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Related Concept Videos

Protein-protein Interfaces02:04

Protein-protein Interfaces

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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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Conserved Binding Sites01:49

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.
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...
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Ligand Binding Sites02:40

Ligand Binding Sites

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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.
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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The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

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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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Ligand Binding and Linkage00:49

Ligand Binding and Linkage

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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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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
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Computational Design of Miniprotein Binders.

Younes Bouchiba1, Manon Ruffini1,2, Thomas Schiex2

  • 1TBI, Université de Toulouse, CNRS, INRAE, INSA, ANITI, Toulouse, France.

Methods in Molecular Biology (Clifton, N.J.)
|March 17, 2022
PubMed
Summary

We developed a computational method to design miniprotein binders, which are promising drug candidates. This approach was successfully applied to create binders targeting the SARS-CoV-2 virus spike protein receptor binding domain (RBD).

Keywords:
Binding affinityComputational protein designMiniprotein bindersMultistate protein designProtein–protein interaction, SARS-CoV-2.

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Area of Science:

  • Computational drug design
  • Protein engineering
  • Structural biology

Background:

  • Miniprotein binders offer advantages over monoclonal antibodies and small molecules, bridging therapeutic efficacy with improved stability and production.
  • They represent a promising class of therapeutics due to their high affinity binding capabilities.
  • The increasing availability of structural data for protein-protein interactions facilitates the design of targeted binders.

Purpose of the Study:

  • To present a generic, structure-based computational approach for designing miniprotein inhibitors.
  • To demonstrate the application of this method for creating miniprotein binders against the SARS-CoV-2 spike protein receptor binding domain (RBD).
  • To highlight the potential broad applicability of this pipeline for various therapeutic targets.

Main Methods:

  • Utilizing a structure-based computational pipeline for miniprotein inhibitor design.
  • Employing artificial intelligence-based protein design methods, including binding energy estimation and multistate design.
  • Generating diverse libraries of potential miniprotein binders.

Main Results:

  • A step-by-step implementation of the computational approach is detailed.
  • The method was successfully applied to design miniprotein binders targeting the SARS-CoV-2 RBD.
  • The pipeline incorporates advanced AI techniques for enhanced binding energy estimation and library generation.

Conclusions:

  • The presented computational approach provides a versatile framework for designing miniprotein binders.
  • This method holds significant potential for developing therapeutics against various protein-protein interactions, including viral targets like SARS-CoV-2.
  • The integration of AI-driven design enhances the efficiency and scope of miniprotein binder development.