Introduction to Chemical Biology

Professor Stuart Conway Introduction to Chemical Biology University of xford Introduction to Chemical Biology ecommended books: Professor Stuart Conway Department of Chemistry, Chemistry esearch Laboratory, University of xford email: stuart.conway@chem.ox.ac.uk Teaching webpage (to download hand- outs): http://conway.chem.ox.ac.uk/teaching.html Biochemistry 4 th Edition by Voet and Voet, published by Wiley, ISB: 978-0- 470-57095- 1. Foundations of Chemical Biology by Dobson, Gerrard and Pratt, published by UP (primer) ISB: 0-19- 924899-0 Amino Acid and Peptide Synthesis by Jones, published by UP (primer) ISB: 0-19- 855668-3 1

Professor Stuart Conway Introduction to Chemical Biology University of xford Amino acids, peptide and proteins slide 9 General features of amino acids slide 10 + 3 - α Proteins constitute 15% of the total mass of cells. Proteins are linear polymers comprised of α- amino acids. The individual amino acids are linked via amide bonds to form polypeptide chains. = side chain, can be one of ~20 groups. 2

Professor Stuart Conway Introduction to Chemical Biology University of xford aturally- occurring amino acids slides 11-16 alanine arginine asparagine aspartic acid Ala, Arg, Asn, Asp, cysteine glutamic acid glutamine glycine Cys, Glu, Gln, Gly, histidine isoleucine leucine lysine is, Ile, Leu, Lys, methionine phenylalanine proline serine Met, Phe, Pro, Ser, threonine tryptophan tyrosine valine Thr, Trp, Tyr, Val, emembering the 1- and 3- letter codes slide 17 First letter: Alanine; Cysteine; Glycine; istidine; Isoleucine; Leucine; Methionine; Proline; Serine; Threonine; Valine. elated letter: asparagie contains ; aspartic acid D is near A aspardic acid ; lysine K is near L. Phonetically suggestive: arginine - ginine; glutamine Q- tamine; Phenylalanine P/F; tryptophan W = double ring; tyrosine. aturally- occurring amino acids slide 18 alanine valine leucine isoleucine Ala, A Val, V Leu, L Ile, I methionine proline phenylalanine glycine Met, M Pro, P Phe, F Gly, G serine threonine cysteine asparagine Ser, S Thr, T Cys, C Asn, glutamine tyrosine histidine tryptophan Gln, Q Tyr, Y is, Trp, W aspartic acid glutamic acid lysine arginine Asp, D Glu, E Lys, K Arg, 3

Professor Stuart Conway Introduction to Chemical Biology University of xford aturally- occurring amino acids slides 19-24 Formula Structure otes glycine + - 3 ydrophobic amino acids alanine C3 + 3 3C + - C3-3 C3 leucine 3C + - 3 C3 3C + valine - 3 C3 S isoleucine methionine + - 3 + proline phenylalanine - + 3 4

Professor Stuart Conway Introduction to Chemical Biology University of xford Polar amino acids serine + 3 + - C3-3 threonine cysteine S + - 3 asparagine 2 + contains amide, weak acid and base, can - bond - 3 2 glutamine as asparagine + - 3 tyrosine + - 3 histidine + - 3 tryptophan + - 3 5

Professor Stuart Conway Introduction to Chemical Biology University of xford Charged amino acids - aspartic acid + 3 - - glutamic acid + 3-3 + lysine + 3 + 2 2 - arginine + 3 - General features of amino acids slide 25 + 3 α - α- Amino acids contain at least one stereogenic centre. Stereochemistry of amino acids slide 26 Using alanine( = C 3 ) as an example, priority can be assigned as above. Therefore, alanine has the (S)- absolute configuration. 6

Professor Stuart Conway Introduction to Chemical Biology University of xford Stereochemistry of amino acids slide 27 For example, L- alanine can be considered analogous to L- glyceraldehyde. The majority of naturally occurring amino acids are L- configured. Implications of amino acid stereochemistry slide 28 7

