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Related Concept Videos

Factors Affecting Protein-Drug Binding: Protein-Related Factors01:20

Factors Affecting Protein-Drug Binding: Protein-Related Factors

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

The Equilibrium Binding Constant and Binding Strength

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Drugs predominantly attach to plasma proteins, with only a small percentage remaining unbound. The unbound portion can be calculated as one minus the bound fraction. Acidic drugs form large, inactive complexes by reversibly binding to plasma albumin, which prevents them from diffusing across biological barriers. These drug-protein complexes act as reservoirs for the drugs. As the concentration of unbound drugs decreases, these complexes quickly dissociate to release the free drug, maintaining...
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Determining protein-drug binding can be achieved through indirect and direct methods, each providing valuable insights into the interaction between proteins and drugs.
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Conserved Binding Sites

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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.
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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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Biocatalytic Tetrapeptide Macrocyclization by Cryptic Penicillin-Binding Protein-Type Thioesterases.

Paisley L Jeannette1, Zachary L Budimir1, Lucas O Johnson1

  • 1James Tarpo Jr. and Margaret Tarpo Department of Chemistry, Purdue University, West Lafayette, Indiana 47906, United States.

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Summary

Researchers discovered WP516, a novel thioesterase enzyme, using bioinformatics. This enzyme efficiently cyclizes various tetrapeptides, expanding possibilities for producing cyclic tetrapeptides (CTPs).

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Area of Science:

  • Biochemistry
  • Bioinformatics
  • Natural Product Synthesis

Background:

  • Cyclic tetrapeptides (CTPs) are valuable natural products with diverse bioactivities.
  • Synthesizing CTPs is challenging due to ring strain and limitations of current chemical methods.
  • Enzymatic approaches for CTP synthesis are sought after for broader substrate scope.

Purpose of the Study:

  • To discover novel enzymes for efficient tetrapeptide cyclization using a bioinformatics-guided approach.
  • To identify and characterize a thioesterase enzyme capable of producing diverse cyclic tetrapeptides.
  • To understand the mechanism behind the enzyme's broad substrate specificity.

Main Methods:

  • Bioinformatic analysis of cryptic nonribosomal peptide synthetase (NRPS) gene clusters.
  • In silico prediction and identification of penicillin-binding type thioesterases (PBP-TEs).
  • Biochemical characterization of the identified enzyme (WP516) with various tetrapeptide substrates.
  • Structural and computational analyses including AlphaFold modeling, covalent docking, molecular dynamics, and mutational studies.

Main Results:

  • The first bioinformatics-guided discovery of a thioesterase (WP516) for peptide cyclization from a cryptic gene cluster.
  • WP516 demonstrates efficient cyclization of a wide range of tetrapeptide substrates.
  • WP516 exhibits a significantly broader substrate scope compared to the previously known tetrapeptide cyclase Ulm16.
  • Structural and computational analyses provided insights into WP516's broad substrate acceptance.

Conclusions:

  • The developed bioinformatics workflow is effective for discovering novel enzymes involved in peptide cyclization.
  • WP516 is a powerful biocatalyst for the production of diverse head-to-tail cyclic tetrapeptides.
  • This discovery offers a new strategy for enzyme discovery in peptide cyclization and biocatalytic CTP production.