Introduction to Protein-Ligand Interactions - Video Tutorials & Practice Problems
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Introduction to Protein-Ligand Interactions
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Video transcript
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 ligand is really just any small substance that can bind and form a complex with a larger biomolecule. And this larger biomolecule here, in most cases is just going to be a protein. And so it's important to note that moving forward in our course, proteins we're going to represent with the capital letter P, and ligands we're going to represent with the capital letter L. And so this reversible binding of a protein to its ligand 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 ligand an interactions. And so we can see that the free protein here can associate with the free ligand to form the protein ligand 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 ligand complex forms, it's also capable of dissociating backwards to form the free protein and the free ligand all over again. And so what you might notice is that this protein ligand 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 ligand 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 ligand interactions, the ligand just binds to the protein but the protein is not going to convert the ligand into a product. And so one thing that we do wanna 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 Ligand Interactions, later in our course we'll be able to talk about how these Protein Ligand Interactions can be biologically relevant. But for now this concludes the basics, and in our next lesson video we'll talk about the rate constants that apply. So, I'll see you guys in that video.
2
concept
Introduction to Protein-Ligand Interactions
Video duration:
3m
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Video transcript
So now that we've introduced the basics of protein ligand interactions, in this video we're going to talk about protein ligand 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 the 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 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 ligand complex. And so the rate constant for the free protein and free ligand association into the protein ligand 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 ligand via this forward reaction here to form the protein ligand 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 ligand 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 ligand complex can indeed dissociate backwards via this, dissociation rate constant k d to form the free ligand and free protein. And so really what's important to note here is that the ratios of these rate constants k a and k d can actually describe the reversible binding of a protein and a ligand. And so the ratios of k a and k d are going to be very very important to biochemists that are studying the reversible binding of a protein and a ligand. And so down below over here, what you can see is that we're showing you the 2 different ratios for the k a and 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 KD over the K a. And so, we'll be able to get more and more practice with these reciprocals 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 a and k d that we cover later in our course, which use the uppercase letter for k. And so we'll talk more about this distinction when we talk about the upper case k a and upper case k d later in our course. But for now, this, concludes our introduction to protein ligand 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.
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Problem
Problem
Which of the following rate law expressions represents a protein-ligand interaction at equilibrium?
A
[PL]ka = [P][L]kd.
B
[PL][P]ka = [L]kd.
C
[L][PL]kd = [P]ka.
D
[L][P]ka = [PL]kd.
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Problem
Problem
Calculate the dissociation rate constant (kd) at equilibrium if [P] = 20 mM, [L] = 10 mM, [PL] = 5 mM, and the association rate constant (ka) = 100 mM-1s-1.