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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...
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Factors Affecting Protein-Drug Binding: Drug-Related Factors

Drug binding to proteins is a complex phenomenon influenced by various drug-related factors, each playing a significant role in the interaction between drugs and proteins within the body.
One crucial factor in drug-protein binding is the drug's lipophilicity or its affinity for fat. More lipophilic drugs tend to have higher binding extents. For example, highly lipophilic drugs like cloxacillin exhibit substantial protein binding, with as much as 95% of the drug binding to proteins. In contrast,...
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...
Factors Affecting Protein-Drug Binding: Protein-Related Factors01:20

Factors Affecting Protein-Drug Binding: Protein-Related Factors

Drug binding to proteins is a key aspect of pharmacokinetics and can influence a drug's distribution, absorption, and elimination in the body. Several factors, including the drug's physiochemical properties, protein concentration, disease states, and the number of binding sites on the protein, influence this process.
The physicochemical properties of a drug play a significant role in its ability to bind to proteins. Lipophilic drugs, which dissolve in fats, oils, and lipids, can be bound by...
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...
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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A Flow Cytometry-Based Cell Surface Protein Binding Assay for Assessing Selectivity and Specificity of an Anticancer Aptamer
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Cation specific binding with protein surface charges.

Berk Hess1, Nico F A van der Vegt

  • 1Max-Planck Institute for Polymer Research, Ackermannweg 10, D-55128 Mainz, Germany.

Proceedings of the National Academy of Sciences of the United States of America
|August 12, 2009
PubMed
Summary
This summary is machine-generated.

The law of matching water affinities fails for protein interactions. Alkali metal ions bind to carboxylates via water molecules, not direct contact, influencing protein stability in salt solutions.

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Area of Science:

  • Biophysics
  • Biochemistry
  • Computational Chemistry

Background:

  • Biological organization relies on precise noncovalent interactions, including ion-protein interactions.
  • The "matching water affinities" law qualitatively predicts ion-pairing based on cation-anion size complementarity.
  • This law is insufficient for understanding cation interactions with carboxylate groups on proteins.

Purpose of the Study:

  • To investigate the binding mechanisms between alkali metal cations and carboxylate anions on protein surfaces.
  • To evaluate the validity of the "matching water affinities" law in this context.
  • To elucidate the role of hydration water in ion-protein interactions and thermodynamic stability.

Main Methods:

  • Utilized molecular simulations with quantitatively accurate models.
  • Analyzed ion-pairing interactions between alkali metal cations (Li+, Na+, K+) and carboxylate ions.
  • Quantified binding affinities and characterized the nature of ion pairs (contact vs. solvent-shared).

Main Results:

  • The "matching water affinities" law inaccurately predicts binding affinities between alkali cations and carboxylates.
  • Observed an increasing binding affinity order: K+ < Na+ < Li+.
  • Demonstrated a stronger preference for forming weak solvent-shared ion pairs over contact ion pairs.
  • Found that direct contact ion pair interactions with protein surfaces are relatively insignificant.

Conclusions:

  • Hydration water plays a crucial role in mediating alkali cation-carboxylate interactions.
  • Thermodynamic stability and protein interactions in alkali salt solutions are primarily governed by water-mediated interactions.
  • The established "matching water affinities" model requires refinement for biological systems involving weak acid anions.