 everyone, also if you're watching it on YouTube. One of the things that I've decided actually is that I'm not gonna cut the videos anymore for Moodle and I'm just gonna put them on YouTube and since the recordings are available for two weeks here on Twitch and you can watch them there, it takes me a lot of time to recode everything. I have to use some weird program for it and that it just takes me like three hours of my time to recode it for Moodle because Moodle has like this 500mb upload limit. So I'm really not wanting to spend three hours every week to just cut the lectures for you guys on Moodle. It's not that I don't want to and if you really want me to then I will do it but I think that since they are available here on Twitch and they are available on YouTube it makes no sense to waste three hours waiting for the stupid program that kind of burns up my CPU the whole time. So just as a note to you guys. Alright so we talked a little bit about history and about how well being a type one or type two diabetic would be an automatic death sentence only like 120 years ago and it's a very amazing discovery so not only insulin of course but the whole protein field is amazing and what we've been able to discover in the last 100 years. Alright so first I want to use some nomenclature right so just to know what we're talking about so an amino acid is a building block and there will be like more talks about amino acids and stuff but an amino acid is a single little molecule which is used in the building of a polypeptide. So a polypeptide is a chain of several amino acids so if I have a single chain of amino acids coupled together or more or less fused together then this is called a polypeptide. We then have something which is called an apoprotein so an apoprotein is one or more polypeptides which are more or less held together by several forces and we will discuss which forces those are but there is no cofactor so and a cofactor is generally a molecule which is not a biomolecule so it can be a zinc atom or an iron atom or something else but so an apoprotein is a non-functioning protein because it doesn't have the cofactor so it doesn't have the zinc molecule which causes the charge or it doesn't have the iron molecule able to bind oxygen and a protein is then defined as an apoprotein with its cofactors so with the zinc molecule or with the iron molecule so just that we got that clear and I will be using apoprotein and protein and polypeptide interchangeably but they are different so just as a warning that I probably am going to mess it up horribly during the whole lecture but when we talk about nomenclature the amino acid is the single building block the polypeptide is a chain the apoprotein is one or more polypeptides with no cofactor and the protein or when you talk about proteins then it means apoproteins with their cofactors included all right so amino acids are alpha amino carboxylic acid and here we see three of them or actually two of them and the general structure of a amino acid so an amino acid is two carbon atoms and an amino group on the one side and and carboxylic acid group on the other side so here we see these the C00 and the OH and of course when you dissolve an amino acid for example like glycine and you put it in water and then the H falls off so there's a slight negative charge on this side of the amino acid and there's a slight positive charge because the amino acid itself is more or less uncharged so this becomes more or less NH3 with one positive charge and this becomes COO with a small negative charge so amino acids are chiral which means that they have a left form and a right form and this is because of the R group here so if you have glycine right you can turn glycine into alanine by instead of having a hydrogen on this side having a CH3 group right so the R here is a carbon atom with three hydrogen atoms coupled to the alpha amino to the alpha carbon so this is called the alpha carbon and the alpha carbon is the thing that we always use so the alpha carbon is the one which has the side chain on it so all amino acids are chiral except for glycine because glycine has a hydrogen on one side and a hydrogen on the other side meaning that no matter how you turn it it will always look the same but if we for example take alanine then alanine has a very specific 3d structure meaning that we can have an L shape and we can have a D shape so and we can have a left and a right kind of handed alanine molecule and these two are different from each other not when it comes to the amount of atoms that they have but they are different from each other based on how they can interact with their environment so there are around 500 different amino acids which are found in nature so we always talk about 26 essential amino acids but there are many many different amino acids some of them are only produced by certain bacterias but you have to remember that almost all naturally occurring amino acids are in the L form and that is very important when you think about about medicine or for example insulin right if you would build insulin from D amino acids instead of L amino acids it would not function these the same because it cannot bind to for example the receptor anymore because the side chains are just pointing in the wrong direction so amino acid is a very simple structure it's two C atoms a nitrogen atom and one part is an acid and the other part is more or less a a base and together of course it's uncharged except for when you have a charged side group but the side group can be literally anything so about chirality and this is more or less one of the best pictures that I could find that explains what chirality is right so here we see just the the alpha or the the main C atom right and here we have then the acid group