Phosphorylation of proteins
Phosphorus, or more precisely phosphate, plays various roles and is found at multiple sites in the human body. I have come to fully understand that it serves critical roles and functions essential for life. Among the various activities of phosphate, I would like to focus in detail on phosphorylation, which has already been briefly mentioned in the previous article. I would like to specifically address the concept of phosphorylation, which constantly appears while studying the cellular signaling processes. In particular, I would like to delve into the phosphorylation of proteins. To begin with, let's briefly look at some very basic aspects of proteins.
Basic structure of proteins
The building blocks of proteins are amino acids. This is similar to how LEGO pieces come together to create various objects. Amino acids can be classified into essential amino acids (9), which the body cannot produce; conditionally essential amino acids (6), which can be synthesized but may cause problems if deficient; and non-essential amino acids (6), which are produced sufficiently, totaling 21. While it is commonly accepted that there are 20 amino acids, I personally believe it is more accurate to consider 21, including selenocysteine, which was discovered later.
All amino acids share a common backbone structure where a central carbon is bonded to an amino group (H2N), a carboxyl group (COOH), and a hydrogen atom (H). Each amino acid has a unique side chain (R group) attached to this common backbone, which defines the characteristics and properties of each amino acid. In other words, except for the R group, all amino acids consist of the same common parts. It is similar to the shape of a bracelet with variously shaped charms connected to the chain.
In the neutral pH aqueous environment of the human body, the amino group acts as a base, accepting a hydrogen ion to become H3N+, while the carboxylic acid acts as an acid, losing a hydrogen ion and ionizing to COO-, thereby acquiring a charge. Interestingly, the charge of both the amino group and the carboxyl group changes depending on whether the surrounding environment is acidic or basic. When the pH becomes low in an acidic environment, the carboxylic acid will accept a hydrogen ion, converting COO- to COOH and neutralizing its charge, while the amino group maintains its positive charge, leading the amino acid to overall carry a positive charge. Of course, whether each R group (side chain) carries a charge also influences the overall charge. When the polar regions of amino acids interact with negatively charged phosphate, it can lead to various outcomes.
If we assume that these amino acids with different chemical properties are a letter of the alphabet, these letters can freely combine (through peptide bonds) to form various words, and these peptides can group together to create proteins with more complex tertiary and quaternary structures. When we closely examine how amino acids are connected, we can see that the common parts of all amino acids consist of amino groups and carboxyl groups that are repeatedly linked, with one water molecule being released during this process, forming covalent bonds and creating a long peptide backbone. It is worth noting that amino acids are not only the basic units of protein synthesis but also serve as neurotransmitters or precursors for producing neurotransmitters.
Proteins not only form the structure and framework of cells, such as in skin, hair, tendons, and collagen, but they also comprise various essential elements that enable cells to perform a range of activities. These include catalytic enzymes, hormone proteins, transport proteins, storage proteins, receptor proteins, gene transcription proteins, antibodies, and transport proteins like hemoglobin. By listing these functions, we can understand the extensive roles of proteins. If we consider that DNA serves as the blueprint for creating these proteins, we come to realize the importance of proteins once again.
Structure and function of proteins
The structure of a protein, composed of one or more polypeptides, is closely related to its function. Since the conformation of a protein determines its function, even slight changes to its structure can alter its function, potentially leading to a complete loss of activity. The covalent bonding within the protein is highly flexible and not fixed, making it relatively easy to modify the structure. For proteins that need to interact dynamically with other molecules or proteins to perform various functions, even minor structural changes can result in significant alterations in their behavior. These changes can impact the protein's function, the degree of activity, the rate of action, or the rate of degradation.
In other words, by targeting specific regions of a protein at particular locations, we can induce changes in its structure to control the protein. For example, in situations where cells must respond immediately to external stimuli, it is obviously much faster and more efficient to slightly modify already synthesized proteins for appropriate use rather than synthesizing new proteins through DNA transcription. This explains why numerous protein modification processes occur within signaling pathways. It is not only a quicker way to respond to the surrounding environment but also a highly effective and convenient method.
Post-translational modifications (PTMs)
For this reason, there is a wide variety of post-translational modifications (PTMs) that occur after protein synthesis, with over 650 different types of protein modifications currently identified.[1] Among these, well-known examples include phosphorylation, acetylation, methylation, glycosylation, ubiquitination, acylation, and cysteine oxidation. Most of these modifications change the protein's structure, activation state, stability, charge, and interactions with other biomolecules by adding or cleaving new molecules, thereby altering its function in biological processes within the cell.
Phosphorylation is involved in cell signaling and the cell cycle, while acetylation and methylation are related to DNA transcription regulation and cellular metabolism. Glycosylation plays a crucial role in protein folding and cell adhesion, and ubiquitination is involved in regulating protein degradation. PTMs expand the chemical composition of amino acids and enable a variety of molecular states, allowing proteins to adopt more diverse and complex forms.
However, among these various types of protein modifications, phosphorylation is the most effective in terms of protein regulation. This is primarily due to the flexible reversibility of phosphorylation. As will be examined in more detail in the following articles, adding a phosphate group to a substrate is called phosphorylation, and subsequently removing that phosphate group allows the protein to revert to its original state. This can be likened to freely pressing and releasing a car's accelerator to control speed, enabling flexible regulation. The actions of kinases and phosphatases make this possible. This is why phosphorylation plays such a crucial role in signaling processes. Specific kinases are phosphorylated to regulate numerous proteins, and in fact, these kinases are also phosphorylated by other kinases. If they are not phosphorylated, they remain in an inactive state. Thus, it is often described that phosphorylation acts like a switch that can be turned on and off. It’s similar to a children's game of freeze tag, where someone must come and say "You're phosphorylated!" for you to move freely and go help others.
[References]
[1] Protein posttranslational modifications in health and diseases: Functions, regulatory mechanisms, and therapeutic implications
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10152985/
