Computational protocol: Cell-Autonomous Gβ Signaling Defines Neuron-Specific Steady State Serotonin Synthesis in Caenorhabditis elegans

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Protocol publication

[…] WD40 repeats are in reference of published predicted GPB-1 sequence []. For homology comparisons, the amino acid sequence of C. elegans GPB-1, human Gβ1 GNB1 (GenBank: CAG33065.1), human Gβ2 GNB2 (GenBank: CAG46530.1) and bovine β1 GNB1 (NCBI reference sequence: NP_786971.2) were aligned using the ClustalW2 software []. The bovine Gβ1 protein shares 100% and 86% amino acid identity to human Gβ1 and C. elegans GPB-1, respectively.Crystal structure of the rat Giα and bovine β1γ2 heterotrimer (PDB entry: 1GP2)[] was used to model the G162E substitution with a focus on the interface between Gβ and Gα switch II helix. The public crystal structural data were downloaded from the protein data bank (http://www.rcsb.org/pdb/explore/explore.do?structureId=1GP2, PDB entry: 1GP2), and displayed as cartoon structures using the PyMOL software (http://www.pymol.org). To model Gβ/Gα switch II helix contacting interface, Gβ-G162 and other contacting residues in the Gβ and Gα identified by the crystallography were manually selected, colored and their side chains displayed. To model the G162E substitution, G162 was manually replaced by E in the Gβ sequence, using the Crystallographic Object-Oriented Toolkit (COOT) [], and modeled again using PyMOL. […]

Pipeline specifications

Software tools Clustal W, PyMOL, Coot
Application Protein structure analysis
Organisms Caenorhabditis elegans
Chemicals Serotonin, Tryptophan