Hey guys, welcome back to The Crux. In this video, we'll try to go over the very fundamental concept of protein modification, also known as post-translational modifications. I will try to give you a very basic overview of it, and these modifications will apply both to prokaryotes as well as eukaryotes. And in our discussion, we'll try to understand the modifications via some specific examples.
After translation or protein synthesis, the polypeptide chain is not ready for performing its task. It first undergoes some folding, which is assuming its primary, secondary, tertiary, or even quaternary structure. I will probably make a video on the topic of protein folding at some later point.
So after folding of the protein, it may still not be completely functional. So additional help is required, which comes in the form of post-translational modifications. And these are...
quite a lot of these modifications that occur depending on the context. And this generally causes a mature protein to form, which is usually the intended functional product. But generally speaking, post-translational modifications can either turn an active protein into its inactive form, or they can turn an inactive protein into its active form. And we'll go over some specific examples of this later.
Essentially, this can be generalized in the form that a protein which has a function x can assume a different function, which is function Y, when the protein is modified. So let's just give a loose definition of post-translational modifications. These are reversible or irreversible chemical changes to proteins after translation.
And these chemical modifications are typically covalent chemical modifications driven by enzymatic reactions. These modifications have names, such as methylation, acetylation, glycosylation, phosphorylation, ubiquitination, proteolysis, protein splicing, and there are many more. But for the sake of this video and brevity, we will try to limit our scope of discussion to these specific ones.
Now, you may ask, what function can post-translation modifications serve, specifically in context of cellular activities? So, generally speaking, everything is dependent on these modifications. But specifically, they affect protein stability, activity, their localization, and they can even control the interaction of proteins with other biomolecules, and these can be nucleic acid, carbohydrates, lipids, or even other proteins. A major impact of modifications is also to control the degradation rate and the recycling of proteins, and they generally regulate their activity in the cell.
The main idea that post-translational modification puts forth is actually quite bigger than all this. In essence, these modifications increase the protein diversity in a cell. Let's take a closer look into this. In a cell, the information is stored in the DNA, which has protein-coding elements, which are genes, and humans have around 20,000 genes that encode for proteins.
And each of these genes can be turned into an RNA through the process of transcription. And I have a complete playlist explaining how this works. And the exons in these RNAs can be concatenated via alternative splicing to make different kinds of mRNAs. And even sometimes, alternative promoters can be used.
to transcribe the same genes, and that results in a different mRNA. Essentially, all these processes, and many more perhaps, are responsible for creating diversity of the mRNA. So one gene in the DNA can produce multiple types of RNA.
And on average, there are about 100,000 or so mRNAs in a cell. And we know that one mRNA can only produce one type of protein. So if we assume that all of these 100,000 mRNAs are unique, you would expect that there would be 100,000 unique proteins in a cell. Turns out that's not true. There are more than a million different functional proteins in a cell.
So how is this possible? Now this is possible because each protein can undergo a certain type of post-translational modification, say for example phosphorylation or acetylation and many more. And depending on these modifications, it can have a different activity and function. And now you see that a single mRNA has the potential to give rise to multiple functional proteins. These post-translational modifications are usually classified into four major categories, depending on the mechanism and the type of modification.
First is the type of functional group that is added, so methylation, acetylation, acylation, phosphorylation, and many more. Second is the addition of a protein tag, which is either ubiquitination, or sumo-elation. Then third, you have the backbone cleavage, which is either porcheolosis or protein splicing.
And then finally, some modifications that can change the nature of amino acids itself. which happens via oxidation, deamination reactions, and other things. These are typically non-enzymatic chemical modifications. So going forward in this video, we'll focus on the modifications that are listed here and we'll try to understand them via very specific examples and see their function.
And towards the end, I will also list the relevance of these modifications to diseases. The list of modifications that we will discuss is a subset of many possible post-translational modifications that exist, so just please keep that in mind that this is not a complete list. Alright, let's dive into the first modification, which is the phosphorylation. And as the name suggests, this is where a phosphate is added to a protein, and this happens to be the most common modification. Around 33% of eukaryotic proteins have this modification at some point in the cell.
And this modification is commonly used in signaling pathways, cell cycle, and growth proteins, and in many other functional proteins. And the type of enzyme that is responsible for this modification is called kinase. Let's just take a look at the example of a signaling cascade to see how this modification is important. Say you have some receptor on the cell membrane, and they receive a signal in the form of a growth factor, or a growth hormone.
