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Related Concept Videos

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...
Assembly of Signaling Complexes01:30

Assembly of Signaling Complexes

Multiprotein signaling complexes are formed in a dynamic process involving protein-protein interactions at the cytoplasmic domain of transmembrane receptors or enzymatic and non-enzymatic proteins associated with the receptor. These complexes ensure the activation and propagation of intracellular signals that regulate cell functions.
Interaction domains in cell signaling
Interaction domains recognize exposed features of their binding partners containing post-translationally modified sequences,...
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...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

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 the...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

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 the...

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Mapping Dysfunctional Protein-Protein Interactions in Disease
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Ligand-binding PAS domains in a genomic, cellular, and structural context.

Jonathan T Henry1, Sean Crosson

  • 1University of Chicago, Chicago, Illinois 60637, USA.

Annual Review of Microbiology
|June 14, 2011
PubMed
Summary

Per-Arnt-Sim (PAS) domains, crucial in bacterial signaling proteins, share a conserved structure despite sequence diversity. Their evolution is linked to ligand binding and cellular location, influencing signal transduction.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Molecular Biology

Background:

  • Per-Arnt-Sim (PAS) domains are ubiquitous signaling modules found across all life kingdoms.
  • In bacteria, they are prevalent in sensor histidine kinases, cyclic-di-GMP synthases/hydrolases, and methyl-accepting chemotaxis proteins.
  • Despite primary sequence divergence, PAS domains exhibit a conserved three-dimensional architecture.

Purpose of the Study:

  • To review the structural foundations of Per-Arnt-Sim (PAS) domains.
  • To explore the evolution of ligand recognition and binding mechanisms within the PAS domain family.
  • To synthesize current knowledge on how PAS domain structure relates to function and signaling.

Main Methods:

  • All-versus-all alignment of 63 solved PAS domain structures.
  • Analysis of structural clades based on topological location and ligand-binding properties.
  • Literature synthesis on PAS domain function, evolution, and ligand interactions.

Main Results:

  • PAS domains form distinct structural clades determined by membrane localization (intra- or extracellular) and bound ligand class.
  • Ligand binding is a key feature, with PAS domains interacting with diverse small-molecule metabolites.
  • Ligand binding can act as a primary signaling cue or modulate responses to secondary signals (gas, redox, photons).

Conclusions:

  • The conserved 3D structure of PAS domains underpins their diverse signaling roles.
  • Structural and functional evolution of PAS domains is closely tied to their ligand-binding capabilities and cellular context.
  • Understanding PAS domain structure-function relationships is critical for deciphering bacterial signaling pathways.