Protein Structure Klemens Wild, BZH,
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1 Protein Structure
2 recommended books
3 Proteins protein definition From gr. proteios (superior, erstrangig) 1836 JJ Berzelius Functions: structural, enzymes, muscle, transport immune system, Linear polymer of amino acid residues. Connection: peptide bond Polypeptide chain 3D structure: 1950s Myoglobin, hemolobin (Kendrew and Perutz)
4 4 levels of protein structure Primary: the linear sequence of amino acids Secondary: the local organization of parts of a polypeptide chain (α-helix, β-sheet) Tertiary: the overall, three-dimensional arrangement of the polypeptide chain (Domain: folding unit) Quaternary: the assembly of two or more polypeptides into a multisubunit complex
5 Part I protein main chain
6 Amino acids the building blocks In general: 2 functional groups α-amino acids R: side chain: 20 different amino acids encoded
7 the building blocks α-carboxyl group pka 2.0 α-amino group pka 9.5
8 The fractional protonation at a certain ph and the pi can be calculated by the Henderson-Hasselbalch equation. pka and pi
9 Absolute configuration the building blocks Amino acids contain asymmetric carbons. α-l amino acids S configuration
10 the peptide bond Condensation reaction ΔG = + 10 kj/mol metastable in water Activation by esterification with CCA-end of t-rnas
11 the peptide bond
12 the peptide bond Ramachandran et al., Biochim. Biophys. Acata 339 (1974), 298
13 The peptide bond has partial double bond character (40%) the peptide bond planarity The peptide bond has a constant dipole µ (3.5 Debye) µ
14 cis and trans peptides Configuration of the peptide bond Peptide bonds are mainly in trans Conformation defined by angle ω& Creighton, Proteins, Copyright 1993 by W.H. Freeman & Co
15 cis and trans peptides Cis bonds cause sterical hindrance. after Creighton, Proteins, Copyright 1993 by W.H. Freeman & Co
16 cis and trans peptides Only proline residues are significantly in cis. after Stryer, Biochemistry, Copyright 2002 by W.H. Freeman & Co
17 the peptide bond Each peptide bond formation requires about 4 ATP and 4 GTP molecules for translation and quality control. The peptide planes are relatively oriented by the rotation around the Φ and Ψ angles. Ramachandran plot
18 Φ and ψ angles after Creighton, Proteins, Copyright 1993 by W.H. Freeman & Co
19 Ramachandran plot Ψ Φ Hoeffken et al., J. Mol. Biol. 204 (1987), 629
20 Ramachandran plot
21 Ramachandran plot Ramachandran plot β-sheet right handed α-helix most favoured regions additionally allowed regions generously allowed regions dis - allowed regions
22 δ+ α - helix 3.6 aar 5.4 Å [ δ-
23 α - helix The α-helix is a helix Helices like to form bundles or coiled coils or transmembrane domains (TMDs)
24 the helical wheel
25 the helical wheel!hydrophobic amphipathic hydrophilic protein core protein surface exposed (membrane) (membrane surface) Branden & Tooze, Protein Structure, 1999 Garland Publ.
26 β-sheet Extended zigzag of peptide chain & Location of side chains alternates & β-sheets form by the alignment of β-strands parallel or antiparallel β-sheets are twisted and like to form β-barrels. after Creighton, Proteins, Copyright 1993 by W.H. Freeman & Co
27 parallel β-sheet
28 antiparallel β-sheet
29 poly-proline helix Ramachandran plot antiparallel β-sheet parallel β-sheet π-helix 3-10 helix left handed α-helix right handed α-helix most favoured regions additionally allowed regions generously allowed regions dis - allowed regions
30 β II β VIa Ramachandran plot inv. γ β V β I β III β VIb β VIII Rose et al., Adv. Prot. Chem. 37 (1985), 1; Chou & Fasman, J. Mol. Biol. 115 (1977), 135; Wilmot & Thornton, J. Mol. Biol. 203 (1988), 221; Richardson, Adv. Prot. Chem. 34 (1981), 167 β III β I β II γ β V
