Background Polygalacturonase inhibiting proteins(PGIPs)play a pivotal role in plant defense against plant patho-gens by inhibiting polygalacturonase(PG),an enzyme produced by pathogens to degrade plant cell wall pecti...Background Polygalacturonase inhibiting proteins(PGIPs)play a pivotal role in plant defense against plant patho-gens by inhibiting polygalacturonase(PG),an enzyme produced by pathogens to degrade plant cell wall pectin.PGIPs,also known as leucine-rich repeat pathogenesis-related(PR)proteins,activate the host’s defense response upon interaction with PG,thereby reinforcing the host defense against plant pathogens attacks.In Egyptian or extra-long staple cotton(Gossypium barbadense),the interaction between PGIP and PG is one of the crucial steps in the defense mechanism against major pathogens such as Xanthomonas citri pv.malvacearum and Alternaria mac-rospora,which are responsible for bacterial leaf blight and leaf spot diseases,respectively.Results To unravel the molecular mechanisms underlying these PR proteins,we conducted a comprehensive study involving molecular modeling,protein-protein docking,site-specific double mutation(E169G and F242K),and molec-ular dynamics simulations.Both wild-type and mutated cotton PGIPs were examined in the interaction with the PG enzyme of a bacterial and fungal pathogen.Our findings revealed that changes in conformations of double-mutated residues in the active site of PGIP lead to the inhibition of PG binding.The molecular dynamics simulation studies provide insights into the dynamic behaviour and stability of the PGIP-PG complexes,shedding light on the intricate details of the inhibitory and exhibitory mechanism against the major fungal and bacterial pathogens of G.barbadense,respectively.Conclusions The findings of this study not only enhance our understanding of the molecular interactions between PGs of Xanthomonas citri pv.malvacearum and Alternaria macrospora and PGIP of G.barbadense but also pre-sent a potential strategy for developing the disease-resistant cotton varieties.By variations in the binding affinities of PGs through specific mutations in PGIP,this research offers promising avenues for the development of enhanced resistance to cotton plants against bacterial leaf blight and leaf spot diseases.展开更多
目的联合使用网络药理学、分子对接和分子动力学模拟技术探讨蛇床子治疗牙周炎伴骨质疏松的活性成分及潜在靶点,并探讨其可能的作用机制。方法通过TCMSP数据库、SwissTargetPrediction数据库并结合文献报道筛选蛇床子的主要化学成分及...目的联合使用网络药理学、分子对接和分子动力学模拟技术探讨蛇床子治疗牙周炎伴骨质疏松的活性成分及潜在靶点,并探讨其可能的作用机制。方法通过TCMSP数据库、SwissTargetPrediction数据库并结合文献报道筛选蛇床子的主要化学成分及作用靶点;采用多种数据库预测牙周炎和骨质疏松的作用靶点;利用Venny 2.1获取蛇床子与牙周炎和骨质疏松的交集靶点;采用STRING数据库构建交集靶点的蛋白相互作用网络(PPI)图并使用Cytoscape 3.9.1软件构建活性成分−交集靶点网络,对其进行拓扑分析筛选关键靶点和核心活性成分;基于Metascape平台对交集靶点进行基因本体论(GO)和京都基因与基因组百科全书(KEGG)富集分析;选取节度点(degree)值排名前5位的核心靶点和核心活性成分,使用Discovery Studio 2019软件对配体和受体进行分子对接,并将结果可视化;使用Gromacs2022.3进行分子动力学模拟,以评估核心活性成分和关键靶点之间相互作用的稳定性。结果筛选得到蛇床子的20个潜在活性成分,蛇床子治疗牙周炎伴骨质疏松的作用靶点116个;对116个交集靶点进行GO和KEGG通路富集分析发现,蛇床子可能通过磷脂酰肌醇3激酶-蛋白激酶、晚期糖基化终产物-糖基化终末产物受体等信号通路发挥治疗作用;分子对接结果发现核心活性成分与关键靶点能够较好地结合,分子动力学模拟进一步验证了香叶木素-AKT1复合体稳定性。结论本研究揭示蛇床子通过多成分、多靶点、多途径的特点治疗牙周炎伴骨质疏松的潜在分子药理机制,为后续药物开发研究及临床应用提供理论基础。展开更多
