A total open question. How would one go about linking a function to a protein given only its structure?
I understand this is a million-dollar question, so vagueness is appreciated.
I have a predicted structure of a protein from de-novo/threading (I-TASSER) followed by extensive simulated annealing MD simulations. There is only DNA work (sequencing), no actual protein experimental work - nothing at all, this is something knew we found. There are also no template structures, i.e., homology modelling efforts have been awful.
Some thoughts I've had:
Are there di-cysteine bonds? Typically extra-cellular proteins have these over intra-cellular proteins.
What is the secondary structure content? i.e., helical vs beta sheet with regards to transmembrane proteins
What is the tertiary structure? Globular, fibrillar, etc.
Are their stretches of exposed hydrophobic residues? i.e., integral membrane proteins.
Are there are metal binding sites e.g., 3x HIS 1 ASP which is very typical for zinc?
Stretches or grooves for protein-protein interaction and/or potential hydrogen bonding?
Given that I have a structure, is there any way of comparing this to 3D structures in the PDB databank? Having said that, if there was, and a match was found, you could safely assume the homology modelling would have worked to begin with.
I appreciate any thoughts you have.
Thanks
Hi Anthony,
I would suggest you to perform a VAST tool search of your protein. The VAST search finds structures that are 3D similar to individual protein molecules, or individual 3D domains.
please share the updates of your result.
regards
Tanuj
Thanks Tanuj,
That is a very interesting find, which I was not aware of. Many thanks.
I am trying computational biology techniques to predict the presence of exons in known protein from PDB database.Is this information enough to predict protein function? and what are the other parameters required to predict the structure and function of a protein?
I appreciate any material or thoughts on this?
Thank you in advance
Here are articles on protein function prediction.
http://www.nature.com/nmeth/journal/v10/n3/full/nmeth.2340.html
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0056833
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0075542
http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003341
http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.0030237
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-162
https://www.eurekalert.org/pub_releases/2007-07/uoia-run071107.php
https://www.sciencedaily.com/releases/2007/07/070712135154.htm
Regards,
Joachim
Respected Sir,
Thank you so much for providing valuable information.
Sincerely
Raman Kumar
- Badges
- Science topic
- Similar topics
- Filing