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Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...
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Correction: Zhang et al. GL-1196 Suppresses the Proliferation and Invasion of Gastric Cancer Cells via Targeting PAK4 and Inhibiting PAK4-Mediated Signaling Pathways. <i>Int. J. Mol. Sci.</i> 2016, <i>17</i>, 470.

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Updated: May 8, 2026

Identification of Kinase-substrate Pairs Using High Throughput Screening
11:13

Identification of Kinase-substrate Pairs Using High Throughput Screening

Published on: August 29, 2015

Structure-based functional site recognition for p21-activated kinase 4.

Jian Wang1, Gang Wang, Yu Sha

  • 1Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China.

Archives of Pharmacal Research
|September 10, 2013
PubMed
Summary
This summary is machine-generated.

Molecular modeling using flexible dinucleotides successfully identified functional sites on p21-activated kinase 4 (PAK4). This structure-based docking approach provides a theoretical basis for enzyme functional site prediction and annotation.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Computational Chemistry

Background:

  • Protein folding principles are crucial for understanding biological function.
  • Molecular modeling methods are advancing the study of protein dynamics.
  • Identifying enzyme functional sites is key to drug discovery and biological research.

Purpose of the Study:

  • To investigate the utility of flexible dinucleotide docking for identifying functional sites on p21-activated kinase 4 (PAK4).
  • To explore structure-based docking as a method for predicting and annotating enzyme active sites.
  • To provide a computational basis for experimental interaction data.

Main Methods:

  • Automated docking of 16 distinct fully flexible dinucleotides (e.g., d(pApA), d(pTpG)) onto the PAK4 kinase domain.
  • Utilizing molecular modeling to simulate dinucleotide-enzyme interactions.
  • Structure-based computational analysis.

Main Results:

  • Automated docking successfully identified potential functional sites on the PAK4 kinase domain.
  • The docking results offer a theoretical framework supporting previous experimental findings.
  • Flexible dinucleotide probes proved effective in mapping enzyme surfaces.

Conclusions:

  • Structure-based docking with flexible dinucleotide probes is a valuable tool for enzyme functional site prediction.
  • This computational approach can guide experimental studies and annotate enzyme functions.
  • The method holds promise for broader applications in enzyme research.