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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 WISDOM: A Workbench for In silico De novo Design of BioMolecules
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AQcalc: A web server that identifies weak molecular interactions in protein structures.

Maral Afshinpour1, Logan A Smith1, Suvobrata Chakravarty1

  • 1Department of Chemistry & Biochemistry, South Dakota State University, Brookings, South Dakota, USA.

Protein Science : a Publication of the Protein Society
|August 19, 2023
PubMed
Summary

We introduce AQcalc, a web server for identifying anion-quadrupole (AQ) interactions. This tool aids in understanding protein structure, function, and disease variants by analyzing these crucial weak molecular interactions.

Keywords:
AlphaFold2MemProtMDanion-quadrupolecation-πdisordered regionsinterfacespost-translational modificationvariantsweak molecular interactions

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Area of Science:

  • Biochemistry and Structural Biology
  • Computational Biology and Bioinformatics

Background:

  • Weak molecular interactions are fundamental to protein structure and function.
  • Computational identification of these interactions is vital for protein studies.

Purpose of the Study:

  • To present AQcalc, a novel web server for identifying anion-quadrupole (AQ) interactions.
  • To analyze the role of AQ interactions in protein structure, function, and disease.

Main Methods:

  • Development of AQcalc web server (https://aqcalcbiocomputing.com/) for detecting AQ interactions.
  • Analysis of AQ, cation-π, and salt bridge clusters in protein models and structures.
  • Comparative analysis of AQ interactions in globular proteins, amyloid fibrils, and protein-lipid bilayers.

Main Results:

  • AQcalc identifies anion-quadrupole (AQ) interactions involving aromatic residues and anions.
  • Disrupted AQ interactions were identified in deleterious disease variants.
  • Amyloid fibrils and protein-lipid bilayers show significantly higher frequencies of AQ interactions compared to globular proteins.

Conclusions:

  • AQcalc is an effective tool for detailed structural analysis of weak molecular interactions.
  • The tool enhances understanding of residue interaction networks and facilitates experimental hypothesis testing.
  • AQcalc's unique ability to report AQ interactions fills a gap in existing web utilities.