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’s dynamics can be provided by atomistic Molecular Dynamics (MD) simulations or coarse grained Elastic Network Models paired with Normal Mode Analysis (ENM-NMA). This article 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 protein structure network and the centrality of the retinal chromophore in differentiating the inactive and active states of the receptor.

Network analysis to uncover the structural communication in GPCRs / Fanelli, Francesca; Felline, Angelo Nicola; Raimondi, Francesco. - In: METHODS IN CELL BIOLOGY. - ISSN 0091-679X. - ELETTRONICO. - 17:(2013), pp. 43-61. [10.1016/B978-0-12-408143-7.00003-7]

Network analysis to uncover the structural communication in GPCRs

FANELLI, Francesca;FELLINE, Angelo Nicola;RAIMONDI, Francesco
2013

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’s dynamics can be provided by atomistic Molecular Dynamics (MD) simulations or coarse grained Elastic Network Models paired with Normal Mode Analysis (ENM-NMA). This article 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 protein structure network and the centrality of the retinal chromophore in differentiating the inactive and active states of the receptor.
2013
17
43
61
Network analysis to uncover the structural communication in GPCRs / Fanelli, Francesca; Felline, Angelo Nicola; Raimondi, Francesco. - In: METHODS IN CELL BIOLOGY. - ISSN 0091-679X. - ELETTRONICO. - 17:(2013), pp. 43-61. [10.1016/B978-0-12-408143-7.00003-7]
Fanelli, Francesca; Felline, Angelo Nicola; Raimondi, Francesco
File in questo prodotto:
Non ci sono file associati a questo prodotto.
Pubblicazioni consigliate

Licenza Creative Commons
I metadati presenti in IRIS UNIMORE sono rilasciati con licenza Creative Commons CC0 1.0 Universal, mentre i file delle pubblicazioni sono rilasciati con licenza Attribuzione 4.0 Internazionale (CC BY 4.0), salvo diversa indicazione.
In caso di violazione di copyright, contattare Supporto Iris

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11380/955093
Citazioni
  • ???jsp.display-item.citation.pmc??? 5
  • Scopus 12
  • ???jsp.display-item.citation.isi??? 12
social impact