Understanding Alpha Helix Structure in Proteins

Hello everyone in this video we'll talk about alpha helix structure which is a common secondary structure of protein. If we talk about protein structure then it can be classified into four different levels. The primary structure, secondary structure, tertiary and the quaternary structure. But this video would focus on the secondary structures. Out of the secondary structures we have alpha helices, beta turns and beta pleated sheet. But today's focus would be totally on alpha helix, its structure, its function, where we find them and how we can study the structure of alpha helix and the factors that stabilize it. So this video is all about that. If you haven't yet subscribed to my channel hit that subscribe button and stay tuned till the end of this video. First of all let's try to understand where do we find alpha helix structures. It can be found in many proteins such as proteins that are receptors and very common example is G protein couple receptor. It has seven transmembrane domain and each transmembrane domain is alpha helix spanning a 10 to 12 amino acid residues. Many transcription factors such as which contains leucine zipper motif that is also an example of alpha helix. So many transcription factor, receptor, ion channels. and many other molecules might have alpha helix confirmation. Now let us try to understand how we can study and gain the information about alpha helix. First we have to start with X-ray crystallography which begins with crystallization of the protein then there is X-ray crystallographic method where we obtain a diffraction pattern while we pass X-ray sample through this crystal. From this diffraction pattern we can convert it into frequency domain to get the electron density map. After Fourier transformation we get this electron density map. Once we get the electron density map it's like the overall outline of a puzzle. And we have to fit our molecule of interest and start building model of it. And ultimately that model might give rise to the protein structure or structure of any molecule. So this is the overall workflow of extra crystallography by which we can understand the protein structure. If you want to know more about extra crystallography click the link in the i button. So the biggest feature of alpha helix is that helix and it was found by Pauling and colleagues around 1940. So alpha helical structure has amino acid in specific orientation. and obviously you can understand the orientation is a helix fashion where four I mean almost four amino acids are there per term 3.6 to be precise so alpha helix has 3.6 residues per turn of the helix all of these residues that are present in the alpha helix are bonded or interacting with each other via al via hydrogen bonding and this hydrogen bonding does not take place in a haphazard manner and there are certain rules that are governing which residues would form hydrogen bonding. Before coming to that rule we should understand that from a scattered structure of protein that means the primary structure making a geometrical structure like helix is a long process it requires a lot of planning organization to make such of geometrically organized structure. So there must be some rule which is governing these interaction which helps to stabilize these kind of helical structures. Let us understand this rule. There is a rule in hydrogen bonding which is ensuring this helical structure is stabilized. Let's imagine a particular amino acid from the N-terbitus and we name it I. Then the next one would be I plus one After that there would be I plus 2, I plus 3 and I plus 4. It turns out the hydrogen bond would be formed between I and I plus 4 amino acid. So the carboxyl group of I and the NH group of the I plus 4 amino acid would form hydrogen bond with each other. Irrespective of the position, this kind of rule is valid throughout the helix. Now let us talk about few special cases when helix is forming. Specific residues such as glutamate are good for helix formation but if glutamate residues are they're in repetition then it might be bad because glutamate residues at pH 7 has negative charges and these negative charges could cause strong electrostatic repulsion and thereby destabilizing the helix. The same goes for the basic amino acids which are lysine or arginine. They are positively charged in pH 7. That is why they can also undergo electrostatic repulsion if they are very close to each other. But if they are dispersed throughout the structure, it might not be a problem. It would be actually favorable in terms of helix formation. Other amino acids such as proline is also termed as helix breaker. Because once proline is present in a secondary structure, it would create a tilt in the secondary structure as you can see here. and the amide hydrogen of proline cannot be contributed, cannot be used to make hydrogen bonds and proline side chain interferes sterically with the backbone and that is why it leads to a tilt of 30 degree corresponding to the helix axis. So obviously we can understand if we have a Proline residue in the secondary structure, it would be ultra destable. It would be destabilizing the helix. So that is why proline is known as helix breaker. Residues in an alpha helix typically adopt specific dihedral angles. And these dihedral angles are really important to define a particular structural characteristics. And the map of dihedral angle is basically the Ramachandran plot. In this Ramachandran plot, this helix falls around minus 60 to minus 45 phi and psi angles. So helix would be