Communications in Physics 33, 73-84 (2023)

ISSN: 0868-3166

Effects of hydrophobic and electrostatic interactions onthe escape of nascent proteins at bacterial ribosomal exit tunnel

Bui Phuong Thuy, Le Duy Manh, Nguyen Thi Hai Yen and Trinh Xuan Hoang

We study the escape process of nascent proteins at the ribosomal exit tunnel of bacte-rial Escherichia coli by using molecular dynamics simulations with coarse-grained and atomisticmodels. It is shown that the effects of hydrophobic and electrostatic interactions on the proteinescape at the E. coli’s tunnel are qualitatively similar to those obtained previously at the exittunnel of archaeal Haloarcula marismortui, despite significant differences in the structures andinteractions of the ribosome tunnels from the two organisms. Most proteins escape efficiently andtheir escape time distributions can be fitted to a simple diffusion model. Attractive interactionsbetween nascent protein and the tunnel can significantly slow down the escape process, as shownfor the CI2 protein. Interestingly, it is found that the median escape times of the considered pro-teins (excluding CI2) strongly correlate with the function Nh+5.9Q of the number of hydrophobicresidues, Nh, and the net charge, Q, of a protein, with a correlation coefficient of 0.958 for theE. coli’s tunnel. The latter result is in quantitative agreement with a previous result for the H.marismortui’s tunnel.

DOI: 10.15625/0868-3166/17434

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