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Related Concept Videos

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...
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...
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...
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 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 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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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Binding pocket optimization by computational protein design.

Christoph Malisi1, Marcel Schumann, Nora C Toussaint

  • 1Max Planck Institute for Developmental Biology, Tübingen, Germany.

Plos One
|January 10, 2013
PubMed
Summary
This summary is machine-generated.

PocketOptimizer is a new computational method for designing protein-ligand binding by modifying protein residues. This tool accurately predicts mutations that enhance binding affinity, aiding in biosensor and enzyme catalyst development.

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Area of Science:

  • Computational biology
  • Protein engineering
  • Molecular modeling

Background:

  • Protein-small molecule interactions are crucial for molecular recognition and biotechnological applications like biosensors and enzyme catalysts.
  • Engineering these interactions computationally is vital for advancing biological studies and applications.

Purpose of the Study:

  • To introduce PocketOptimizer, a novel computational method for designing protein-small ligand binding.
  • To modify protein binding pocket residues to improve or establish small molecule binding.
  • To provide a benchmark dataset for assessing in silico ligand binding design methods.

Main Methods:

  • PocketOptimizer utilizes a modular pipeline of customizable molecular modeling tools.
  • It employs a receptor-ligand scoring function to estimate binding free energy.
  • A benchmark set of proteins with experimentally determined structures and varying ligand affinities was compiled.

Main Results:

  • PocketOptimizer correctly predicts the higher affinity mutant in approximately 69% of cases within the benchmark set.
  • The method excels at introducing stabilizing hydrogen bonds and improving geometric complementarity between ligand and binding pocket.
  • The developed benchmark dataset facilitates comparison of mutant binding pocket affinities.

Conclusions:

  • PocketOptimizer offers a robust computational approach for engineering protein-ligand interactions.
  • The method's success in predicting affinity-enhancing mutations has significant implications for protein design.
  • The new benchmark dataset addresses a critical need for evaluating in silico protein design tools.