Protein Structure Study Guide

Protein Structure Remember: 🡪 There are 20 types of amino acids in proteins 🡪 Polypeptides that form proteins are folded (forming 3D shape) to perform a specific function 🡪 Proteins have different structures because of difference in amino acids and their order ____________________________________________________________________________________ 🡪 Although there are many protein structures, few of them are active 🡪 Native Conformations:3D structure of properly folded, stable, functional, and repeated every time when this protein is synthesized ___________________________________________________________________________ Levels of protein structure 🡪 Primary structure: the sequence of amino acid residues that is present in a polypeptide chain 🡪 Secondary structure: the localized organization and structures of parts of a polypeptide chain, at this level of protein structure I know if the protein contains α-helices, β-sheets and there quantities, but I don’t know the final 3D shape and how they are organized 🡪 Tertiary structure: the final 3D structure and/or arrangement of all the amino acids residues of a polypeptide chain , at this level of protein structure we add the extra groups that are not made of amino acids to the polypeptide chain 🡪 Quaternary structure (the only structure that contains more than one polypeptide): describes the number and relative positions of the subunits in a multimeric protein What is multimeric protein ? A: a type of protein that is made of multiple polypeptides crosslinked (connected) with each other ____________________________________________________________________________________ In this picture, you can see: To summarize primary structure: starts from N terminus to the C terminus Secondary structure: we have α-helices, β-sheets, and other structural components Tertiary structure: when we know the orientation of 3D form of protein Quaternary structure: multimeric protein ___________________________________________________________________________________ Primary structure 🡪 This structural level is very simple but it’s very important for the final 3D shape of the protein 🡪 Small changes in the amino acid sequence may make the protein non-functional 🡪 All the information needed for the folding of protein into the final functional form are found in the primary structure ____________________________________________________________________________________ Example to show the effect of mutations in the primary structure: Sickle cell anemia (genetic disease) notes: Glutamate (Glu): have acidic properties, while Valine (Val): is a nonpolar molecule, so replacing Glu with Val will cause big changes in the amino acid Remember: Hemoglobin consist 4 chains: 2 β and 2 α This mutation causes aggregation of , while hemoglobin hemoglobin is biconcave in normal cases and the thickness in the middle 🡪 Bendable red blood cell (because it’s biconcave) of the red blood cell is small is a very important feature when is pass in small capillary, In normal case,blood cell is bendable so transportation of oxygen will be more efficient 🡪 Because Val is non-polar, it’s not preferred to it to be exposed to water,so hemoglobin accumulate and Val in each hemoglobin forms hydrophobic interaction with another Val to be isolated from the aqueous environment, this will affect the shape of blood cells to be sickle, sickle cells can’t bend once moving in small capillaries, they’re going to be relatively rigid and this would cause non-efficient oxygen transfer and also clotting in blood vessels and tissues . ____________________________________________________________________________________ Secondary structure As you can see, the rotation is around the whole circled unit not within the bond itself (red line), this would result in the orientation of R groups of adjacent amino acids in opposite directions as we discussed before, so they are in trans configurations 🡪This structure forms due to the non-covalent interactions between the backbone atoms and groups e.g.(Carbonyl carbon, amine group) 🡪 The contributing factor to the formation of this structure is the properties of the peptide bond 🡪 Properties of peptide bonds: 1.they are rigid because of the resonance structure, 2. It’s single sometimes and double sometimes 🡪 The two bonds within each amino acid residue freely rotate: *)the bond between the α-carbon and the amino nitrogen *)the bond between the α-carbon and the carboxyl carbon Common secondary structures 🡪 A hydrogen-bonded, local arrangement of the backbone of a polypeptide chain. 🡪 Polypeptide chains can fold into regular structures such as: Alpha helix, Beta-pleated sheet, Turns and Loops ____________________________________________________________________________________ α helix it looks like a helical rod, it has a spiral shape The helix has an average of 3.6 amino acids per turn (means that 60% of the fourth amino acid will be in the turn and the rest of it will be in the next turn) (notice that the turn is not a closed circle, it’s closed at different level) The pitch of the helix (the linear distance between corresponding points on successive turns) is 5.4 Å( 1 Å = 10^–10 m) It is very stable because of the linear hydrogen bondings that forms between the oxygen of the carbonyl, and the hydrogen of the amine group from another layer. Amino acids not found in α helices Examples of molecules that aren’t suitable to be a part of α helix: 🡪 Glycine: too small Factors that determine if the sequence will form a helix or 🡪 Proline: other secondary structure: The primary sequence of certain *) No rotation around N-Cα bond region, remember that all info necessary for formation of *) No hydrogen bonding of α amino protein shape are inherited or found in primary sequence group This is because of the formation of the ring between the backbone and the R chain that causes bending the molecule 🡪Close proximity of a pair of charged amino acids with similar charges, for example: if we have two histidines with negative charges on them there would be repulsion, this would be unstable. 