Professor Stuart Conway Introduction to Chemical Biology University of xford Implications of amino acid stereochemistry slide 29 - Me C 2 Me candida antarctica lipase C 2 C 2 Me C 2 Me ydrogen bonding slide 30 ydrogen bonds are one of the most important non- covalent interactions in biological systems. There is a significant electrostatic component to - bonding. ydrogen bonding slide 31 owever, orbital interactions are also an important component of - bonding. - bonds can be viewed as having a σ- bonding component. Consequently, there is an optimum orientation for - bonding. 8

Professor Stuart Conway Introduction to Chemical Biology University of xford ydrogen bonding slide 32-3 + + 3 2 - The optimum angle for - bonding is where the X- bond points directly to the lone pair, such that the angle is 180 - Bond strength can vary between 16 and 60 kjmol - 1. General features of amino acids slide 33 + 3 α - The amino group is basic and the carboxylate group is acidic. General features of amino acids slide 34 glycine acetic acid glycine methyl ester aliphatic amine + 3-3 C - + Me 3 + 3 The acid of glycine is more acidic than acetic acid, due to the electron- withdrawing effect of the ammonium ion. The amine of glycine is more basic than that of glycine methyl ester. owever, glycine s amino group is less basic than aliphatic amines, due to the electron- withdrawing effect of the carboxylic acid. 9

Professor Stuart Conway Introduction to Chemical Biology University of xford Isoelectric point of amino acids slide 35 The enderson- asselbalch equation: Calculating the isoelectric point for glycine: The p at which a molecule carries no net charge is its isoelectric point. The isoelectric point (pi) of amino acids is calculated by applying the enderson- asselbalch equation. Isoelectric point of charged amino acids slide 37 - + 3 - Calculating pi for amino acids with charged side chains is slightly more complex. 10

Professor Stuart Conway Introduction to Chemical Biology University of xford Isoelectric point of charged amino acids slide 39 3 + + 3 - EDX chemistry of cysteine slide 40 owever, in contrast to hydroxyl groups, thiols do not form strong hydrogen bonds. In general, sulfur containing side chains (C, M) are relatively non- polar. The thiol (C) has the unique property of being the most readily oxidised of all side chains. When two thiols are oxidised a disulfide bond results. Two cysteines linked by a disulfide bond are known as a cystine. Disulfide bonds are important structural features of some proteins. 11

Professor Stuart Conway Introduction to Chemical Biology University of xford EDX chemistry of cysteine - keratin slide 41 Disulfide bridges stabilise protein 3- dimensional structure. Amino acid synthesis slide 43 Br 2 Br 3 2 C 2 PCl 3 C 2 C 2 The Strecker Synthesis of amino acids slide 44 4 Cl ac 2 C Cl 2 2 12

Professor Stuart Conway Introduction to Chemical Biology University of xford The Strecker Synthesis of amino acids slide 45 + 3 + ± + + 2 3 2 C + + - C The Strecker Synthesis of amino acids slide 46 2 C 2 + + 2 2 2 2 + 2 + 3 2 ± + 2 2 2 + The Bucherer- Bergs synthesis of amino acids slide 47 C 3 ( 4 ) 2 C 3 KC C 3 a 2 2 C 3 13

Professor Stuart Conway Introduction to Chemical Biology University of xford The Bucherer- Bergs synthesis of amino acids slide 48 4 Cl ac 2 C Cl 2 2 The Bucherer- Bergs synthesis of amino acids slide 49 C 2 C C 3 - C C 3 Et C C 3 Et Et C C C 3 C 3 The Bucherer- Bergs synthesis of amino acids slide 50 2 2 C 3 C 3 C 3 2 Asymmetric amino acid synthesis: The Schöllkopf method slide 51 Me Me 1. BuLi 2. BnBr Me Me Ph Cl C 2 Me - Cl + 3 Bn 73% yield 85% ee 14

