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Comparative Study of Elastic Network Model and Protein Contact Network for Protein Complexes: The Hemoglobin Case

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      Abstract

      The overall topology and interfacial interactions play key roles in understanding structural and functional principles of protein complexes. Elastic Network Model (ENM) and Protein Contact Network (PCN) are two widely used methods for high throughput investigation of structures and interactions within protein complexes. In this work, the comparative analysis of ENM and PCN relative to hemoglobin (Hb) was taken as case study. We examine four types of structural and dynamical paradigms, namely, conformational change between different states of Hbs, modular analysis, allosteric mechanisms studies, and interface characterization of an Hb. The comparative study shows that ENM has an advantage in studying dynamical properties and protein-protein interfaces, while PCN is better for describing protein structures quantitatively both from local and from global levels. We suggest that the integration of ENM and PCN would give a potential but powerful tool in structural systems biology.

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      Most cited references 75

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      Network biology: understanding the cell's functional organization.

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        Anisotropy of fluctuation dynamics of proteins with an elastic network model.

        Fluctuations about the native conformation of proteins have proven to be suitably reproduced with a simple elastic network model, which has shown excellent agreement with a number of different properties for a wide variety of proteins. This scalar model simply investigates the magnitudes of motion of individual residues in the structure. To use the elastic model approach further for developing the details of protein mechanisms, it becomes essential to expand this model to include the added details of the directions of individual residue fluctuations. In this paper a new tool is presented for this purpose and applied to the retinol-binding protein, which indicates enhanced flexibility in the region of entry to the ligand binding site and for the portion of the protein binding to its carrier protein.
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          Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis.

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            Author and article information

            Affiliations
            1Center for Systems Biology, School of Electronic and Information Engineering, Soochow University, Suzhou 215006, China
            2Unit of Chemical-Physics Fundamentals in Chemical Engineering, Department of Engineering, Università Campus Bio-Medico di Roma, Rome, Italy
            3Environment and Health Department, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Roma, Italy
            Author notes

            Academic Editor: Hesham H. Ali

            Journal
            Biomed Res Int
            Biomed Res Int
            BMRI
            BioMed Research International
            Hindawi Publishing Corporation
            2314-6133
            2314-6141
            2017
            22 January 2017
            : 2017
            5294226
            10.1155/2017/2483264
            Copyright © 2017 Guang Hu et al.

            This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

            Funding
            Funded by: National Natural Science Foundation of China
            Award ID: 21203131
            Award ID: 81302700
            Funded by: Natural Science Foundation of the Jiangsu Higher Education Institutions
            Award ID: 12KJB180014
            Award ID: 13KJB520022
            Funded by: China Postdoctoral Science Foundation
            Award ID: 2013M531406
            Award ID: 2016M590495
            Categories
            Review Article

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