Ribosomal Protein Analysis

Hamilton, R.S.^1,2

¹ Centre for Trophoblast Research, ² Department of Physiology, Development, & Neuroscience, University of Cambridge, Downing Site, Cambridge, CB2 3DY,

Citation

Hamilton, R.S. (2019) DOI

Abstract

To be added

Downloading and pre-processing ribosome structure CIF and annotation files

Ribosome 3D Coordinates (CIF)

Download the human 80s ribosome structure from RCSB: 6EK0.cif

Structure Chain to Ribosomal Protein Naming Conversion

This is a horrible hack at the moment, but the easiest way to like the structure file chain naming to the ribosomal protein naming conventions. Start by saving the html source as txt.

cat 6EK0.source.copy.txt | grep -v "^Protein" | grep -v "^Full" | \
grep -v "^Molecule" | grep -v "^Find" | grep -v "Mutations" | \
sed 's/Entity ID: //g' | sed 's/Gene Names: //g' > 6EK0.source.copy.ed.txt

To Do:

Create a permanent look up table linking the CIF to official ribosomal protein names

Calculating Ribosomal Protein Surface Scores

perl RibosomeStructure.pl 6ek0.cif 6EK0.source.copy.ed.csv

Output

40s: Cn   Dist Description
40s: SG 113.84 S6; RPS6
40s: SI 107.44 S8; RPS8
40s: SM 100.57 S12; RPS12

To Do:

Add cut off for output e.g. score of 100
Use permanent look up table in output

Visualisation using Pymol

Set up Pymol

viewport 1000,1000
set ignore_case, off

Desired script output

colour red, chain LR #Rpl19
...
colour red, chain S12 #Rps12

Create MPG movies from Pymol PNG

Pymol Movie Creation

Movie: Program: Camera Loop: Y-Roll: 16 seconds

Pymol Save Movie as PNGs

File: Save Movie as: PNG

Convert Pymol Movie PNGs to MPG using ImageMagick

convert -delay 6 -quality 99 <filename>_*.png <filename>_movie.mpg

References

Links

Description	URL
Publications	bioRxiv, Journal and DOI (To be updated on publication)

Contact

Contact rsh46 -at- cam.ac.uk

darogan/Ribosomal-Protein