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Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

5.2K
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...
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Ligand Binding Sites02:40

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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...
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The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

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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:
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Related Experiment Video

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Author Spotlight: Unveiling the Structural and Dynamic Aspects of Glycan Molecular Recognition
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Deciphering Cryptic Binding Sites on Proteins by Mixed-Solvent Molecular Dynamics.

S Roy Kimura1, Hai Peng Hu2, Anatoly M Ruvinsky3

  • 1Schrödinger KK , 17th Fl, Marunouchi Trust Tower North, 1-8-1 Marunouchi, Chiyoda-ku, Tokyo, Japan.

Journal of Chemical Information and Modeling
|May 25, 2017
PubMed
Summary
This summary is machine-generated.

Molecular dynamics simulations using mixed solvents reveal hidden protein binding pockets. This approach aids in drug discovery by identifying potential ligand binding sites not seen in static protein structures.

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Area of Science:

  • Biophysics
  • Computational Chemistry
  • Drug Discovery

Background:

  • Molecular dynamics (MD) simulations in mixed solvents are increasingly used in protein biophysics and drug discovery.
  • Applications include protein folding, surface characterization, fragment screening, allostery, and druggability assessment.

Purpose of the Study:

  • To systematically investigate how organic solvent mixtures in water can expose cryptic ligand binding pockets in apo proteins.
  • To determine if MD simulations of apo proteins using cosolvents can induce binding sites observed in holo structures.

Main Methods:

  • Performed MD simulations of eight diverse PDB proteins in explicit mixed solvents (water with organic probes).
  • Analyzed conformational changes on protein surfaces induced by cosolvent simulations.
  • Compared simulation-induced structures with available holo structures.

Main Results:

  • Cosolvent MD simulations successfully induced conformational changes on protein surfaces.
  • These induced changes revealed cryptic binding pockets not apparent in apo crystal structures.
  • The study examined various biological systems, probe choices, concentrations, and the druggability of induced pockets.

Conclusions:

  • Mixed solvent MD simulations are effective in uncovering cryptic ligand binding sites.
  • This methodology offers a valuable approach for drug discovery by identifying previously hidden pockets.
  • The findings highlight the utility of dynamic simulation approaches for characterizing protein-ligand interactions.