Introduction to Protein-Ligand Interactions

in this video, we're going to begin our introduction to protein ligand interactions by starting off with the basics. So first, what exactly is a ligand? Well, a lie again is really just any small substance that can reverse obl e bind and form a complex with a larger bio molecule. And this larger bio molecule here, in most cases is just going to be a protein. And so it's important to note that moving forward and our course proteins were going to represent what the capital letter p and lie Gans. We're going to represent what? The capital letter l and so this reversible binding of a protein too. It's like and is really described by the simple expression shown right here and notice that we have the same exact simple expression shown down below for protein like and interactions. And so we can see that the free protein here can associate with the free ligand toe form the protein Ligon complex, which we're going to abbreviate with pl moving forward. And we can tell that this interaction here is a reversible one because we have these equilibrium arrows here, which means that once the protein, leg and complex forms. It's also capable of dissociating backwards toe form, the free protein and the free ligand all over again. And so what you might notice is that this protein, like in interaction, looks kind of familiar. And that's because it really does resemble the enzyme substrate interaction that we talked about in our previous lesson videos, where we know that the free enzyme can associate with the free substrate to form the enzyme substrate complex. And this is also a reversible process, just like the protein like in interactions. And so really, the main difference between these protein ligand interactions and the enzyme substrate interactions is that the enzyme in the enzyme substrate interaction is catalyzing a reaction, which means that ultimately this substrate we know is going to be converted into a product, whereas this is not the case with protein ligand interactions. When it comes to protein Liggan interactions, the lie again just binds to the protein. But the protein is not going to convert the lie again into a product. And so one thing that we do want to be careful of is not to confuse the P here that we have for protein with the P that we used in our previous lesson videos for product. And so now that we understand the basics of protein leg in interactions later in our course, we'll be able to talk about how these protein leg in interactions can be biologically relevant. But for now, this concludes the basics, and in our next listen video, we'll talk about the rate constants that apply, So I'll see you guys in that video.

So now that we've introduced the basics of protein like an interactions in this video, we're going to talk about protein like an rate constants. And so we already know from way back in our previous lesson videos that every single reaction has a rate constant that we abbreviate with lower case letter K, which indicates the reaction rate, efficiency and probability under set conditions. And so, of course, we already know that the higher the value of the rate constant K, the more likely it is that the reaction is going to be faster and again. Every single reaction has a rate constant K, including the reactions that form and break down the protein like and complex. And so the rate constant for the free protein and Free Ligand Association into the protein like and complex is referred to as just the association rate constant and is abbreviated as just k A, where the A here represents association and so down below. What we can see is that the free protein can associate with the free like an via this Ford reaction here to form the protein like in complex via the association rate, constant K A and of course, the opposite rate constant is going to be the rate constant for the protein, leg and complex dissociation backwards into the free protein and free ligand. And this dissociation rate constant is referred to as just the dissociation rate constant and is abbreviated as K D, where the D here represents dissociation and so down below. We can see that the protein leg in complex can indeed associate backwards via this dissociation rate constant K d to form the free leg in and free protein. And so really, what's important to note here is that the ratios of these rate constants K a N k d. Can actually describe the reversible binding of a protein and enough like an And so the ratios of K and K D are going to be very, very important to biochemists, that air studying the reversible binding of a protein and a lagging and so down below, over here. What you can see is that we're showing you the two different ratios for the K in the K D. The first ratio is just going to be the K A over the K d. And of course, the second ratio is just going to be the reciprocal, which is going to be the K D over the K A. And so we'll be able to get more and more practice with these reciprocal as we move forward in our course. And so what I want you guys to take note now is that these rate constants K A and K D are using the lower case letter K. And so this is going to be different than the K and K D that we cover later in our course, which use the uppercase letter for K. And so we'll talk Maura, about this distinction when we talk about the upper case K and upper case K d. Later in our course. But for now, this concludes our introduction to protein, leg and rate constants, and we'll be able to get a little bit of practice in our next couple of videos, so I'll see you guys there.