4.7 Review

Integration of network models and evolutionary analysis into high-throughput modeling of protein dynamics and allosteric regulation: theory, tools and applications

Journal

BRIEFINGS IN BIOINFORMATICS
Volume 21, Issue 3, Pages 815-835

Publisher

OXFORD UNIV PRESS
DOI: 10.1093/bib/bbz029

Keywords

molecular dynamics; normal mode analysis; structural bioinformatics; allostery; protein interactions; genomic medicine

Funding

  1. National Natural Science Foundation of China [31872723]
  2. China Postdoctoral Science Foundation [2016M590495]
  3. Jiangsu College Natural Science Research Key Program [17KJA520004]
  4. Jiangsu Planned Projects for Postdoctoral Research Funds [1601168C]
  5. Priority Academic Program Development (PAPD) of Jiangsu Higher Education Institutions

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Proteins are dynamical entities that undergo a plethora of conformational changes, accomplishing their biological functions. Molecular dynamics simulation and normal mode analysis methods have become the gold standard for studying protein dynamics, analyzing molecular mechanism and allosteric regulation of biological systems. The enormous amount of the ensemble-based experimental and computational data on protein structure and dynamics has presented a major challenge for the high-throughput modeling of protein regulation and molecular mechanisms. In parallel, bioinformatics and systems biology approaches including genomic analysis, coevolution and network-based modeling have provided an array of powerful tools that complemented and enriched biophysical insights by enabling high-throughput analysis of biological data and dissection of global molecular signatures underlying mechanisms of protein function and interactions in the cellular environment. These developments have provided a powerful interdisciplinary framework for quantifying the relationships between protein dynamics and allosteric regulation, allowing for high-throughput modeling and engineering of molecular mechanisms. Here, we review fundamental advances in protein dynamics, network theory and coevolutionary analysis that have provided foundation for rapidly growing computational tools for modeling of allosteric regulation. We discuss recent developments in these interdisciplinary areas bridging computational biophysics and network biology, focusing on promising applications in allosteric regulations, including the investigation of allosteric communication pathways, protein-DNA/RNA interactions and disease mutations in genomic medicine. We conclude by formulating and discussing future directions and potential challenges facing quantitative computational investigations of allosteric regulatory mechanisms in protein systems.

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