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Abstract
Intra–molecular interactions within complex systems play a pivotal role in the biological function. They form a major challenge to computational structural proteomics. The network paradigm treats any system as a set of nodes linked by edges corresponding to the relations existing between the nodes. It offers a computationally efficient tool to meet this challenge. Here, we review the recent advances in the use of network theory to study the topology and dynamics of protein– ligand and protein–nucleic acid complexes. The study of protein complexes networks not only involves the topological classification in term of network parameters, but also reveals the consistent picture of intrinsic functional dynamics. Current dynamical analysis focuses on a plethora of functional phenomena: the process of allosteric communication, the binding induced conformational changes, prediction and identification of binding sites of protein complexes, which will give insights into intra–protein complexes interactions. Furthermore, such computational results may elucidate a variety of known biological processes and experimental data, and thereby demonstrate a huge potential for applications such as drug design and functional genomics. Finally we describe some web–based resources for protein complexes, as well as protein network servers and related bioinformatics tools.
Keywords: Allosteric communication paths, binding sites prediction, conformational changes, network theory, protein–ligand interactions, protein-nucleic acid interactions
Current Protein & Peptide Science
Title:The Topology and Dynamics of Protein Complexes: Insights from Intra– Molecular Network Theory
Volume: 14 Issue: 2
Author(s): Guang Hu, Jianhong Zhou, Wenying Yan, Jiajia Chen and Bairong Shen
Affiliation:
Keywords: Allosteric communication paths, binding sites prediction, conformational changes, network theory, protein–ligand interactions, protein-nucleic acid interactions
Abstract: Intra–molecular interactions within complex systems play a pivotal role in the biological function. They form a major challenge to computational structural proteomics. The network paradigm treats any system as a set of nodes linked by edges corresponding to the relations existing between the nodes. It offers a computationally efficient tool to meet this challenge. Here, we review the recent advances in the use of network theory to study the topology and dynamics of protein– ligand and protein–nucleic acid complexes. The study of protein complexes networks not only involves the topological classification in term of network parameters, but also reveals the consistent picture of intrinsic functional dynamics. Current dynamical analysis focuses on a plethora of functional phenomena: the process of allosteric communication, the binding induced conformational changes, prediction and identification of binding sites of protein complexes, which will give insights into intra–protein complexes interactions. Furthermore, such computational results may elucidate a variety of known biological processes and experimental data, and thereby demonstrate a huge potential for applications such as drug design and functional genomics. Finally we describe some web–based resources for protein complexes, as well as protein network servers and related bioinformatics tools.
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Cite this article as:
Hu Guang, Zhou Jianhong, Yan Wenying, Chen Jiajia and Shen Bairong, The Topology and Dynamics of Protein Complexes: Insights from Intra– Molecular Network Theory, Current Protein & Peptide Science 2013; 14 (2) . https://dx.doi.org/10.2174/1389203711314020004
DOI https://dx.doi.org/10.2174/1389203711314020004 |
Print ISSN 1389-2037 |
Publisher Name Bentham Science Publisher |
Online ISSN 1875-5550 |
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