🡪 Amino acids with branches at the β-carbon atom (valine, threonine, and isoleucine), for example: Valine in amino acid has a branching on the first carbon in the R chain, so this branching make the molecule large very early along the R chain, same the threonine, so if valine and threonine are beside each other this would need large space and this isn’t available in α helix 🡪 appearance of amino acids with large chains next to each other (e.g. represent of two triptans beside each others as they have large R chains) Note: Number of rotations in α helix depends on the amino acids that are present in their structure ____________________________________________________________________________________ Amphipathic α helices When looking to α helices from up (as in picture 1) R chains are going to be directed outside of the helix 🡪so this allows for more space to fit R chains, because this is a large circle with a large circumference so this gives more space for R chains to fit the helix 🡪 The numbered atoms and groups (green and yellow circles) are involved in peptide bond formation and involved and they are backbone atoms and groups 🡪 Once these helices are formed and if helices are inserted into a membrane they need to pass through the bilayer so they must have a region of hydrophobicity to fit beside the hydrophobic tails, that’s why the inserted amino acids are hydrophobic amino acids 🡪 If we have a channel (as in picture 2) that is made just of helices, and suppose that this channel for example transfer Ca⁺² that are charged molecules, it’s outside surface must be hydrophobic and it’s inside surface must be hydrophilic (Dr. diala supposed that green circles in picture 1 are hydrophilic amino acids and yellow circles to be hydrophobic), So this helix is Amphipathic, remember that single helices are hydrophobic ___________________________________________________________________________________ β pleated sheet (β sheet) 🡪 They are composed of two or more straight chains (β strands) that are hydrogen bonded side by side, so they are crosslinked with each other and this would affect the mechanical properties of the β sheets (hydrogen bond is between carbonyl’s oxygen and the hydrogen of the amine group). 🡪 These are zig-zag like chains strandβ β sheet might be oriented in the same orientation or in the opposite directions as shown in this picture β sheets can form between many strands, typically 4 or 5 but as many as 10 or more, this depends on the type of protein. Such β sheets can be purely parallel, purely anti-parallel, or mixed a single protein may contains β sheet, and may contains α helix, and may contains both N terminus (it’s beginning) C terminus (it’s end) N terminus C terminus C terminus N terminus * )Q: What can be a component of β sheets? Amino acids with branched chains like: Valine, threonine and Isoleucine, they can be found next to each other (more explanation in the below box and picture) and the large aromatic amino acids (phenylalanine, tryptophan, and tyrosine) tend to be present in β-sheets, as they can be found next to each other because there is more space because the R chains are distributed alternatively (one upward and one downward) important note: we may find Valine or tyrosine for example in α helix, but they can’t be beside each other. *)Q: Why we don’t find proline in β sheets? ( Proline) tends to disrupt β strands, so we don’t find it in β strands and sheets, because the presence of the ring structure interferes with the zig-zag shape of the β sheet, specifically that the ring structure is found between the back bone and the R chain, also the amine group due to the formation of the ring structure don’t have hydrogen, so it can’t form hydrogen bonds as an amine group of the backbone with the oxygen of the carbonyl carbon -turnsβ *) side-chains are in trans position, one of them is upward and the other is downward, so they are far away from each other and there’s enough space for R chain to be located in a β sheet whether R chain is branched or not β - turns Turns are compact, U-shaped secondary structures They are also known as β turn or hairpin bend ,they’re kind of flexible structure, they can move easily, so they need relatively to contain small amino acids, that’s why they contain GLY (small amino acid). They contain PRO amino acid, and because of it’s bent structure, it’s suitable to be found in β turns They’re mainly found connecting between α helices or β sheets Glycine and proline are commonly present in turns Super-secondary structures (Between secondary and tertiary structure) (not like the final 3D shape) 🡪They are regions in proteins that contain an ordered organization of secondary structures. 🡪There are at least two types: Motifs and Domains Motif (module) A motif is a repetitive super-secondary structure, which can often be repeated and organized into larger motifs, it’s made of secondary structural elements but organized in a certain way. It usually constitutes a small portion of a protein (typically less than 20 amino acids). In general, motifs may provide us with information about the folding of proteins, but not the biological function of the protein. Motifs can be very simple as in the picture (there are only 2 helices and 1 loop) (instead of helix there may be a sheet) They also can be loop sheets The loop in the “Helix-loop-helix” is larger than the turn in the “Helix-turn-helix” (only difference between them), these are the variable parts of the protein structure (a motif doesn’t do any function, it’s just related to folding) Immunoglobulin: the shape of antibodies A domain 🡪A domain is a compactly folded region of polypeptide found in proteins with similar function and/or structure.