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Related Concept Videos

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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Conserved Binding Sites01:49

Conserved Binding Sites

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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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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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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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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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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
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Modeling Binding Affinity of Pathological Mutations for Computational Protein Design.

Miguel Romero-Durana1, Chiara Pallara1, Fabian Glaser2

  • 1Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain.

Methods in Molecular Biology (Clifton, N.J.)
|December 4, 2016
PubMed
Summary

Computational methods offer efficient ways to study protein-protein interactions and identify key binding residues. These techniques analyze phylogenetic, structural, and energetic properties, advancing proteomics research.

Keywords:
AMBER packageBiomolecular dynamics simulationConSurfEvolutionary conservationHot-spots identificationIn silico alanine scanningInterface predictionProtein–protein dockingProtein–protein interactionspyDock

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Area of Science:

  • Biochemistry
  • Computational Biology
  • Structural Biology

Background:

  • Protein-protein interactions are crucial for biological processes and understanding them is vital for medicine.
  • Experimental methods like X-ray crystallography and NMR spectroscopy provide structural data but are resource-intensive.
  • Identifying residues critical for protein binding is a significant challenge in biological research.

Purpose of the Study:

  • To review computational protocols for modeling protein-protein interfaces.
  • To highlight methods for analyzing phylogenetic, structural, and energetic properties of interface residues.
  • To present computational approaches as alternatives to experimental characterization of protein interactions.

Main Methods:

  • Review of existing computational protocols for protein-protein interface analysis.
  • Methods discussed include estimation of evolutionary conservation of amino acid positions.
  • Protocols cover energetic contributions of residues to binding affinity.

Main Results:

  • Computational approaches significantly aid in characterizing protein interactions and identifying key residues.
  • These methods assist in understanding biological and pathological phenomena.
  • Technological advances enable comprehensive analysis from evolutionary to energetic properties.

Conclusions:

  • Computational methods are a powerful breakthrough in proteomics for studying protein-protein interfaces.
  • These techniques can assist or replace expensive and time-consuming experimental efforts.
  • Modeling phylogenetic, structural, and energetic properties provides valuable insights into protein binding.