Professor Stuart Conway Introduction to Chemical Biology University of xford Amino acids - Summary slide 52 There are 20 proteinogenic α- amino acids, differing in their side chain structure. All but glycine are chiral, and this affects protein secondary structure. Polar amino acids are involved in hydrogen bonding. Charged amino acids affect the acid- base chemistry of proteins. Cysteine plays an important functional role through EDX chemistry. atural and unnatural amino acids can be made by chemical synthesis. Peptide bonds slide 54 + 3 1 - + 3 2 - - 2 + 3 1 2 - This is formally a dehydration reaction ( 2 is lost). Peptides are linear polymers that link together in a head- to- tail fashion rather than forming branched chains. - 2-3 + + 3 15

Professor Stuart Conway Introduction to Chemical Biology University of xford Peptide bonds slide 56 The amide bond structure is deceptively simple and contains an unexpected property, which is partly responsible for protein stability. Peptide bonds slide 57 The delocalisation can be represented using curly arrows, but this implies that there is a movement of electrons between the nitrogen and the oxygen, which is not true! A better representation may be to show the electrons delocalised across the, C and atoms. owever, this representation is not useful for drawing mechanisms. Peptide bonds slide 58 A molecular orbital approach shows the nitrogen lone pair in the p- orbital overlapping with the carbonyl π*- orbital. If this representation is correct, it implies that the C- bond has some double bond character. 16

Professor Stuart Conway Introduction to Chemical Biology University of xford Peptide bonds slide 59 X- ay crystal structures (above) and M provide evidence that amide bonds are planar. This bond length implies that the C- bond has some double bond character, which is supported by the planar nature of the amide unit. The partial double bond character is responsible for restricted rotation around the C- amide bond. Peptide bonds slide 60 88 kj mol - 1 is required to rotate the amide bond of,- dimethylformamide (DMF), so at room temperature the amide bond is locked. Two peaks for the methyl groups are visible in the 1 M spectrum of this compound at room temperature. These peaks coalesce at higher temperature, where more energy is available - increasing the rate of C- bond rotation. 17

Professor Stuart Conway Introduction to Chemical Biology University of xford Peptide bonds slide 61 The partial double bond character of the amide bond means that there are two main possible conformations that can be adopted by amides. These are with the - groups cis or trans. This conformation avoids an unfavourable steric clash between C- atoms in the main protein chain. Peptide bonds - proline slide 62 The steric clash present in the cis conformation is similar to that of the clash in other peptide bonds, and to that in the trans proline peptide bond. ence the cis peptide conformation of proline is not significantly disadvantaged over the trans conformation. 18

Professor Stuart Conway Introduction to Chemical Biology University of xford Peptide bonds and ester bonds slide 63 Esters are less reactive than acid chlorides because of donation from the oxygen p- orbital into the carbonyl π*- orbital. Peptide bonds and ester bonds slide 64 The second oxygen atom in the ester group differs from the amide nitrogen, in that it has one less substituent, but an extra lone pair. 19

Professor Stuart Conway Introduction to Chemical Biology University of xford Peptide bonds and ester bonds slide 65 3 C C 3 In the trans conformation an additional interaction, between the other oxygen lone pair and the C- σ*- orbital is possible, which stabilises this conformation, even when the trans conformation appears to be sterically disfavoured. These stereoelectronic effects have a profound influence on the reactivity of esters. Peptide bonds slide 66 Understanding the interaction between amide units tells us about protein structure. As the amide units are planar there is only free rotation around two bonds in the main peptide chain. These are the - C α bond and the C- C α bond. 20

Professor Stuart Conway Introduction to Chemical Biology University of xford Peptide bonds slide 67 C α C The - C α dihedral angle is labelled Φ (Phi). C Peptide bonds slide 68 Peptide bonds slide 69 CC C C C C L- Amino acids are expected to prefer conformations where Φ = - 60 to - 180. 21