31 Which secondary structure is formed? propensities Secondary structures can be predicted.
32 side chains amino acid side chains
33 Amino acid classification: amino acid classes 1. Aliphatic 2. Proline (imino acid) 3. Hydroxyl (polar) 4. Acidic 5. Amide (polar) 6. Basic 7. Histidine 8. Aromatic 9. Sulfur containing
34 G Gly Glycine 1. Aliphatic Glycine R: -H Glycine is not asymmetric High conformational flexibility molecular mass: 57 dalton frequency: 7.2 % All aliphatic residues are chemically inert. Structural role (hydrophobic core) after Creighton, Proteins, Copyright 1993 by W.H. Freeman & Co; amino acid frequency McCaldon & Argos, Proteins 4 (1988), 99
35 1. Aliphatic Alanine R: -CH 3 A Ala Alanine molecular mass: 71 dalton frequency: 8.3 % after Creighton, Proteins, Copyright 1993 by W.H. Freeman & Co; amino acid frequency McCaldon & Argos, Proteins 4 (1988), 99
36 1. Aliphatic Valine R: -CH-(CH 3 ) 2 V Val Valine molecular mass: 99 dalton frequency: 6.6 % after Creighton, Proteins, Copyright 1993 by W.H. Freeman & Co; amino acid frequency McCaldon & Argos, Proteins 4 (1988), 99
37 1. Aliphatic Leucine R: -CH 2 -CH-(CH 3 ) 2 L Leu Leucine molecular mass: 113 dalton frequency: 9.0 % after Creighton, Proteins, Copyright 1993 by W.H. Freeman & Co; amino acid frequency McCaldon & Argos, Proteins 4 (1988), 99
38 1. Aliphatic Isoleucine I Ile Isoleucine molecular mass: 113 dalton frequency: 5.2 % Note: Additional asymmetric β-carbon. after Creighton, Proteins, Copyright 1993 by W.H. Freeman & Co; amino acid frequency McCaldon & Argos, Proteins 4 (1988), 99
39 1. Proline (imino acid) R: -CH 2 -CH 2 -CH 2 - Side chain is bonded to main chain nitrogen. Rigid breaks secondary structures P Pro Proline molecular mass: 97 dalton frequency: 5.1 % black = protein main chain after Creighton, Proteins, Copyright 1993 by W.H. Freeman & Co; amino acid frequency McCaldon & Argos, Proteins 4 (1988), 99
40 2. Hydroxyl (polar) Serine R: -CH 2 -OH Hydroxyl group is polar but chemically inert. S Ser Serine molecular mass: 87 dalton frequency: 6.9 % after Creighton, Proteins, Copyright 1993 by W.H. Freeman & Co; amino acid frequency McCaldon & Argos, Proteins 4 (1988), 99
41 2. Hydroxyl (polar) Threonine R: -CH(-CH) 3 (-OH) Note: Additional asymmetric β-carbon. T Thr Threonine molecular mass: 101 dalton frequency: 5.8 % after Creighton, Proteins, Copyright 1993 by W.H. Freeman & Co; amino acid frequency McCaldon & Argos, Proteins 4 (1988), 99
42 3. Acidic D Asp Aspartate Aspartic acid (Aspartate) R: -CH 2 -COOH Used for ionic and polar interactions molecular mass: (active sites, metal chelating) 115 dalton frequency: 5.3 % pka: 4.0 shaded = partial double bond after Creighton, Proteins, Copyright 1993 by W.H. Freeman & Co; amino acid frequency McCaldon & Argos, Proteins 4 (1988), 99
