School of Biotechnology and Bioinformatics, D.Y. Patil Deemed to be University, Navi Mumbai, India.
CSIR-National Chemical Laboratory, Pune, India.
Methods Mol Biol. 2024;2780:257-280. doi: 10.1007/978-1-0716-3985-6_13.
The interactions of G-protein-coupled receptors (GPCRs) with other proteins are critical in several cellular processes but resolving their structural dynamics remains challenging. An increasing number of GPCR complexes have been experimentally resolved but others including receptor variants are yet to be characterized, necessitating computational predictions of their interactions. Although integrative approaches with multi-scale simulations would provide rigorous estimates of their conformational dynamics, protein-protein docking remains a first tool of choice of many researchers due to the availability of open-source programs and easy to use web servers with reasonable predictive power. Protein-protein docking algorithms have limited ability to consider protein flexibility, environment effects, and entropy contributions and are usually a first step towards more integrative approaches. The two critical steps of docking: the sampling and scoring algorithms have improved considerably and their performance has been validated against experimental data. In this chapter, we provide an overview and generalized protocol of a few docking protocols using GPCRs as test cases. In particular, we demonstrate the interactions of GPCRs with extracellular protein ligands and an intracellular protein effectors (G-protein) predicted from docking approaches and test their limitations. The current chapter will help researchers critically assess docking protocols and predict experimentally testable structures of GPCR complexes.
G 蛋白偶联受体 (GPCRs) 与其他蛋白质的相互作用在许多细胞过程中至关重要，但解析它们的结构动力学仍然具有挑战性。越来越多的 GPCR 复合物已被实验解析，但其他包括受体变体的复合物仍有待表征，这需要对它们的相互作用进行计算预测。尽管多尺度模拟的综合方法可以提供其构象动力学的严格估计，但由于开源程序的可用性和具有合理预测能力的易于使用的网络服务器，蛋白质-蛋白质对接仍然是许多研究人员的首选工具。蛋白质-蛋白质对接算法在考虑蛋白质柔性、环境效应和熵贡献方面的能力有限，通常是更综合方法的第一步。对接的两个关键步骤：采样和评分算法有了很大的改进，并且已经针对实验数据对其性能进行了验证。在本章中，我们提供了一些对接方案的概述和通用协议，使用 GPCR 作为测试案例。特别是，我们展示了从对接方法预测的 GPCR 与细胞外蛋白质配体和细胞内蛋白质效应物 (G 蛋白) 的相互作用，并测试了它们的局限性。本章将帮助研究人员批判性地评估对接方案，并预测 GPCR 复合物的可实验测试结构。