here we have the amino group here we have the side chain and here we have the hydrogen and no matter how you turn this one you can never make a right one out of it so this is a left one and this is a right one and the best way to think about this is to kind of imagine turning this one right and if you would turn this one then as soon as this as as you would turn it head then then it would flip around so that it's a it's a stereo thing right it's like a putting a mirror and the mirror image left in the mirror image is right for you and and right for the mirror image is left for you and chirality is a difficult subject because like chirality is difficult to understand but I think that if you think about a mirror standing in front of a mirror then chirality can be explained as when you raise your left hand then the mirror image actually raises its right hand so from from the perspective of the mirror so chirality is very important in amino acids because like I said naturally occurring amino acids all have the left handed shape form um while we can also chemically synthesize the amino acids but generally L amino acids are very beneficial because when you make a a medicine and then the medicine needs to be in the L form for your body to kind of hook on to the molecule to have a proper binding and generally the D form of amino acids are very very toxic because your your body can't handle it and it it will not bind to the thing that you think it binds to so chirality is very important when synthesizing method medicine so in total there are 21 more or less essential amino acids which occur in almost any living creature without these 21 um you're gonna have a very bad time and we divide amino acids into very different groups so um the groups are of course based on the side chain and the side chain coupled to the standard more or less amino structure right so we can have for example electrically charged side chain so um we can have positive charge where we for example have the R group being something like this so we see the amino acid right and this is then the at this little thing is normally where you would write the R group so here we have the alpha carbon here we have the other carbon for the um for the acid group here we have the amino for the for the base group and then here we have the side chain and if this side chain carries a positive charge then it is a positively charged side chain and some examples of these are arganine histidine and lysine so the arganine histidine and lysine molecules are a are a are positively charged side chains we also have amino acids which have a negative side chain like aspartic acid or glutamaic acid and these have a negative charge it's just the way that it is all right i saw that testosterone redeemed a digital sketch that's really nice so you saved up two thousand points um what do you want me to sketch for you because of course like i need to have a topic to sketch so we're going to take like five minutes and i'm going to do a a guinea pig oh my god that's that's one of the hardest things to sketchy as well i'm so bad at sketching animals i knew it i knew it i knew it all right so it's drawing time all right let me actually show you guys the drawing so um let's see where the pen is and let's just remove what we have so you want to have a guinea pig a guinea pig is really really hard let's let's just start off with drawing some eyes right so if you have some eyes then at least that that's something that we have a guinea pig all right then a guinea pig has a very distinct head shape and it has a very distinct nose and mouth as well all right so guinea pig looks like this because it has this little pig nose otherwise it's not a guinea pig and of course yeah it has big teeth so let's give it at least some big teeth it starts looking like a beaver a little bit like that's that's not really what i wanted to um but yeah it's a chewing animal right so sort of big teeth are something that we we definitely want to have all right then they're very furry right so we have to have a lot of fur um for the guinea pig oh my god this is gonna be so bad do guinea pigs actually have whiskers i think they do right so they probably have like these big whiskers um like a like a rat or a or a this is so terrible i know i know i was it was fire oh my god yeah it's gonna be a horrible guinea pig but at least the guinea pig like it has like things like this right and uh i want to offer 2.7k for no guinea pig poor guinea pig poor guinea pig all right so it looks kind of like this right and it's very very furry and fluffy and they have different shapes and does it have a tail does a guinea pig have a tail that's a good question i don't know um at least it has feet so no it doesn't have a tail how do you mean it doesn't have a tail like i thought all animals except humans have tails you see them every day in rim yeah but the rimworld guinea pigs are very stylized right so let's give it some feet as well and then uh so what is a very very uh pick the nose a little bit bigger and then we do like a little bit more fur i had guinea pigs yeah i think that everyone had guinea pigs when they were younger right and uh everyone probably killed like one or two guinea pigs by dropping them they're very sensitive to being dropped even from like small heights they they don't survive that um if you are set a tail you definitely had no guinea pig definitely not a pigtail though yeah we can give it a little pigtail just so that it's like a guinea pig right all right so then uh and a guinea pig is often found in cages right because they they you shouldn't let your guinea pig just run wild so let's just do a little cage structure around the guinea pig so that it has somewhere to live uh of course we want to do something like this