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.
Export Options
About this article
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 |
Call for Papers in Thematic Issues
Advancements in Proteomic and Peptidomic Approaches in Cancer Immunotherapy: Unveiling the Immune Microenvironment
The scope of this thematic issue centers on the integration of proteomic and peptidomic technologies into the field of cancer immunotherapy, with a particular emphasis on exploring the tumor immune microenvironment. This issue aims to gather contributions that illustrate the application of these advanced methodologies in unveiling the complex interplay ...read more
Nutrition and Metabolism in Musculoskeletal Diseases
The musculoskeletal system consists mainly of cartilage, bone, muscles, tendons, connective tissue and ligaments. Balanced metabolism is of vital importance for the homeostasis of the musculoskeletal system. A series of musculoskeletal diseases (for example, sarcopenia, osteoporosis) are resulted from the dysregulated metabolism of the musculoskeletal system. Furthermore, metabolic diseases (such ...read more
Protein Folding, Aggregation and Liquid-Liquid Phase Separation
Protein folding, misfolding and aggregation remain one of the main problems of interdisciplinary science not only because many questions are still open, but also because they are important from the point of view of practical application. Protein aggregation and formation of fibrillar structures, for example, is a hallmark of a ...read more
Related Journals
- Author Guidelines
- Graphical Abstracts
- Fabricating and Stating False Information
- Research Misconduct
- Post Publication Discussions and Corrections
- Publishing Ethics and Rectitude
- Increase Visibility of Your Article
- Archiving Policies
- Peer Review Workflow
- Order Your Article Before Print
- Promote Your Article
- Manuscript Transfer Facility
- Editorial Policies
- Allegations from Whistleblowers
Related Articles
-
Nucleic Acids Electro-transfer: From Bench to Bedside
Current Drug Metabolism Meet Our Editorial Board Member
Current Molecular Pharmacology Crimean-Congo Hemorrhagic Fever Virus in Pakistan
Infectious Disorders - Drug Targets Pulmonary Hypertension and Lung Transplantation
Current Hypertension Reviews Neuropsychiatric Systemic Lupus Erythematosus
Current Neuropharmacology Video Games and Sleep: An Overlooked Challenge
Adolescent Psychiatry In Vitro Models of Human T Cell Development: Dishing Out Progenitor T Cells
Current Immunology Reviews (Discontinued) Gabapentin and Pregabalin for the Acute Post-operative Pain Management. A Systematic-narrative Review of the Recent Clinical Evidences
Current Drug Targets Conference Report:
CNS & Neurological Disorders - Drug Targets Adenosine A2A Receptor Antagonists and Parkinsons Disease: State of the Art and Future Directions
Current Pharmaceutical Design Onychomycosis: Current Understanding and Strategies for Enhancing Drug Delivery into Human Nail Tissue
Current Drug Research Reviews Examination of Hippocampal Differences Between Alzheimer Disease, Amnestic Mild Cognitive Impairment and Normal Aging: Diffusion Kurtosis
Current Alzheimer Research Oxidative Stress and Antioxidants in Neurological Diseases: Is There Still Hope?
Current Drug Targets Genetic Studies on the Role of T-Type Ca2+ Channels in Sleep and Absence Epilepsy
CNS & Neurological Disorders - Drug Targets Placental Drug Transporters
Current Drug Metabolism Machine Learning, Molecular Modeling, and QSAR Studies on Natural Products Against Alzheimer’s Disease
Current Medicinal Chemistry Implications of Nanotechnology in Healthcare
Nanoscience & Nanotechnology-Asia PET/MR Tomographs: A Review with Technical, Radiochemical and Clinical Perspectives
Current Radiopharmaceuticals Rho GTPase Effector Functions in Tumor Cell Invasion and Metastasis
Current Drug Targets Monoaminergic Neurotransmission: The History of the Discovery of Antidepressants from 1950s Until Today
Current Pharmaceutical Design