title: The Semantics of the Modular Architecture of Protein Structures.
abstract: Protein structures can be conceptualized as context-aware self-organizing systems. One of its emerging properties is a modular architecture. Such modular architecture has been identified as domains and defined as its units of evolution and function. However, this modular architecture is not exclusively defined by domains. Also, the definition of a domain is an ongoing debate. Here we propose differentiating structural, evolutionary and functional domains as distinct concepts. Defining domains or modules is confounded by diverse definitions of the concept, and also by other elements inherent to protein structures. An apparent hierarchy in protein structure architecture is one of these elements, where lower level interactions may create noise for the definition of higher levels. Diverse modularity-molding factors such as folding, function, and selection, can have a misleading effect when trying to define a given type of module. It is thus important to keep in mind this complexity when defining modularity in protein structures and interpreting the outcome modularity inference approaches.
authors.affiliation: Department of Biochemistry and Molecular Biology, Faculty of Medicine, Dalhousie University, PO Box 15000 Halifax, Nova Scotia, Canada B3H 4R2. jshleap@dal.ca.
authors.forename: Jose Sergio
authors.initials: JS
authors.lastname: Hleap
authors.forename: Christian
authors.initials: C
authors.lastname: Blouin
mesh_terms: D000818:Animals; D001665:Binding Sites; D005075:Biological Evolution; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation; D054730:Protein Interaction Domains and Motifs; D011506:Proteins / Q000737:chemistry*; D012660:Semantics; D013329:Structure-Activity Relationship
chemical_list: D011506:Proteins