Inhibitory effect of truncated isoforms on GPCR dimerization predicted by combinatorial computational strategy

• Published in: Computational and structural biotechnology journal Vol. 23; pp. 278 - 286
• Main Authors: Li, Mengke, Qing, Rui, Tao, Fei, Xu, Ping, Zhang, Shuguang
• Format: Journal Article
• Language: English
• Published: Netherlands Research Network of Computational and Structural Biotechnology 01.12.2024; Elsevier
• Subjects: AlphaFold2 prediction; Complex structure prediction; GPCR oligomerization; Molecular docking; Transmembrane truncation; Complex structure prediction; GPCR oligomerization; AlphaFold2 prediction; Transmembrane truncation; Molecular docking
• ISSN: 2001-0370; 2001-0370
• DOI: 10.1016/j.csbj.2023.12.008

G protein-coupled receptors (GPCRs) play a pivotal role in fundamental biological processes and disease development. GPCR isoforms, derived from alternative splicing, can exhibit distinct signaling patterns. Some highly-truncated isoforms can impact functional performance of full-length receptors, suggesting their intriguing regulatory roles. However, how these truncated isoforms interact with full-length counterparts remains largely unexplored. Here, we computationally investigated the interaction patterns of three human GPCRs from three different classes, ADORA1 (Class A), mGlu2 (Class C) and SMO (Class F) with their respective truncated isoforms because their homodimer structures have been experimentally determined, and they have truncated isoforms deposited and identified at protein level in Uniprot database. Combining the neural network-based AlphaFold2 and two physics-based protein-protein docking tools, we generated multiple complex structures and assessed the binding affinity in the context of atomistic molecular dynamics simulations. Our computational results suggested all the four studied truncated isoforms showed potent binding to their counterparts and overlapping interfaces with homodimers, indicating their strong potential to block homodimerization of their counterparts. Our study offers insights into functional significance of GPCR truncated isoforms and supports the ubiquity of their regulatory roles.