Mahdizadeh Sayyed Jalil, Pålsson Emil, Carlesso Antonio, Chevet Eric, Eriksson Leif A
Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Göteborg, Sweden.
Faculty of Biomedical Sciences, Euler Institute, Università della Svizzera Italiana (USI),, Lugano 6904, Switzerland.
J Chem Inf Model. 2022 Sep 12;62(17):4247-4260. doi: 10.1021/acs.jcim.2c00735. Epub 2022 Aug 12.
A range of methodologies were herein employed to study the unconventional XBP1 mRNA cleavage mechanism performed by the unfolded protein response (UPR) mediator Inositol Requiring Enzyme 1α (IRE1). Using Protein-RNA molecular docking along with a series of extensive restrained/unrestrained atomistic molecular dynamics (MD) simulations, the dynamical behavior of the system was evaluated and a reliable model of the IRE1/XBP1 mRNA complex was constructed. From a series of well-converged quantum mechanics molecular mechanics well-tempered metadynamics (QM/MM WT-MetaD) simulations using the Grimme dispersion interaction corrected semiempirical parametrization method 6 level of theory (PM6-D3) and the AMBER14SB-OL3 force field, the free energy profile of the cleavage mechanism was determined, along with intermediates and transition state structures. The results show two distinct reaction paths based on general acid-general base type mechanisms, with different activation energies that perfectly match observations from experimental mutagenesis data. The study brings unique atomistic insights into the cleavage mechanism of XBP1 mRNA by IRE1 and clarifies the roles of the catalytic residues H910 and Y892. Increased understanding of the details in UPR signaling can assist in the development of new therapeutic agents for its modulation.
本文采用了一系列方法来研究由未折叠蛋白反应（UPR）介质肌醇需要酶1α（IRE1）执行的非常规XBP1 mRNA切割机制。通过蛋白质 - RNA分子对接以及一系列广泛的受限/无约束原子分子动力学（MD）模拟，评估了系统的动力学行为，并构建了IRE1 / XBP1 mRNA复合物的可靠模型。使用Grimme色散相互作用校正的半经验参数化方法6理论水平（PM6 - D3）和AMBER14SB - OL3力场进行了一系列收敛良好的量子力学分子力学加权元动力学（QM / MM WT - MetaD）模拟，确定了切割机制的自由能分布以及中间体和过渡态结构。结果显示基于一般酸碱类型机制的两条不同反应路径，具有不同的活化能，与实验诱变数据的观察结果完美匹配。该研究为IRE1切割XBP1 mRNA的机制带来了独特的原子层面见解，并阐明了催化残基H910和Y892的作用。对UPR信号传导细节的更多理解有助于开发用于调节它的新型治疗药物。