corresponding to this particular region and there are different regions for other particular secondary structures such as beta pleated sheet or right-handed or left-handed helix. Coming to the helix sense, helix could be right-handed or left-handed. Right-handed helix are the most common ones found in biological system. It's very easy to understand right-handed helix. Try to point your thumb towards the helix axis and your curled fingers direction would tell you the sense of the helix. Now alpha helix which is left which has a left helicity or a right helicity would be found in different locations in a Ramachandran plot as depicted here. Also, there are helix propensities. That means the probability of an amino acid to be found in a particular helix. This governs many factors. I mean, that means which of these amino acids might be incorporated to form a helix structure. Amino acids like alanine, leucine, methionine are helix makers. That means if these amino acids are present in a protein sequence they would readily form alpha helical structures. Whereas other amino acids such as glycine and proline are known as helix breakers. They break the helix but they are very good in terms of beta turn. That is why helix propensity index tells us by a particular score that what is the probability that one particular amino acid would form a helix. Now let me tell you these alpha helix structures have a peptide, lot of peptide bonds and each peptide bond might have slightly dipole, dipole interaction among them. So alpha helix acquires a net positive charge in one side and negative charge in other side due to dipole interaction. And these charges need to be neutralized in order to gain stability and this is done by specifically negatively charged residues in the N-terminus and positively charged residues in the C-terminus positively charged residues such as arginine and lysine would help to neutralize the net negative charge whereas negatively charged amino acid would help to neutralize the partial positive charge due to dipole and this ensures the helix becomes stable. So let's just summarize the factors which are affecting helix stability. First of all electrostatic repulsion, second bulkiness of adjacent R groups of amino acids, hydrogen bonding between I and I plus 4 amino acid is absolutely crucial. Presence of proline or glycine really destabilize the helix. So these are helix breakers. And lastly interaction between amino acids and the residues at the end determines the helical stability. So the alpha helical structure can be studied nicely with extra crystallography and this is the best way of studying protein structure because high resolution protein structures can be obtained from this methodology. But other than that there are very quick and easier ways to gain information about protein secondary structure such as circular dichroism spectroscopy. If you need detailed information about any of these topics you can click on the link in the i button. Now circular dichroism spectroscopy gives us a specific signature of several secondary structures. In fact circular dichroism spectroscopy is a best method to study secondary structural changes. For example alpha helix, beta plated sheet or random coils would have a characteristic signature in a circular dichroism spectra. Now let's say we have an unknown protein and we would try to plot that unknown protein in this particular graph and we would see it would match with which particular structure. In this case you can see in the blue broken line it's our unknown protein and it is kind of overlapping with the alpha helical structure. So we can conclude that majority of the secondary structure present in this protein would be alpha helix. Coming to our next example that if we take another protein and plot its series spectra Look at it. It kind of match with the beta pleated sheet signature. That means this particular protein might have majority of beta pleated sheet in its structure. So these kind of nitty-gritty details about secondary structures can be obtained with the help of circular dichroism spectroscopy. But other than these two techniques there is a recent development of cryo electron microscopy which can tell us more about protein structure but what is really different about all of these techniques is the resolution the highest resolution can be obtained by extra crystallography whereas circular dichroism spectroscopy is not it can give information about protein secondary structure but it does not tell us about the high resolution structure whereas cryo electron microscopy is kind of high resolution but not as much as extra crystallography. So with that we had learned quite a lot in this particular video. We talked about the structure of alpha helix, the integrated details of it, factors that affect helix stability and ultimately we learned the techniques by which we can study alpha helix structure. So I hope this video was helpful and informative to you. If you like this video give it a big thumbs up, don't forget to like share and subscribe and you can also get my courses in unacademy which is Biggest learning platform in India use my code AP10 to get a 10% discount and do let me know in the comment How you like my videos? Thank you guys

But this video would focus on the secondary structures. Out of the secondary structures we have alpha helices, beta turns and beta pleated sheet. But today's focus would be totally on alpha helix, its structure, its function, where we find them and how we can study the structure of alpha helix and the factors that stabilize it.