right and like and we make a nice nice cage for the guinea pig and then we can also hide some of the the horrible mistakes all right good so let's do something like this and then we have a guinea pig in a box and it's uh it's very small yeah guinea pigs are pretty small all right so and then of course because it's a very wild animal it needs to have like cages right so like these bars so that it cannot escape so that we can just have it like this just make sure that we hide part of the figure just by having some like metal bar so that it's behind it and of course like when you're drawing you should actually draw from the front to the back ghoul says no tail yeah no we figured that out but i gave it a little pigtail so that you can see that it's a guinea pig oh all right so this is this is this is definitely worth your two thousand denny bucks that you spend on this stuff this all right drawing time i love drawing shit makes you really think about what you want to draw but uh yeah starting off with a guinea pig is really really hard i'd hope for someone to just come and say like oh draw me a tree um so let's give it some blue eyes right so blue eyed guinea pig and then make uh make a little bit of more color of it so like let's do that like this because they're generally like brownish right so and uh guinea pig very good very good and then of course we don't want to do the teeth to do this so like there's a little bit of color so they are a little bit brownish and they are this is the worst guinea pig ever where's the carrot yeah that's a good one because guinea pigs eat carrots right so we can just have like a carrot on the side um so let's put that here and uh in the thing so let's just have a carrot which looks like this and then carrot of course have some green additional leaves so let's make some green leaves for the carrot and of course it needs to have like a feeding tray or something like that for the water so we just put a like thing here on the side so that it has water and and of course there's this little funnel so that it can drink from it and let's put some water in as well can have like a guinea pig there needs to be Anna's hand because she wants to pet it well I don't think that anyone actually wants to pet a guinea pig like this you paid for a guinea pig all right so what do you think guys is this a beautiful guinea pig or not it it has all of the features a guinea pig needs um like it has the eyes of a guinea pig like um we can actually make the eyes a little bit reddish because they are kind of crazy ish right so we can have like a little bit crazy guinea pig perfect looks more like Frankenstein kitty poor thing it's something yes yes I definitely agree next time a panda please well if you save up 2000 points um it looks like a caged bee yeah although bee doesn't have whiskers right so at least it has whiskers and it has the the pigtail so we can actually make like a very orangey pigtail on the back um so let me get like a real pig color so we have like a really nice guinea pig tail all right I'm hope you're happy testes out is like uh you're the first one 2000 denny bucks here's your beautiful guinea pig I'll actually sign it as well so that that you know that that I made it live for you on stream all right so I'll just sign it using my normal signature and uh there you go and it is uh 2021 right so it's uh and and let's write down that it's a guinea pig as well so guinea pig good good good good good good all right so that's your drawing are you proud I'm proud I'm proud like I love drawing so it's good to have you guys force me to draw a little bit all right so amino acids right so amino acids come in different groups so the first group group number a is amino acids with an electric electrically charged side chain eb positive be it negative the next group of amino acids is group number b which have polar uncharged side chains so polar means that they are more or less hydrophilic right so these amino acids are very good at dissolving in water and this is because they have these OH groups which actually make them able to make hydrogen bonds and so polar uncharged side chains they don't have a charge but they are very good with a reacting with water um then we have some special cases so some special cases are for example cysteine and cylate no cysteine and these are very special because these have this um um sulfur atom and the sulfur atom allows them to make bindings to each other what a waste of time you mean the drawing the drawing is not a waste of time drawings are all wait there's always time for a nice drawing so the the the the s group so the s molecules the um the sulfur molecules they allow to bind so they can make a bridge so a sulfur bridge which allows two peptide chains to kind of be coupled together so they are causing two chains to kind of bind to them and be um connected to each other um we have here one which is glycine glycine is a little bit special because it has a relatively uh high high p k a um and it just has an n h2 um it has no it has no side group right so it's just the amino acid without any side group so glycine only one which is not affected by stereochemistry um which means that the left and the right molecule are the same and then we have proline and proline is a little bit different because we see here that we have the carbon atom right then we have the side chain actually folding back on the amino group so the nice thing about proline is is that it's flat so it's kind of a flat surface so if you think about proteins as being a um as being like a more or less molecular crane or a molecular um machine then the proline is kind of what gives it a plane to orient on right so proline because it's a flat uh amino acid it it it's just something that other amino acids can