{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,31]],"date-time":"2025-12-31T12:19:44Z","timestamp":1767183584695,"version":"build-2065373602"},"reference-count":54,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2024,8,27]],"date-time":"2024-08-27T00:00:00Z","timestamp":1724716800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Ministry of Science, Technological Development and Innovation of the Republic of Serbia","award":["451-03-66\/2024-03\/200168","451-03-66\/2024-03\/200026"],"award-info":[{"award-number":["451-03-66\/2024-03\/200168","451-03-66\/2024-03\/200026"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Computation"],"abstract":"<jats:p>This study investigates the influences and environmental preferences of amide\u2013\u03c0 interactions, a relatively unexplored class of charge-free interactions, in oligomeric phycocyanins. In a data set of 20 proteins, we observed 2086 amide\u2013\u03c0 interactions, all of which were part of the protein backbone. Phe and Tyr residues were found to be involved in amide\u2013\u03c0 interactions more frequently than Trp or His. The most favorable amide\u2013\u03c0 interactions occurred within a pair distance range of 5\u20137 \u00c5, 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\u2013\u03c0 interactions. Our ab initio calculations revealed that most amide\u2013\u03c0 interactions have energy from 0 to \u22122 kcal\/mol. Stabilization centers of phycocyanins showed that all residues in amide\u2013\u03c0 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\u2013\u03c0 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.<\/jats:p>","DOI":"10.3390\/computation12090172","type":"journal-article","created":{"date-parts":[[2024,8,27]],"date-time":"2024-08-27T06:19:01Z","timestamp":1724739541000},"page":"172","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Amide\u2013\u03c0 Interactions in the Structural Stability of Proteins: Role in the Oligomeric Phycocyanins"],"prefix":"10.3390","volume":"12","author":[{"given":"Luka M.","family":"Breberina","sequence":"first","affiliation":[{"name":"Faculty of Chemistry, Department of Biochemistry, University of Belgrade, 11158 Belgrade, Serbia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4311-1731","authenticated-orcid":false,"given":"Mario V.","family":"Zlatovi\u0107","sequence":"additional","affiliation":[{"name":"Faculty of Chemistry, Department of Organic Chemistry, University of Belgrade, 11158 Belgrade, Serbia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1847-9318","authenticated-orcid":false,"given":"Sr\u0111an \u0110.","family":"Stojanovi\u0107","sequence":"additional","affiliation":[{"name":"Institute of Chemistry, Technology and Metallurgy, Department of Chemistry, National Institute of the Republic of Serbia, University of Belgrade, 11000 Belgrade, Serbia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0932-889X","authenticated-orcid":false,"given":"Milan R.","family":"Nikoli\u0107","sequence":"additional","affiliation":[{"name":"Faculty of Chemistry, Department of Biochemistry, University of Belgrade, 11158 Belgrade, Serbia"}]}],"member":"1968","published-online":{"date-parts":[[2024,8,27]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1023\/A:1024954911473","article-title":"Phycobiliproteins and phycobilisomes: The early observations","volume":"76","year":"2003","journal-title":"Photosynth. 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