(collection of secondary elements that bind together and do a specific function) 🡪 Domains with similar conformations are associated with the particular function. 🡪 A structural domain may consist of 100– 200 residues in various combinations of α helices, β sheets, turns, and random coils. 🡪 They fold independently of the rest of the protein, and form structural element inside the protein 🡪Domains may also be defined in functional terms: a) enzymatic activity b)binding ability (e.g., a DNA-binding domain, it acts as a transcription factor) 🡪If we find a domain inside a specific protein, I can know it’s function, for example, if we find a domain in an enzyme, therefore the function of the domain is phosphorylation. Tertiary structure The overall conformation of a polypeptide chain (just one polypeptide chain with one N terminus and C terminus) The three-dimensional arrangement of all the amino acids residues The spatial arrangement of amino acid residues that are far apart in the sequence Cylinder structure:each cylinder represents a helix space filling structure: gives more information of the surface of the protein and types of atoms on surface protein surface map: gives more information about the surface only trace structure: Represents the primary structure taking the 3D shape 4 2 3 1 Remember: The formation of the secondary structural elements is related of the formation of non-covalent interactions specially hydrogen bonds between the backbone atoms. 1)Hydrogen bonds between the backbone atoms 2) bond between Serine (on right) and asparagine (on left) 3)Salt bridge (ionic interaction) (between basic and acidic amino acid) (side chains that have opposite charges) 4) Hydrophobic interactions, a pocket is formed that is isolated from aqueous environment 5) disulfide bridge between two cysteine residues in an oxidizing environment, they lose their hydrogens and connect to each other Note: any bond that isn’t numbered dr. Diala read it only without explanation Non-covalent interactions Hydrogen bonds occur not only within and between polypeptide chains but with the surrounding aqueous medium. Charge-charge interactions (salt bridges) occur between oppositely charged R-groups of amino acids. Charge-dipole interactions form between charged R groups with the partial charges of water. the same charged group can form either hydrogen bonding or electrostatic interactions van der Waals attractions There are both attractive and repulsive van der Waals forces that control protein folding. Although van der Waals forces are extremely weak, they are significant because there are so many of them in large protein molecules. This interaction contribute to the protein folding although relatively very weak in comparison to the other non-covalent interactions, but the number of these bonds contribute the stability of the molecule Remember: electrons rotate so the place of positive and negative charges may change Hydrophobic interactions Can polar amino acids be found in the interior?...YES Polar amino acids can be found in the interior of protein In this case, they form hydrogen bonds with other polar amino acids or with the polypeptide backbone, they won’t interact with hydrophobic amino acids They play important roles in the function of the protein also non-polar amino acids may be on the surface under certain conditions (not usual) mostly non polar amino acids are found interior, specially for soluble proteins and that can be transferred from one side to another, not the associated with membrane ()A system is more thermodynamically (energetically) stable when hydrophobic groups are clustered together rather than extended into the aqueous surroundings () hydrophobic interactions are forces that cluster hydrophobic side chains next to each other and isolate them from the aqueous environment (e.g.) in channels, remember α helices that need to be inserted to the membrane, they have the outside of protein made of hydrophobic amino acids, as we described before Stabilizing factors 🡪There are two forces that do not determine the three dimensional structure of proteins, but stabilize these structures: Disulfide bonds (type of covalent bond that forms between cysteine amino acids specifically and only) and Metal ions ( at tertiary structure prosthetic groups -non protein components- are added like metal ions, heme groups, sugars in glycoproteins, lipids as in lipoproteins….) Disulfide bonds The side chain of cysteine contains a reactive sulfhydryl group (—SH), which can oxidize to form a disulfide bond (—S— S—) to a second cysteine. The crosslinking of two cysteines to form a new amino acid, called cystine. (we are talking here about a cysteine in an amino acid connecting with a cysteine in another amino acid) e.g. of protein that contains disulfide bridge is insulin metal ions (*) Several proteins can be complexed to a single metal ion that can stabilize protein structure by forming: 1)Covalent interaction (myoglobin) myoglobin contains heme groups that contain (Fe²⁺) another example of metallic structure that represent in protein structure is (Zn) that is found in transcription factors 2)Salt bridges (carbonic anhydrase) carbonic anhydrase is responsible of forming a salt bridge between( Zn2+) and H₂O molecule, this facilitates the formation of H₂CO as a result of the reaction between H₂O and CO₂ as we talked about that in the buffer system.