Listen,
The cell doesn't just change the pH (which isn't in an integer scale, it has infinite range to it - and on a logarithmic axis), and the protein magically folds correctly. There are hundreds of different cell pathways for processing proteins to get them into a specific shape before being "shuttled" to the proper place.
This is a subject that people spend their entire lives studying, and that is just for a single protein much less every peptide combination possible.
Saying one sequence will fold like another because they are similar polypeptides in similar conditions is like saying two people with similar traits will act the same under the same circumstances or that two apple trees will taste the same since you planted the seeds in the same soil. It's possible, but really unlikely. Just a single difference in CELL PROTEIN PROCESSING will change everything and your program goes out the window.
Now you're talking about having users input their specific cell pathways to try to determine exactly what happens as a sum of those pathways and then GUESSING how all those variables are weighted.
Remember, even if you think you got it right you'll have to use X-ray crystallography to find out if you're right. Old school, and classic, but also very very difficult and time consuming.
-SG
The closest I've been able to find (at least as far as I understand what you are asking for) is PSCDB - the Protein Structural Change DataBase, but that one seems heavily focused on structural changes induced by ligand binding, not pH or temperature changes etc.There are likely also some databases out there with information on what the physiological range is for enzymes or other proteins. But it may not have any info on exactly why they lose their function beyond those parameters - whether it's due to a distinct structural change, or they start to denature, or undergo some other non-structural changes that inhibit their function.What I am fairly certain you will NOT find, is a database with a large number of proteins documenting in detail how their structure changes with changes with environmental parameters. There just aren't that many proteins that have been documented to switch between distinct structural conformations. And for those proteins we do know about, the characterization of the parameter space will typically be very coarse, e.g. something like "this protein has conformation X at pH 7, but conformation Y at pH 5 in the presence of Ca+".Patrik--On Thursday, December 7, 2017 at 7:10:01 PM UTC-8, Cory J. Geesaman wrote:Does anyone know of a set of categorizations for proteins which provide good coverage of all the observed structural conformations?
Examples of what I'm referring to would be the pH, salinity, temperature, and possibly reducing agent concentrations.
The purpose is to try to classify different stable folded proteins for each set of possible changes, so if for instance there's a hard cutoff at a pH of 3 where lower doesn't do anything, or greater than 100C or more than a 90% saturation of salt, or more than a 2% solution with reducing agents (a specific reducing agent or in general,) etc that would be helpful to know. Additionally, if there is somewhat of a gradient that would be helpful (e.g. will a protein fold different at a pH of 6, 7, and 8 - and if so are there known transition points?)
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