VeloPro: A pipeline integrating Ribo-seq and AlphaFold deciphers association patterns between translation velocity and protein structure features

Abstract

VeloPro integrates Ribo-seq data and AlphaFold2-predicted 3D protein structure information for characterization of the association patterns between translation velocity and many protein structure features in prokaryotic and eukaryotic organisms across different taxonomical clades such as bacteria, fungi, protozoa, nematode, plants, insect, and mammals. We illustrated that association patterns between translation velocity and protein structure features differ across organisms, partially reflecting their taxonomical relationship.

Figure 1

Workflow of VeloPro. (A) Pipeline for translation velocity quantification including adapter trimming, mapping, calibration, and normalization. (B) Pipeline for protein structure features determination from AlphaFold. (C) Schematic of the comparative data analysis and visualization between translation velocity and protein structure features used in this study.

Figure 2

Comparisons of scaled footprints between the structured (i.e., α‐helix and β‐sheet) and coil regions in 12 organisms. p‐Values were calculated by two‐sided Wilcoxon rank‐sum test.

Figure 3

Heatmap of partial Spearman correlation coefficients between scaled footprints and protein structure features in 12 organisms. The mean of the partial correlation coefficients of all the analyzed genes is shown. Bonferroni‐corrected p‐value for multiple testing was calculated by one sample t‐test for the deviation of the mean from zero: *p < 0.05, **p < 2.2e−5, ***p < 2.2e−10, ****p < 2.2e−15. N.S, not significant. The raw values of the means and the Bonferroni‐corrected p‐values are shown in Supporting Information S2: Table S6.