Suleman Muhammad, Luqman Muhammad, Wei Dong-Qing, Ali Shahid, Ali Syed Shujait, Khan Abbas, Khan Haji, Ali Zafar, Khan Wajid, Rizwan Muhammad, Ullah Naeem
Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan.
Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China.
Heliyon. 2023 Apr;9(4):e15083. doi: 10.1016/j.heliyon.2023.e15083. Epub 2023 Mar 31.
The SARS COV-2 and its variants are spreading around the world at an alarming speed, due to its higher transmissibility and the conformational changes caused by mutations. The resulting COVID-19 pandemic has imposed severe health consequences on human health. Several countries of the world including Pakistan have studied its genome extensively and provided productive findings. In the current study, the mCSM, DynaMut2, and I-Mutant servers were used to analyze the effect of identified mutations on the structural stability of spike protein however, the molecular docking and simulations approaches were used to evaluate the dynamics of the bonding network between the wild-type and mutant spike proteins with furin. We addressed the mutational modifications that have occurred in the spike protein of SARS-COV-2 that were found in 215 Pakistani's isolates of COVID-19 patients to study the influence of mutations on the stability of the protein and its interaction with the host cell. We found 7 single amino acid substitute mutations in various domains that reside in spike protein. The H49Y, N74K, G181V, and G446V were found in the S1 domain while the D614A, V622F, and Q677H mutations were found in the central helices of the spike protein. Based on the observation, G181V, G446V, D614A, and V622F mutants were found highly destabilizing and responsible for structural perturbation. Protein-protein docking and molecular simulation analysis with that of furin have predicted that all the mutants enhanced the binding efficiency however, the V622F mutant has greatly altered the binding capacity which is further verified by the K value (7.1 E) and therefore may enhance the spike protein cleavage by Furin and increase the rate of infectivity by SARS-CoV-2. On the other hand, the total binding energy for each complex was calculated which revealed -50.57 kcal/mol for the wild type, for G181V -52.69 kcal/mol, for G446V -56.44 kcal/mol, for D614A -59.78 kcal/mol while for V622F the TBE was calculated to be -85.84 kcal/mol. Overall, the current finding shows that these mutations have increased the binding of Furin for spike protein and shows that D614A and V622F have significant effects on the binding and infectivity.
严重急性呼吸综合征冠状病毒2（SARS-CoV-2）及其变体正在以惊人的速度在全球传播，这是由于其更高的传播性以及突变引起的构象变化。由此产生的新冠疫情对人类健康造成了严重的健康后果。包括巴基斯坦在内的世界上几个国家对其基因组进行了广泛研究，并提供了富有成效的研究结果。在本研究中，使用了mCSM、DynaMut2和I-Mutant服务器来分析已识别突变对刺突蛋白结构稳定性的影响，然而，采用分子对接和模拟方法来评估野生型和突变型刺突蛋白与弗林蛋白酶之间的结合网络动态。我们研究了在215例巴基斯坦新冠患者分离株中发现的SARS-CoV-2刺突蛋白发生的突变修饰，以研究突变对蛋白质稳定性及其与宿主细胞相互作用的影响。我们在刺突蛋白的各个结构域中发现了7个单氨基酸替代突变。在S1结构域中发现了H49Y、N74K、G181V和G446V，而在刺突蛋白的中央螺旋中发现了D614A、V622F和Q677H突变。基于观察结果，发现G181V、G446V、D614A和V622F突变体具有高度不稳定作用，并导致结构扰动。与弗林蛋白酶的蛋白质-蛋白质对接和分子模拟分析预测，所有突变体均提高了结合效率，然而，V622F突变体极大地改变了结合能力，这通过K值（7.1 E）得到进一步验证，因此可能增强弗林蛋白酶对刺突蛋白的切割，并增加SARS-CoV-2的感染率。另一方面，计算了每个复合物的总结合能，野生型为-50.57 kcal/mol，G181V为-52.69 kcal/mol，G446V为-56.44 kcal/mol，D614A为-59.78 kcal/mol，而V622F的总结合能计算为-85.84 kcal/mol。总体而言，当前研究结果表明，这些突变增加了弗林蛋白酶与刺突蛋白的结合，并表明D614A和V622F对结合和感染性有显著影响。
