# Structural Biochemistry/Enzyme Regulation/Reversible covalent modification

After a molecule is covalently attached to an enzyme, the activity, or catalytic activity, of the enzyme can be changed. In this regulatory strategy, the donor molecule provides the modifying group. The acceptor molecule is usually an enzyme molecule which accepts the modifying group therefore changing its activity. The acceptor is usually a serine, threonine, or tyrosine residue, amino acids that contain hydroxide. The process of the covalent modification may be reversible, but not in all cases. One common example of covalent regulation is protein phosphorylation.

## Examples

The examples of the covalent modification strategy are acetylation/deacytilation; phosphorylation/dephosphorilation; myristoylation; ADP ribosylation; farnesylation; sulfation; ubiquitination. However, phosphorylation and acytilation are the most common examples. In phosphorylation, ATP donates a phosphate to the hydroxyl group of a cytosine or tyrosine. The reaction yields ADP and a phosphate ester (phosphorylated protein). In the case of phosphorylation, glucose homeostasis is the function that is modified in the glycogen phosphorylase protein. In case of acytilation, the donor molecule is acetyl CoA. The DNA packing function can be modified in the histon protein.

## Regulation of the activities of the target proteins

The phosphorylation reaction is used in almost every metabolic process; moreover, approximately 30% of the known proteins are phosphorylated. The enzyme which catalyzes the phosphorylation process is protein kinase. The human genome contains about 500 homologs for this enzyme. The donor molecule that provides modifying group for that process of the catalytic modification is an ATP molecule. The acceptor molecule has to contain one of the OH groups containing amino acids in its sequence (such as serine, threonine, or tyrosine). In the process of phosphorylation, the ɤ-phosphoryl group from ATP molecule attacks the OH containing amino acid in the protein molecule. This process can ONLY occur within the cell. Proteins that are located outside the cell are not able to go though the phosphorylation regulation.
Protein phosphotases are another type of enzyme which catalyze the process of the removal of phosphate group from the protein molecule. This is also known as dephosphorylation. This enzyme deactivates the flag on the protein that was activated by the kinase. Protein phosphatase removes the phosphoryl group that is attached to the protein. However, those enzymes are required to increase the reaction rate of the phosphorylation/dephosphorylation reactions.
Protein phosphorylation adds two negative charges, forms 2-3 hydrogen bonds, is a reversible modification, kinetics can be adjusted to physiological process, amplifies signal, and ATP coordinates signaling with bio-energetics.

## Phosphorylation can control the activity of proteins

1. An attached phosphoryl group gives an additional negative charge (2-) to the modified protein. Presence of the negative charge can be a source for the electrostatic interaction with other proteins which contain positive charge or within the same protein with positively charged amino acids.
2. A phosphoryl group is also able to form an additional interaction, as a result of the ability to form three H-bondings.
3. Phosphorylation process gives large expand of free energy.
4. The phosphorylation process can take time in the range between one second and few hours depending on the physiological process.
5. The donor molecule for phosphorylation, ATP, is represented as a unit of energy currency required for the regulation in the metabolic processes.
Phosphorylation is a covalent modification that controls the activity of enzymes and other proteins. Signals can be greatly amplified by this modification because one kinase has the potential to create an exponential chain effect on various target molecules. An example of this would be the sensitivity of human eyes in reaction to a photon. Protein kinase regulatory activations can be reversed by protein phosphatases, a hydrolysis reaction of connected phosphates. Cyclic AMP, an intercellular messenger, can activate protein kinase A. Cyclic AMP activates Protein Kinase A by altering the quaternary structure. The effects of cAMP in eukaryotic cells are due to activation of PKA by cAMP.The activation of that multifunctional kinase is accomplished by cAMP binding to the regulatory subunit of the enzyme, which frees the functional sites of protein kinase A. When a inhibitor is bound to a Protein kinase A, it binds between the domain of the enzyme in a cleft.
PKA in muscle has 2 subunits: Regulatory (R) subunit and catalytic (C) subunit. The binding of cAMP to the regulatory subunit relieves its inhibition of the catalytic subunit.
Regulation of PKA: PKA is activated when four molecules of cAMP bind to it; this dissociates the inhibited holoenzyme(R$_2$C$_2$) into a regulatory subunit (R$_2$) and two catalytically active subunits (C).

## References

Berg, Jeremy M. John L. Tymoczko. Lubert Stryer. Biochemistry Sixth Edition. New York: W.H. Freeman, and Company 2007.