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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...
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...
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:

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Related Experiment Video

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Modeling Ligands into Maps Derived from Electron Cryomicroscopy
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Carbohydrate-binding proteins: Dissecting ligand structures through solvent environment occupancy.

Diego F Gauto1, Santiago Di Lella, Carlos M A Guardia

  • 1Departamento de Quimica Inorganica, Analitica, y Quimica Fisica, INQUIMAE-CONICET, Universidad de Buenos Aires, Argentina.

The Journal of Physical Chemistry. B
|June 3, 2009
PubMed
Summary

Displacing tightly bound water molecules from protein binding sites is key for understanding ligand interactions. This study reveals a direct correlation between water site occupancy and ligand binding, offering insights for drug design.

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Biochemical and Structural Characterization of the Carbohydrate Transport Substrate-binding-protein SP0092
08:53

Biochemical and Structural Characterization of the Carbohydrate Transport Substrate-binding-protein SP0092

Published on: October 2, 2017

Area of Science:

  • Biochemistry and Molecular Biophysics
  • Computational Chemistry and Structural Biology

Background:

  • Protein-ligand complex formation involves significant solvent reorganization and displacement of bound water molecules.
  • The role of water molecules in ligand binding, particularly at carbohydrate recognition sites, is crucial but not fully understood at the microscopic level.
  • Understanding water displacement is essential for characterizing binding free energy and kinetics.

Purpose of the Study:

  • To investigate the thermodynamic and kinetic contributions of surface-associated water molecules to protein-ligand binding.
  • To develop and apply analysis tools linking solvation properties to ligand binding in carbohydrate-binding proteins.
  • To extend the analysis of water molecule roles to a broader range of structurally characterized protein-ligand complexes.

Main Methods:

  • Utilized molecular dynamics (MD) simulations in explicit water solvent.
  • Applied statistical mechanics analysis to compute and analyze thermodynamic properties of water molecules.
  • Defined and analyzed 'water sites' (WS) based on the thermodynamic properties of strongly bound water molecules.

Main Results:

  • Identified a direct correlation between the probability of water molecules occupying defined water sites (p(v)) and the likelihood of ligand hydroxyl groups binding within the protein.
  • Demonstrated that the occupancy of high p(v) water sites is indicative of potential ligand binding interactions.
  • Extended these findings across diverse proteins including concanavalin-A, galectin-3, cyclophilin-A, and bacterial sialidase modules.

Conclusions:

  • The solvation structure of carbohydrate recognition domains is intricately linked to protein-ligand complex formation.
  • Targeting high p(v) water sites with hydroxyl-containing functional groups can enhance protein affinity and specificity.
  • This approach offers a strategy for designing improved drugs, particularly glycomimetic drugs, by optimizing ligand-protein interactions.