And let's assume for clarity that this receptor is an epidermal growth factor receptor. In this pathway, when this factor binds the receptor, these receptors get phosphorylated, and they activate an enzyme called RAF, which happens to be a kinase. And this enzyme takes its substrate protein, MEK, which is typically inactive and adds a phosphorylate to it, and this makes it active.
And this active MEK also happens to be a kinase. and it activates another downstream protein by adding a phosphate to it. And this phosphorylated ERK, which is also a kinase, can target many other cytoplasmic proteins, and it can be transported into the nucleus. And there it can phosphorylate transcription factors.
Now notice that only phosphorylated ERK can be transported into the nucleus. So this again highlights that phosphorylation can change the function and localization of a protein. So in the nucleus, the phosphorylated ERK can activate a transcription factor, which can then bind to a specific promoter of a gene, or a regulatory element like an enhancer, and turn the expression of a gene on.
And because this was the case of a growth factor signaling cascade, the genes that get turned on will probably drive cell growth and proliferation. Alright, now all these phosphates that get attached to these proteins, where do they come from? Well, the substrate for phosphorylation is ATP.
So each of these transition steps in this pathway require ATP, which is the energy currency of a cell. And now it also makes sense that why you need to eat more and better if your body needs to grow and develop, which is when a growth factor or growth hormone is released. Here's another quick example of phosphorylation. Remember C-terminal domain of the RNA polymerase, which gets phosphorylated at different steps at different places during transcription? And this phosphorylation changes how polymerase functions and what proteins it can bind with.
Since we're on the topic of transcription factors in DNA, let's talk about methylation and acetylation, where the modification results in the functional group transfer, which is either methyl group or the acetyl group. And this is perhaps the most common modification that occurs in histones, which are proteins that make up the chromatin. In chromatin, DNA is wrapped around histones, and generally speaking, if histones are methylated, the packaging of DNA increases and then the DNA cannot be accessed.
On the other hand, if the same histones are acetylated, the packaging density decreases and therefore the DNA becomes open and accessible. This is something that we also talked about in transcription when we were discussing the problem of histones which block the transcription. So generally speaking, these methylation and acetylation of histones can lead to different parts of chromatin being open and closed.
which are either euchromatin or heterochromatin state. Talking about substrates, the methyl is transferred from its substrate which is the SAM. This is the same substrate that we saw in mRNA capping video. And the acetyl group comes from its substrate acetyl coenzyme A.
You may have seen this in biochemistry when discussing metabolism. So the third modification on our list is glycosylation which is just the addition of some sugar molecule. This sugar can either be a simple monosaccharide or a complex polysaccharide. And glycosylation is involved in protein folding, protein conformation, its stability, activity, and distribution in a cell. And after phosphorylation, it is perhaps one of the most important post-translational modifications.
Let's look at an example where this is useful. In blood cells, you have membrane proteins called glycoproteins, which have sugars attached to them, and that's why they're called glycoproteins. And oftentimes, these sugars are very specifically attached, and this depends on the genes that are present in a person. And this specific form of sugar determines the ABO or AB blood group of person. And that's a very common example of glycosylation.
Similarly, glycans, which is another type of complex sugar, acts as a checkpoint in protein trafficking in the endoplasmic reticulum, and it controls the distribution of a specific protein. And if you read more on glycosylation, you may find that glycosylation is further subdivided into N, O, and C-linked glycosylation, which is just a nomenclature based on the sugar-peptide bond. Alright, so next is the ubiquitination.
which is the addition of a small protein tag known as ubiquitin. And this modification is very specific to eukaryotes, and it is responsible for the degradation of a protein. And this can occur in the context of cell growth, proliferation, or even cell death. And the idea of ubiquitination is fairly simple.
The protein gets tagged with either a single ubiquitin, or multiple of them, and then a shuttle protein comes in and attaches to it, and takes it away for degradation. And the destination of the shuttle is a proteosome, which looks like this cylindrical trash can where proteins enter from one side and bits and pieces of shredded protein comes out of the other end. And ubiquitin is usually not degraded and is recycled.
This ubiquitination is commonly used when proteins are misfolded or left unfolded and they need to be degraded. Proteins that have to be maintained in steady state levels also undergo turnover. which is usually done by ubiquitination modification. Since ubiquitination only occurs in eukaryotes, the prokaryotic analog to ubiquitin is called prokaryotic ubiquitin-like proteins.
