Proteins are made up of amino acids. Protein has basically primary (1-D), secondary (2-D), and tertiary (3-D) structures exhibiting different types of functions. Nanoparticles (NPs) have unique properties that may be useful in a diverse range of applications, and consequently, they have attracted significant interest. Particularly in the bio-medical field, the use of nanovaccines and nano-drugs is being intensively researched. The temperature and pKa values of the amino acids in the proteins have great importance about the pH-dependence of the protein stability. Many experiments have been carried out in the last few decades to re-engineer the temperature and pH-activity and pH-stability profile of the proteins. Some of the earlier results predicts a sets of point mutations that will change the pKa values of a set of target residues in each direction, thus allowing for targeted re-design of the pH-dependent characteristics of the proteins. In this work, molecular dynamics (MD) studies are carried out by re-designing pKa values of some of the protein’s amino acids in the carbon nanotube and the protein system. In our earlier studies, a variation in temperature was observed to play an important role in the dynamics of protein around the carbon nanotube. The pH value of the protein is modified with the help of H++ server. Detailed molecular dynamics simulations of 100 ns each are carried out to further study the behaviour of this protein under the influence of the pH change environment. A shape change is observed in the protein surrounding around the carbon nanotube at a pH value other than physiological pH. Towards the end of the simulation, very interesting results are observed in the interaction of CNT with protein at a low pH of 6.5. Protein is observed to be wrapping around the CNT thus forming a corona like structure. Comparatively very less interaction is observed between CNT and protein at a higher pH of 10.