title: The architectural design of networks of protein domain architectures.
abstract: Protein domain architectures (PDAs), in which single domains are linked to form multiple-domain proteins, are a major molecular form used by evolution for the diversification of protein functions. However, the design principles of PDAs remain largely uninvestigated. In this study, we constructed networks to connect domain architectures that had grown out from the same single domain for every single domain in the Pfam-A database and found that there are three main distinctive types of these networks, which suggests that evolution can exploit PDAs in three different ways. Further analysis showed that these three different types of PDA networks are each adopted by different types of protein domains, although many networks exhibit the characteristics of more than one of the three types. Our results shed light on nature's blueprint for protein architecture and provide a framework for understanding architectural design from a network perspective.
authors.affiliation: Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan, Republic of China.
authors.forename: Chia-Hsin
authors.initials: CH
authors.lastname: Hsu
authors.forename: Chien-Kuo
authors.initials: CK
authors.lastname: Chen
authors.forename: Ming-Jing
authors.initials: MJ
authors.lastname: Hwang
mesh_terms: D019143:Evolution, Molecular; D053263:Gene Regulatory Networks; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry / Q000235:genetics*
chemical_list: D011506:Proteins
keywords: domain accretion; network expansion; protein domain architecture; protein evolution