Amide–π Interactions in the Structural Stability of Proteins: Role in the Oligomeric Phycocyanins

• Published in: Computation Vol. 12; no. 9; p. 172
• Main Authors: Breberina, Luka M, Zlatovic, Mario V, Stojanovic, Srdan D, Nikolic, Milan R
• Format: Journal Article
• Language: English
• Published: Basel MDPI AG 01-09-2024
• Subjects: ab initio method; Amides; amide–π interactions; Composition; Datasets; hot-spot regions; Hydrogen; interfaces; Ligands; Phycocyanin; phycocyanins; Pigments; Properties; Proteins; Residues; stabilization centers; Structural stability; Structure; Serbia; United States > US
• ISSN: 2079-3197; 2079-3197
• DOI: 10.3390/computation12090172

This study investigates the influences and environmental preferences of amide–π interactions, a relatively unexplored class of charge-free interactions, in oligomeric phycocyanins. In a data set of 20 proteins, we observed 2086 amide–π interactions, all of which were part of the protein backbone. Phe and Tyr residues were found to be involved in amide–π interactions more frequently than Trp or His. The most favorable amide–π interactions occurred within a pair distance range of 5–7 Å, with a distinct angle preference for T-shaped ring arrangements. Multiple interaction patterns suggest that approximately 76% of the total interacting residues participate in multiple amide–π interactions. Our ab initio calculations revealed that most amide–π interactions have energy from 0 to −2 kcal/mol. Stabilization centers of phycocyanins showed that all residues in amide–π interactions play a crucial role in locating one or more such centers. Around 78% of the total interacting residues in the dataset contribute to creating hot-spot regions. Notably, the amide–π interacting residues were found to be highly evolutionarily conserved. These findings enhance our understanding of the structural stability and potential for protein engineering of phycocyanins used as bioactive natural colorants in various industries, including food and pharmaceuticals.