Local motifs in proteins combine to generate global functional moves

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Atılgan, Ali Rana and Atılgan, Canan (2012) Local motifs in proteins combine to generate global functional moves. Briefings in Functional Genomics (Sl), 11 (6). pp. 479-488. ISSN 2041-2649 (Print) 2041-2657 (Online)

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Official URL: http://dx.doi.org/10.1093/bfgp/els027


Literature on the topological properties of folded proteins that has emerged as a field in its own right in the past decade is reviewed. Physics-based construction of coarse-grained models of proteins from knowledge of all-atom coordinates of the average structure is discussed. Once network is thus obtained with the node and link information, local motifs provide plethora of information on protein function. The hierarchical structure of the proteins manifested in the interrelations of local motifs is emphasized.Motifs are also related to modularity of the structure, and they quantify shifts in the landscapes upon conformational changes induced by, e.g. ligand binding. Redundancy emerges as a balance between local and global network descriptors and is related to the collectivity of the protein motions. Introducing weight on links followed by sequential removal of least cohesive contacts allows interactions in proteins to be represented as the superposition of essential and redundant sets. Lack of the former makes the network non-functional, while the latter ensures robust functioning under a wide range of perturbation scenarios.

Item Type:Article
Uncontrolled Keywords:amino-acid contacts, assortative coordination, weighted networks, redundant links, allosteric communication, collective dynamics
Subjects:Q Science > QD Chemistry > QD450-801 Physical and theoretical chemistry
Q Science > Q Science (General)
ID Code:20403
Deposited By:Canan Atılgan
Deposited On:27 Nov 2012 16:44
Last Modified:31 Jul 2019 15:11

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