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Spatiotemporal Control of Protein Activity through Optogenetic Allosteric Regulation
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How protein topology controls allosteric regulations.

Juan Xie1, Gaoxiang Pan2, Yibo Li3

  • 1Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.

The Journal of Chemical Physics
|March 15, 2023
PubMed
Summary
This summary is machine-generated.

Protein topology significantly influences allosteric regulation and the location of allosteric sites, including cryptic ones. A new method, TopoAlloSite, predicts these sites using protein structure, aiding drug design.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Biology

Background:

  • Allostery is a key protein regulatory mechanism.
  • The relationship between protein topology and allosteric regulation is not well understood.
  • Specific protein structures are frequently observed in allosteric proteins.

Purpose of the Study:

  • To investigate how protein topology influences allosteric regulation.
  • To identify patterns in the distribution of allosteric sites based on protein structure.
  • To develop a computational method for predicting allosteric site locations.

Main Methods:

  • Extraction of protein topology graphs at the fold level.
  • Analysis of fold combinations and domain/subunit arrangements in allosteric proteins.
  • Development of TopoAlloSite, a kernel support vector machine method using subgraph-matching kernels.

Main Results:

  • Allosteric proteins predominantly feature multiple domains or subunits.
  • Allosteric sites are frequently located between domains of the same fold type.
  • TopoAlloSite accurately predicted known cryptic allosteric sites in several proteins.

Conclusions:

  • Protein topology is a major determinant of allosteric regulation.
  • The location of allosteric sites, including cryptic ones, is linked to protein topology.
  • TopoAlloSite offers an efficient approach for identifying cryptic allosteric sites and potential drug targets.