基金CABin grant(F.no.Agril.Edn.4-1/2013-A&P)Indian Council of Agricul-tural Research,Ministry of Agriculture and Farmers’Welfare,Govt.of India and Department of Biotechnology,Govt.of India for BIC project grant(BT/PR40161/BTIS/137/32/2021)。
文摘Background Polygalacturonase inhibiting proteins(PGIPs)play a pivotal role in plant defense against plant patho-gens by inhibiting polygalacturonase(PG),an enzyme produced by pathogens to degrade plant cell wall pectin.PGIPs,also known as leucine-rich repeat pathogenesis-related(PR)proteins,activate the host’s defense response upon interaction with PG,thereby reinforcing the host defense against plant pathogens attacks.In Egyptian or extra-long staple cotton(Gossypium barbadense),the interaction between PGIP and PG is one of the crucial steps in the defense mechanism against major pathogens such as Xanthomonas citri pv.malvacearum and Alternaria mac-rospora,which are responsible for bacterial leaf blight and leaf spot diseases,respectively.Results To unravel the molecular mechanisms underlying these PR proteins,we conducted a comprehensive study involving molecular modeling,protein-protein docking,site-specific double mutation(E169G and F242K),and molec-ular dynamics simulations.Both wild-type and mutated cotton PGIPs were examined in the interaction with the PG enzyme of a bacterial and fungal pathogen.Our findings revealed that changes in conformations of double-mutated residues in the active site of PGIP lead to the inhibition of PG binding.The molecular dynamics simulation studies provide insights into the dynamic behaviour and stability of the PGIP-PG complexes,shedding light on the intricate details of the inhibitory and exhibitory mechanism against the major fungal and bacterial pathogens of G.barbadense,respectively.Conclusions The findings of this study not only enhance our understanding of the molecular interactions between PGs of Xanthomonas citri pv.malvacearum and Alternaria macrospora and PGIP of G.barbadense but also pre-sent a potential strategy for developing the disease-resistant cotton varieties.By variations in the binding affinities of PGs through specific mutations in PGIP,this research offers promising avenues for the development of enhanced resistance to cotton plants against bacterial leaf blight and leaf spot diseases.
文摘目的联合使用网络药理学、分子对接和分子动力学模拟技术探讨蛇床子治疗牙周炎伴骨质疏松的活性成分及潜在靶点,并探讨其可能的作用机制。方法通过TCMSP数据库、SwissTargetPrediction数据库并结合文献报道筛选蛇床子的主要化学成分及作用靶点;采用多种数据库预测牙周炎和骨质疏松的作用靶点;利用Venny 2.1获取蛇床子与牙周炎和骨质疏松的交集靶点;采用STRING数据库构建交集靶点的蛋白相互作用网络(PPI)图并使用Cytoscape 3.9.1软件构建活性成分−交集靶点网络,对其进行拓扑分析筛选关键靶点和核心活性成分;基于Metascape平台对交集靶点进行基因本体论(GO)和京都基因与基因组百科全书(KEGG)富集分析;选取节度点(degree)值排名前5位的核心靶点和核心活性成分,使用Discovery Studio 2019软件对配体和受体进行分子对接,并将结果可视化;使用Gromacs2022.3进行分子动力学模拟,以评估核心活性成分和关键靶点之间相互作用的稳定性。结果筛选得到蛇床子的20个潜在活性成分,蛇床子治疗牙周炎伴骨质疏松的作用靶点116个;对116个交集靶点进行GO和KEGG通路富集分析发现,蛇床子可能通过磷脂酰肌醇3激酶-蛋白激酶、晚期糖基化终产物-糖基化终末产物受体等信号通路发挥治疗作用;分子对接结果发现核心活性成分与关键靶点能够较好地结合,分子动力学模拟进一步验证了香叶木素-AKT1复合体稳定性。结论本研究揭示蛇床子通过多成分、多靶点、多途径的特点治疗牙周炎伴骨质疏松的潜在分子药理机制,为后续药物开发研究及临床应用提供理论基础。
