AKMT Lys pred

Type	Python Script
Download	aKMT_Lys_pred.py
Author(s)	Troels Schwarz-Linnet
License	BSD
This code has been put under version control in the project Pymol-script-repo

Overview

Chu et al. has compiled a large information of peptides which are methylated in Sulfolobus Islandicus. The mass-spec data is available at: http://www.mcponline.org/content/15/9/2908/suppl/DC1 in

• Supplemental Table S2a revisied (.xlsx, 6.5 MB) - Supplemental Table S2a revisied : mcp.M115.057778-3.xlsx
• Supplemental Table S2a revisied (.xlsx, 4.8 MB) - Supplemental Table S2a revisied : mcp.M115.057778-4.xlsx

The authors has tried to find correlation with amino acids in 1D, with 7 residues up and downstream to the lysines. The authors also tried to first predict secondary structure in the chain, and then find correlation. They made a weblogo figure http://weblogo.threeplusone.com with their findings. There seems to be a preference for helical structure and Glutamic acid (E), Isoleucin (I), Leucin (L) and Valine (V) seems to be dominant with 7 residues up/downstream to the methylated lysines.

This script should try to make an analysis this for 3D, with residues up and downstream in angstrom distance to the residue of interest.

PDB structures in Sulfolobus Islandicus

Following structures was found June 2017

• www.rcsb.org -> Search advanced
• Biology -> Source organism -> Sulfolobus organism

4G2D || test

PDB id	Info	Text	Authors	Released	Method	Residue Count	Macromolecule	Gene Name(s)	UniProtKB AC	NCBI - Accession Numbers

Orange	Apple
Bread	Pie
Butter	Ice cream

Example

test

References

For Mass-Spec data
aKMT Catalyzes Extensive Protein Lysine Methylation in the Hyperthermophilic Archaeon Sulfolobus islandicus but is Dispensable for the Growth of the Organism'
Chu, Yindi; Zhu, Yanping; Chen, Yuling; Li, Wei; Zhang, Zhenfeng; Liu, Di; Wang, Tongkun; Ma, Juncai; Deng, Haiteng; Liu, Zhi-Jie; Ouyang, SongyingHuang, Li
Molecular & Cellular Proteomics 2016, Vol 15, Issue 9, 2908-2923, DOI: 10.1074/mcp.M115.057778