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Related Concept Videos

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...
Solubility03:00

Solubility

Solution, Solubility, and Solubility Equilibrium
A solution is a homogeneous mixture composed of a solvent, the major component, and a solute, the minor component. The physical state of a solution—solid, liquid, or gas—is typically the same as that of the solvent. Solute concentrations are often described with qualitative terms such as dilute (of relatively low concentration) and concentrated (of relatively high concentration).
In a solution, the solute particles (molecules, atoms, and/or ions)...
Solubility Equilibria03:07

Solubility Equilibria

Solubility equilibria are established when the dissolution and precipitation of a solute species occur at equal rates. These equilibria underlie many natural and technological processes, ranging from tooth decay to water purification. An understanding of the factors affecting compound solubility is, therefore, essential to the effective management of these processes. This section applies previously introduced equilibrium concepts and tools to systems involving dissolution and precipitation.
The...
Factors Affecting Solubility04:01

Factors Affecting Solubility

Compared with pure water, the solubility of an ionic compound is less in aqueous solutions containing a common ion (one also produced by dissolution of the ionic compound). This is an example of a phenomenon known as the common ion effect, which is a consequence of the law of mass action that may be explained using Le Chȃtelier’s principle. Consider the dissolution of silver iodide:
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...
Factors Affecting Dissolution: Drug pKa, Lipophilicity and GI pH01:21

Factors Affecting Dissolution: Drug pKa, Lipophilicity and GI pH

Drug absorption within the gastrointestinal (GI) tract is a complex process influenced by several critical factors, including the site pH, the drug's dissociation constant (pKa), and the drug's lipophilicity. The GI tract exhibits a pH gradient, with an acidic environment in the stomach and a more alkaline environment in the small intestine. This pH variation directly affects the ionization state of drugs.
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Related Experiment Video

Updated: May 26, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Sequence-based prediction of protein solubility.

Federico Agostini1, Michele Vendruscolo, Gian Gaetano Tartaglia

  • 1Centre for Genomic Regulation (CRG) and Universitat Pompeu Fabra (UPF), Dr. Aiguader, 88, Barcelona 08003, Spain.

Journal of Molecular Biology
|December 17, 2011
PubMed
Summary
This summary is machine-generated.

Protein solubility and aggregation rates are significantly correlated, suggesting a link between thermodynamic stability and kinetic barriers. This finding aids in predicting protein solubility computationally.

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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Area of Science:

  • Biochemistry
  • Computational Biology
  • Protein Science

Background:

  • Protein aggregation is implicated in various diseases.
  • Understanding the factors governing protein aggregation is crucial.

Purpose of the Study:

  • To investigate the relationship between protein thermodynamics (solubility) and kinetics (aggregation rates).
  • To develop a predictive model for protein solubility at the proteome level.

Main Methods:

  • Compared protein solubility with aggregation rates using a database of in vitro reconstituted translation system data.
  • Utilized physicochemical properties for developing a solubility prediction method.

Main Results:

  • A significant correlation was found between protein solubility and aggregation rates.
  • The correlation suggests a link between thermodynamic stability and kinetic barriers in protein aggregation.
  • A computational method for predicting protein solubility was developed.

Conclusions:

  • Thermodynamic stability and kinetic barriers are closely linked in protein aggregation.
  • The developed method enables computational proteome-level studies on protein solubility and aggregation.