Professor Stuart Conway Introduction to Chemical Biology University of xford Peptide bonds slide 70 CC C C C C Glycine ( = ) is less constrained as the atom causes less steric interactions. Peptide bonds slide 71 Proline is more constrained than the other amino acids. Peptide bonds slide 72 We can determine Ψ (Psi) by looking down the C- C α bond and observing the angle between the two nitrogen atoms. 22

Professor Stuart Conway Introduction to Chemical Biology University of xford Peptide bonds slide 73 C α C 3 C C C Peptide bonds slides 74 & 75 anticlockwise)rotation)of)the rear)substituents)by)60 C clockwise)rotation)of)the rear)substituents)by)60 C C anticlockwise)rotation)of)the rear)substituents)by)further)60 C C clockwise)rotation)of)the rear)substituents)by))further)60 In order to minimise unfavourable steric interactions, L- amino acids are expected to prefer conformations where Ψ (Psi) -60 or +120 to +180. Peptide bonds - summary slide 76 L- Amino acids are expected to prefer conformations where Φ = - 60 to - 180. L- Amino acids are expected to prefer conformations where Ψ (Psi) -60 or +120 to +180. 23

Professor Stuart Conway Introduction to Chemical Biology University of xford amachandran plots slide 77 The combined values of Φ (Phi) and Ψ (Psi) can be summarised on a conformational map, which is known as a amachandran plot (after G.. amachandran). ~75% of the plot (i.e. most combinations of Φ and Ψ are inaccessible). amachandran plots slide 78 nly three small regions of the map are physically accessible to a polypeptide chain. All common types of regular secondary structure fall within the allowed regions of a amachandran plot. 24

Professor Stuart Conway Introduction to Chemical Biology University of xford amachandran plots slide 79 The amachandran plot for glycine demonstrates that these residues have far greater conformation freedom than other amino acids. amachandran plots slide 80 The above plot shows the conformation angle distribution of all non- Gly/Pro residues superimposed on the amachandran plot. The conformations that lie in the forbidden regions represent a twist in the peptide bond of a few degrees, which makes these conformations accessible. 25

Professor Stuart Conway Introduction to Chemical Biology University of xford Peptides - summary slide 81 As the amide unit is planar, there are only two dihedral angles to be considered when thinking about protein conformation. The - C α dihedral angle is labelled Φ (Phi). The C- C α dihedral angle is labelled Ψ (Psi). The combined values of Φ (Phi) and Ψ (Psi) can be summarised on a conformational map, which is known as a amachandran plot. nly three small regions of the map are physically accessible to a polypeptide chain. Peptide bonds - synthesis slide 82 2 2 2 26

Professor Stuart Conway Introduction to Chemical Biology University of xford Peptide bonds - synthesis slide 83 2 X 2 2 2 X 2 2 2 2 X 2 X 2 As there are three nucleophiles in the system, there is the possibility for many products to form. Peptide bonds - synthesis slide 84 2 PG PG 2 A protecting group (PG) can be attached to a functional group to stop it reacting in subsequent transformation, before being removed. A good protecting group requires the following properties: o o o Both amine and carboxylic acid protecting groups are important for peptide synthesis. Peptide bonds - synthesis slide 85 2 1. Et, + 2. Cl Et + 3 Cl - Methyl and ethyl esters prevent action as an acid or a nucleophile. 27

Professor Stuart Conway Introduction to Chemical Biology University of xford Peptide bonds - synthesis slide 86 + 2 2 The t- butyl ester is more commonly used as a carboxylic acid protecting group in peptide synthesis. This group is easily added and removed under acid conditions. Peptide bonds - synthesis slide 87 + 3 2 3 The steric bulk of t- butyl alcohol means that standard coupling conditions are inefficient when preparing t- butyl esters. eaction of isobutene, via a carbocation, is a more efficient method of preparation. The amine is protonated and therefore not nucleophilic. 28

