|Project's title||Effect of the ribosomal tunnel shape and interactions on the folding and escape of nascent proteins|
|Research hosting institution||Graduate University of Science and Technology|
|Project leader’s name||Ph.D. Bui Phuong Thuy|
|Project duration||30/09/2020 - 31/12/2022|
|Project’s budget||408 million VND|
|Goal and objectives of the project||
The study's aim is to clarify the role of shape and hydrophobic and electrostatic interactions of ribosomal exit tunnels on the post-translational escape of nascent proteins. The study also revealed conserved features as well as differences in the escape of proteins at the ribosomal exit tunnel across all three domains of life. As such, enriching our understanding of how the ribosomal machinery works - a complex molecular machinery, optimized to do the job of making proteins quickly and efficiently, exactly.
- Theoretical results:
• The ribosomal exit tunnel has many structural and chemical elements that could affect the post-translational escape of nascent proteins. These elements include the irregular shape of the tunnel, the exposed hydrophobic side-chains of the ribosomal proteins and the charged amino acids on tunnel's surface. The exit tunnels from different organisms of different domains of life, as the ones considered in our study, show significant differences in structural and physico-chemical properties beside certain similarities. The present study shows that despite all these differences of the exit tunnels, the protein escape process has conserved mechanisms across the domains of life.
• First, it is shown that the escape process follows the simple diffusion mechanism described by the diffusion model. This property holds true for twelve proteins of distinct native structures and diverse physico-chemical properties within two different protein models that are given with and without non-native interactions.
• Second, the median escape time, tesc, positively correlates with both the number of hydrophobic residues, Nh, and the net charge, Q, of protein, with a sufficient statistical significance in most cases. This property underlines the simple mechanism that attraction between the protein and the tunnel slows down the protein escape while repulsion speeds it up.
• These results reinforce our understanding of the protein escape process as the one that is simple and predictable. Note that variations of the escape time among proteins still exist and extreme delays of the escape can happen with proteins that have very strong electrostatic attraction to the tunnel.
• From an evolutionary perspective, it could be that the exit tunnels of S. cerevisiae and H. sapiens have evolved to deal with a larger number of proteins in their genomes in suppressing the escape time. The argument for this hypothesis is that a too slow escape of a nascent protein from the exit tunnel could hamper the ribosome productivity, thus it is beneficial to have an exit tunnel that allows all proteins in the genome to escape efficiently.
|Novelty and actuality and scientific meaningfulness of the results||
- Our study is the first to show that the post-translational escape follows a simple diffusion mechanism described by the diffusion model, which is conserved across the domains of life.
- Our study shows a positive correlation between the median escape time and the number of hydrophobic residues and the total charge, thereby suggesting a mechanism of the tunnel to control the escape time in a simple way.
- From an evolutionary perspective, it could be that the exit tunnels of S. cerevisiae and H. sapiens have evolved to deal with a larger number of proteins in their genomes in suppressing the escape time.
|Products of the project||
- Publications in ISI journals:
 P. T. Bui and T. X. Hoang, "The protein escape process at the ribosomal exit tunnel has conserved mechanisms across the domains of life", The Journal of Chemical Physics , 158, 015102 (2023), https://doi.org/10.1063/5.0129532
 P. T. Bui and T. X. Hoang, “Hydrophobic and electrostatic interactions modulate protein escape at the ribosomal exit tunnel”, Biophysical Journal, 120, 4798–4808 (2021) https://doi.org/10.1016/j.bpj.2021.09.027
- Publications in national journals:
 P. T. Bui, L. D. Manh, N.T.H. Yen and T. X. Hoang, “Effects of hydrophobic and electrostatic interactions on the escape of nascent proteins at bacterial ribosomal exit tunnel”, Communications in Physics, 33(1), (2023), ACCEPTED, https://doi.org/10.15625/0868-3166/17434
|Images of project||