Understanding Kimotripsin: The Key Serine Protease and Its Specificity
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Introduction
In the realm of biochemistry, understanding enzymes is crucial, especially those involved in peptide bond cleavage. Kimotripsin is a prominent example of a serine protease that effectively catalyzes the cleavage of peptide bonds on the carboxy-terminal of large hydrophobic non-polar amino acids such as methionine, phenylalanine, tyrosine, and tryptophan. This article delves into the mechanism of action of Kimotripsin, focusing on its catalytic triad, specificity, and comparison with other serine proteases in our digestive system.
The Catalytic Triad: Power Behind Catalysis
The enzyme Kimotripsin possesses a unique feature known as the catalytic triad, which consists of three specific amino acid residues: aspartate, histidine, and cysteine. This triad is essential for the cleavage of peptide bonds, enabling the enzyme to break down proteins efficiently.
Mechanism of Action
The catalytic triad functions through two primary processes:
- Covalent Catalysis: In this process, the enzyme forms a transient covalent bond with the substrate, facilitating bond cleavage.
- Acid-Base Catalysis: The histidine residue acts as a base that accepts a proton from the peptide bond, increasing the electrophilicity of the carbonyl carbon and making it more susceptible to nucleophilic attack.
Together, these two catalytic mechanisms empower Kimotripsin to effectively cleave peptide bonds in specific substrates.
Specificity of Kimotripsin
Despite using the same catalytic triad as other serine proteases, Kimotripsin’s specificity arises from the unique structural features of its active site, particularly the S1 pocket.
The S1 Pocket
The S1 pocket is a hydrophobic region that accommodates the side chains of amino acids. This pocket is relatively long and deep, and it preferentially binds to non-polar and bulky hydrophobic amino acids. The specificity of Kimotripsin can be summarized as follows:
- Preferred Amino Acids: Methionine, phenylalanine, tyrosine, and tryptophan, all of which contain large hydrophobic side chains.
- Mechanism of Binding: Only amino acids with long non-polar side chains fit into this pocket without causing significant electrostatic repulsion.
The shape and hydrophobic characteristics of the S1 pocket are crucial in determining the enzyme's substrate preference.
Comparison with Other Serine Proteases
Trypsin and Elastase
In our digestive systems, Kimotripsin is not alone; two other prominent serine proteases, Trypsin and Elastase, also utilize the catalytic triad. However, each protease has distinct functions due to variations in the S1 pocket structure.
Trypsin
- Substrate Preferences: Cleaves at the carboxy end of lysine and arginine, which carry positive charges.
- Structural Features: The S1 pocket contains an aspartate residue that stabilizes the positively charged side chains of lysine and arginine, allowing specificity for these amino acids.
Elastase
- Substrate Preferences: Targets small hydrophobic amino acids such as glycine, alanine, and leucine.
- Structural Features: Contains two valine residues that narrow the S1 pocket, only allowing smaller side chains to fit and preventing larger residues from entering.
Enzyme Mechanism Variation
Although all three proteases utilize the same catalytic triad, their differences in the S1 pocket structure lead to unique specificity in the peptide bonds they cleave.
Conclusion
In summary, Kimotripsin exemplifies how structural characteristics and the catalytic triad work together to accomplish specific enzymatic functions. The enzyme’s ability to cleave peptide bonds at the carboxy end of certain hydrophobic amino acids is a direct result of its unique S1 pocket shape. By understanding the mechanisms and specificities of serine proteases like Kimotripsin, researchers can appreciate the complexity of biochemical reactions in digestion and protein metabolism.
kimot Tron is a sering protease and it has the ability to catalyze the cleavage of peptide bonds on the carboxy end of
large hydrophobic non-polar amino acids for instance kimot Trion Cleaves at the carboxy end of methionine phenol alanine
tyrosine as well as tryptophan now as we discussed previously it's the presence of the catalytic Triad inside the active
side of kyrion that actually gives it the power of catalysis gives it the ability to actually cleave those peptide
bonds so remember the catalytic Triad is basically this collection of three individual residues aspartate histadine
and cine which work together to basically promote the cleavage of those peptide bonds now the question Still
Remains what exactly gives kyrion its specificity what gives Kim trips in the ability to only cleave on the carboxy
end of specific amino acids those amino acids that contain bulky hydrophobic side chain groups now to answer this
question we actually have to study the shape of the active side the structure of that enzyme if we examine the active
side of that enzyme we're going to find something called the S1 pocket and the S1 pocket in kimat tripid is basically
that real region to which that side chain group will actually move into and if we examine the shape and structure of
the S1 pocket we're going to find that it's relatively long so relatively deep and mostly hydrophobic so non-polar and
because of that structure of the S1 pocket only those amino acids that contain side chain groups that are long
nonpolar do not have any charges will actually be able to fit into that pocket into the active side without creating
too much electric repulsion so amino acids such as methine phenol alanine tyrosine and tryptophan so once again
it's the catalytic Triad in the active side it's the presence of these three individual amino acids that give kimot
Tron its catalytic power the ability to actually catalyze the cleavage of those peptide bonds but it's this long and
narrow shape and the fact that it's mostly hydrophobic it's the shape of the S1 pocket that actually gives katriin
its specific nature its specificity to cleave only on the carboxy and of specific side chain
groups now as we discussed in our uh study of proteases we basically said there are many different types of
proteases that exist in inside our body and inside nature now so far we focused on seing proteases and we use kimot
tripson as the prototypical sering proteas but of course in our body in our digestive system for example we have