43 E Glu Glutamate 3. Acidic Glutamic acid (Glutamate) R: -CH 2 -CH 2 -COOH Used for ionic and polar interactions molecular mass: 129 dalton frequency: 6.2 % pka: 4.4 shaded = partial double bond after Creighton, Proteins, Copyright 1993 by W.H. Freeman & Co; amino acid frequency McCaldon & Argos, Proteins 4 (1988), 99
44 N Asn Asparagine 5. Amide (polar) Asparagine R: -CH 2 -CONH 2 Amid form of aspartic acid black = double bond relatively inert but amide is labile molecular mass: 114 dalton frequency: 4.4 % after Creighton, Proteins, Copyright 1993 by W.H. Freeman & Co; amino acid frequency McCaldon & Argos, Proteins 4 (1988), 99
45 5. Amide (polar) Glutamine R: -CH 2 -CH 2 -CONH 2 Amid form of glutamic acid Q Gln Glutamine molecular mass: 128 dalton frequency: 4 % black = double bond after Creighton, Proteins, Copyright 1993 by W.H. Freeman & Co; amino acid frequency McCaldon & Argos, Proteins 4 (1988), 99
46 5. Amide (polar) Glutamine spontaneously cyclises at N-terminus pyrrolidone carboxylic acid Q Gln Glutamine Creighton, Proteins, Copyright 1993 by W.H. Freeman & Co
47 6. Basic K Lys Lysine Lysine R: -(CH 2 ) 4 -NH 2 non-ionised Lys is a potent nucleophile! molecular mass: frequency: 128 dalton 5.7 % pka: after Creighton, Proteins, Copyright 1993 by W.H. Freeman & Co; amino acid frequency McCaldon & Argos, Proteins 4 (1988), 99
48 6. Basic Arylation K Lys Lysine 2,4,6-trinitrobenzene sulfonate absorbance at 367 nm Creighton, Proteins, Copyright 1993 by W.H. Freeman & Co
49 6. Basic acetylation by anhydrides (reversible) K Lys Lysine Creighton, Proteins, Copyright 1993 by W.H. Freeman & Co
50 K Lys Lysine reversible Schiff base with Aldehydes Example: PLP (Vit. B6) Creighton, Proteins, Copyright 1993 by W.H. Freeman & Co
51 6. Basic Arginine R: -(CH 2 ) 3 -NH-C-(NH 2 ) 2 used for ionic and polar interactions (i.e. nucleotides) R Arg Arginine molecular mass: 156 dalton frequency: 5.7 % shaded = partial double bond pka: 12 Guanidinium group planar after Creighton, Proteins, Copyright 1993 by W.H. Freeman & Co; amino acid frequency McCaldon & Argos, Proteins 4 (1988), 99
52 H His Histidine 7. Histidine Contains very reactive imidazole ring Nucleophilic and acid-base reactions active site molecular mass: 137 dalton black = double bond pka: 6-7 frequency: 2.2 % after Creighton, Proteins, Copyright 1993 by W.H. Freeman & Co; amino acid frequency McCaldon & Argos, Proteins 4 (1988), 99
53 pka: 6-7 H His Histidine an aromatic heterocycle with one pyrrole N (δ 1 ) and one pyridine N (ε 2 ) The two nitrogens contribute 3 valence electrons to the aromatic ring. In the neutral imidazole ring, six π-electrons are de-localised over five p-orbitals in the five atoms of the imidazole ring. This makes for three bonding molecular orbitals. after Creighton, Proteins, Copyright 1993 by W.H. Freeman & Co and Kyte, Structure in Protein Chemistry, 1995 by Garland Publ. Inc.
54 + H His Histidine - after Kyte, Structure in Protein Chemistry, 1995 by Garland Publ. Inc.
