Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences, Hyderabad, India.
Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences, Hyderabad, India.
J Biol Chem. 2021 Nov;297(5):101271. doi: 10.1016/j.jbc.2021.101271. Epub 2021 Oct 5.
The recognition of carbohydrates by lectins plays key roles in diverse cellular processes such as cellular adhesion, proliferation, and apoptosis, which makes it a therapeutic target of significance against cancers. One of the most functionally active lectins, galectin-3 is distinctively known for its specific binding affinity toward β-galactoside. However, despite the prevalence of high-resolution crystallographic structures, the mechanistic basis and more significantly, the dynamic process underlying carbohydrate recognition by galectin-3 are currently elusive. To this end, we employed extensive Molecular Dynamics simulations to unravel the complete binding event of human galectin-3 with its native natural ligand N-acetyllactosamine (LacNAc) at atomic precision. The simulation trajectory demonstrates that the oligosaccharide diffuses around the protein and eventually identifies and binds to the biologically designated binding site of galectin-3 in real time. The simulated bound pose correlates with the crystallographic pose with atomic-level accuracy and recapitulates the signature stabilizing galectin-3/oligosaccharide interactions. The recognition pathway also reveals a set of transient non-native ligand poses in its course to the receptor. Interestingly, kinetic analysis in combination with a residue-level picture revealed that the key to the efficacy of a more active structural variant of the LacNAc lay in the ligand's resilience against disassociation from galectin-3. By catching the ligand in the act of finding its target, our investigations elucidate the detailed recognition mechanism of the carbohydrate-binding domain of galectin-3 and underscore the importance of ligand-target binary complex residence time in understanding the structure-activity relationship of cognate ligands.
凝集素识别碳水化合物在多种细胞过程中发挥着关键作用，如细胞黏附、增殖和凋亡，这使其成为癌症治疗的重要靶点。半乳糖凝集素-3 是最具功能活性的凝集素之一，其独特之处在于其对 β-半乳糖苷的特异性结合亲和力。然而，尽管具有高分辨率晶体结构，但目前仍不清楚半乳糖凝集素-3识别碳水化合物的机制基础，更不用说动态过程了。为此，我们采用广泛的分子动力学模拟，以原子精度揭示人源半乳糖凝集素-3与其天然配体 N-乙酰乳糖胺（LacNAc）的完整结合事件。模拟轨迹表明，寡糖在蛋白质周围扩散，最终实时识别并结合到半乳糖凝集素-3的生物指定结合位点上。模拟的结合构象与晶体构象具有原子级精度的相关性，并再现了稳定半乳糖凝集素-3/寡糖相互作用的特征。识别途径还揭示了在其到达受体的过程中一组短暂的非天然配体构象。有趣的是，动力学分析与残基水平的图片相结合，揭示了 LacNAc 的更活跃结构变体的效力的关键在于配体抵抗与半乳糖凝集素-3解离的能力。通过捕捉配体寻找其靶标的过程，我们的研究阐明了半乳糖凝集素-3碳水化合物结合域的详细识别机制，并强调了配体-靶标二元复合物停留时间在理解同源配体的结构-活性关系中的重要性。
