a Institute of Theoretical Chemistry , Jilin University , Changchun , China.
b College of Chemistry and Biology , Beihua University , Jilin , China.
J Biomol Struct Dyn. 2019 Aug;37(13):3445-3455. doi: 10.1080/07391102.2018.1517609. Epub 2018 Nov 17.
Rhomboid proteases can catalyze peptide bond cleavage and participate in abundant biological processes encompassing all branches of life; however, the pathway for substrate entry into its active site remains ambiguous. Here, the two possible pathways are preliminarily determined through molecular dynamics: One pathway is between Tm2 and Tm5, and the other is between Loop3 and Loop5. Then, the umbrella sampling simulations are performed to investigate the more feasible pathway for substrate entry. The results show that free energy barriers along the two pathways are similar; in the pathway 1, Trp236 and Trp157 as pivotal residues are responsible for the rotation of substrate in the binding process; in the pathway 2, among some important residues, the residue His150 plays an important role in substrate entry. Further, combining with previous experiment results, it is concluded that the substrate is inclined to enter into the active site along pathway 2. Our results are important for further understanding the function and catalysis mechanism of rhomboid proteases. Communicated by Ramaswamy H. Sarma.
菱形蛋白酶可以催化肽键的断裂，并参与包括生命所有分支的丰富生物过程；然而，底物进入其活性部位的途径仍不清楚。在这里，通过分子动力学初步确定了两种可能的途径：一种途径是在 Tm2 和 Tm5 之间，另一种途径是在 Loop3 和 Loop5 之间。然后，进行伞状采样模拟以研究底物进入的更可行途径。结果表明，两条途径的自由能障碍相似；在途径 1 中，关键残基 Trp236 和 Trp157 负责在结合过程中底物的旋转；在途径 2 中，在一些重要残基中，残基 His150 在底物进入中起重要作用。此外，结合以前的实验结果，得出结论，底物倾向于沿途径 2 进入活性部位。我们的结果对进一步了解菱形蛋白酶的功能和催化机制很重要。由 Ramaswamy H. Sarma 传达。
