Mechanism of translocation by Bacteriophage T7 Helicase gp4 using AWSEM-Suite

In the process of DNA replication, the efficient unwinding of the duplex parental DNA is mediated by DNA helicases. Helicases are chemo-mechanic motors that use the energy of ATP hydrolysis to translocate unidirectionally along with DNA. Helicase gp4 from bacteriophage T7 is a model system for studying helicase in DNA replication. However, how ATP hydrolysis drives the conformational changes and the unidirectional translocation remains elusive. Here, molecular dynamics simulations using coarse-grained protein model AWSEM-Suite and DNA model 3SPN2 were applied to explore the global energy landscape of the helicase gp4 translocation along ssDNA.

 

We built the initial model based on the structures of gp4. The umbrella sampling was used to capture the large-scale conformational changes and analyze the free energy landscape and translocation. By comparing the simulations from ATP, ADP, and apo forms, we suggested that the translocation process can be broken into several rotation-guided steps. Furthermore, three intermediate states were identified during the progress that indicates the transition states. In summary, the AWSEM model can probe the translocation's conformational changes and provide insights into it.