more or less orient itself towards so those are special cases um of course we have of course also the opposite of the um un polar uncharged side chains which are the hydrophilic side chains we also have a lot of amino acids which have hydrophobic side chains and of course these ones are generally so the the polar un uncharged side chains are generally found on the outside of proteins because they interact with water and these ones the hydrophobic side chains are generally found within the protein so if you think about a protein as being like a globule like a ball then the outside of the ball is hydrophilic and because it needs to be dissolved in water while the inside of the ball generally is made out of hydrophobic side chains there's many different ways of of defining different groups within the amino acids but the alanine and all of these like tryptophan and they are hydrophobic which means that they don't like water which means that they are generally found in the inside and of course the different side chains they they have their own function and they they make it so that you can mix and match them like lego blocks and then build up something which is a very useful protein all right so that's all I wanted to say about amino acids so for the exam remember that there are four different types of amino acids they are charged and charged of course comes in two types then we have the hydrophilic we have the hydrophobic and then we have the special cases and the special cases are mostly the cysteine so the the s group here which allows you to couple multiple chains multiple polypeptides together into a single molecule so polypeptides are amino acids which are chained together using peptide bonds and if you would write them down then they are always written down from the n-terminus at the left to the c-terminus at the right right so we we write them down we start off with the first amino acid from the n-terminus and so here we can see that we have a ch3 side group and then you can see that the that the acid of the first amino acid is coupled to the um amino group of the second one and then we have the second side chain and then the same thing and these are called peptide bonds so um amino acids are coupled together using peptide bonds to form a polypeptide so it's very comparable to dna where we write down the amino acids from the n to the c-terminus in dna we always write from five prime to three prime and that's just the way that we kind of determine it however in uh proteins we can have two cysteines right so two of these ones which have um a sulfur group and these can form disulfide bonds so two sulfur groups can more or less couple together and what happens is that then the primary structure is not a single flat um or a single line of of of amino acids anymore right so if we would write down here we see oxytocin which is the the happy molecule if you would write down the primary structure of cytotoxin not cytotoxin but oxytocin if you would write it down we start at the n-terminus and at the c-terminus but because these two cysteines in the molecule coupled together using this disulfide bond so two sulfur molecules coupling together this is how you write down the structure so the structure is not like dna or rna where you just write atc gg atc now the primary structure already has a little bit of a a wiggle or some other things in there and this is because of the two cysteine bonds um and so oxytocin happy molecule hey it has like a couple of amino acids um but there is this double this disulfide bond which makes the primary structure not a singular kind of linear thing but it it has this little hump in there so when we talk about the primary structure of insulin for example this molecule which is massively important um is that if we have disulfide bonds it it's possible not only that it's forming bonds within a single peptide but a disulfide bond can also join two polypeptides and then we have a very complex primary structure already right so what we see here is we see that we write it down from the n-terminus to the c-terminus so this is the first the alpha chain of um insulin this is the beta chain of of insulin they they are different right they are just two different polypeptides which come together but because of these bridges right so you see that here there's a disulfide bond between the cysteine of the alpha chain and another cysteine of the alpha chain but the second cysteine here can couple to the beta chain and the same thing here so at the primary structure of insulin if you would write it down on paper you would have to write down that there are two chains right that these chains have disulfide bonds and then of course both of these chains are written down from n-terminus to c-terminus but the primary structure is already very very complex compared to for example the primary structure of DNA which is just a a a t c c t g right just the sequence so remember that when you write down proteins and you want to write down the the primary structure you already have to deal with the fact that these two um sulfur molecules can form a disulfide bond all right so then the next structural level is the secondary structure so the secondary structure is the 3d form of local segments of biopolymers so secondary structure also occurs for RNA right we did a secondary structure prediction of RNA at the assignments DNA also has a secondary structure but for DNA and RNA that's it right there is nothing above this this secondary structure but for proteins there actually is but in proteins there are two secondary structures which we more or less identify and those are the alpha helices and the beta sheets so the structure the secondary structure in proteins does not describe specific atom positions in a three-dimensional