Identification of a carbohydrate recognition motif of purinergic receptors

Abstract

As a major class of biomolecules, carbohydrates play indispensable roles in various biological processes. However, it remains largely unknown how carbohydrates directly modulate important drug targets, such as G-protein coupled receptors (GPCRs). Here, we employed P2Y purinoceptor 14 (P2Y14), a drug target for inflammation and immune responses, to uncover the sugar nucleotide activation of GPCRs. Integrating molecular dynamics simulation with functional study, we identified the uridine diphosphate (UDP)-sugar-binding site on P2Y14, and revealed that a UDP-glucose might activate the receptor by bridging the transmembrane (TM) helices 2 and 7. Between TM2 and TM7 of P2Y14, a conserved salt bridging chain (K2.60-D2.64-K7.35-E7.36 [KDKE]) was identified to distinguish different UDP-sugars, including UDP-glucose, UDP-galactose, UDP-glucuronic acid, and UDP-N-acetylglucosamine. We identified the KDKE chain as a conserved functional motif of sugar binding for both P2Y14 and P2Y purinoceptor 12 (P2Y12), and then designed three sugar nucleotides as agonists of P2Y12. These results not only expand our understanding for activation of purinergic receptors but also provide insights for the carbohydrate drug development for GPCRs.

Highly accurate carbohydrate-binding site prediction with DeepGlycanSite

“…In general, carbohydrate binding specificity could result from limited amino acid changes within a common protein fold 25 , 26 . In addition, the same protein domain could bind to different carbohydrates 27 – 29 . Therefore, it is important to include homologous proteins binding to different carbohydrates.…”

Nanopore-based glycan sequencing: state of the art and future prospects

“…First, the resolution and sensitivity of nanopore sensing to glycans especially neutral glycans need further improvement. It will be solved by nanopore engineering methods, which include site-directed mutation, 38 genetic code expansion (GCE), 125 glycan recognition module grafting, 126,127 integrated adaptors, 128 glycan derivatization including tags with different sizes or properties, 37 reversible host–guest interactions, 129 etc. 130 The future novel sensors derived from the de novo protein design 81 and glycan porins/transporters will be more glycan-matched.…”