Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India.
Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India.
Biophys J. 2021 May 4;120(9):1765-1776. doi: 10.1016/j.bpj.2021.03.001. Epub 2021 Mar 9.
Amyotrophic lateral sclerosis (ALS) and frontotemporal lobe degeneration (FTLD) are two inter-related intractable diseases of motor neuron degeneration. Fused in sarcoma (FUS) is found in cytoplasmic accumulation of ALS and FTLD patients, which readily link the protein with the diseases. The RNA recognition motif (RRM) of FUS has the canonical α-β folds along with an unusual lysine-rich loop (KK-loop) between α1 and β2. This KK-loop is highly conserved among FET family proteins. Another contrasting feature of FUS RRM is the absence of critical binding residues, which are otherwise highly conserved in canonical RRMs. These residues in FUS RRM are Thr286, Glu336, Thr338, and Ser367, which are substitutions of lysine, phenylalanine, phenylalanine, and lysine, respectively, in other RRMs. Considering the importance of FUS in RNA regulation and metabolism, and its implication in ALS and FTLD, it is important to elucidate the underlying molecular mechanism of RNA recognition. In this study, we have performed molecular dynamics simulation with enhanced sampling to understand the conformational dynamics of noncanonical FUS RRM and its binding with RNA. We studied two sets of mutations: one with alanine mutation of KK-loop and another with KK-loop mutations along with critical binding residues mutated back to their canonical form. We find that concerted movement of KK-loop and loop between β2 and β3 facilitates the folding of the partner RNA, indicating an induced-fit mechanism of RNA binding. Flexibility of the RRM is highly restricted upon mutating the lysine residues of the KK-loop, resulting in weaker binding with the RNA. Our results also suggest that absence of the canonical residues in FUS RRM along with the KK-loop is equally important in regulating its binding dynamics. This study provides a significant structural insight into the binding of FUS RRM with its cognate RNA, which may further help in designing potential drugs targeting noncanonical RNA recognition.
肌萎缩侧索硬化症（ALS）和额颞叶变性（FTLD）是两种相互关联的运动神经元退行性疾病。融合肉瘤（FUS）在 ALS 和 FTLD 患者的细胞质中积累，这使得该蛋白与这些疾病密切相关。FUS 的 RNA 识别基序（RRM）具有典型的α-β折叠结构，以及α1 和β2 之间不寻常的赖氨酸丰富环（KK-环）。这个 KK-环在 FET 家族蛋白中高度保守。FUS RRM 的另一个显著特征是缺乏关键结合残基，而这些残基在典型的 RRMs 中高度保守。FUS RRM 中的这些残基分别是 Thr286、Glu336、Thr338 和 Ser367，它们分别被赖氨酸、苯丙氨酸、苯丙氨酸和赖氨酸取代。考虑到 FUS 在 RNA 调节和代谢中的重要性及其在 ALS 和 FTLD 中的作用，阐明 RNA 识别的潜在分子机制非常重要。在这项研究中，我们使用增强采样的分子动力学模拟来理解非典型 FUS RRM 的构象动力学及其与 RNA 的结合。我们研究了两组突变：一组是 KK-环的丙氨酸突变，另一组是 KK-环突变加上关键结合残基回复到其典型形式。我们发现，KK-环和β2 与β3 之间的环的协同运动促进了配对 RNA 的折叠，表明 RNA 结合的诱导契合机制。突变 KK-环的赖氨酸残基会极大地限制 RRM 的柔韧性，导致与 RNA 的结合减弱。我们的结果还表明，FUS RRM 中缺乏典型残基和 KK-环同样重要，有助于调节其结合动力学。这项研究为 FUS RRM 与其同源 RNA 结合提供了重要的结构见解，这可能有助于设计针对非典型 RNA 识别的潜在药物。