space now it just describes that part of the protein will form either a helix or it will form a sheet so talking a little bit more about alpha helices is that and so a single protein chain in a helical structure is a alpha helix so it looks more or less well it doesn't look like this but the way that we write it down is either using a helix and like we see here and then we see an undetermined part so part which is not having any shape and then we see that it couples to a secondary a second alpha helix and then we have again an unstructured part and then we see that this part now comes into a beta sheet so but for for alpha helices it turns so a single turn of the helix right so you're above the same in 3.6 amino acids so every turn of the helix is 3.6 amino acids big and the shape is maintained by having hydrogen bonding between the CO and the HN for amino acids earlier so the CO group of one amino acid couples to the it makes a hydrogen bond to the HN group of an amino acid for amino acids earlier so there's two ways of showing alpha helix when in a 3d diagram or in a secondary structure diagram for proteins and that is using a helix which is more or less how it's depicted here but in a lot of cases people use the toilet roll representation so the toilet roll representation is like this so here we can see the different alpha helices so if we would just count then this protein here has one two three small alpha helices and one two three four bigger alpha helices so longer alpha helices furthermore it seems to have one two beta sheets which are the the arrows so remember that the amino acid side chains are on the outside of the helix so they point outwards and not only do they point outwards but they always point towards the N-terminus of the protein so it's a helix and every time there is a side chain of each of the amino acids they point outwards but kind of towards the N-terminus so I have a figure of that as well so what we see here is we see then the the the C being coupled to the N right so this is a peptide bond here we see the alpha and then the side chain is here so the side chain sticks out to the outside of the helix but it also always points towards the N-terminus of the of the of the peptide yes peptide is okay here and then we see another one another one another one and another one and then four four amino acids later we see that there's a hydrogen bridge between the N-H group of the four amino acids earlier compared to the current amino acids that we're looking at right so an alpha helix is a very very structured part of a protein and the structured part of the protein is there because we have hydrogen bonds so had the primary structure of a peptide is determined by atomic bonds like a disulfide bond or a peptide bond the secondary structure like alpha helices are determined by hydrogen bonds so a different force is responsible for keeping this into an alpha helical structure we also have beta sheets the other secondary structure again it is a flat structure kept in place by hydrogen bonds and it is two strands of a polypeptide that fold back on itself so here we see for example an anti-parallel beta sheet and we see that this is one part of the peptide chain which then turns and loops around and comes back through the other side so it is more or less again a flat surface and had there are two important forms they are parallel or anti-parallel I already told you that they are shown in an as an arrow when we look at a third a tertiary structure of a protein but have what you have to remember is that for the anti-parallel sheet what happens is that the side chains are pointing towards each other and then they are pointing away from each other and then they are pointing again towards each other and away from each other so of course you can imagine that when you have an anti-parallel beta sheet that these side chains cannot be too long because if you have very long side chains then of course they start hitting each other and they start interfering with each other when you have an anti-parallel beta sheet this is different from when you have a parallel beta sheet because when you have a parallel beta sheet the two side chains point towards the same direction right so they point towards the left side then the next one points towards the right side and both of them do right so you have side chains which point in the same direction and of course based on the anti-parallel or being parallel they can have different shapes one of the things that you can see here is that the hydrogen bond in an anti-parallel sheet is much closer so it's much tighter than in a parallel sheet so parallel beta sheets are not as tightly bound together as an anti-parallel sheet of course this also depends on the length of the sheet right so it's just a polypeptide which folds back on itself and because of hydrogen bridging it forms a kind of sheet like structure so a more or less a plane in 3d all right so how do we determine if a protein has alpha helices or beta sheets well this is where ramagandran plots come in so ramagandran plots are plots of the torsion angles of the residues contained in a peptide so we have so here we have again a polypeptide chain right so we see the N being coupled to the alpha C atom right and then we have the C with the O which is then coupled to the next so this is the peptide bond here and here we see the other peptide bond and this is the one which has the side chain right so this is this is determined by C beta so here we see that if we look at the alpha atom we have a rotational angle of the nitrogen atom relative to the C alpha atom and we also have the phi angle psi angle so we have the phi angle and we have the psi angle which are the two angles which determine how much stress there is in the