Simulation to analysis nonsynonymous SNV effect to FGF6

Question

[Shicheng Guo]

I hope to get some suggestion, what kinds of protein structure simulation can allow me to analysis the effect to these nonsynonymous in the exon of FGF6 genes?

FGF6 . nonsynonymous SNV FGF6:NM_020996:exon3:c.G563A:p.R188Q

FGF6 . nonsynonymous SNV FGF6:NM_020996:exon3:c.A521T:p.D174V

FGF6 . stopgain FGF6:NM_020996:exon3:c.G514T:p.E172X

FGF6 . nonsynonymous SNV FGF6:NM_020996:exon3:c.C485T:p.T162I

FGF6 . nonsynonymous SNV FGF6:NM_020996:exon2:c.C449T:p.T150M

FGF6 . nonsynonymous SNV FGF6:NM_020996:exon2:c.G445A:p.A149T

FGF6 . synonymous SNV FGF6:NM_020996:exon2:c.C444T:p.Y148Y

FGF6 . synonymous SNV FGF6:NM_020996:exon2:c.C444T:p.Y148Y

FGF6 . synonymous SNV FGF6:NM_020996:exon2:c.T417C:p.V139V

FGF6 . nonsynonymous SNV FGF6:NM_020996:exon2:c.C388G:p.L130V

FGF6 . nonsynonymous SNV FGF6:NM_020996:exon2:c.A358G:p.I120V

FGF6 . . . FGF6 . nonsynonymous

SNV FGF6:NM_020996:exon1:c.G187A:p.A63T FGF6 . nonsynonymous

SNV FGF6:NM_020996:exon1:c.T107C:p.V36A FGF6 . nonsynonymous

SNV FGF6:NM_020996:exon1:c.G86T:p.G29V

Thanks.

Answer 1

[Kevin Blighe]

Please take a look at my answer here, in particular the section entitled 'Protein modelling (from amino acid sequence)': A: pathogenicity predictors of cancer mutations

Through the link, you can have access to numerous tools that attempt to predict the change in conformation of the protein due to the mutation. You usually have to provide the entire amino acid sequence though.

Kevin

[Shicheng Guo]

Awesome!! Thanks Kevin.

https://www.proteinmodelportal.org/?pid=modelling_interactive

This is working!!

[Kevin Blighe]

Great - note that all are for academic / research use only.

[Shicheng Guo]

Get the simulated protein structure, however, totally don't know what's the difference. What the hell it is...

[Kevin Blighe]

What did you receive in your email - a PDB file? You can view the site of the mutation in Jmol. I believe that there are functions in Jmol that allow you to search for amino acid residues. Then, you can see if, for example, if differences appear over the wild-type.

Sorry, I am not aware of any automated method to do this.

[Shicheng Guo]

Thanks Kevin, I checked the simulated structure with Cn3D. Jmol is better than Cn3D?

[Shicheng Guo]

RasMol vs JMOL vs Cn3D

For more advanced uses, such as command line control, you can install RasMol. Some scientific websites are using JMOL, a Java-based viewer, for rendering molecules in 3-D. JMOL and similar tools may replace Chime eventually, but for now, Chime is the program used most for viewing small molecules from websites.

If you would like to view macromolecules in 3-D, download and install Cn3D. This program should be all you need to visualize proteins of interest. For advanced users, investigate Protein Explorer, a RasMol derivative.

[Kevin Blighe]

Thank you for the information, Shicheng