Structural basis of ligand specificity and channel activation in an insect gustatory receptor
Data files
Apr 12, 2024 version files 67.02 GB
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BmGr9-apo-8VC1-nolipid-prod.dcd.gz
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BmGr9-apo-8VC1-nolipid-system.pdb
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BmGr9-apo-8VC1-nolipid-system.psf
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BmGr9-apo-8VC1-popc-prod-wat.dcd.gz
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BmGr9-apo-8VC1-popc-system.pdb
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BmGr9-apo-8VC1-popc-system.psf
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BmGr9-apo-8VC1-pope-prod-wat.dcd.gz
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BmGr9-apo-8VC1-pope-system.pdb
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BmGr9-apo-8VC1-pope-system.psf
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GRs-uniref50-alignment-BmGr9-mapped.fasta
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GRs-uniref50-alignment.fasta
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ORs-uniref50-alignment-MhOr5-mapped.fasta
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ORs-uniref50-alignment.fasta
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README.md
Apr 12, 2024 version files 67.02 GB
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BmGr9-apo-8VC1-nolipid-prod.dcd.gz
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BmGr9-apo-8VC1-nolipid-system.pdb
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BmGr9-apo-8VC1-nolipid-system.psf
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BmGr9-apo-8VC1-popc-prod-wat.dcd.gz
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BmGr9-apo-8VC1-popc-system.pdb
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BmGr9-apo-8VC1-popc-system.psf
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BmGr9-apo-8VC1-pope-prod-wat.dcd.gz
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BmGr9-apo-8VC1-pope-system.pdb
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BmGr9-apo-8VC1-pope-system.psf
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GRs-uniref50-alignment-BmGr9-mapped.fasta
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GRs-uniref50-alignment.fasta
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ORs-uniref50-alignment-MhOr5-mapped.fasta
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ORs-uniref50-alignment.fasta
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README.md
Abstract
Gustatory Receptors (GRs) are critical for insect chemosensation and are potentialtargets for controlling pests and disease vectors, making their structural investigation avital step towards such applications. We present structures of Bombyx mori Gr9(BmGr9), a fructose-gated cation channel, in agonist-free and fructose-bound states.BmGr9 forms a tetramer similar to distantly related insect Olfactory Receptors (ORs).Upon fructose binding, BmGr9’s channel gate opens through helix S7b movements. Incontrast to ORs, BmGR9’s ligand-binding pocket, shaped by a kinked helix S4 and ashorter extracellular S3-S4 loop, is larger and solvent accessible in both agonist-freeand fructose-bound states. Also unlike ORs, fructose binding by BmGr9 involves helixS5 and a pocket lined with aromatic and polar residues. Structure-based sequencealignments reveal distinct patterns of ligand-binding pocket residue conservation in GRsubfamilies associated with different ligand classes. These data provide insight into themolecular basis of GR ligand specificity and function.
README
Molecular dynamics (MD) simulations and multiple sequence alignments in the paper "Structural basis of ligand specificity and channel activation in an insect gustatory receptor".
Alignments and simulations created and performed by Sanket Walujkar under the supervision of Prof. Rachelle Gaudet.
Description of the data and file structure
There are four FASTA files containing four different multiple sequence alignments.
- ORs-uniref50-alignment.fasta: Full length alignment of 3885 odorant receptor (OR) sequences from the Uniref50 database.
- ORs-uniref50-alignment-MhOr5-mapped.fasta: Alignment of the same 3885 OR sequences but only columns corresponding to Machilis hrabei OR5 (PDB: 7LIC).
- GRs-uniref50-alignment.fasta: Full length alignment of 1854 gustatory receptor (GR) sequences from the Uniref50 database.
- GRs-uniref50-alignment-BmGr9-mapped.fasta: Alignment of the same 1854 GR sequences but only columns corresponding to Bombyx mori Gr9 (PDB: 8VC1, 8VC2; Uniprot: B3GTD7)
There are coordinates, topology, and trajectory files for three different MD simulations.
1. MD simulation of apo *Bm*Gr9 with POPC lipids in the intersubunit fenestrations.
BmGr9-apo-8VC1-popc-system.psf: CHARMM topology file.
BmGr9-apo-8VC1-popc-system.pdb: Initial coordinates file.
BmGr9-apo-8VC1-popc-prod-wat.dcd.gz: Gzipped trajectory file for the 200-ns production run.
2. MD simulation of apo *Bm*Gr9 with POPE lipids in the intersubunit fenestrations.
BmGr9-apo-8VC1-pope-system.psf: CHARMM topology file.
BmGr9-apo-8VC1-pope-system.pdb: Initial coordinates file.
BmGr9-apo-8VC1-pope-prod-wat.dcd.gz: Gzipped trajectory file for the 200-ns production run.
3. MD simulation of apo *Bm*Gr9 with no lipids in the intersubunit fenestrations.
BmGr9-apo-8VC1-nolipid-system.psf: CHARMM topology file.
BmGr9-apo-8VC1-nolipid-system.pdb: Initial coordinates file.
BmGr9-apo-8VC1-nolipid-prod.dcd.gz: Gzipped trajectory file for the 200-ns production run.
Usage
The multiple sequence alignment files can be viewed and analyzed using any sequence visualization and analysis softwares such as clustal/jalview/Geneious etc.
MD simulations can be visualized and analyzed using molecular visualization software such as PyMOL and VMD.