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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:
Bonding and Strength of Aggregate01:12

Bonding and Strength of Aggregate

The bond between aggregate particles and the cement matrix is significantly influenced by the shape and surface texture of the aggregates. High-strength concretes benefit from a rougher texture, which leads to stronger bonding due to greater adhesion. Angular aggregates with larger surface areas also enhance this bond. The bonding quality, however, is complex to assess as no universally accepted test exists. Good bonding is indicated when a crushed concrete specimen shows some aggregate...
Noncovalent Attractions in Biomolecules02:35

Noncovalent Attractions in Biomolecules

Noncovalent attractions are associations within and between molecules that influence the shape and structural stability of complexes. These interactions differ from covalent bonding in that they do not involve sharing of electrons.
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Noncovalent Attractions in Biomolecules02:35

Noncovalent Attractions in Biomolecules

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Van der Waals Interactions01:24

Van der Waals Interactions

Atoms and molecules interact with each other through intermolecular forces. These electrostatic forces arise from attractive or repulsive interactions between particles with permanent, partial, or temporary charges. The intermolecular forces between neutral atoms and molecules are ion–dipole, dipole–dipole, and dispersion forces, collectively known as van der Waals forces.

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Related Experiment Video

Updated: May 25, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Optimizing ring assembly reveals the strength of weak interactions.

Eric J Deeds1, John A Bachman, Walter Fontana

  • 1Center for Bioinformatics and Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66047, USA. deeds@ku.edu

Proceedings of the National Academy of Sciences of the United States of America
|February 7, 2012
PubMed
Summary

Optimizing protein ring assembly requires balancing subunit interaction strengths. Computational models reveal that intermediate affinities maximize efficiency for homomeric rings, while heteromeric rings benefit from at least one weak interaction.

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Related Experiment Videos

Last Updated: May 25, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Biology

Background:

  • Cellular processes depend on multiprotein complexes with precise quaternary structures.
  • Ring-like structures, such as proteasomes and AAA+ ATPases, are common in biology.
  • Understanding the evolution of their assembly pathways is crucial.

Purpose of the Study:

  • To investigate evolutionary challenges in the assembly dynamics of ring-like protein structures.
  • To identify how subunit interaction strengths affect assembly efficiency and yield.
  • To predict optimal interaction affinities for both homomeric and heteromeric rings.

Main Methods:

  • Development of computational models to simulate protein complex assembly dynamics.
  • Analysis of assembly trajectories under varying interaction strengths.
  • Comparison of model predictions with affinities estimated from solved protein structures.

Main Results:

  • A 'deadlocked plateau' in assembly dynamics occurs with overly strong subunit interactions, causing delays and reduced yield.
  • Weak interactions lead to instability of key intermediates, also delaying assembly.
  • Intermediate interaction affinities optimize assembly efficiency for homomeric rings.
  • Heteromeric rings assemble efficiently and robustly when incorporating at least one weak subunit interaction.

Conclusions:

  • The study provides an evolutionary explanation for the prevalence of weak interactions in heteromeric ring structures.
  • Findings offer insights into the assembly of complex stacked rings like the proteasome.
  • The work lays groundwork for designing synthetic self-assembling ring-like protein structures.