Related Experiment Video
Updated: Jun 24, 2025
12:05
RIBO-seq in Bacteria: a Sample Collection and Library Preparation Protocol for NGS Sequencing
Published on: August 7, 2021
8.2K
VeloPro: A pipeline integrating Ribo-seq and AlphaFold deciphers association patterns between translation velocity
Bian Bian1,2, Toshitaka Kumagai3, Yutaka Saito1,2,4,5
1Department of Computational Biology and Medical Sciences Graduate School of Frontier Sciences, The University of Tokyo Kashiwa Japan.
Imeta
|June 13, 2024
Summary
VeloPro links translation speed with protein structures across diverse species. These associations vary by organism, reflecting evolutionary relationships and providing insights into protein synthesis.
Area of Science:
- Molecular Biology
- Bioinformatics
- Structural Biology
Background:
- Ribosome profiling (Ribo-seq) measures translation speed.
- Protein structure influences cellular functions.
- Understanding the link between translation and structure is crucial.
Purpose of the Study:
- To investigate the relationship between translation velocity and protein structure features.
- To analyze these associations across diverse organisms and taxonomic groups.
- To identify organism-specific patterns in translation-protein structure relationships.
Main Methods:
- Integration of Ribo-seq data with AlphaFold2-predicted 3D protein structures.
- Comparative analysis of association patterns in prokaryotes and eukaryotes.
- Examination across various taxa including bacteria, fungi, protozoa, nematodes, plants, insects, and mammals.
Main Results:
- Identified distinct association patterns between translation velocity and protein structure features.
- Demonstrated that these patterns differ significantly across different organisms.
- Showcased that observed variations partially correlate with the taxonomical relatedness of organisms.
Conclusions:
- Translation velocity and protein structure associations are not universal.
- Organism-specific patterns reflect evolutionary history and biological context.
- VeloPro provides a framework for exploring genotype-phenotype relationships at the translational level.
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