Dear All,
I want to do constant pH MD for an enzyme. For the analysis, I want to know, is there any way to calculate pH of static pdb structure? I have pKa (individual residue) and charge (whole protein).
PS: I already did the simulation using, H++ server and Gromacs.
If you have the amino acid sequence, you can calculate the pI of the enzyme using ExPASy: https://web.expasy.org/compute_pi/
Using PROPKA, you can calculate the pKa of an entire protein for different forcefields. Link: http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/
Go through this article: Numerical calculations of the pH of maximal protein stability.
Article Numerical calculations of the pH of maximal protein stabilit...
I think what you meant is the protonation states of the sidechain residues at a particular pH. You can set that manually by consulting the pKa values of the individual amino acid residues. Or, you may use some automated programs (e.g. Schrodinger Maestro Academic version) to assign correct protonation states for the side chains at certain pH.
Farzane Jalalypour You cannot cange the pKa; you can change the protonation state of the amino acids. For example, at pH below 6, both the N in the histidine ring will remain protonated. But at neutral pH only one N in the histidine ring will reamin as NH. So, these are the changes you can make manually.
Uttam Pal thank you.
so after I calculate pka in one of websites I cant define a Pka that I calculated for one of the residues? Right?( ın the case I need it)
pKa is an intrinsic property. You cannot possibly use the pKa values directly. For each residue there would be as many pKa values as there are acid base groups in the residue. But, based on the pKa values and the pH of the system, you can assign the protonation states of the residues.
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