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

【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(acylcarrier 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。

[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.