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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 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 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...
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...
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

Updated: Jul 5, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Proline-rich proteins--deriving a basis for residue-based selectivity in polyphenolic binding.

A K Croft1, M K Foley

  • 1School of Chemistry, University of Wales Bangor, Bangor, Gwynedd. a.k.croft@bangor.ac.uk

Organic & Biomolecular Chemistry
|April 19, 2008
PubMed
Summary
This summary is machine-generated.

Minimal proline-based models demonstrate superior binding selectivity for phenol, surpassing other amino acid models. This enhanced molecular recognition involves cooperative effects and C-H-pi interactions, not just hydrogen bonds.

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Residue-Specific Exchange of Proline by Proline Analogs in Fluorescent Proteins: How "Molecular Surgery" of the Backbone Affects Folding and Stability
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Residue-Specific Exchange of Proline by Proline Analogs in Fluorescent Proteins: How "Molecular Surgery" of the Backbone Affects Folding and Stability

Published on: February 3, 2022

Area of Science:

  • Supramolecular Chemistry
  • Organic Chemistry
  • Computational Chemistry

Background:

  • Understanding molecular recognition is crucial for designing selective binding agents.
  • Amino acid derivatives are explored as scaffolds for molecular recognition due to their inherent chirality and functional groups.
  • Phenol derivatives are common targets in host-guest chemistry and drug design.

Purpose of the Study:

  • To investigate the binding selectivity of proline-based models towards phenol.
  • To elucidate the binding mechanism and contributing factors beyond traditional hydrogen bonding.
  • To compare the binding affinities of different amino acid-based models.

Main Methods:

  • Proton Nuclear Magnetic Resonance ((1)H NMR) titration experiments were conducted in chloroform (CDCl(3)).
  • Density Functional Theory (DFT) calculations were employed to model binding interactions.
  • Hunter's molecular recognition toolbox model was applied to analyze binding contributions.

Main Results:

  • Proline-based models exhibited enhanced binding selectivity for phenol compared to other protected amino acid residues.
  • Sarcosine models showed intermediate binding constants, suggesting cooperative binding effects.
  • Binding is not solely due to hydrogen bond strength but also involves C-H-pi interactions and amide rotational freedom.

Conclusions:

  • Minimal proline-based models offer a promising platform for selective phenol recognition.
  • Cooperative binding and non-classical interactions like C-H-pi bonds are key to the observed selectivity.
  • The findings provide insights into designing novel molecular receptors with tailored binding properties.