dihedral angle
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welcome back friends welcome to another video tutorial from somos biology in this video lecture we will be talking about dihedral angles which are also known as torsional angles okay I will talk about the dihedral angles and will also talk about the importance of dihedral angles in maintaining the protein structure especially the protein secondary structure and will also see and talk about Ramachandran plot which gives us the idea about what kind of torsional angle will ultimately fit to what type of secondary structure of the proteins so let us see the relation between torsional angles and the Ramachandran plot and protein structure so let us begin with this the idea of torsional angles of dihedral angles originated from a three dimensional space angle idea now what does that mean if you look at here the whole idea of torsional angles will talk about for the proteins or the amino acid chain which is also known as polypeptide so if you look at this polypeptide it contains 1 2 3 different amino acid chains linked with one another now if you look at here there is an in terminal of the amino acid this is the N terminal and this is the C terminal of the amino acid okay so these are the 2 different terminals that we depict here now in this case the peptide bonds are this one c o n h this will be known as the peptide bond because these are separate amino acids linked with this bond here now one thing you should look very carefully here is that this nitrogen always carry lone pair of electron as a result in a resonance property this lone pair of electron can form another bond between this C carbonyl carbon and the nitrogen so as they form this bond a partial a-side bond between carbonyl carbon and nitro previously there was on one one so now it kind of behave like two ones in between the carbonyl carbon and the nitrogen that are involved in a peptide linkage now that is called a peptide bond and as I told you if you look at here that peptide bond contains two bond characteristics so it is a it is a partially double bond character of the peptide bond it acts like partially double bonded bond now in this case this partial double bonds that
we can see and here you see the turbine e this is the alpha carbon that are placed in between now as a result of this double bond partial double bond nature of the peptide linkage this amino acids or all those molecules cannot rotate around this bond it will be unable to rotate around this partial double bond character okay because it is kind of a double bond feature it is restricted to rotate so all this amoenus is this side and this side cannot rotate on the other hand if you look here there are two other bonds that you also find one is this carbonyl carbon and C alpha carbon the bond between them this one another one is the bond between the carbonyl carbon then the nitrogen and the carbonyl term so these are the Alpha carbon sorry so these are the two bonds that we can see the Alpha carbon in the middle in the left you see the bond between nitrogen and the alpha carbon this is one type of bond and the other bond is the bond between carbonyl carbon and the Alpha carbon those are two different bonds and those bonds have specific names here the bond between the NC alpha is known as the Phi bond and the bond between C alpha C is known as the Sai bond so let me light write them here this is Phi bond this is sy bond two different bonds are there now this is up to the link and only the peptide bond but now youll see how we talk about angles in here the simple thing I can tell you about the dihedral angles is that lets begin with some structure say hydrogen if we look at the structure of hydrogen we can break it down like to two hydrogen linked with each other so there is no chance of formation of any angle or bond so to define nitrogen geom at geometry of the hydrogen what you can say is that the two hydrogen molecules they are separate by a specific distance one when you when you say the distance it defines how theyre linked and what is the total geometry so only distance is sufficient for telling the geometry of hydrogen now if you take water the structure of water says somehow like this okay so oxygen attached with
two hydrogen earlier you only say the distance and you get the geometry right but here let us say you know the distance between oxygen and water this this hydrogen and water and this hydrogen and water you know that and you are telling that distance let us say this is distance X this is y now my question is will it clear will it give you the clear view of the geometry the answer is no because distance is not enough in this case you also tale you need need to tell talk about the angle between this two hand of hydrogen linked with oxygen so this angle is required so for this three molecule content in this case C atom content actually in this case a3 they are linked you need to use to distance and one angle to get the geometry correct on the other hand if you take hydrogen peroxide for example I do not know whether I can see bottom-1 so let me draw it here so let us say now we take hydrogen peroxide h2o2 this is another molecule and four different atoms are linked now and in this case let us say we have o o h h this is what we have here okay I do not think whether you can see me but this is how the structure look like for example of hydrogen peroxide now in this case as their four point so this was a two point we only distances enough three points to distance one angle now there are four points here in this case in this four point conditions we need to talk about two different angles if you think one is here another one is here two different angles we need to talk about just if you look at the structure of peptide bond here you will find also four different points in C alpha C and these are the four different regions you will find in between okay in C alpha C in this between you will find four different points 1 2 3 4 so 4 different points are present so the similar structure here so whenever you have 4 different points and the molecule will be in the 3-dimensional shape in that case there are angles that are formed between planes instead of forming between lines because you know if I draw
a line it will be a 2 dimensional if I draw a plane 3 dimensional space so that is what we are talking about here so if I look at here I told you the angle between this two line and this 2 line but we are now calculating this as plane so lets imagine this plane this line as a plane imagine this line as another plane so what we have we have two different planes attached with one another something like that this is one plane this is another plane attached with each other like that and there will be an angle between two planes and their the angle will be known as the torsional angle a dihedral angle you can see that thing here from this the distance between NC alpha and C you will also find that and because you know in this C alpha hydrogen is attached our interest right R is the side chain hydrogen is let us to if you look at here you will find that plane you will find that four points and in each of the side this is a four point this is another four point so from that what you will find there will be two planes creating angles in this bond two more planes creating angles in this bond right so there will be two different angles one in the between the N and C alpha there two different planes creating angles known as Phi angle and on the other hand another between C alpha and C two different planes again creating another angle known as Sai so Phi angle in the Phi bond Sai angle in the Sai bond now this angles can change they can go brought narrower or broader this angle can change so this properties will be changing if you look at here those properties will change and the angles are changing distance are changing and due to the change of those angles the rotation quality will also vary the rotation quality will also change for example you say from these two different bonds the rotations are possible because they are not double bonds the single bond so rotation around that bond is possible so we have two different angles in which the rotation is possible because there will be limit to each of those angles right now how much those rotations
if it is not involved with any sort of angle formation or if its not even a three-dimensional structure then we can say it can move any place in the same plane but protein is a three-dimensional structure and we know it is not only the rotation around the bond but while it is rotating the angle is also changing because due to this angle the rotation is the rotation is defined by this angles actually okay so let us say they have a specific angle of plus 60 degree so once they have the angle of plus 60 degree the rotation will be possible up to a certain extent only and only up to that certain extent the protein structure can be stable prior to that or or let us say over that angle or if you change the angle then only the structure will be changed so for a specific angle there will be a specific way of rotation and that will give a specific structure to the peptide chain so let us say if the angle is plus 160 degree they are going to rotate at certain extent that is going to give them the idea of or the structure of beta sheet as a secondary structure okay because this Hamming asses will try to rotate they try to interact they try to form hydrogen bonds between themselves to finally produce a fully functional three-dimensional protein now how they will fold and how they those army nurses will interact that complete thing will depend on that the degree of angle and that will regulate the rotational freedom of all those bonds that will ultimately create whether that amino acid sequence having the specific degree of angles can ultimately form alpha helix or beta sheet or any loop structure okay so that is the idea of torsional angles so if you know the torsional angles it will be very important and helpful for us to identify that whether this polypeptide chain is going to form beta helix beta beta sheet or alpha helix or parallel beta hat beta sheet or anti parallel beta sheet or is it going to form a right-handed helix or a left-handed helix we can get all these ideas by looking at the torsional angles or dihedral angles because they are the same things here okay that is all about the dihedral angles
tags:
suman bhattacharjee, shomus biology, torsional angle, dihedral angle, Ramachandran plot, si and phi angle of proteins, Peptide bond, alpha helix, beta sheet,…
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