Aguilar-Carrillo Yovani, Soto-Urzúa Lucía, Martínez-Martínez María De Los Ángeles, Becerril-Ramírez Mirian, Martínez-Morales Luis Javier
Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Av. San Claudio y Av. 24 Sur, Col. San Manuel Ciudad Universitaria, Puebla 72570, Mexico.
Polymers (Basel). 2024 Feb 23;16(5):611. doi: 10.3390/polym16050611.
Sp7 produces PHB, which is covered by granule-associated proteins (GAPs). Phasins are the main GAPs. Previous studies have shown phasins can regulate PHB synthesis. When grows under stress conditions, it uses sigma factors to transcribe genes for survival. One of these factors is the σ factor. This study determined the possible interaction between phasins and the σ factor or phasin-σ factor complex and DNA. Three-dimensional structures of phasins and σ factor structures were predicted using the I-TASSER and SWISS-Model servers, respectively. Subsequently, a molecular docking between phasins and the σ factor was performed using the ClusPro 2.0 server, followed by molecular docking between protein complexes and DNA using the HDOCK server. Evaluation of the types of ligand-receptor interactions was performed using the BIOVIA Discovery Visualizer for three-dimensional diagrams, as well as the LigPlot server to obtain bi-dimensional diagrams. The results showed the phasins (Pha4 or Pha5)-σ factor complex was bound near the -35 box of the promoter region of the C gene. However, in the individual interaction of PhaP5 and the σ factor, with DNA, both proteins were bound to the -35 box. This did not occur with PhaP4, which was bound to the -10 box. This change could affect the transcription level of the C gene and possibly affect PHB synthesis.
Sp7产生聚羟基丁酸酯（PHB），其被颗粒相关蛋白（GAPs）所覆盖。phasins是主要的GAPs。先前的研究表明phasins可以调节PHB的合成。当在应激条件下生长时，它会使用σ因子来转录生存所需的基因。其中一个因子是σ因子。本研究确定了phasins与σ因子或phasins-σ因子复合物与DNA之间可能的相互作用。分别使用I-TASSER和SWISS-Model服务器预测了phasins的三维结构和σ因子的结构。随后，使用ClusPro 2.0服务器对phasins与σ因子进行分子对接，接着使用HDOCK服务器对蛋白质复合物与DNA进行分子对接。使用BIOVIA Discovery Visualizer绘制三维图以及使用LigPlot服务器获取二维图来评估配体-受体相互作用的类型。结果表明，phasins（Pha4或Pha5）-σ因子复合物结合在C基因启动子区域的-35框附近。然而，在PhaP5与σ因子以及DNA的单独相互作用中，两种蛋白质都结合在-35框上。PhaP4则不然，它结合在-10框上。这种变化可能会影响C基因的转录水平，并可能影响PHB的合成。