Professor Stuart Conway Introduction to Chemical Biology University of xford Peptide bonds - synthesis slide 88 + 2 2 2 Due to steric bulk, t- butyl esters are hydrolysed via and A AL 1 mechanism. This can be viewed as S 1 substitution of the t- butyl group. Peptide bonds - synthesis slide 89 + C t- Butyl deprotection is often achieved using a mixture of acetic acid and formic acid. Formic acid acts as a hydride donor to scavenge the t- butyl cation. 29

Professor Stuart Conway Introduction to Chemical Biology University of xford Peptide bonds - synthesis slide 90 Protecting group Structure Protects From Protection Deprotection Peptide bonds - synthesis slide 91 2 BnCCl base Ph The carboxylbenzyl (Cbz, Z) nitrogen protecting group is added by treating amines with benzyl chloroformate and a weak base. Cbz groups can be removed using the same conditions as for removing benzyl ethers, 2 and Pd or Br. Peptide bonds - synthesis slide 92 Cl 2 Ph Et 3 + Ph Ph 30

Professor Stuart Conway Introduction to Chemical Biology University of xford Peptide bonds - synthesis slide 93 2, Pd Ph 2 + 2 Cbz groups can be removed by any conditions that cleave a benzyl group. The carbamate decomposes to give the amino acid and C 2. Peptide bonds - synthesis slide 94 Boc 2 2 t- Butyloxycarbonyl (Boc) is another nitrogen- protecting group. Boc groups can be removed using dilute aqueous acid. 31

Professor Stuart Conway Introduction to Chemical Biology University of xford Peptide bonds - synthesis slide 95 2 base + Peptide bonds - synthesis slide 96 + + 2 2 Peptide bonds - synthesis slide 97 2 Cl base Fluorenylmethyloxycarbonyl (Fmoc) is another nitrogen- protecting group. 32

Professor Stuart Conway Introduction to Chemical Biology University of xford Peptide bonds - synthesis slide 98 + 2 2 The fluorenyl proton is relatively acidic (pk a ~25) and can be deprotonated with mild bases, such as piperidine. Although the anion is stabilised, elimination occurs, forming the carbamate, which releases C 2 and the free amine. Peptide bonds - synthesis slide 99 base The fluorene (B not fluorine) group is more acidic than we might expect, with a pk a value of ~25. Delocalisation of the negative charge in the planar anion stabilised the conjugate base. 33

Professor Stuart Conway Introduction to Chemical Biology University of xford Peptide bonds - synthesis slide 100 - Pg + 3 C 3 Pg C 3 - Pg 2 C 3 + 3 - Pg X Peptide bonds - synthesis slide 101 BnCCl 2 base Cbz Bn Ts Bn Li Bn Cbz Cbz Bn The amine can be selectively Cbz protected. Benzylation, followed by Li hydrolysis of the more electrophilic ester gives Cbz- Asp bezyl ester. 34

Professor Stuart Conway Introduction to Chemical Biology University of xford Peptide bonds - synthesis slide 102 Cbz Bn Cl Cl Cl Ts toulene reflux Cbz Bn Cl Cl Cl - Cl + 3 base C 3 - Bn + 3 C 3 2, Pd C 3 Cbz Peptide bonds - synthesis slide 103 Bn Cl Bn Cl Cl Cbz Cl Cl Cbz Cl Bn Cbz X The electron- withdrawing nature of the ester activates the ester to attack by nucleophiles. It would be more convenient to activate the acid directly in situ. 35

Professor Stuart Conway Introduction to Chemical Biology University of xford Protein structure Secondary structure slide 104 Protein secondary structure is the local spatial arrangement of polypeptide backbone atoms, without regard to the conformations of their side chains. Protein structure Tertiary structure slide 105 The distinction between secondary structure is somewhat vague. 36

