Molecular dynamics simulations investigate the pathway of substrate entry active site of rhomboid protease

Abstract

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

Keywords:

• Rhomboid protease
• substrate entry
• pathway
• umbrella sampling simulations

Acknowledgments

This work was support in part by National Natural Science Foundation of China (NSFC) (21373099, 21573090, 81573063), Jilin Province Department of Education project (JJKH20180334KJ), Jilin Province Science and Technology Development Plan (20150101005JC), the Ministry of Education of China (21030061110020) and the Project of Beihua University (202116143), Shanghai Municipal Commission of Health and Family Planning (20140388), andClinical Research and Training project (SHDC12017X25) provided by Shanghai Shen Kang Hospital Development Center.

Disclosure statement

No potential conflict of interest was reported by the authors.

Supplemental data

The supplementary material is linked to the article https://doi.org/10.1080/07391102.2018.1517609 online.