Bacteriophages are the natural predators of bacteria and are available abundantly everywhere in nature. Lytic phages can specifically infect their bacterial host (through attachment to the receptor) and use their host replication machinery to replicate rapidly, a feature that enables them to kill a disease-causing bacteria. Hence, phage attachment to the host bacteria is the first important step of the infection process. It is reported in this study that the receptor could be an LPS which is responsible for the attachment of the Sfk20 phage to its host (Shigella flexneri 2a). Phage Sfk20 bacteriolytic activity was examined for preliminary optimization of phage titer. The phage Sfk20 viability at different saline conditions was conducted. The LC–MS/MS technique used here for detecting and identifying 40 Sfk20 phage proteins helped us to get an initial understanding of the structural landscape of phage Sfk20. From the identified proteins, six structurally significant proteins were selected for structure prediction using two neural network systems: AlphaFold2 and ESMFold, and one homology modeling software: Phyre2. Later the performance of these modeling systems was compared using various metrics. We conclude from the available and generated information that AlphaFold2 and Phyre2 perform better than ESMFold for predicting Sfk20 phage protein structures.

中文翻译：

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基于使用结构预测方法的比较研究的志贺氏菌噬菌体 Sfk20 的蛋白质组学分析和蛋白质结构预测

噬菌体是细菌的天然捕食者，在自然界中随处可见。裂解噬菌体可以特异性感染其细菌宿主（通过附着于受体）并利用其宿主复制机制快速复制，这一功能使它们能够杀死致病细菌。因此，噬菌体附着到宿主细菌上是感染过程的第一个重要步骤。据报道，该研究中的受体可能是LPS，它负责Sfk20噬菌体与其宿主（福氏志贺氏菌2a）的附着。检查噬菌体 Sfk20 溶菌活性以初步优化噬菌体滴度。进行噬菌体 Sfk20 在不同盐水条件下的活力。这里使用的 LC-MS/MS 技术检测和鉴定 40 种 Sfk20 噬菌体蛋白，帮助我们初步了解噬菌体 Sfk20 的结构景观。从鉴定的蛋白质中，使用两种神经网络系统：AlphaFold2和ESMFold以及一种同源建模软件：Phyre2，选择了六种结构上重要的蛋白质进行结构预测。后来使用各种指标对这些建模系统的性能进行了比较。我们从现有和生成的信息中得出结论，AlphaFold2 和 Phyre2 在预测 Sfk20 噬菌体蛋白结构方面比 ESMFold 表现更好。