So this video is all about that. If you haven't yet subscribed to my channel hit that subscribe button and stay tuned till the end of this video. First of all let's try to understand where do we find alpha helix structures.

It can be found in many proteins such as proteins that are receptors and very common example is G protein couple receptor. It has seven transmembrane domain and each transmembrane domain is alpha helix spanning a 10 to 12 amino acid residues. Many transcription factors such as which contains leucine zipper motif that is also an example of alpha helix. So many transcription factor, receptor, ion channels.

and many other molecules might have alpha helix confirmation. Now let us try to understand how we can study and gain the information about alpha helix. First we have to start with X-ray crystallography which begins with crystallization of the protein then there is X-ray crystallographic method where we obtain a diffraction pattern while we pass X-ray sample through this crystal.

From this diffraction pattern we can convert it into frequency domain to get the electron density map. After Fourier transformation we get this electron density map. Once we get the electron density map it's like the overall outline of a puzzle.

And we have to fit our molecule of interest and start building model of it. And ultimately that model might give rise to the protein structure or structure of any molecule. So this is the overall workflow of extra crystallography by which we can understand the protein structure.

If you want to know more about extra crystallography click the link in the i button. So the biggest feature of alpha helix is that helix and it was found by Pauling and colleagues around 1940. So alpha helical structure has amino acid in specific orientation. and obviously you can understand the orientation is a helix fashion where four I mean almost four amino acids are there per term 3.6 to be precise so alpha helix has 3.6 residues per turn of the helix all of these residues that are present in the alpha helix are bonded or interacting with each other via al via hydrogen bonding and this hydrogen bonding does not take place in a haphazard manner and there are certain rules that are governing which residues would form hydrogen bonding.

Before coming to that rule we should understand that from a scattered structure of protein that means the primary structure making a geometrical structure like helix is a long process it requires a lot of planning organization to make such of geometrically organized structure. So there must be some rule which is governing these interaction which helps to stabilize these kind of helical structures. Let us understand this rule. There is a rule in hydrogen bonding which is ensuring this helical structure is stabilized.

Let's imagine a particular amino acid from the N-terbitus and we name it I. Then the next one would be I plus one After that there would be I plus 2, I plus 3 and I plus 4. It turns out the hydrogen bond would be formed between I and I plus 4 amino acid. So the carboxyl group of I and the NH group of the I plus 4 amino acid would form hydrogen bond with each other.

Irrespective of the position, this kind of rule is valid throughout the helix. Now let us talk about few special cases when helix is forming. Specific residues such as glutamate are good for helix formation but if glutamate residues are they're in repetition then it might be bad because glutamate residues at pH 7 has negative charges and these negative charges could cause strong electrostatic repulsion and thereby destabilizing the helix. The same goes for the basic amino acids which are lysine or arginine. They are positively charged in pH 7. That is why they can also undergo electrostatic repulsion if they are very close to each other.

But if they are dispersed throughout the structure, it might not be a problem. It would be actually favorable in terms of helix formation. Other amino acids such as proline is also termed as helix breaker. Because once proline is present in a secondary structure, it would create a tilt in the secondary structure as you can see here.

and the amide hydrogen of proline cannot be contributed, cannot be used to make hydrogen bonds and proline side chain interferes sterically with the backbone and that is why it leads to a tilt of 30 degree corresponding to the helix axis. So obviously we can understand if we have a Proline residue in the secondary structure, it would be ultra destable. It would be destabilizing the helix.

So that is why proline is known as helix breaker. Residues in an alpha helix typically adopt specific dihedral angles. And these dihedral angles are really important to define a particular structural characteristics.

