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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...
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...
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...
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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Related Experiment Video

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Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
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Evolution of 'ligand-diffusion chreodes' on protein-surface models: a genetic-algorithm study.

Sayed-Amir Marashi1, Mehdi Kargar, Ali Katanforoush

  • 1Department of Biotechnology, University College of Science, University of Tehran, Enghelab Avenue, Tehran, Iran. marashie@khayam.ut.ac.ir

Chemistry & Biodiversity
|December 18, 2007
PubMed
Summary
This summary is machine-generated.

Ligand diffusion pathways can evolve on protein surfaces, guided by genetic algorithms. This evolution optimizes pathways to reduce ligand travel time to the active site, enhancing protein function.

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Area of Science:

  • Computational biology
  • Biophysics
  • Protein dynamics

Background:

  • Lattice models simulate ligand diffusion on protein surfaces.
  • Pre-existing pathways ('chreodes') can reduce ligand travel steps to active sites.

Purpose of the Study:

  • Investigate if ligand-diffusion pathways can evolve on protein surfaces.
  • Determine if evolution can shorten ligand travel length to the active site.

Main Methods:

  • Utilized a genetic algorithm approach.
  • Modeled ligand diffusion on protein surfaces using lattice models.
  • Applied selection pressure for reduced travel length.

Main Results:

  • Demonstrated the evolution of ligand-diffusion pathways.
  • Showed that evolved pathways effectively shorten travel length.
  • Identified specific residue properties contributing to pathway optimization.

Conclusions:

  • Ligand-diffusion pathways can be computationally evolved on protein surfaces.
  • Evolutionary optimization of pathways significantly enhances ligand access to active sites.
  • Results offer insights into protein functional evolution and drug design.