| Title: | Unveiling polyphenol-protein interactions : a comprehensive computational analysis |
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| Authors: | ID Lešnik, Samo (Author)
ID Jukič, Marko (Author)
ID Bren, Urban (Author) |
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| Files: |  s13321-025-00997-3.pdf (5,61 MB)
MD5: D7B60C3CF9B0B0D59697AB28CBBB1A59
 https://link.springer.com/article/10.1186/s13321-025-00997-3
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| Language: | English |
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| Work type: | Article |
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| Typology: | 1.01 - Original Scientific Article |
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| Organization: | FKKT - Faculty of Chemistry and Chemical Engineering
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| Abstract: | Our study investigates polyphenol-protein interactions, analyzing their structural diversity and dynamic behavior. Analysis of the entire Protein Data Bank reveals diverse polyphenolic structures, engaging in various noncovalent interactions with proteins. Interactions observed across crystal structures among diverse polyphenolic classes reveal similarities, underscoring consistent patterns across a spectrum of structural motifs. On the other hand, molecular dynamics (MD) simulations of polyphenol-protein complexes unveil dynamic binding patterns, highlighting the influx of water molecules into the binding site and underscoring limitations of static crystal structures. Water-mediated interactions emerge as crucial in polyphenol-protein binding, leading to variable binding patterns observed in MD simulations. Comparison of high- and low-resolution crystal structures as starting points for MD simulations demonstrates their robustness, exhibiting consistent dynamics regardless of the quality of the initial structural data. Additionally, the impact of glycosylation on polyphenol binding is explored, revealing its role in modulating interactions with proteins. In contrast to synthetic drugs, polyphenol binding seems to exhibit heightened flexibility, driven by dynamic water-mediated interactions, which may also facilitate their promiscuous binding. Comprehensive dynamic studies are, therefore essential to understand polyphenol-protein recognition mechanisms. Overall, our study provides novel insights into polyphenol-protein interactions, informing future research for harnessing polyphenolic therapeutic potential through rational drug design. |
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| Keywords: | polyphenols, polyphenol-protein complexes, molecular dynamics simulations, noncovalent interactions, water-mediated interactions, glycosylation, dynamic behavior |
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| Publication status: | Published |
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| Publication version: | Version of Record |
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| Submitted for review: | 11.04.2024 |
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| Article acceptance date: | 25.03.2025 |
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| Publication date: | 10.04.2025 |
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| Publisher: | BioMed Central |
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| Year of publishing: | 2025 |
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| Number of pages: | 21 str. |
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| PID: | 20.500.12556/DKUM-94367  |
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| UDC: | 547 |
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| ISSN on article: | 1758-2946 |
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| COBISS.SI-ID: | 233496067 |
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| DOI: | 10.1186/s13321-025-00997-3 |
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| Copyright: | © The Author(s) 2025 |
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| Publication date in DKUM: | 14.08.2025 |
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| Views: | 315 |
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| Downloads: | 7 |
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| Metadata: |    |
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| Categories: | Misc.
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