many other examples of searing proteases the question is what is the mechanism that these other seing proteases
actually Ed to cleave peptide bonds well it turns out other serum proteases also use this same catalytic Triad and what
that means is they also carry out the catalysis process by using the same exact mechanism namely Cove valent
catalysis and acidbase catalysis and two examples of other serum proteases inside our digestive system that also contain
only sering protease that utilizes this catalytic Triad in fact Tron and elastase are two other sering proteases
found in our digestive system that use this same exact catalytic Triad and therefore the same exact mechanism of
catalysis that we spoke about in the previous lecture now the question is why do we have different types of CM
proteases inside our body body and the question is what exactly differentiates tripson elastase and kimat Trion if they
have the same exact catalytic Triad well remember it's the catalytic Triad that gives the enzyme its catalytic power
that gives the protease the ability to cleave those peptide bonds but it's the shape of that active side the S1 pocket
that determines the specificity of that protease the type of eptide Bond it actually breaks and so the difference
between Kima trips and tripson and El lastas is not in the type of catalytic Triad used but it's in the shape of that
particular S1 pocket the structure of that S1 pocket as we'll see in just a moment as a result of a slight variation
in the S1 pocket of tripson and Al last days we see that these other serm proteases cleave other amino acid so all
the trips in El last days use the same mechanism so coent catalysis and acid-based catalysis which we spoke
about in the previous lecture they differ in their specificity and that has to do uh and that has to do to the fact
that there is a slight structural difference in the S1 pocket in tripson as well as alasas and let's see what
these differences are and what they result so let's begin with Trion so Tron catalyzes the cleavage of peptide bonds
on the carboxy end of Lysine and Arginine and if you recall lysine and Arginine both contain positive charges
on their side chain groups now the question is why is this true so tripson uses the same exact catalytic Triad that
kimat Trion uses but what gives this Tron the difference in specificity well if we examine the S1
pocket of tripson at the bottom of that S1 pocket we're going to see we're going to see a residue that we don't see in
the S1 pocket of Kima tripson at the bottom of the tripson S1 pocket we have a negatively chared side chain that came
from the aspartate that we see in tripson and we don't see in Kima tripson so as a result of the negatively chared
side chain of aspartate 189 that is found at the bottom of the S1 tripson pocket we see that this tripon only
Cleaves at the carboxy end of those amino acids which are long and contain a positive charge at the end and these
happen to be lysine and Arginine so if we examine the following hypothetical polypeptide we have glycine this one
here we have lysine this one here we have glycine this one we have Arginine this one and we have glycine this one
now the only ones that contain positive charges are these two amino acids and only these amino acids will be able to
actually fit into the pocket of Tron and at the end will be able to actually interact in a stabilizing manner so the
positive charges of these two side chain groups will interact with the negative charges of of the of this aspartate 189
and that and that will create a stabilizing effect it will neutralize the net charge in that space and that
will create a very stable effect so at the bottom of the active side of tripson is an aspartate residue and the negative
charge of the aspartate side chain group will stabilize those amino acids that contain side chain groups with positive
charges namely the lysine and the Arginine and so the only bonds that tripson will be able to cleave are this
Bond and this Bond here so at the carboxy end of Lysine and Arginine so we see that a very tiny
variation in the structure of the S1 pocket in tripson gives tripson uh a different specificity than that of kimat
Trion and finally let's move on to AAS days so if we examine the S1 pocket of elast days we'll see the presence of two
additional valine and valine if you recall are these small or valine molecules have these small relatively
small hydrophobic chains and notice where these two valins are positioned they're positioned opposite of each
other and they essentially play the role of blocking the majority of the bottom portion of that S1 pocket and so what
that means is when the side chain group of the amino acid moves into the S1 pocket it cannot actually occupy this
space here because this blocks as a result of the stair Kinder of the hydrophobic properties of these side
chain groups and so only those amino acids that have relatively small side chain groups and which are non-polar so
uncharged will be able to fit into this pocket and so we see that elastase Cleaves peptide bonds on the carboxy end
of small hydrophobic amino acids such as glycine valine alanine valine alanine Lucine and isoline as well as Seine so
if we have this hypothetical polypeptide chain we have glycine lysine alanine phenol alanine glycine so the only ones
which have a small hydrophobic side chain are glycine alanine as well as glycine at the end so
the only two peptide bonds that are going to be cleaved are this peptide bond so on the carboxy end of glycine as
well as this one on the carboxy end of alanine so lysine and phenol alanine are not small ones this one has a large long
one and it's positively charged although this one is is uh non-polar hydrophobic it's too large to actually fit into this
pocket because these two valins block the majority of that pocket and even though this is a glycine there's no bond
on the car boxal side and so nothing will be cleaved on this side by last days and so we see that two Valiant
residues found in the S1 pocket of el lastes block off the majority of the pocket in El lastes and this allows the
last days to only cleave small hydrophobic residues and so we see that the majority of the serum proteases
found inside our body for instance kimat Trion Tron as well as elastase although they use the same catalytic Triad to
basically catalyze the cleavage of the peptide bonds they actually differ in the types of amino acids that they
cleave types of peptide bonds that they cleave as a result of these structural differences and shapes in the S1 pockets