Professor Stuart Conway Introduction to Chemical Biology University of xford Protein structure Quaternary structure slide 106 Each individual polypeptide chain subunit is shown in a different colour. Protein structure Primary structure slide 108 Determining the primary sequence of a protein consist of three conceptual parts: Determine the number of polypeptide chains (subunits) in the protein. Cleave the protein s disulfide bonds. Separate and purify the unique subunits. Determine the subunits amino acid composition. Fragment the individual subunits at specific points to yield peptides small enough to be sequenced directly. Separate and purify the fragments. Determine the amino acid sequence of each peptide fragment. epeat the above with a different fragmentation selectivity. Span the cleavage points between one set of peptide fragments and the other. By comparison, the sequences of these sets of polypeptides can be arranged in the order that they occur in the subunit, thereby establishing the amino acid sequence. Finally, elucidate the positions of any disulfide bonds. 37

Professor Stuart Conway Introduction to Chemical Biology University of xford Protein structure Primary structure slide 109-2 - 3 + + 3 Prepare the protein for sequencing: Determine the number of polypeptide chains (subunits) in the protein. Each polypeptide chain (if not chemically blocked or circular) has an - terminal residue and a C- terminal residue. By identifying these end groups, we can establish the number of chemically distinct polypeptide chains in a protein. e.g. insulin has equal amounts of - terminal Phe and Gly residues, which indicates that it has equal numbers of two different subunits. Protein structure Primary structure slide 110 Use of dansyl reagents 2 2 1 S 1 3 2 1 2 3 Ph S The Sanger method slide 111 + - +- F 2 1 3 2 - - + 2 F 1 3 2 2 2 1 + 3 2-3 - 2 2 1 3 2 38

Professor Stuart Conway Introduction to Chemical Biology University of xford Use of dansyl reagents slide 112 S Cl 2 1 3 2 S 1 3 2 3 + S 1 + 3 2-3 - Edman degradation slide 113 C + S 2 1 3 2 Ph S 1 3 2 anhydrous F 3 CC 2 1 S Ph + 1 Ph S + 2 2 3 39

Professor Stuart Conway Introduction to Chemical Biology University of xford Protein structure Primary structure slide 114 1 1 3-2 2 + 3 2 3 - + 3 2 2 + 3 + 3 2 C- terminus identification is less reliable than - terminus identification. The most reliable chemical method is hydrazinolysis, in which only the C- terminal amino acid is not converted into the hydrazine derivative. owever, there are many side reactions. Carboxypeptidase enzymes also selectively cleave C- terminal residues, but their selectivity for certain side chains causes problems. Protein structure Primary structure slide 115 3 C S C Br 3 C S + C 3 C S C 2 2 Cyanogen bromide specifically cleaves peptide bonds after Met residues. This selectivity is can be explained mechanistically. 40

Professor Stuart Conway Introduction to Chemical Biology University of xford Protein structure Primary structure slide 116 ther reagents that cleave at specific points in a peptide chain are: - Iodosobenzoate: after Trp residues. ydroxylamine: Asp- Gly bonds. 2- itro- 5- thiocyanobenzoate: amino side of Cys residues Enzymes can also be use to perform selective bond cleavage: Trypsin: after Lys and Arg residues. Clostripain after Arg residues. Staphylococcal protease: after Asp and Glu (under certain conditions). Protein structure α- helices slide 117 nly one helical polypeptide conformation has simultaneously allowed conformational angles and a favourable hydrogen- binding pattern. This striking element of secondary structure is known as the α- helix. Protein structure α- helices slide 119 For a polypeptide made from L- amino acids, the residues in the helix have the following torsion angles: 41

Professor Stuart Conway Introduction to Chemical Biology University of xford Protein structure α- helices slide 120 The core of the α- helix is tightly packed; its atoms are in van der Waals contact across the helix. The carbonyl oxygen atom of the n th residue points along the helix to hydrogen bond with the - of the (n + 4) residue. This arrangement results in a strong hydrogen bond with an - distance of ~2.8 Å (slightly shorter - distance shown left). 42