And the map of dihedral angle is basically the Ramachandran plot. In this Ramachandran plot, this helix falls around minus 60 to minus 45 phi and psi angles. So helix would be corresponding to this particular region and there are different regions for other particular secondary structures such as beta pleated sheet or right-handed or left-handed helix. Coming to the helix sense, helix could be right-handed or left-handed.

Right-handed helix are the most common ones found in biological system. It's very easy to understand right-handed helix. Try to point your thumb towards the helix axis and your curled fingers direction would tell you the sense of the helix.

Now alpha helix which is left which has a left helicity or a right helicity would be found in different locations in a Ramachandran plot as depicted here. Also, there are helix propensities. That means the probability of an amino acid to be found in a particular helix.

This governs many factors. I mean, that means which of these amino acids might be incorporated to form a helix structure. Amino acids like alanine, leucine, methionine are helix makers.

That means if these amino acids are present in a protein sequence they would readily form alpha helical structures. Whereas other amino acids such as glycine and proline are known as helix breakers. They break the helix but they are very good in terms of beta turn.

That is why helix propensity index tells us by a particular score that what is the probability that one particular amino acid would form a helix. Now let me tell you these alpha helix structures have a peptide, lot of peptide bonds and each peptide bond might have slightly dipole, dipole interaction among them. So alpha helix acquires a net positive charge in one side and negative charge in other side due to dipole interaction.

And these charges need to be neutralized in order to gain stability and this is done by specifically negatively charged residues in the N-terminus and positively charged residues in the C-terminus positively charged residues such as arginine and lysine would help to neutralize the net negative charge whereas negatively charged amino acid would help to neutralize the partial positive charge due to dipole and this ensures the helix becomes stable. So let's just summarize the factors which are affecting helix stability. First of all electrostatic repulsion, second bulkiness of adjacent R groups of amino acids, hydrogen bonding between I and I plus 4 amino acid is absolutely crucial.

Presence of proline or glycine really destabilize the helix. So these are helix breakers. And lastly interaction between amino acids and the residues at the end determines the helical stability.

So the alpha helical structure can be studied nicely with extra crystallography and this is the best way of studying protein structure because high resolution protein structures can be obtained from this methodology. But other than that there are very quick and easier ways to gain information about protein secondary structure such as circular dichroism spectroscopy. If you need detailed information about any of these topics you can click on the link in the i button. Now circular dichroism spectroscopy gives us a specific signature of several secondary structures.

In fact circular dichroism spectroscopy is a best method to study secondary structural changes. For example alpha helix, beta plated sheet or random coils would have a characteristic signature in a circular dichroism spectra. Now let's say we have an unknown protein and we would try to plot that unknown protein in this particular graph and we would see it would match with which particular structure. In this case you can see in the blue broken line it's our unknown protein and it is kind of overlapping with the alpha helical structure.

So we can conclude that majority of the secondary structure present in this protein would be alpha helix. Coming to our next example that if we take another protein and plot its series spectra Look at it. It kind of match with the beta pleated sheet signature.

That means this particular protein might have majority of beta pleated sheet in its structure. So these kind of nitty-gritty details about secondary structures can be obtained with the help of circular dichroism spectroscopy. But other than these two techniques there is a recent development of cryo electron microscopy which can tell us more about protein structure but what is really different about all of these techniques is the resolution the highest resolution can be obtained by extra crystallography whereas circular dichroism spectroscopy is not it can give information about protein secondary structure but it does not tell us about the high resolution structure whereas cryo electron microscopy is kind of high resolution but not as much as extra crystallography. So with that we had learned quite a lot in this particular video.

We talked about the structure of alpha helix, the integrated details of it, factors that affect helix stability and ultimately we learned the techniques by which we can study alpha helix structure. So I hope this video was helpful and informative to you. If you like this video give it a big thumbs up, don't forget to like share and subscribe and you can also get my courses in unacademy which is Biggest learning platform in India use my code AP10 to get a 10% discount and do let me know in the comment How you like my videos?

Thank you guys

Transcript for:Understanding Alpha Helix Structure in Proteins

Transcript for:
Understanding Alpha Helix Structure in Proteins