55 F Phe Phenylalanine 8. Aromatic Phenylalanine Hydrophobic and inert protein core molecular mass: 147 dalton shaded = partial double bond frequency: 3.9 % after Creighton, Proteins, Copyright 1993 by W.H. Freeman & Co; amino acid frequency McCaldon & Argos, Proteins 4 (1988), 99
56 Y Tyr Tyrosine 8. Aromatic Tyrosine Less hydrophobic due to hydroxyl group Used for ligand interactions Absorbs at 280 nm shaded = partial double bond molecular mass: 163 dalton frequency: 3.2 % pka: 11 after Creighton, Proteins, Copyright 1993 by W.H. Freeman & Co; amino acid frequency McCaldon & Argos, Proteins 4 (1988), 99
57 W Trp Tryptophane 8. Aromatic Tryptophane Indole ring important for absorption and flourescence molecular mass: 186 dalton shaded = partial double bond frequency: 1.3 % black = double bond after Creighton, Proteins, Copyright 1993 by W.H. Freeman & Co; amino acid frequency McCaldon & Argos, Proteins 4 (1988), 99
58 Phe Trp Tyr Wetlaufer, Adv. Protein Chem. 17 (1962), 303
59 Phe Trp Tyr Creighton, Proteins, Copyright 1993 by W.H. Freeman & Co
60 C Cys Cysteine 9. Sulfur containing Cysteine R: -CH 2 -SH Thiol group is most reactive side chain active sites Thiolate is a potent nucleophile! Sensitive to oxidation! pka: molecular mass: 103 dalton frequency: 1.7 % after Creighton, Proteins, Copyright 1993 by W.H. Freeman & Co; amino acid frequency McCaldon & Argos, Proteins 4 (1988), 99
61 C Cys Cysteine 9. Sulfur containing cysteine oxidation disulfide formation Cellular system to prevent oxidation: Creighton, Proteins, Copyright 1993 by W.H. Freeman & Co
62 C Cys Cysteine 9. Sulfur containing thiole-disulfide exchange Creighton, Proteins, Copyright 1993 by W.H. Freeman & Co
63 9. Sulfur containing Cleland s reagent C Cys Cysteine DTT Creighton, Proteins, Copyright 1993 by W.H. Freeman & Co
64 C Cys Cysteine 9. Sulfur containing Ellman Assay DTNB di-thio-bis-nitrobenzoic acid after Creighton, Proteins, Copyright 1993 by W.H. Freeman & Co
65 9. Sulfur containing C Cys Cysteine alkylation at basic ph pka: Creighton, Proteins, Copyright 1993 by W.H. Freeman & Co
66 9. Sulfur containing C Cys Cysteine p-mercuribenzoic acid Creighton, Proteins, Copyright 1993 by W.H. Freeman & Co
67 9. Sulfur containing Methionine R: -CH 2 -CH 2 -S-CH 3 Long and flexible and hydrophobic M Met Methionine less sensitive to oxidation molecular mass: 131 dalton frequency: 2.4 % after Creighton, Proteins, Copyright 1993 by W.H. Freeman & Co; amino acid frequency McCaldon & Argos, Proteins 4 (1988), 99
68 9. Sulfur containing M Met Methionine methionine oxidation by air Creighton, Proteins, Copyright 1993 by W.H. Freeman & Co
69 A Venn diagram showing the relationship of the 20 naturally occurring amino acids Taylor, W. R. The Classification of Amino Acid Conservation. J. Theor. Biol. 119 (1986), ; Livingstone & Barton, Meth. Enzymol. 266 (1996),
70 Essential amino acids I Ile, L Leu, V Val, W Trp, F Phe, M Met, K Lys, T Thr
71 Modified amino acids
72 phosphorylation O-phosphonoserine, O-phosphonothreonine, O-phosphonotyrosine, O-phosphonoglutamate, N-phosphonolysine, N-phosphonohistidine, N-phosphonoarginine, S-phosphonocysteine Jack Kyte, Structure in Protein Chemistry, 1995 by Garland Publ. Inc.; Uy, R. & Wood, F., Science 198 (1977),
73 glycosylation O-(polymannosyl)serine, O-(polymannosyl)threonine, O-[oligo(α1,2)galactosyl]serine, O-(3-O-(β-glucosyl)-α-fucosyl]threonine, O-[2-O-(α-glucosyl)-β-galactosyl)-5-hydroxylysine, O-(β-xylosyl)serine, O-[4-O-(β-galactosyl)-β-xylosyl]serine, S-digalactosylcysteine, S-triglucosylcysteine, O-(glucosylarabinosyl)hydroxyproline, O-(N-acetylglucosaminyl)serine Jack Kyte, Structure in Protein Chemistry, 1995 by Garland Publ. Inc.; Uy, R. & Wood, F., Science 198 (1977),
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