Chapter 3: Amino Acids and Peptides

Chapter 3: Amino Acids and Peptides BINF 6101/8101, Spring 2018

Outline 1. Overall amino acid structure 2. Amino acid stereochemistry 3. Amino acid sidechain structure & classification 4. Non-standard amino acids 5. Amino acid ionization 6. Formation of the peptide bond 7. Disulfide bonds

Protein Sequence

Amino Acids q Proteins are linear polymers of amino acids connected by peptide bonds amino acids are the building blocks of proteins q There are 20 standard amino acids. Asparagine was first found in 1806 and the last amino acid discovered (Threonine) was in 1938 (over 130 years later!!) q All 20 amino acids share common structural features: a-amino acids

General Structure of an Amino Acid --The twenty α-amino acids are encoded by the genetic code --Share the generic structure: a carboxyl group and an amino group bonded to the same a-carbon --differ in R group or side chain

1. Overall amino acid structure 2. Amino acid stereochemistry 3. Amino acid sidechain structure & classification 4. Non-standard amino acids 5. Amino acid ionization 6. Formation of the peptide bond 7. Disulfide bonds

Stereoisomerism in α-amino Acids Enantiomers (mirror images) --All amino acids are chiral except for glycine --Proteins only contain L amino acids Perspective Fischer projection

Stereoisomerism in α-amino Acids

Important Terms q Hydrophobic: tending to avoid an aqueous environment. Hydrophobic molecules are non-polar and uncharged. Amino acids with this property are usually buried within the hydrophobic core of the protein. Aliphatic: carbon atoms are joined together in straight or branched open chains rather than in rings. Aromatic: contains an aromatic ring system. q Hydrophilic: tending to interact with water. Hydrophilic molecules are polar and charged. Generally found on protein surface and exposed to aqueous environment. Hydrophobic core Hydrophilic surface

Amino Acids Amino Acids 3-Letter 1-Letter Alanine Arginine Asparagine Aspartic acid Cysteine Glutamic acid Glutamine Glycine Histidine Isoleucine Leucine Lysine Methionine Phenylalanine Proline Serine Threonine Tryptophan Tyrosine Valine Ala Arg Asn Asp Cys Glu Gln Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val A R N D C E Q G H I L K M F P S T W Y V Carboxyl: D, E Hydroxyl: S, T Sulfhydryl: C Guanidine: R Imidazole: H Amido: N, Q

Nonpolar, Aliphatic R Groups

Aromatic R Groups These amino acid side chains absorb UV light at 270 280 nm

Polar, Uncharged R Groups

Positively Charged R Groups

Negatively Charged R Groups

FYI: Codes for Rare or Ambiguous Amino Acids UGA UAG *B, Z: ambiguous from protein sequencing techniques, now obsolete; *J: ambiguous from mass spectrometry for getting protein sequence

The Classification is Actually More Complicated M.J. Betts, R.B. Russell. (2003) Amino acid properties and consequences of substitutions

Essential Amino Acids for Humans Question: How many amino acid types we need to get from diet? (In other words, what are the amino acids that cannot be synthesized by our body?) Cannot be synthesized by humans Must be provided in diet Bacteria and plants can synthesize all 20 amino acids Histidine (H) Isoleucine (I) Leucine (L) Lysine (K) Methionine (M) Phenylalanine (F) Threonine (T) Tryptophan (W) Valine (V) KVWaIT FILM

Atom Naming for Amino Acids C CA CB CG CD CE O, OXT z 7 NZ N ζ NZ

Atom Naming in PDB PDB: Protein Data Bank http://www.rcsb.org/pdb/home/home.do atomic symbol remoteness indicator branch designator Greek letters "A" for alpha, "B" for beta, "G" for gamma, "D" for delta, "E" for epsilon, "Z" for zeta, and "H" for eta. C, N, O, S 1, 2, 3