amino acid and if we if we determine if we can determine the the angles then we can plot the phi angle on the x-axis which is the N C alpha bond or we can plot and we can plot the psi on the y-axis and that is the C alpha C bonding right so the secondary C which is there this method was developed in 1963 by ramagandran that's why it's called a ramagandran plot and there are online tools available to generate them from a pdb file right so if you do an experiment and you do an x-ray crystallography experiment then in the end what you get if you if if you have so the machine does the x-ray experiment then you get your electron density map then within the electron density map you fit your polypeptide in there and then once you have this this structure right so once you have this 3d structure you can use this pdb file which stores the atomic coordinates of each of the atoms just upload it here and then it will generate a ramagandran plot for you so how does a ramagandran plot look like well a ramagandran plot looks more or less like this this is more or less a kind of schematic representation so it shows the favorite regions in dark green and the allowed regions in light green from the torsion angles in alpha helices and beta sheets right so if we have a right-handed alpha helix we see that the phi angle is around minus 45 while the psi angle is also around minus 45 degrees right so however if we see that the phi angle is actually different right if it's plus 90 degrees to around 135 degrees while the psi angle is around like 90 and then we see that we have a parallel beta sheet which shows up here an anti-parallel beta sheet would show up here and we have a collagen helix which we don't care about much but that's like a third secondary structure that there is that's the collagen helix which is over here if we have a left-handed alpha helix then the left-handed alpha helix is a positive 45 phi angle and a positive 45 degree phi angle so based on this we can determine if it's if if inside of the protein we have alpha helices if this is a right or a left-sided alpha helix or if we have a beta sheet which is parallel or anti-parallel oh crap i thought i had a real thing a real one because then normally you make these plots and then these plots don't look more these are the areas where you can determine but when you when you upload one of these structures then this structure will give you for give you each amino acid will be plotted on here and then you can see oh like amino acid 50 to 60 they form an alpha helix because you see like 10 points here right so the the plot looks like little numbers and so every amino acid from beginning to end has a number and then the numbers are plotted on this plot and then you can see oh like 10 to 25 is a right-handed alpha helix 50 to 73 is a left-handed alpha helix so and you can generate these plots from PDB structures so you can kind of investigate which part of the protein is in which configuration or in which 2d configuration i thought i had a real one but just go here right just go to the PDB so to the protein database download your favorite protein from there throw it into this tool and then it will generate one of these plots for you and then you can indeed see that part if you take a protein which consists only of alpha helix's and then most of the numbers will be in this area and because then or in this area because it might be a left or a right-handed side of helix but that's that's how you can kind of figure out what the secondary structure of a protein is just based on the on the location of the atoms all right so one level higher we have the tertiary structure so the first so the primary structure is based on atomic bonding the secondary structure is based on hydrogen bridges right so again a relatively strong atomic force but the tertiary structure of the protein is its three-dimensional structure as defined by the atomic coordinates right so the 3d structure is really how the thing looks in in real life and had the forces on the tertiary structure that keep the tertiary structure in place is because there is ionic bonding so a positive side chain bonding with a negative side chain there can of course be hydrogen bonding as well so hydrogen bonding also plays a role at the third level but generally hydrogen bonding structure consists of the second level then we have things like hydrophobic and hydrophilic interactions right so how does the protein when it when it hits water how does the how do the hydrophobic parts kind of clump together and how do the hydrophilic parts make it dissolve in water and of course the disulfide bonds but the disulfide bonds and the hydrogen bonding these and so the disulfide bonds are the primary structure hydrogen bonding is secondary structure and then for the tertiary structure you also consider ionic bonding so positive side change with negative side change and you in and you also consider the hydrophobic hydrophilic interactions so how does this generally look well it generally looks somewhat like this so here you see that this protein has a lot of beta sheets and it has a massive alpha helix and had the way that it's structured is like this and this now has a relationship to the real positions of the atoms in the protein when we talk about quaternary structure so one level higher then we talk about the arrangement of multiple proteins or coiling proteins in a multi subunit complex with the cofactor so here we still talk for tertiary structure we still talk about peptide chains so singular or two peptide chains coupled with disulfide bonds or three coupled with disulfide bonds but when we have when we talk about the quaternary structure we talk about proteins which are for example hemoglobin which you see here and so hemoglobin has four