Protein Structure and Function. Amino acid structure
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1 Protein Structure and Function Lecture 2b: Amino acid structure and properties Amino acid structure Un-ionized form Dipolar form (zwitterion) 2 Amine (α-amino) Carboxylic acid C 3 C Side chain 1
2 Ionization state vs p Predominant forms 3 C 3 C 2 C p 1 p 7 p 11 Chirality at C-alpha L-amino acid D-amino acid 3 C Chiral center C 3 L- and D-amino acids 2
3 Aliphatic side chains Glycine (Gly, G) Alanine (Ala, A) Valine (Val, V) 3 C 3 C 3 C C 3 C 3 C C 3 Leucine (Leu, L) Isoleucine (Ile, I) 3 C 3 C C 2 3 C C 3 C C C 3 C 2 C 3 Aromatic side chains Phenylalanine (Phe, F) C 3 C 2 Tyrosine (Tyr, Y) C 3 C 2 Tryptophan (Trp, W) C 3 C 2 C 3 C 2 istidine (is, ) Imidazole ring Indole ring 3
4 Spectroscopic properties of aromatic amino acids UV Absorbance Phe, λ max 256 nm Tyr, λ max 275 nm Trp, λ max 280 nm Fluorescence Phe, λ max 282 nm Tyr, λ max 303 nm Trp, λ max 348 nm Environment affects the observed spectrum Can be used to probe conformational changes Basic side chains Lysine (Lys, K) Arginine (Arg, ) 3 C 3 C C 2 C 2 C 2 C 2 C 2 C 2 3 C
5 Acid and amide side chains Aspartate (Asp, D) Asparagine (Asn, ) C C 3 3 C 2 C 2 2 Glutamate (Glu, E) C 3 C 2 Glutamine (Gln, Q) C 3 C 2 C 2 C 2 2 ydroxyl and sulfur-containing side chains Serine (Ser, S) Threonine (Thr, T) Methionine (Met, M) 3 C 3 C 3 C C 2 3 C C C 2 C 2 S Cysteine (Cys, C) C 3 3 C C 2 S 5
6 Proline Alanine (Ala, A) Proline (Pro, P) 3 C 2 C C 3 Pyrrolidine ring Side chain atom nomenclature δ ε γ β α δ2 β γ δ1 α δ γ1 β α γ2 Lysine (Lys, K) Leucine (Leu, L) Isoleucine (Ile, I) β-branched 6
7 Amino acid pk a Amino acid Arginine (Arg, ) Aspartic Acid Cysteine Glutamic acid istidine Lysine Tyrosine -C( 2 ) 2 -C -S -C Im -3 -C pka of side chain Backbone , -C Side chain polarity onpolar Ala, Val, Leu, Ile, Met, Cys, Trp, Phe, Pro Ambiguous Gly (nonpolar), is (may be charged) Polar Ser, Thr, Asn, Gln, Tyr Charged Asp, Glu, Lys, Arg 7
8 Amino acid names, abbreviations, mnemonics Alanine Ala A Arginine Arg -ginine Asparagine Asn As Aspartate Asp D AsparDic acid Cysteine Cys C Glutamine Gln Q Q-tamine Glutamate Glu E GluEtamic acid Glycine Gly G istidine is Isoleucine Ile I Amino acid names, abbreviations, mnemonics Leucine Leu L Lysine Lys K K, letter before L Methionine Met M Phenylalanine Phe F Fenylalanine Proline Pro P Serine Ser S Threonine Thr T Tryptophan Trp W double ring Tyrosine Tyr Y tyrosine Valine Val V 8
9 Peptide bond formation Amino-terminal or -terminal residue Carboxy-terminal or C-terminal residue Cis vs trans peptide bond Peptide bonds are overwhelmingly trans Cis peptide bonds result in Cα-Cα repulsion Cα Cα Exception: cis Xaa-proline Cδ 2 -C C- Cα Cα 9
10 Cis/trans peptide bond statistics Disulfide bonds S S 4 5 Cysteines oxidized to Cystine (a dimer of two cysteines). Inter- and intra-chain S-S bonds possible. 10
11 Cyclic peptide Cyclosporin Prevents rejection following organ or bone marrow transplants Amino Acid Alanine Arginine Asparagine Abbrev Ala Arg Asn Sym A Mass Pept mass C Aspartic Acid Asp D Cysteine Glutamine Glutamic acid Glycine Cys Gln Glu Gly C Q E G istidine is Isoleucine Ile I Leucine Leu L Lysine Lys K Methionine Met M Phenylalanine Phe F Proline Pro P Serine Ser S Threonine Thr T Tryptophan Trp W Tyrosine Tyr Y Valine Val V
12 Protein sequence As small as 25 amino acids to as large as 3000 amino acids for fibrous proteins. Typically residues Sequence comparisons and analysis can be used to construct evolutionary trees. emoglobin and myoglobin Sequence similarity to a known protein can be used to deduce the structure and function of a new protein. Mutations, natural and recombinant, provide information on critical residues. Summary Proteins are made up of one or more polypeptide chains Primary structure = amino acid sequence ften referred to as the 1D structure of the protein But remember, amino acids are 3D objects 20 common α-amino acids found in proteins L-isomers Average MW of an amino acid in a protein is daltons eactive functional groups in some side chains Peptide bond is almost always trans p-dependent ionization state 12
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