DOI: 10.5061/dryad.cc2fqz6dp
title: Structural basis of ligand specificity and channel activation in an insect gustatory receptor

description: 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.
description: 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. 1. ORs-uniref50-alignment.fasta: Full length alignment of 3885
 odorant receptor (OR) sequences from the Uniref50 database. 2.
 ORs-uniref50-alignment-MhOr5-mapped.fasta: Alignment of the same 3885 OR
 sequences but only columns corresponding to *Machilis hrabei* OR5 (PDB:
 7LIC). 3. GRs-uniref50-alignment.fasta: Full length alignment of 1854
 gustatory receptor (GR) sequences from the Uniref50 database. 4.
 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.