I hope you can help in these matters.
1) What is the difference between sequence and structural comparison between proteins?
2) Which website or software is good to use to perform this task?
3) how to interpret results?
4) can I only compare the kinase domain between different proteins? Not the whole protein or chain.
Thanks
Hello,
Sir as per my knowledge
1. if two proteins are having same sequence its doesn't mean that they will have the same function but if they have same structure there is a chance of having same function
same sequence can fold differently
http://www.nature.com/scitable/topicpage/protein-misfolding-and-degenerative-diseases-14434929
2. For sequence similarity you can us multalin, clusterW for structural similarity phyre2 server can be used
3. For interpretation % similarity /RMSD value could be considered
4. I am not sure if whole protein or chain can be compared on any web server....sorry for this...
Good Luck......
Hi.
To answer questions 1&2:
In sequence comparison, one simply measures the extent to which two or more protein sequences are alike, and this can be measured by a Local or Global alignment. The result of such comparison is usually a number in "percents": for instance, protein 1 and protein 2 have 60% sequence similarity (or sequence identity). This comparison can be made using free software such as the BioEdit.
However, when comparing two protein 3-D structures, you are measuring the similarity between different structural regions and amino acid side-chain conformations. This is usually measured via RMSD and is usually in Angstroms. A tool mostly used for this purpose is SPDBV which is also available for free. You can use the following link for download: https://spdbv.vital-it.ch/disclaim.html#
The answer to your 3rd question depends mostly on the kind of study you are conducting. But the higher the similarity percentage is, the more the proteins may be alike. This is also true about structural comparison; if you are studying two enzymes, a lower RMSD between the two structures shows a higher structural similarity.
Hope this was helpful. If you needed more info on the tools or software, let me know!
In summary,
you may compare the sequences of proteins with clustal w method and calculate their similarity scores.
and about the 3D structures you can align the structures based on their backbone atoms and calculate their RMSDs with respect to each other.
1) What is the difference between sequence and structural comparison between proteins?
This is a complex question, the answer to which depends upon what you are trying to accomplish by doing the comparison.
2) Which website or software is good to use to perform this task?
https://books.google.com/books?id=l6moDgAAQBAJ&printsec=frontcover&dq=protein+structure&hl=en&sa=X&ved=0ahUKEwikv6uCu7LXAhVEw4MKHbIQA9gQ6AEILzAB#v=onepage&q=protein%20structure&f=false
Article Methods of Protein Structure Comparison
https://www.rcsb.org/pdb/home/home.do
http://www.cathdb.info
http://pfam.xfam.org
https://www.cgl.ucsf.edu/chimera/
3) how to interpret results?
See #1.
4) can I only compare the kinase domain between different proteins? Not the whole protein or chain.
Sure. https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/super.html
Thank you all for your comprehensive responses.
I'll try your suggestions and will get back to you in case of encountered problems.
Thanks again!
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