Ghosh Ambarnil, Nandy Ashesh, Nandy Papiya
Physics Department, Jadavpur University, Kolkata, India.
BMC Struct Biol. 2010 Feb 22;10:6. doi: 10.1186/1472-6807-10-6.
Catalytic activity of influenza neuraminidase (NA) facilitates elution of progeny virions from infected cells and prevents their self-aggregation mediated by the catalytic site located in the body region. Research on the active site of the molecule has led to development of effective inhibitors like oseltamivir, zanamivir etc, but the high rate of mutation and interspecies reassortment in viral sequences and the recent reports of oseltamivir resistant strains underlines the importance of determining additional target sites for developing future antiviral compounds. In a recent computational study of 173 H5N1 NA gene sequences we had identified a 50-base highly conserved region in 3'-terminal end of the NA gene.
We extend the graphical and numerical analyses to a larger number of H5N1 NA sequences (514) and H1N1 swine flu sequences (425) accessed from GenBank. We use a 2D graphical representation model for the gene sequences and a Graphical Sliding Window Method (GSWM) for protein sequences scanning the sequences as a block of 16 amino acids at a time. Using a protein sequence descriptor defined in our model, the protein sliding scan method allowed us to compare the different strains for block level variability, which showed significant statistical correlation to average solvent accessibility of the residue blocks; single amino acid position variability results in no correlation, indicating the impact of stretch variability in chemical environment. Close to the C-terminal end the GSWM showed less descriptor-variability with increased average solvent accessibility (ASA) that is also supported by conserved predicted secondary structure of 3' terminal RNA and visual evidence from 3D crystallographic structure.
The identified terminal segment, strongly conserved in both RNA and protein sequences, is especially significant as it is surface exposed and structural chemistry reveals the probable role of this stretch in tetrameric stabilization. It could also participate in other biological processes associated with conserved surface residues. A RNA double hairpin secondary structure found in this segment in a majority of the H5N1 strains also supports this observation. In this paper we propose this conserved region as a probable site for designing inhibitors for broad-spectrum pandemic control of flu viruses with similar NA structure.
流感神经氨酸酶（NA）的催化活性有助于子代病毒粒子从受感染细胞中洗脱，并防止其由位于主体区域的催化位点介导的自我聚集。对该分子活性位点的研究已导致开发出有效的抑制剂，如奥司他韦、扎那米韦等，但病毒序列中的高突变率和种间重配以及最近关于奥司他韦耐药菌株的报道强调了确定额外靶点以开发未来抗病毒化合物的重要性。在最近一项对173个H5N1 NA基因序列的计算研究中，我们在NA基因的3'末端鉴定出一个50个碱基的高度保守区域。
我们将图形和数值分析扩展到从GenBank获取的更多H5N1 NA序列（514个）和H1N1猪流感序列（425个）。我们对基因序列使用二维图形表示模型，对蛋白质序列使用图形滑动窗口方法（GSWM），每次将序列作为16个氨基酸的块进行扫描。使用我们模型中定义的蛋白质序列描述符，蛋白质滑动扫描方法使我们能够比较不同菌株在块水平的变异性，这与残基块的平均溶剂可及性显示出显著的统计相关性；单个氨基酸位置的变异性则无相关性，表明化学环境中伸展变异性的影响。在靠近C末端处，GSWM显示描述符变异性较小，平均溶剂可及性（ASA）增加，这也得到了3'末端RNA保守预测二级结构以及3D晶体结构的视觉证据的支持。
所鉴定的末端片段在RNA和蛋白质序列中都高度保守，特别重要的是它暴露于表面，并且结构化学揭示了该伸展在四聚体稳定中的可能作用。它也可能参与与保守表面残基相关的其他生物学过程。在大多数H5N1菌株的该片段中发现的RNA双发夹二级结构也支持这一观察结果。在本文中，我们提出这个保守区域作为设计抑制剂的可能位点，用于对具有相似NA结构的流感病毒进行广谱大流行控制。
