Pka of residues in an active site of protein

  • Thread starter johndude222
  • Start date
  • Tags
    Protein
In summary, The pKa of histidine in a protein active site can be affected by the presence of surrounding negative residues. By making the surrounding residues negative, the pKa of histidine increases as it becomes more stable in its protonated form. This is due to the thermodynamic effect of stabilizing the protonated form in a negatively charged environment.
  • #1
johndude222
1
0
Here is a little concept I have difficulty reasoning it out and I was hoping if someone can guide me through it.

pKa of amino acid residues in a protein active site. Take histidine for example, below pH of 6.0 it stays positively charged but above pH of 6.0 it becomes neutral with the removal of a hydrogen on its side chain.

Now if we make the its surrounding negative (i.e. all the nearby residues are negatively charged), the pKa of histidine side chain increases because histidine itself likes to remain positively charged in this negatively charged environment. That makes sense.

However, given that the hydrogen ion been removed is positive, doesn't other negatively charged residues want that hydrogen from the histidine (as opposite charges attract) and therefore it should be easier to remove that hydrogen (therefore pKa decreases).

I don't understand why the pKa increases in this context.
 
Chemistry news on Phys.org
  • #2
Remember that pKa is measuring a thermodynamic quantity (the equilibrium constant of the acid dissociation reaction). If we add negative charges to the histidine environment we stabilize the protonated form relative to the deprotonated form and so the pKa increases (the equilibrium favours the reactant side more than it did).
 

1. What is the significance of the pKa of residues in an active site of protein?

The pKa of residues in an active site of protein is important because it determines the ionization state of the amino acids in the active site. This, in turn, affects the protein's function and the binding of substrates or ligands.

2. How is the pKa of residues in an active site of protein determined?

The pKa of residues in an active site of protein can be experimentally determined using techniques such as NMR spectroscopy or site-directed mutagenesis. It can also be predicted using computational methods.

3. What factors can affect the pKa of residues in an active site of protein?

The pKa of residues in an active site of protein can be influenced by the local electrostatic environment, the presence of neighboring amino acids, and the binding of substrates or cofactors. Additionally, changes in temperature and pH can also affect the pKa of residues.

4. How does the pKa of residues in an active site of protein impact enzyme kinetics?

The pKa of residues in an active site of protein can affect enzyme kinetics by influencing the rate of substrate binding, catalysis, and product release. It can also affect the specificity and efficiency of enzyme-substrate interactions.

5. Can the pKa of residues in an active site of protein be altered?

Yes, the pKa of residues in an active site of protein can be altered by mutations, changes in the local environment, or through the use of small molecule modulators. This can have significant impacts on the function and regulation of the protein.

Similar threads

Replies
5
Views
2K
Replies
1
Views
5K
Replies
5
Views
1K
  • Biology and Chemistry Homework Help
Replies
1
Views
5K
  • Biology and Chemistry Homework Help
Replies
5
Views
6K
Replies
10
Views
2K
Replies
10
Views
3K
Replies
4
Views
3K
  • Biology and Chemistry Homework Help
Replies
11
Views
19K
  • Atomic and Condensed Matter
Replies
4
Views
3K
Back
Top