Programme

P.11 -- Poster, VCTP-45

Date: Tuesday, 13 October 2020

Time: 08:30 - 10:00

Effects of hydrophobic and electrostatic interactions of the ribosomal exit tunnel on the escape and folding of nascent proteins

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

(1) Duy Tan University; (2) Institute of Physics, Vietnam Academy of Science and Technology

After the determination of ribosome structures, there has been increasing attention to understanding the role of the ribosomal exit tunnel in protein biosynthesis and folding inside cells. In recent works, we have shown that the exit tunnel, as a passive conduit with only excluded volume interaction, has a significant impact on the escape process and early post-translational folding of nascent proteins. In the present study, we continue to study the impact of the tunnel on the escape and folding processes by considering the effects of hydrophobic and electrostatic interactions between the tunnel and nascent chains. The study is carried out by using molecular dynamics simulation method with an atomistic model of the ribosome tunnel and a coarse-grained Go-like model for nascent proteins. We show that while the hydrophobic interaction slows down the protein escape process, the electrostatic interaction may speed it up depending on the net charge of a protein. Interestingly, like the escape time, the folding time at the tunnel also follows a proposed diffusion model of a drifting Brownian particle in a linear potential field, suggesting that the tunnel helps proteins to bypass a free energy barrier for folding which would exist without the tunnel.

Presenter: Bui Phuong Thuy

Presentation file: