Molecular dynamics simulation studies on binding of activator and inhibitor to Munc13-1 C1 in the presence of membrane

Abstract

Munc13-1 is a presynaptic active zone protein that plays a critical role in priming the synaptic vesicle and releasing neurotransmitters in the brain. Munc13-1 acts as a scaffold and is activated when diacylglycerol (DAG)/phorbol ester binds to its C1 domain in the plasma membrane. Our previous studies showed that bryostatin 1 activated the Munc13-1, but resveratrol inhibited the phorbol ester-induced Munc13-1 activity. To gain structural insights into the binding of the ligand into Munc13-1 C1 in the membrane, we conducted 1.0 μs molecular dynamics (MD) simulation on Munc13-1 C1–ligand–lipid ternary system using phorbol 13-acetate, bryostatin 1 and resveratrol as ligands. Munc13-1 C1 shows higher conformational stability and less mobility along membrane with phorbol 13-acetate and bryostatin 1 than with resveratrol. Bryostatin 1 and phorbol ester remained in the protein active site, but resveratrol moved out of Munc13-1 C1 during the MD simulation. While bryostatin 1-bound Munc13-1 C1 showed two different positioning in the membrane, phorbol 13-acetate and resveratrol-bound Munc13-1 C1 only showed one positioning. Phorbol 13-acetate formed hydrogen bond with Ala-574 and Gly-589. Bryostatin 1 had more hydrogen bonds with Trp-588 and Arg-592 than with other residues. Resveratrol formed hydrogen bond with Ile-590. This study suggests that different ligands control Munc13-1 C1’s mobility and positioning in the membrane differently. Ligand also has a critical role in the interaction between Munc13-1 C1 and lipid membrane. Our results provide structural basis of the pharmacological activity of the ligands and highlight the importance of membrane in Munc13-1 activity.

Communicated by Ramaswamy H. Sarma

Keywords:

• Activator
• inhibitor
• molecular dynamics
• presynaptic
• Munc13-1
• lipid membrane
• phorbol ester
• diacylglycerol
• resveratrol
• bryostatin 1
• molecular docking

Acknowledgements

MD simulations were performed using the server at the Center for Advanced Computing and Data Systems (CACDS) of the University of Houston.

Disclosure statement

The authors declare no competing financial interest.

Author contributions

JD designed and YY performed the study. JD and YY wrote the paper.

Additional information

Funding

This research has been supported by funding from National Institutes of Health Grants, 1R01AA022414 to J.D.