Professor Stuart Conway Introduction to Chemical Biology University of xford Protein structure β- sheets slide 121 an#parallel(β)sheets parallel&β'sheets C" C" " C C" Again, these structures contain repeating Φ and Ψ angles that fall in the allowed region of the amachandran plot. There are two types of β- sheet structure: o o Protein structure β- sheets slide 122 For a polypeptide made from L- amino acids, the residues in antiparallel β- sheets have the following torsion angles: 43

Professor Stuart Conway Introduction to Chemical Biology University of xford Protein structure β- sheets slide 123 In antiparallel, β- sheets the polypeptide strands run in opposite directions. All β- sheets have a two residue repeat unit of ~7.0 Å. Again, this arrangement results in a strong hydrogen bond with a near optimal - distance. Protein structure β- sheets slide 124 Complementary hydrogen- bonding occurs between amino acids in each chain. Again, this arrangement results in a strong hydrogen bond with a near optimal - distance. This results in a rippled or pleated structure. 44

Professor Stuart Conway Introduction to Chemical Biology University of xford Protein structure β- sheets slide 125 For a polypeptide made from L- amino acids, the residues in parallel β- sheets have the following torsion angles: Protein structure β- sheets slide 126 Phe Leu Ile Asp Leu Asp Ile Trp Ile Ala In parallel, β- sheets the polypeptide strands run in the same direction. All β- sheets have a two residue repeat unit of ~7.0 Å. Again, hydrogen- bonding occurs between amino acids in each chain. This results in a staggered pattern of hydrogen- bonding. 45

Professor Stuart Conway Introduction to Chemical Biology University of xford Protein structure β- sheets slide 127 β- sheets are common motifs in proteins. They consist of 2-22 strands, with 6 being most common. β- sheets can be up to 15 residues long, with an average of 6. This reduced stability may be attributed to the distorted hydrogen- bonding in parallel β- sheets. Protein structure β- sheets slide 128 β- sheets have a slight right- handed helical twist. 46

Professor Stuart Conway Introduction to Chemical Biology University of xford Protein structure β- sheets slide 129 Multiple parallel β- sheets, in this case 7, can arrange themselves into a β- barrel. Protein structure - β- turns slide 130 Both α- helices and β- sheets can be viewed as repetitive secondary structure. owever, there are also important elements of non- repetitive secondary structures. 47

Professor Stuart Conway Introduction to Chemical Biology University of xford Protein structure - β- turns slide 131 Type I β- turn Type II β- turn There are two types of β- turns, Type I and Type II. Each comprises four key amino acids. Protein structure - β- turns slide 132 Type I β- turn Phe Ser Ile The turn is stabilised by at least one hydrogen bond. A type I β- turn has the following torsion angles: Protein structure - β- turns slide 133 Type II β- turns also link successive strands of antiparallel β- sheets. 48

Professor Stuart Conway Introduction to Chemical Biology University of xford Protein structure - β- turns slide 134 Type II β- turn is Gln The type II turn is also stabilised by at least one hydrogen bond. A type II β- turn has the following torsion angles: Protein structure - β- turns slide 135 Type I β- turn Type II β- turn Type I and type II β- turns differ in the C α2 - C α3 amide bond orientation. The 180 flip in the bond is reflected in the torsion angles. 49

Professor Stuart Conway Introduction to Chemical Biology University of xford Protein structure - β- turns slide 136 is Gln In order to form the hydrogen bond in both types of turn, significant disruption in the ideal conformation occurs (cf torsion angles). In type II turns, the oxygen atom of residue 2 crowds the side chain carbon of residue 3, which is therefore usually a glycine. Protein structure - β- turns slide 137 Globular proteins (a traditional classification) are globe- like and usually soluble in aqueous solution. 50

Professor Stuart Conway Introduction to Chemical Biology University of xford Protein structure - β- turns slide 138 Protein structure - β- turns slide 139 Many fibrous proteins (eg collagen, above) such as those in skin, tendon and bone function as structural materials that have a protective, connective or supportive role in living organisms. 51