containing 5% PIP2 without applied tension (+1 bar) and with applied tension (-30 bar).

Cite as:

Contact: a.kalli@leeds.ac.uk

2. TERMS OF USE
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Unless otherwise stated, this dataset is licensed under a Creative Commons Attribution 4.0 International Licence: https://creativecommons.org/licenses/by/4.0/.

3. PROJECT AND FUNDING INFORMATION
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This study was supported by British Heart Foundation (BHF) PhD Studentships to K.A.S (FS/4yPhD/F/20/34130D) and J.A.K. (FS/19/59/34896D), BHF Project Grants PG/21/10595 and PG/21/10515 to A.C.K., J.S. and D.J.B., BHF Intermediate Fellowship FS/17/2/32559 to J.S., a BHF Programme Grant RG/17/11/33042 to D.J.B., J.S. and R.F. and BHF Mautner Fellowships to E.C.-B. and M.D.. The computational work was undertaken on ARC3 and ARC4, part of the High Performance Computing facilities at the University of Leeds, UK. This project also made use of time on HPC granted via the UK High-End Computing Consortium for Biomolecular Simulation, HECBioSim (http://hecbiosim.ac.uk), supported by EPSRC (grant no. EP/R029407/1).

4. CONTENTS
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The data has been divided into 6 dataset zip files:

[dataset] [name] [description]
1 WT_EM_CG.zip Coarse-grained MD simulation data for the wildtype human PIEZO1 simulated in an endothelial membrane containing 5% PIP2.
2 WT_0PIP2_CG.zip Coarse-grained MD simulation data for the wildtype human PIEZO1 simulated in an endothelial membrane containing 0% PIP2.
3 SHM_CG.zip Coarse-grained MD simulation data for the SHM human PIEZO1 simulated in an endothelial membrane containing 5% PIP2.
4 WT_AA.zip All-atom MD simulation data for the wildtype human PIEZO1 simulated in an endothelial membrane containing 5% PIP2 at +1 bar and -30 bar tensions.
5 SHM_AA.zip All-atom MD simulation data for the SHM human PIEZO1 simulated in an endothelial membrane containing 5% PIP2 at +1 bar and -30 bar tensions.
6 Sourcedata.zip Source data for the experimental figures included in the publication.

.tpr files are GROMACS binary input run files for a simulation

.gro files are the coordinates from the final frame of a simulation

.xtc files are the GROMACS simulation trajectories, thinned to 10% of their original size (due to memory limitations) by only writing every 10th frame from the original.

Coarse-grained datasets include simulation data for 5 replica simulations named sim1 to sim5.

5. METHODS
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1. Description of methods used for collection/generation of data:

The simulation data were generated using coarse grained molecular dynamics simulations of a full-length structural model of human PIEZO1, and a model endothelial membrane. These were run using v2.2 of the Martini CG force field and GROMACS 5.0.7 (CG simulations) or CHARMM36 force field and GROMACS 2016 (atomistic simulations).

Experimental data was generated by patch-clamp electrophysiology and intracellular calcium measurement.

PIEZO orthologues across eukaryotes were selected for multiple sequence alignment to look at the conservation of positive charge in the regions expected to form the handshake helices. 15 PIEZO orthologues were selected: Human PIEZO1 (Uniprot: Q92508), Mouse PIEZO1 (Uniprot: E9PUQ9), Mouse PIEZO2 (Uniprot: Q8CD54), Dog (Uniprot: A0A8I3MUY4), Zebrafish (Uniprot: A0A8N7TDV6), Pig (Uniprot: A0A480F0E9), Tufted Duck (Uniprot: A0A6J3DPG2), Bovine (Uniprot: F1MD64), Cat (Uniprot: A0A337SVB0), Koala (Uniprot: A0A6P5KK49), Western European Hedgehog (Uniprot: A0A1S3WLZ8), Rhesus Macaque (Uniprot: A0A5F7ZT10), Chicken (Uniprot: A0A8V0Y724), Atlantic Cod (Uniprot: A0A8C4YZ71), Arabidopsis thaliana (Uniprot: F4IN58). Multiple sequence alignment was performed on 15 PIEZO orthologues using Clustal Omega program.

The structure of the mouse PIEZO1 (PDB:6B3R) was used as a template for the modelling of the human PIEZO1. The structure of PIEZO2 (PDB:6KG7) is shown in Figure S1.

2. Methods for processing the data:

Due to storage limitations the trajectories have been thinned to 10% of their original frames.

3. This work was undertaken on ARC3 and ARC4, part of the High Performance Computing facilities at the University of Leeds, UK and on ARCHER2, the UK national supercomputing service.