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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...
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:
Gene Families01:57

Gene Families

Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
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.
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...
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...

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Related Experiment Video

Updated: May 13, 2026

Modeling Ligands into Maps Derived from Electron Cryomicroscopy
09:30

Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Published on: July 19, 2024

Small ligand-globin interactions: reviewing lessons derived from computer simulation.

Luciana Capece1, Leonardo Boechi, Laura L Perissinotti

  • 1Departamento de Química Inorgánica, Analítica, y Química Física, Universidad de Buenos Aires, Buenos Aires, Argentina.

Biochimica Et Biophysica Acta
|March 9, 2013
PubMed
Summary

Computer simulations reveal how small molecules like oxygen and carbon monoxide interact with globins. These atomistic studies enhance understanding of ligand migration and binding modulation by protein structures.

Keywords:
Computer simulationGlobinHeme proteinMolecular dynamicsQM/MM

Related Experiment Videos

Last Updated: May 13, 2026

Modeling Ligands into Maps Derived from Electron Cryomicroscopy
09:30

Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Published on: July 19, 2024

Area of Science:

  • Biophysics
  • Computational Chemistry
  • Biochemistry

Background:

  • Globins are essential proteins involved in oxygen transport and sensing.
  • Understanding small ligand interactions with globins is crucial for various biological processes.
  • Previous studies have explored these interactions using experimental and theoretical methods.

Purpose of the Study:

  • To review the application of classical and quantum-mechanical atomistic computer simulations for investigating small ligand interactions with globins.
  • To highlight how simulation tools have advanced the understanding of ligand migration and binding.
  • To provide insights into the modulation of protein-ligand binding by heme structure and amino acid interactions.

Main Methods:

  • Utilizing classical and quantum-mechanical atomistic computer simulation tools.
  • Analyzing ligand migration and its relation to kinetic association rate constants (kon).
  • Reviewing studies on various ligands including O2, NO, CO, HS(-), F(-), and NO2(-).

Main Results:

  • Demonstrated the role of heme structure, proximal effects, and distal amino acid interactions in modulating protein-ligand binding.
  • Presented findings on ligand migration and kinetic association rates.
  • Showcased how computer simulations have deepened the understanding of small ligand-globin interactions over the past decade.

Conclusions:

  • Atomistic computer simulations are powerful tools for elucidating small ligand interactions with globins.
  • These simulations provide valuable insights into the mechanisms of ligand binding and modulation.
  • The reviewed studies exemplify the significant contribution of computational methods to biophysical and biochemical research.