title: Network analysis to uncover the structural communication in GPCRs.
abstract: Protein structure network (PSN) analysis is one of the graph theory-based approaches currently used to investigate the structural communication in biomolecular systems. Information on system dynamics can be provided by atomistic molecular dynamics simulations or coarse-grained Elastic Network Models paired with Normal Mode Analysis (ENM-NMA). This chapter describes the application of PSN analysis to uncover the structural communication in G protein-coupled receptors (GPCRs). Strategies to highlight changes in structural communication upon misfolding mutations, dimerization, and activation are described. Focus is put on the ENM-NMA-based strategy applied to the crystallographic structures of rhodopsin in its inactive (dark) and signaling active (meta II (MII)) states, highlighting clear changes in the PSN and the centrality of the retinal chromophore in differentiating the inactive and active states of the receptor.
authors.affiliation: Dulbecco Telethon Institute (DTI), Rome, Italy; Department of Chemistry, University of Modena and Reggio Emilia, Modena, Italy.
authors.forename: Francesca
authors.initials: F
authors.lastname: Fanelli
authors.forename: Angelo
authors.initials: A
authors.lastname: Felline
authors.forename: Francesco
authors.initials: F
authors.lastname: Raimondi
mesh_terms: D018360:Crystallography, X-Ray; D006801:Humans; D056004:Molecular Dynamics Simulation; D009154:Mutation; D017510:Protein Folding; D054730:Protein Interaction Domains and Motifs; D055503:Protein Multimerization; D012243:Rhodopsin / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D012984:Software
chemical_list: D012243:Rhodopsin
keywords: Allosteric communication; Elastic network model; GPCRs; Molecular dynamics simulations; Normal mode analysis; Protein structure graphs; Protein structure networks