Some proteins change their conformation based on protonation state of particular residues like aspartic acid. Some kinases are examples for this. For example, in case of Abl kinase, protonated D381 residue favours inactive DFG-out conformation, and de-protonated D381 favors active DFG-in conformation ( doi: 10.1073/pnas.0811223106 ). The pKa of COOH in the side-chain of aspartic acid is 3.81. So, does is mean that only when the environment ph3.81.
Thanks
The pKa depends on the location of the amino acid in the protein (solvent-exposed vs buried) and can be modulated by binding of metal ions. These two factors are exploited by many enzymes that catalyze proton transfer reactions.
as Martin Klvana said, enviornment has huge effect on protonation state. for example, if you have arginine around glutamate, glu is most likely going to be deprotonated, while if there are negatively charged residues around Glu, its going to be protonated.
Also, there could be local ph variation which may regulate this activity depending on protonation state. like lysosome has a pH of ~4.5-5. You need to be careful with such test-tube based biophysical/biochemical studies though as it may not be relevant to physiology at all. Not all protein can tolerate a pH of 4 or 4.5.
Martin Klvana Dhiraj Srivastava
Is there a way to predict the pKa of a particular residue in a given protein structure and environment?
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