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Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
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Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
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Protein-Drug Binding: Determination Methods01:22

Protein-Drug Binding: Determination Methods

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Determining protein-drug binding can be achieved through indirect and direct methods, each providing valuable insights into the interaction between proteins and drugs.
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Protein-protein Interfaces02:04

Protein-protein Interfaces

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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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Protein Folding Quality Check in the RER01:29

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ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
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Ligand Binding and Linkage00:49

Ligand Binding and Linkage

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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...
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Related Experiment Video

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A Protocol for Computer-Based Protein Structure and Function Prediction
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TWN-RENCOD: A novel method for protein binding site comparison.

Kwang-Eun Choi1, Anand Balupuri1, Nam Sook Kang1

  • 1Graduate School of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, South Korea.

Computational and Structural Biotechnology Journal
|January 9, 2023
PubMed
Summary
This summary is machine-generated.

A new method, TWN-based residue encoding (TWN-RENCOD), compares protein binding sites by analyzing water networks. This approach better predicts drug activity variations compared to existing methods.

Keywords:
Binding site comparison methodDrug repurposingProtein binding siteSunitinibWater network

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Chemistry

Background:

  • Diverse proteins often share similar binding sites, crucial for drug discovery and development.
  • Existing binding site comparison methods may not fully explain variations in drug activity across related proteins.
  • Water molecules and their topological water networks (TWNs) significantly influence protein structure and function.

Purpose of the Study:

  • To introduce a novel method, TWN-based residue encoding (TWN-RENCOD), for comparing protein binding sites.
  • To enhance the understanding of binding site characteristics by analyzing the aqueous environment.
  • To improve the prediction of drug activity variations against protein targets.

Main Methods:

  • Developed TWN-RENCOD, a method that encodes binding sites based on topological water networks.
  • Applied TWN-RENCOD to compare the binding sites of nine protein kinases.
  • Evaluated the method's performance in correlating with drug activity differences.

Main Results:

  • TWN-RENCOD effectively compares the aqueous environments within protein binding sites.
  • The method demonstrated a better correlation with the activity variations of Sunitinib across nine protein kinases compared to existing methods.
  • TWN-RENCOD provides a novel perspective on binding site analysis.

Conclusions:

  • TWN-RENCOD offers a promising new approach for protein binding site comparison.
  • Analyzing topological water networks can significantly improve the understanding of binding site properties and drug-protein interactions.
  • This method has potential applications in drug discovery, off-target identification, and drug repurposing.