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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.
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A peptide bond covalently attaches amino acids through a dehydration reaction. One amino acid's carboxyl group and another amino acid's amino group combine, releasing a water molecule. The resulting bond is the peptide bond. The products that such linkages form are peptides. As more amino acids join this growing chain, the resulting chain is a polypeptide. Each polypeptide has a free amino group at one end. This end has the N-terminal, or the amino-terminal, and the other end has a free...
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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...
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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...
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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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Drug-receptor bonds are formed through various chemical forces when drugs interact with target cells. Covalent bonds, strong and irreversible, are exemplified by DNA-alkylating anticancer agents that inhibit cell division. However, such irreversible drug binding lacks selectivity and can modify the DNA of the surrounding healthy cells. Covalent binding often contributes to tissue toxicity, as seen with chloroform and paracetamol metabolites binding to the liver, causing hepatotoxicity.
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Kinetic Screening of Nuclease Activity using Nucleic Acid Probes
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Binding Interactions of Peptide Aptamers.

Roger R C New1,2, Tam T T Bui3, Michal Bogus1

  • 1Vaxcine (UK) Limited, London Bioscience Innovation Centre, London NW1 0NH, UK.

Molecules (Basel, Switzerland)
|December 29, 2020
PubMed
Summary
This summary is machine-generated.

Cyclic peptides demonstrate enhanced binding affinity compared to linear peptides. This study confirms that cyclic configurations improve ligand interactions, offering benefits for peptide aptamer development.

Keywords:
cyclic peptidefluorescence enhancementhydrogen bondlipo-amino acidpeptide aptamerpeptide therapeutics

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Drug Discovery

Background:

  • Peptide aptamers are short amino acid chains that bind ligands like antibodies.
  • Therapeutic targets include peptide chains or loops on protein receptors involved in cell communication.
  • Cyclic peptides are hypothesized to offer greater conformational rigidity for stronger binding interactions.

Purpose of the Study:

  • To investigate the binding interactions of cyclic peptides versus linear peptides.
  • To test the hypothesis that cyclic configurations enhance binding strength.
  • To compare the binding of a model cyclic decamer with linear peptide constructs.

Main Methods:

  • A model cyclic decamer was used for interaction studies.
  • Binding affinities were compared between the cyclic decamer and its linear counterpart.
  • A series of linear peptide constructs were analyzed for interaction strength.

Main Results:

  • The cyclic configuration of the peptide significantly increased binding strength.
  • Binding interactions were stronger when a cyclic peptide acted as the ligand compared to linear peptides.
  • The study confirmed the benefits of cyclic peptide structures for enhanced binding.

Conclusions:

  • Cyclic peptide structures confer advantages in binding affinity over linear peptides.
  • This finding supports the use of cyclic peptides in developing more effective peptide aptamers.
  • The conformational rigidity of cyclic peptides enhances ligand interactions, crucial for therapeutic applications.