基于AlphaFold 2和分子对接探讨非还原型聚酮合酶的碳甲基化程序

C-methylation programming of non-reducing polyketide synthases: based on AlphaFold 2 and molecular docking

摘要:

【目的】探讨非还原型聚酮合酶(non-reducing polyketide synthase, NR-Pks)的碳甲基化程序差异的原因。【方法】以红色红曲菌(Monascus ruber) M7中红曲色素和桔霉素的NR-Pks为研究对象，采用生物信息学方法和AlphaFold 2软件，分析了这两种NR-Pks及其各结构域的序列和结构差异。再基于分子对接等技术，比较了它们的碳甲基转移酶结构域(C-methyltransferase domain, CMeT)分别与其他结构域及其中间产物的结合特征。【结果】两种NR-Pks各结构域的序列和结构相似性高，但其整体结构差异大，表明碳甲基化差异可能源于结构域互作差异。进一步分析发现，桔霉素Pks的CMeT比红曲色素Pks的更容易结合携带底物的酰基载体蛋白结构域(acyl carrier protein, ACP)，使其中间产物更容易受到CMeT催化。CMeT和β-酮酰基合成酶结构域(β-ketosynthase domain, KS)相比，与甲基受体底物的结合自由能更低。【结论】NR-Pks中的CMeT能通过与KS竞争，从而影响其产物的碳甲基化程度。研究结果为Pks的碳甲基化程序研究提供了新思路。

Abstract:

[Objective] To explore the reasons for differences in the C-methylation programming of non-reducing polyketide synthases (NR-Pkss). [Methods] We used bioinformatics tools and AlphaFold 2 to compare the domain sequences and structures of the NR-Pkss involved in the synthesis of Monascus pigment and citrinin in Monascus ruber M7, i.e., Mr-PksPT and Mr-PksCT. Furthermore, we employed molecular docking to compare the binding of C-methyltransferase domains (CMeTs) with other domains and the intermediates of the two NR-Pkss. [Results] The large differences of the overall structure and the high similarity of domain sequence and structure between the two NR-Pkss suggested that the differences of C-methylation programming between NR-Pkss may be resulted from domain interactions. The CMeT of Mr-PksCT was more likely to bind to the acyl carrier protein (ACP) carrying the substrate than that of Mr-PksPT, making the intermediate more easily catalyzed by CMeT. Moreover, CMeT had lower binding free energy to methyl receptor substrate than the β-ketosynthase domain (KS). [Conclusion] The CMeTs of NR-Pkss can affect the C-methylation of the products by competing with KS. The findings provide a new idea for the study of C-methylation programming of Pkss.