This is a read-only mirror of pymolwiki.org
Difference between revisions of "AKMT Lys pred"
| Line 30: | Line 30: | ||
{| class="wikitable" style="margin: auto;" | {| class="wikitable" style="margin: auto;" | ||
| − | + | ! Orange !! Apple | |
| − | |||
|- | |- | ||
| − | | Bread | + | | Bread | Pie |
| − | | Pie | ||
|- | |- | ||
| Butter | | Butter | ||
Revision as of 11:32, 17 June 2017
| 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
| PDB id | Info | Text | Authors | Released | Method | Residue Count | Macromolecule: | Gene Name(s) | UniProtKB AC | NCBI - Accession Numbers |
|---|
| Orange | Apple |
|---|---|
| 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