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Related Concept Videos

The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
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...
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-Drug Binding: Determination Methods01:22

Protein-Drug Binding: Determination Methods

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 WISDOM: A Workbench for In silico De novo Design of BioMolecules
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Published on: July 25, 2013

A structure-based benchmark for protein-protein binding affinity.

Panagiotis L Kastritis1, Iain H Moal, Howook Hwang

  • 1Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, 3584CH Utrecht, The Netherlands.

Protein Science : a Publication of the Protein Society
|January 8, 2011
PubMed
Summary
This summary is machine-generated.

This study presents a diverse dataset of 144 protein-protein complexes with high-resolution structures and measured affinities. This resource aids in developing better models for predicting protein interaction strength from structure.

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Published on: January 26, 2024

Area of Science:

  • Structural Biology
  • Biophysics
  • Computational Biology

Background:

  • Understanding protein-protein interactions is crucial for deciphering biological processes.
  • Accurate prediction of binding affinity from structural data remains a challenge.

Purpose of the Study:

  • To curate a comprehensive dataset of protein-protein complexes for benchmarking computational models.
  • To analyze the relationship between structural changes and binding affinity in protein association.

Main Methods:

  • Assembled a nonredundant set of 144 protein-protein complexes with available high-resolution structures for both complexed and unbound states.
  • Included complexes with diverse biological functions (e.g., G-protein, receptor, antibody, enzyme interactions).
  • Utilized biophysical methods to measure dissociation constants (K(d)) ranging from 10^-5 to 10^-14 M.

Main Results:

  • Observed significant conformational changes, including large movements and disorder-to-order transitions, in most complexes upon association.
  • Identified nine pairs of related complexes with similar structures but vastly different affinities, highlighting the impact of subtle changes.
  • The dataset includes diverse binding affinities, providing a wide range for model testing.

Conclusions:

  • The curated dataset serves as a valuable benchmark for biophysical models aiming to link protein structure to binding affinity.
  • Accounting for conformational changes and unbound states is essential for accurate affinity prediction.
  • This resource facilitates the development of more predictive models for protein-protein interactions.