You would have to figure out some sort of Principle Component Analysis (PCA) algorithm to determine what you are most concerned about when it comes to how things 'differ'. It has a lot to do with compressing 1000s of variables into a single dimensional field so you can graph it and people will actually understand it in a visual sense.
pH is very important to proteins, but remember that's sort of because hydrogen ions are positively charged. Proteins need to have specific amino acids protonated or deprotonated in order to properly associate with the nearest amino acids in the sequence, as well as amino acids further away in the sequence. Other positively charged ions like Calcium and Magnesium can also interfere.
Don't forget : adding different salts, sugars, and peptides to an aqueous solution will change the way things dissolve, for lack of a better way of saying it. The hydration shells start to change, the viscosity, and the way HYDROPHOBIC MOLECULES FOLD is very complex.
If you figure this out, every company in the world that designs recombinant proteins will just throw money at you.
Again. Best of luck.
pH is very important to proteins, but remember that's sort of because hydrogen ions are positively charged. Proteins need to have specific amino acids protonated or deprotonated in order to properly associate with the nearest amino acids in the sequence, as well as amino acids further away in the sequence. Other positively charged ions like Calcium and Magnesium can also interfere.
Don't forget : adding different salts, sugars, and peptides to an aqueous solution will change the way things dissolve, for lack of a better way of saying it. The hydration shells start to change, the viscosity, and the way HYDROPHOBIC MOLECULES FOLD is very complex.
If you figure this out, every company in the world that designs recombinant proteins will just throw money at you.
Again. Best of luck.
-SG
On Thu, Dec 7, 2017 at 9:04 PM Cory J. Geesaman <cory@geesaman.com> wrote:
I'm aiming for more of a blanket id system, of the sort:
{
sequence,
chunk,
temp,
pH,
salinity,
reducingAgentConcentration
}
where sequence is the actual sequence of amino acids, chunk would be a pointer to something like the clustering functionality of MSM Builder, and the others are some integer or floating/double point precision number mapping to all the critical regions of each attribute in the smallest possible manner (i.e. if a linear or logarithmic pH scale with 4 bits is plenty to encompass all the possible folds given the other parameters, then I don't want to use a 64-bit floating point number as I would like to be able to actually simulate ever combination for a given protein, or more accurately a polypeptide given reasonable computational limits with current technology.)
On Thursday, December 7, 2017 at 10:27:55 PM UTC-5, Bryan Jones wrote:Are you asking about some particular protein? I don't think you could specify any general parameters as the limit for all proteins. Some proteins are much more tolerant of extreme conditions than others. Proteins are evolved for particular conditions, but those conditions are different for different proteins, and some proteins, by chance, happen to be even more tolerant than they were selected to be. Some proteins, espicially those from extremophile organisms, show surprising tolerance for pH extremes or temperature extremes or high salinity. That being said, if you want to find conditions that are almost guaranteed to completely unfold almost all proteins, look at the conditions usually used to prep samples for running protein gels: a bunch of soap (SDS) and reducing agent (beta mercaptoethanol or dithiothreitol) and heated to almost boiling.On Thu, Dec 7, 2017 at 10:10 PM Cory J. Geesaman <co...@geesaman.com> 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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