Programme

P.30 -- Poster, VCTP-44

Date: Tuesday, 30 July 2019

Time: 08:30 - 10:00

The geometry of ribosomal exit tunnel affects post-translational escape of nascent proteins

Phuong Thuy Bui (1) and Trinh Xuan Hoang (2)

(1) Institute of Theoretical and Applied Research, Duy Tan University, Hanoi 100000, Vietnam (2) Institute of Physics, Vietnam Academy of Science and Technology, 10 Dao Tan, Ba Dinh, Hanoi, Vietnam

We study the escape of nascent proteins at the ribosomal exit tunnel by using the Go-like model for proteins and a real atomistic tunnel taken from the PDB structure of a ribosome of archeon Haloarcula Marismortui. The full translation and escape process of nascent proteins at the tunnel were simulated by using Langevin dynamics. We show that at the temperature relevant to the physiological conditions, the escape time of protein G (GB1) follows quite well the one-dimensional diffusion model proposed in our earlier works. The escape time distribution of GB1 and the relationship between its folding and the escape obtained for the real exit tunnel is similar to those for simple cylinder model. Compared to an equivalent cylinder tunnel, the real tunnel induces a higher probability of trapping small proteins inside the tunnel and a broader escape time distribution. This probability is shown to be depend on temperature, the friction coefficient and the translation speed. Within a range of translation speed, slower translation leads to less trapped protein.

Presenter: Bui Phuong Thuy