AQcalc

AQcalc identifies and analyzes anion-quadrupole (AQ) interactions in protein structures to characterize weak molecular interactions involving aromatic residues such as tryptophan (Trp), tyrosine (Tyr), and phenylalanine (Phe) with anions such as aspartate (Asp), glutamate (Glu), and phosphate ions for insights into protein structure, function, and dynamics.

Key Features:

• Identification of Anion-Quadrupole (AQ) Interactions: Detects AQ interactions within proteins and at interfaces including protein-protein, protein-nucleic acids, and protein-lipid bilayer interfaces.
• Cluster detection with other weak interactions: Identifies clusters that include AQ interactions alongside cation-π interactions and salt bridges.
• Application to theoretical models: Analyzes weak interactions in protein models when experimental structures are unavailable.
• Variant impact analysis: Identifies deleterious variants, including oncogenic and germline mutations, that disrupt AQ interactions and reports their frequency and impact relative to cation-π interactions.
• Comparative structural analysis: Reports that AQ interactions occur more frequently in amyloid fibrils than in globular proteins and that AQ interactions are detected three times more often than hydrogen-bonded AQ (HBAQ) interactions in fibrils and five times more frequently at protein-lipid bilayer interfaces.
• Unique residue interaction reporting: Provides explicit reporting of AQ interactions within residue interaction networks to facilitate identification of weak but significant contacts for experimental follow-up.

Scientific Applications:

• Structural Biology: Enables detailed analysis of how weak AQ and related interactions contribute to protein stability, conformation, and function.
• Disease Research: Supports investigation of molecular mechanisms by analyzing variants that disrupt AQ interactions, including oncogenic and germline mutations.
• Protein Engineering: Informs design and modification of proteins by predicting interaction networks that include AQ interactions to alter stability or binding properties.

Methodology:

AQcalc employs computational algorithms to scan protein structures for AQ interactions and related clusters using structural data derived from experimental structures or theoretical models.