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Related Concept Videos

Ligand Binding Sites02:40

Ligand Binding Sites

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.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Ligand Binding Sites02:40

Ligand Binding Sites

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.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Conserved Binding Sites01:49

Conserved Binding Sites

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.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Protein-protein Interfaces02:04

Protein-protein Interfaces

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 polypeptide...
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

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 polypeptide...
Ligand Binding and Linkage00:49

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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Single-Molecule Measurement of Protein Interaction Dynamics Within Biomolecular Condensates
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Single-Molecule Measurement of Protein Interaction Dynamics Within Biomolecular Condensates

Published on: January 5, 2024

Rapid protein-ligand costructures from sparse NOE data.

Dipen M Shah1, Eiso A B, Tammo Diercks

  • 1Leiden Institute of Chemistry, Leiden University, Leiden 2300RA, The Netherlands.

Journal of Medicinal Chemistry
|November 14, 2012
PubMed
Summary

This study presents a fast method for determining protein-ligand structures using Nuclear Magnetic Resonance (NMR) and selective labeling. This approach aids in early-stage drug discovery by defining binding sites and ligand orientation efficiently.

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Area of Science:

  • Structural Biology
  • Biophysics
  • Drug Discovery

Background:

  • Determining protein-ligand complex structures is crucial for understanding biological mechanisms and designing drugs.
  • Traditional methods for structural determination can be time-consuming and resource-intensive.

Purpose of the Study:

  • To develop an efficient and rapid method for generating protein-ligand costructures.
  • To utilize sparse Nuclear Magnetic Resonance (NMR) data combined with selective isotope labeling.

Main Methods:

  • Employed solution-NMR spectroscopy with sparse Nuclear Overhauser Effect (NOE) data.
  • Incorporated selective isotope labeling to enhance data quality and reduce complexity.
  • Applied computational docking to generate the structural model.

Main Results:

  • Successfully generated a docked model of the Hsp90 N-terminal ATPase domain bound to a small molecule ligand.
  • Utilized only 21 intermolecular NOEs to define the ligand's binding site and orientation.
  • Demonstrated the efficiency and accuracy of the sparse NOE approach.

Conclusions:

  • The presented method offers an efficient way to rapidly determine protein-ligand structures.
  • This technique is valuable for the early stages of fragment-based drug discovery.
  • The approach can accelerate the identification and optimization of drug candidates.