different polypeptide chains two times an alpha chain two two times a beta chain so the beta chains are in red and the alpha chains here are in blue but here you also see the structures of the proteins surrounding the four iron molecules so that they are the the the thing that makes hemoglobin able to kind of attach an oxygen molecule or attach four oxygen molecules because every hemoglobin molecule binds four atoms of oxygen and it does that because it has these four iron ions in there and those are depicted more or less here with their kind of structure that holds these iron atoms in place so quaternary structure is different from tertiary structure because it doesn't consider a single polypeptide chain or polypeptide chains which have been fused or linked together using disulfide bonds no it it consists of how different poly of apo proteins come together and form the real protein i hope that's clear first level second level third level fourth level all right so and because the structure is very very very very important when we talk about proteins right because proteins can only function because of their structure so there are many different computational tools to to predict protein structure be it secondary structure be tertiary structure be it be a quaternary structure so these tools can be divided into five different groups and of course there are also tools which are kind of borrowing from two or more groups but the first group is the up in the geo prediction so that means that you predict the secondary or tertiary protein structure just from the sequence of the amino acids then we have secondary structure prediction so secondary structure prediction predicts alpha helices and beta sheets for example by using rachmarachan plot then we have for example also a trans membrane helix prediction so that will predict if an alpha helix is actually going through a lipid membrane then we have thread and folding recognition algorithms which work based on previously learned structures from other proteins which have a structure and then there's also homology modeling which uses knowledge about the 3d structure of other related proteins to predict the structure of the protein that you're currently looking at so different structure prediction tools we will run through a couple of these categories just to show you some of the tools that that are in this group and how they are called and where you can use them so up in each your prediction like i said is an algorithm is an algorithmic process by which a protein tertiary structure is predicted from its primary sequence so you give it the primary sequence so just the basic amino acid order and then what it will try to do is predict how the tertiary structure of the protein will look like so it had a computer will model the hydrogen bridges the disulfide bonds but it will also try to figure out the the ionic forces and it will also try and figure out the what was the fourth force i always forget that one hydrophobic interactions actually the fourth level and i forgot to tell you guys this this is based on van de Waal's force so van de Waal's force is the force that applies to things when you put it in water that things kind of like to clump together so but up in each your prediction is still one of these remaining unsolved questions in biology no one can really do it there are some programs that try to do it but it is one of the top 125 outstanding issues in modern computer science so you can become like world famous by solving or by writing an algorithm which when fed the primary sequence of amino acids predicts the protein tertiary structure so the atomic location of each of the of the of each of the atoms within the protein there are some tools that do this one of my favorite is folding at home which is part of the Berkeley kind of ecosystem so the Berkeley ecosystem started years ago with the search for extraterrestrial intelligence sati i think that most people know what sati is if you don't know what sati is definitely google it um what what it does is that it uses computers like my computer and your computer you install a program on it and what the program does it contacts one of the Berkeley servers and ask for a job so in the old days when like i started computers um which is well very old but in like the 1995 you had the first sati program so what they did is they have all of these radio telescopes all around the world and in these radio telescope recordings they look for ex messages sent by extraterrestrials so what they would do is you would just get for example five minutes of recording sent to your computer you compute if there is a signal in there and then you send your results back and by doing this by using thousands and thousands of computers all over the world um they hope to find extraterrestrial life this infrastructure is also nowadays used for folding proteins so what happens is is that they want to fold for example a very big protein so everyone gets a little piece of it right so your computer gets like 15 amino acids and then on these 15 amino acid it it tries to simulate all of these different forces disulfide bonds and these kinds of things so folding at home is a project where you can contribute your excess computer time when you're not playing computer games or streaming online or or doing other things with your computer and the computer can actually help fold proteins folding at home um same as sati at home uses the same infrastructure really interesting project by Berkeley University fold it is a different approach fold it is a computer game for your mobile phone where you are sneakily folding proteins and earning points for it because like two side chains are not allowed to touch each other um and two hydro uh hydrophobic side chain will never kind