Kulakova Anna M, Khrenova Maria G, Zvereva Maria I, Polyakov Igor V
Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia.
Institute of Biomedical Chemistry, 119121 Moscow, Russia.
Int J Mol Sci. 2024 Dec 25;26(1):73. doi: 10.3390/ijms26010073.
ORF2p (open reading frame 2 protein) is a multifunctional multidomain enzyme that demonstrates both reverse transcriptase and endonuclease activities and is associated with the pathophysiology of cancer. The 3D structure of the entire seven-domain ORF2p complex was revealed with the recent achievements in structural studies. The different arrangements of the CTD (carboxy-terminal domain) and tower domains were identified as the "closed-ring" and "open-ring" conformations, which differed by the hairpin position of the tower domain, but the structural diversity of these complexes has the potential to be more extensive. To study this, we performed sub-microsecond all-atom molecular dynamics simulations of the entire ORF2p complex with different starting configurations. The obtained molecular dynamic trajectories frames were assigned to several clusters following the dimension reduction to three principal components of the 1275 distances feature matrix. Five and six clusters were obtained for the "open" and "closed" ring models, respectively. While the fingers-palm-thumb core retains its rigid configuration during the MD (molecular dynamics) simulations, all other domains display the complicated dynamic behavior not observed in the experimental structures. The EN (endonuclease) and CTD domains display significant translations and rotations while their internal structures stay rigid. The CTD domain can either form strong contacts with the tower or be far apart from it for both formal "open" and "closed" ring states because the tower hairpin position is not the only determining factor of the protein complex configuration. While only the "thumb up" conformation is observed in all the trajectories, the active site can be obstructed by the movement of the CTD domain. Thus, molecular modeling and machine learning techniques provide valuable insights into the dynamical behavior of the ORF2p complex, which is hard to uncover with experimental methods, given the complexity and size of the object.
ORF2p（开放阅读框2蛋白）是一种多功能多结构域酶，具有逆转录酶和内切核酸酶活性，与癌症的病理生理学相关。随着结构研究的最新成果，整个七结构域ORF2p复合物的三维结构得以揭示。CTD（羧基末端结构域）和塔状结构域的不同排列被确定为“闭环”和“开环”构象，它们的区别在于塔状结构域的发夹位置，但这些复合物的结构多样性可能更广泛。为了研究这一点，我们对具有不同起始构型的整个ORF2p复合物进行了亚微秒级全原子分子动力学模拟。在将1275个距离特征矩阵降维到三个主成分后，将获得的分子动力学轨迹帧分配到几个簇中。“开环”和“闭环”模型分别获得了五个和六个簇。虽然在分子动力学模拟过程中，指-掌-拇指核心保持其刚性构型，但所有其他结构域都表现出实验结构中未观察到的复杂动态行为。EN（内切核酸酶）和CTD结构域显示出显著的平移和旋转，而它们的内部结构保持刚性。对于正式的“开环”和“闭环”状态，CTD结构域既可以与塔状结构域形成紧密接触，也可以与之相距甚远，因为塔状发夹位置不是蛋白质复合物构型的唯一决定因素。虽然在所有轨迹中只观察到“拇指向上”构象，但活性位点可能会被CTD结构域的移动所阻碍。因此，分子建模和机器学习技术为ORF2p复合物的动态行为提供了有价值的见解，鉴于该对象的复杂性和大小，用实验方法很难揭示这些见解。