In short, they're called pup proteins. The modification is referred to as pupillation. So essentially, just small puppies get added to proteins and those proteins get degraded. The fifth modification is the sumoillation, which is also an addition of a small protein tag.
called SUMO. SUMO stands for Small Ubiquitin-like Modifier. But unlike ubiquitin, SUMO proteins are not degradation tags.
Just a side note on SUMO tags that they are very rare compared to other modifications that we have seen. SUMOylation, despite being rare, is used to direct proteins in and out of nucleus and cytoplasm, so they're required for transport. They even regulate proteins that are involved in transcription and stress response. especially ones in the DNA damage repair. Here's a nice example of sumoilation.
In cell division, centrosomes are present in the cytosol during prophase and anaphase, and when the cell has gone through anaphase into the telophase, the nucleus is reconstructed, and the centrosomes are sumoilated at that step, and this sumo modification makes the centrosomes go into the nucleus. If they're retained in the cytoplasm, they are ubiquitin-related, and this means that the 26S proteosome trash can will simply eat them. But if they move into nucleus, the centrosomes will hide away from the proteosome, because proteosomes are not found in the nucleus, so they avoid degradation. And that's one sort of example where SUMO modifications are involved in transport of proteins and help regulate their stability. The sixth modification on our list is proteolysis, which is simply breaking off these very stable peptide bonds in a protein.
You need to break some bonds to release, let's say, signal peptides. Some precursor enzymes mature into active enzymes after cleaving a specific part of a protein. Antigen processing in immune system and signaling pathways also sometimes requires peptide bond cleavage.
Let's take a look at an example of this. Oftentimes in a cell, the endoplasmic reticulum will have ribosomes that directly synthesize a protein into the lumen of the reticulum. This is the case when insulin has to be produced. and direct translation into the endoplasmic reticulum is directed by a signal peptide in this precursor protein known as pre-proinsulin. But soon this signal peptide is cleaved off, and you end up with a protein called proinsulin.
But still, this is not ready to use protein. So some more peptide bonds are broken off, and this results in a final functional insulin protein. And the remaining peptide, known as C-peptide, is degraded off.
And you can probably guess which type of post-translation modification is required to degrade this C-peptide. The enzymes that do proteolysis are, generally speaking, known as proteases, which are further classified into serine proteases, cysteine proteases, zinc metalloproteases, and the list goes on. Here's one more example of this. Blood clots are formed when thrombin, which is a kind of protease, chops up the fibrinogen, and fibrinogen usually does not polymerize, but if it's chopped up, it can form fibrin, and fibrin can form polymers, and this forms the clot when an injury happens. Alright, on to the last modification, and this one is a bit bizarre.
This is called protein splicing, which is the removal of amino acids from a protein. And these amino acids can be a domain or a subunit that have an enzymatic activity. The concept of protein splicing is very analogous to the RNA splicing, where you have exons and introns. In proteins, you call them X-teens and intines.
And typically, there is only one intine present in a given protein. And it is very rare that proteins have intines. And intines tend to be self-splicing for the most part, and they are sometimes referred to as selfish elements.
But recent studies have shown that this may not be the case. They are usually very important for mediating stress response in response to temperature and pH changes. And a lot of DNA polymerase genes, damage repair genes, helicases have entines in them.
Most often, entines code for some sort of endonuclease, and these are like restriction enzymes. But keep in mind that protein splicing has only been observed in lower eukaryotes like yeast, and it is very common in bacteria. and entines are not found in humans at all.
Alright, now that you understand some of these post-translational modification and their functions, it should not be a surprise that defects in these modifications can result in a variety of diseases. The most obvious ones are the defects in methylation, acetylation, and phosphorylation of, let's say, a transcription factor or a proto-oncogene that can easily result in cancer. Glycosylation defects in context of immunoglobulins can impact immunity.
For instance, defects in sugar transfer to antibodies can increase the chances of HIV invasion. Liver cirrhosis is another example where defect in glycosylation is observed. Even problems associated with ubiquitination can cause diseases. For instance, a protein called survivin, which is typically marked for degradation in survivin, is responsible for cell growth and proliferation. But if it is not degraded, then it results in cancer.
And it is also linked to to some cases of ulcers and inflammatory bowel disease. Defects in proteases can result in blood clotting problems and even diabetes if insulin cannot be processed from its precursor. There are of course many other examples and cases, but this summary video should provide you with a fairly decent idea of post-translational modifications. And that is it for this particular video.
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