title: Comparative Study of Elastic Network Model and Protein Contact Network for Protein Complexes: The Hemoglobin Case.
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.
authors.affiliation: Center for Systems Biology, School of Electronic and Information Engineering, Soochow University, Suzhou 215006, China.
authors.forename: Guang
authors.identifier: 0000-0002-8754-1541
authors.initials: G
authors.lastname: Hu
authors.affiliation: Unit of Chemical-Physics Fundamentals in Chemical Engineering, Department of Engineering, Università Campus Bio-Medico di Roma, Rome, Italy.
authors.forename: Luisa
authors.initials: L
authors.lastname: Di Paola
authors.affiliation: Center for Systems Biology, School of Electronic and Information Engineering, Soochow University, Suzhou 215006, China.
authors.forename: Zhongjie
authors.initials: Z
authors.lastname: Liang
authors.affiliation: Environment and Health Department, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Roma, Italy.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Giuliani
mesh_terms: D000494:Allosteric Regulation; D019295:Computational Biology / Q000379:methods*; D006454:Hemoglobins / Q000378:metabolism*; D008954:Models, Biological; D046912:Multiprotein Complexes / Q000378:metabolism*; D025941:Protein Interaction Mapping; D055503:Protein Multimerization; D015398:Signal Transduction
chemical_list: D006454:Hemoglobins; D046912:Multiprotein Complexes