Unveiling polyphenol-protein interactions

ǂa ǂcomprehensive computational analysis

Samo Lešnik (Avtor), Marko Jukič (Avtor), Urban Bren (Avtor)

Povzetek

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.

Ključne besede

polyphenols;polyphenol-protein complexes;molecular dynamics simulations;noncovalent interactions;water-mediated interactions;glycosylation;dynamic behavior;

Podatki

Jezik:	Angleški jezik
Leto izida:	2025
Tipologija:	1.01 - Izvirni znanstveni članek
Organizacija:	UM FKKT - Fakulteta za kemijo in kemijsko tehnologijo
Založnik:	BioMed Central
UDK:	547
COBISS:	233496067
ISSN:	1758-2946
Št. ogledov:	0
Št. prenosov:	1
Ocena:	0 (0 glasov)
Metapodatki:

Ostali podatki

Sekundarni jezik:	Slovenski jezik
Sekundarne ključne besede:	polifenoli;simulacija dinamike molekul;nekovalentne interakcije;
Vrsta dela (COBISS):	Članek v reviji
Strani:	21 str.
Letnik:	ǂVol. ǂ17
Zvezek:	ǂarticle no. ǂ50
Čas izdaje:	2025
DOI:	10.1186/s13321-025-00997-3
ID:	27082480