I am interested to collect thermal stability of different proteins, i.e., their Tm values. Is there any easiest way to find the Tm using only RCSB PDB ID? Suppose I would like to get Tm value of 1M8U PDB file.
Thanks in advance,
Kalyanashis Jana
Try this:
Article ProtDataTherm: A database for thermostability analysis and e...
Thank you very much Adam for reply and suggestion. I have tried to get Tm from ProtDataTherm web server, however, I could not understand how to get the desired Tm value. I did the following steps
1) find out PFAM ID from https://pfam.xfam.org/
2) E.g., PFAM for 1M8U is PF00030
3) I have used PFAM ID for the thermal stability value at http://profiles.bs.ipm.ir/ softwares/protdatatherm 4) Finally, the web server provides different type of protein sequence.
But I how can I get the Tm value from this protein sequence (Attached ProtDataTherm results)
Sincerely yours,
Kalyanashis Jana
Dear Kalyanashis Jana,
I’m afraid that indeed the suggested program will not be able to answer your question.
The set-up of this program is based on grouping proteins (roughly) into groups for their known temperature where they are stable (obviously thermophilic proteins form the upper group). The program integrates known experimental effects of mutations but does not include the Tm or denaturation midpoint data (since most of them are simple not known (yet)).
An approach what comes close to what you are looking for is decribed in:
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003689
https://www.nature.com/articles/srep23257
That ultimately led to the program called PopMuSiC:
https://soft.dezyme.com/
Hope this helps you any further.
Dear Rob Keller,
Thank you very much for your reply. The above mentioned articles are helpful and broadly covered thermal stability topic. HoTMuSiC web server can also predict the thermal stability values of a protein from a given PDB ID. However, I have been looking for just experimental thermal stability values.
The ProTherm has large experimental data set on thermal stability as well as Biophysical J. 2011, 101, 217–227 (Article How Do Thermophilic Proteins and Proteomes Withstand High Temperature?
) and J. Phys. Chem. Ref. Data, 2016, 45, 023104 (Article High-quality Thermodynamic Data on the Stability Changes of ...
) cover a large number of proteins. Therefore, I am looking forward to other source of experimental thermal stability values.Thank you once again for your suggestions.
Sincerely yours,
Kalyanashis Jana
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