of be close to hydrophilic side chain and since humans are very good at this the idea of fold it was like let's make an app for people on their mobile phone so that we can use all of the brain power of people that is out there to have them help us solve proteins and structures so what you do is you you just install the folded app um and then you get little puzzles and these puzzles are like rotate um this little molecule so that it's in the best configuration so the least amount of stress right so that two two hydrophobic chains are not pointing towards each other so and this is a really interesting project because fold it actually made some massive contributions to protein prediction or initial prediction for proteins because what they did is they they studied how people solve these different puzzles that they get and then try to abstract the kind of algorithm which people run in their mind to kind of extract that and put that back into a computer um and then there's also the human proteome folding project which is a big project set up by all kinds of university to do um protein folding um but i think that the folding at home and just contributing access computer power that you have to solve uh to to help people fold proteins and fold it which is a really interesting like approach where you just use an app um with a game and hey you have people play the game and people well they know that they're folding proteins but like the idea is that it's just a fun game so okay you solve it as quickly as possible and you get points for how good your folding of the protein was so up in your prediction still an unsolved question one of these things that if you are able to solve this yeah then you will become one of the most famous computer scientists in modern history so secondary structure prediction is more or less a solved problem right so going from the primary structure to the secondary structure is relatively easy because you only have to take into account the um the atomic binding right so um the disulfide bonds and the other thing that you have to take into account is the hydrogen bridging so only two out of four forces you have to take into account currently we can predict local secondary structures not the whole secondary structure but locally like if you if you give if you have a protein which is a thousand's amino acid long and you then zoom in on like 20 of them then we can with an 80 accuracy predict if this is an alpha helix a beta sheet or a collagen helix so that is more or less a solved problem and there are some tools out there when you want to do local secondary structure prediction like raptor axe and sim pret and just another secondary structure protein predictor that's the name so yet no it's yet another secondary structure protein predictor um so and that those are different computational tools which you can feed um your amino acid sequence and then it will look at parts of this protein so it will just more less um do a sliding window through the protein and for each of these windows predict what is the chance that it's an alpha helix what is the chance that it's a beta sheet and then it will give you this secondary structure prediction and then we can do that with around 80 accuracy if you want to predict transmembrane helices which is a little bit different because those are alpha helices which have hydrophobic side chains on the side so that they can integrate into membranes so head like they form like these pores on the side of the cell or they they form like these pores which allow like transport of electrons and other stuff from the inside of the cell to the outside so this is also a relatively solved issue we can kind of predict with like 60 to 80 accuracy if something is going to be a transmembrane helix because we know how how thick a lipid bilayer is and we know how an alpha helix should look like so that it that it punches a hole um through um the cell wall um you can use HMM top which uses hidden Markov models there's memsat which uses a neural network um we have phobias which uses homology prediction so it it is a model trained on homologous proteins where we know that they are having transmembrane helices and then we can have like think tools like cctop which are constrained consensus topology um so had they used like known topology and they constrain there and they do a consensus voting on so it's kind of a machine learning approach as well all right 303 let's see what's the next one let's do an example um good um let me actually show you guys the example and then um i'm gonna um just have it run during the break so we'll have a 10 minute break so for example let's do a structure prediction of the human insulin receptor using cctop right so the first thing that we do is we click the link and we go to firefox um so that's actually the other firefox right so here we see the insulin receptor hey it shows you all of the different types and sites so head and this is the the the protein structure um so the protein the amino acid sequence of the protein um but of course we want to have an infasta format so we click on fasta and then it just gives us the fasta file which is just the amino acid sequence of the insulin receptor for human um then we go to the cctop prediction tool and that should open up or not it doesn't open up come on there we go all right so the only thing that we do is we just take the fasta sequence right from ncbi we just throw it in cctop and then we just say submit good so this is all that you do and now it's doing its work so it it well we're in the queue um but after we're out of the queue it will show us what it predicted for our secondary structure um for cctop all right i'm going to take a break this time it is going to be sloth i hope so um i will stop the recording so