Grupo de Investigacion en Mutaciones & Biotecnología Vegetal, Facultad de Agronomía, Universidad Nacional Agraria La Molina, Av. La Molina s/n., Lima 12175, Peru.
Doctoral Program in Biological Sciences and Engineering, National Agrarian University La Molina, Av. La Molina s/n., Lima 12175, Peru.
Biomolecules. 2021 Nov 25;11(12):1761. doi: 10.3390/biom11121761.
RuBisCO is the most abundant enzyme on earth; it regulates the organic carbon cycle in the biosphere. Studying its structural evolution will help to develop new strategies of genetic improvement in order to increase food production and mitigate CO emissions. In the present work, we evaluate how the evolution of sequence and structure among isoforms I, II and III of RuBisCO defines their intrinsic flexibility and residue-residue interactions. To do this, we used a multilevel approach based on phylogenetic inferences, multiple sequence alignment, normal mode analysis, and molecular dynamics. Our results show that the three isoforms exhibit greater fluctuation in the loop between αB and βC, and also present a positive correlation with loop 6, an important region for enzymatic activity because it regulates RuBisCO conformational states. Likewise, an increase in the flexibility of the loop structure between αB and βC, as well as Lys330 (form II) and Lys322 (form III) of loop 6, is important to increase photosynthetic efficiency. Thus, the cross-correlation dynamics analysis showed changes in the direction of movement of the secondary structures in the three isoforms. Finally, key amino acid residues related to the flexibility of the RuBisCO structure were indicated, providing important information for its enzymatic engineering.
RuBisCO 是地球上最丰富的酶；它调节生物圈中的有机碳循环。研究其结构进化将有助于开发新的遗传改良策略，以增加粮食产量和减少 CO 排放。在本工作中，我们评估了 RuBisCO 同工型 I、II 和 III 的序列和结构进化如何定义其固有灵活性和残基-残基相互作用。为此，我们使用了基于系统发育推断、多重序列比对、正常模式分析和分子动力学的多层次方法。我们的结果表明，这三种同工型在 αB 和 βC 之间的环上表现出更大的波动，并且与 loop6 呈正相关，loop6 是一个重要的酶活性区域，因为它调节 RuBisCO 的构象状态。同样，增加 αB 和 βC 之间环结构的灵活性，以及 loop6 中的 Lys330（同工型 II）和 Lys322（同工型 III），对于提高光合作用效率很重要。因此，交叉相关动力学分析显示了三种同工型中二级结构运动方向的变化。最后，指出了与 RuBisCO 结构灵活性相关的关键氨基酸残基，为其酶工程提供了重要信息。
