Energetic and frustration analysis of SARS-CoV-2 nucleocapsid protein mutations

The ongoing COVID-19 spreads worldwide with the ability to evolve in diverse human populations. The nucleocapsid (N) protein is one of the mutational hotspots in the SARS-CoV-2 genome. The N protein is an abundant RNA-binding protein critical for viral genome packaging. It comprises two large domains including the N-terminal domain (NTD) and the C-terminal domain (CTD) linked by the centrally located linker region. Mutations in N protein have been reported to increase the severity of disease by modulating viral transmissibility, replication efficiency as well as virulence properties of the virus in different parts of the world. To study the effect of N protein missense mutations on protein stability, function, and pathogenicity, we analyzed 228 mutations from each domain of N protein. Further, we have studied the effect of mutations on local residual frustration changes in N protein. Out of 228 mutations, 11 mutations were predicted to be deleterious and destabilized. Among these mutations, R32C, R191C, and R203 M mutations fall into disordered regions and show significant change in frustration state. Overall, this work reveals that by altering the energetics and residual frustration, N protein mutations might affect the stability, function, and pathogenicity of the SARS-CoV-2.

持续蔓延的新型冠状病毒肺炎（COVID-19）已在全球范围内扩散，且具备在不同人群中演化的能力。核衣壳（N）蛋白是严重急性呼吸综合征冠状病毒2型（SARS-CoV-2）基因组中的突变热点区域之一。N蛋白是一种丰度较高的RNA结合蛋白，对病毒基因组的包装过程至关重要。它包含两个大型结构域，即由中央连接区相连的N端结构域（NTD）与C端结构域（CTD）。已有研究表明，全球多地的N蛋白突变可通过调控病毒的传播能力、复制效率以及毒力特性，加重疾病严重程度。为探究N蛋白错义突变对蛋白质稳定性、功能及致病性的影响，本研究分析了来自N蛋白各结构域的228处突变。此外，本研究还探讨了突变对N蛋白局部残基受挫（residual frustration）状态变化的影响。在228处突变中，有11处被预测为有害且会导致蛋白稳定性下降。在上述突变中，R32C、R191C以及R203M突变位于无序区域，且其受挫状态发生了显著变化。综上，本研究表明，N蛋白突变可通过改变蛋白质的能量学特性与残基受挫状态，影响严重急性呼吸综合征冠状病毒2型的稳定性、功能及致病性。