MRNA transcription before and after transcription, the earliest, storage function when the minimum PH value. MiRNA and mRNA move when the second, the highest PH value after protein formation. Also, the molecular weight is related.

Remember that physiological pH is 7.41, and it can be assumed that most if not all proteins including enzymes (e.g., proteins that function in the lysosome, where the pH is 4.5-5.0) function at this pH.  So, yes, of course you can do HM at different pHs to satisfy your curiosity, but just keep in mind the physiological pH criterion when interpreting your results.  HTH.

I think the question is also relevant to mild basic and acidic pHs, which are common in physiological environments, and the structure of protein can change. Histidines in a protein are most commonly affected due to this shift, protonated (or positively charged) at mild acidic and deprotonated (or neutral) at mild basic. If you are able to define these two residue types and accordingly manipulate the energy function (increased electrostatic contribution for protonated state), you might be able to see alternate conformations of exposed or partially exposed histidine side chains and backbone.

Respected Vicente Mendoza Reyes,

can you please suggest me the software or server which can be used for HM using different PH value.

@AbdulNasir: I myself have not done any HM where I could vary the ambient pH. So I can only suggest to you to search the internet for "Homology Modeling with pH adjustment" or anything to that effect.  But I think a better way to go about your objective is to go to the PDB website and search for "crystallization pH" (or just "pH") in the keyword box. This will hopefully give you a list of proteins crystallized at different pHs, from which you can then cull out identical or similar proteins that were crystallized at different pHs. You can then compare their structures to each other and make your own hypotheses.  HTH.

You can do the typical HM to get a model of your structure if it has not been crystallographically determined. Then, study the effect of pH using two molecular dynamic simulation experiments, one using a box containing the protein and higher-pH solution, the other using a box filled with the protein and lower-pH solution. Then, compare the folds of resulted structures using structural alignment, etc.

Yes i would go with Ebrahim Barzegari statement.

First you make your model using homology modeling concept, later you can perform dynamic simulation in different pH and compare the results.

thanks Ebrahim Barzagari andPramodkumar P Gupta for your comments