通过将高覆盖率的古代基因组序列与现代人类的基因组序列进行比较，已经确定了特定的遗传差异。例如，在神经肿瘤腹侧抗原 1 (NOVA1) 中发现了人类特异性取代，NOVA1 是一种 RNA 结合蛋白，可调节神经元前 mRNA 的选择性剪接。氨基酸取代导致 NOVA1 中 197 位异亮氨酸变为缬氨酸（古代：I197，现代人类：V197）。先前的研究已经利用基因编辑技术来比较古代和现代人类皮质类器官中NOVA1的形式，然而，结构和分子细节需要进一步研究。使用计算机方法，生成了 NOVA1 的现代人类 (WT) 和古代 (V197I) 结构。此外，还检查了 NOVA1 的结构，该结构在第 68 位（G68V）处包含甘氨酸至缬氨酸的取代（G68V），该取代发生在 RNA 结合界面处。随后进行蛋白质-RNA 对接来模拟 NOVA1 变体与 RNA 的相互作用，并使用经典分子动力学 (MD) 模拟进一步评估复合物。根据 MM-PBSA 分析，WT (-956.8 ± 32.6 kcal/mol)、V197I (-975.4 ± 65.6 kcal/mol) 和 G68V (-946.7 ± 34.3 kcal/mol) 复合物之间的结合自由能相似。研究结果强调了蛋白质-RNA 复合物的结合和稳定性，与 WT NOVA1 蛋白相比，在古老的变体和 G68V 变体中仅观察到适度的结构变化。需要进一步澄清以增强我们对 NOVA1 突变对选择性剪接和疾病发展影响的理解。特别是，描述 NOVA1 基因中多个突变的影响非常重要。版权所有 © 2024 作者。由爱思唯尔有限公司出版。保留所有权利。

By comparing the high-coverage archaic genome sequences to those of modern humans, specific genetic differences have been identified. For example, a human-specific substitution has been found in neuro-oncological ventral antigen 1 (NOVA1) - an RNA-binding protein that regulates the alternative splicing of neuronal pre-mRNA. The amino acid substitution results in an isoleucine-to-valine change at position 197 in NOVA1 (archaic: I197, modern human: V197). Previous studies have utilised gene editing technology to compare the archaic and modern human forms of NOVA1 in cortical organoids, however, the structural and molecular details require further investigation. Using an in silico approach, the modern human (WT) and archaic (V197I) structures of NOVA1 were generated. Moreover, the structure of NOVA1 containing a glycine-to-valine substitution at position 68 (G68V), which occurs at the RNA-binding interface, was examined for comparison. Protein-RNA docking was subsequently performed to model the interaction of NOVA1 variants with RNA and the complexes were evaluated further using classical molecular dynamics (MD) simulations. Based on the MM-PBSA analysis, the binding free energies were similar between the WT (-956.8 ± 32.6 kcal/mol), V197I (-975.4 ± 65.6 kcal/mol), and G68V (-946.7 ± 34.3 kcal/mol) complexes. The findings highlight the binding and stability of protein-RNA complexes with only modest structural changes observed in the archaic and G68V variants compared to the WT NOVA1 protein. Further clarification is required to enhance our understanding of the impact of NOVA1 mutations on alternative splicing and disease development. In particular, delineating the effect of multiple mutations in the NOVA1 gene is of importance.Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.