Network-based models as tools hinting at nonevident protein functionality
Atılgan, Canan and Okan, Osman Burak and Atılgan, Ali Rana (2012) Network-based models as tools hinting at nonevident protein functionality. Annual Review of Biophysics, 41 . pp. 205-225. ISSN 1936-122X (Print) 1936-1238 (Online)
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Official URL: http://dx.doi.org/10.1146/annurev-biophys-050511-102305
Network-basedmodels of proteins are popular tools employed to determine dynamic features related to the folded structure. They encompass all topological and geometric computational approaches idealizing proteins as directly interacting nodes. Topology makes use of neighborhood information of residues, and geometry includes relative placement of neighbors. Coarsegrained approaches efficiently predict alternative conformations because of inherent collectivity in the protein structure. Such collectivity is moderated by topological characteristics that also tune neighborhood structure: That rich residues have richer neighbors secures robustness toward random loss of interactions/nodes due to environmental fluctuations/mutations. Geometry conveys the additional information of force balance to network models, establishing the local shape of the energy landscape. Here, residue and/or bond perturbations are critically evaluated to suggest new experiments, as network-based computational techniques prove useful in capturing domain movements and conformational shifts resulting from environmental alterations. Evolutionarily conserved residues are optimally connected, defining a subnetwork that may be utilized for further coarsening.
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