Programme

P.52 -- Poster, VCTP-47

Date: Thursday, 4 August 2022

Time: 08:30 - 10:00

Effects of hydrophobic and electrostatic interactions on the escape of proteins at archaeal and bacterial ribosomal exit tunnels

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

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

We study the escape process of nascent proteins at the ribosome exit tunnels of archaeal Haloarcula marismortui and bacterial Escherichia coli by using combined coarse-grained and atomistic models and molecular dynamics simulations. It is shown that for both types of organisms the electrostatic and hydrophobic interactions of the exit tunnel have similar effects on the escape of small globular proteins. The escape time distribution always maps to a simple diffusion model in various types of the tunnel model, with and without electrostatic and hydrophobic interactions. An exception is found for the escape of CI2 protein, wherein the hydrophobic interaction of the bacteria exit tunnel significantly slows down the escape process. We also find that the median escape time strongly correlates with the number of hydrophobic residues, N_h, and the net charge, Q, of a protein. Interestingly, the correlation coefficient 0.958 and a combined quantity of N_h + 5.9Q for E.coli (excluding CI2 protein) is quite the same as those for Haloarcula marismortui.

Presenter: Bui Phuong Thuy