PDB: Protein Data Bank http://www.rcsb.org/pdb/home/home.do

The PDB File Format ATOM 1 N PRO A 2 22.126 26.173 0.149 1.00 28.61 N ATOM 2 CA PRO A 2 21.848 26.169 1.597 1.00 27.50 C ATOM 3 C PRO A 2 20.582 25.363 1.875 1.00 26.69 C ATOM 4 O PRO A 2 19.724 25.215 0.973 1.00 26.48 O ATOM 5 CB PRO A 2 21.874 27.626 1.981 1.00 28.55 C ATOM 6 CG PRO A 2 21.899 28.434 0.721 1.00 29.65 C ATOM 7 CD PRO A 2 21.761 27.465-0.440 1.00 28.77 C ATOM 8 N LYS A 3 20.499 24.795 3.073 1.00 22.80 N ATOM 9 CA LYS A 3 19.360 23.972 3.469 1.00 22.07 C ATOM 10 C LYS A 3 18.610 24.700 4.597 1.00 18.49 C ATOM 11 O LYS A 3 19.262 25.140 5.536 1.00 17.98 O ATOM 12 CB LYS A 3 19.669 22.668 4.145 1.00 24.58 C ATOM 13 CG LYS A 3 20.495 21.675 3.360 1.00 36.59 C ATOM 14 CD LYS A 3 20.652 20.419 4.220 1.00 48.23 C ATOM 15 CE LYS A 3 19.341 19.779 4.628 1.00 53.43 C ATOM 16 NZ LYS A 3 19.502 19.003 5.891 1.00 57.07 N ATOM 17 N ALA A 4 17.319 24.698 4.389 1.00 17.98 N ATOM 18 CA ALA A 4 16.468 25.371 5.384 1.00 17.19 C Record name Atom number Atom name Residue name Chain ID Residue number X-coordinate Y-coordinate Z-coordinate Occupancy B-factor (aka Temp factor) Atom type

Numbers are used to discriminate between similar positions CB CG CB CB CG CD1 CD2 CG2 OG1 OD1 ND2 Here are some harder examples CB CG CD1 CB CG CD2 CB CG CE3 CD2 CZ3 CD2 NE2 ND1 CE1 CE1 CE2 CZ OH CD1 NE1 CE2 CZ2 CH2

Side-chain Torsion Angles -With the exception of Ala and Gly, all sidechains also have torsion angles. -To do on your own: - Count the # of chi s in each amino acid. - Determine why Ala doesn t have a chi angle. Chi1: N-CA-CB-CG Chi2: CA-CB-CG-CD Chi3: CB-CG-CD-CE Chi4: CG-CD-CE-NZ

Side Chain Torsion Angles Number of c No c Only one c 1 c 1, c 2 c 1, c 2, c 3 c 1, c 2, c 3, c 4 c 1, c 2, c 3, c 4, c 5 Amino Acid Types Gly, Ala Cys, Ser, Thr, Val Asn, Asp, His, Ile, Leu, Phe, Pro, Tyr, Trp Gln, Glu, Met Lys Arg Take this amino acid as an example

Side Chain Torsion Angles q The different conformations of the sidechain as a function of χ 1 are referred to as gauche(+), trans and gauche(-). q The amino acid is viewed along the Cβ-Cα bond www.cryst.bbk.ac.uk

In case you forgot.. CH 3 -CH 2 -CH 2 -CH 3 Newman projections

Side Chain Torsion Angles q It has been shown in the 70s by Janin et al. that different side-chain conformations don not have equal distribution over the dihedral angle space. Rather they tend to cluster at specific regions of the space. Janin J, Wodak S. Conformation of amino acid side-chains in proteins, J Mol Biol. 1978,125(3):357-86

Side Chain Torsion Angles Distribution of side-chain torsion angles for 6,638 leucine residues (403 crystal structures). The two major rotamers are labeled "1" and "2. G.J. Kleywegt and T.A. Jones, Acta Cryst. D54, 1119-1131 (1998). Right image from Dunbrack s lab

Side Chain Torsion Angles http://dunbrack.fccc.edu/

Proline: Side Chain Torsion Angles http://dunbrack.fccc.edu/bbdep2010/figures/pro0_x1.gif

q Rotamer: Rotational isomer Side Chain Rotamers q Rotamers are generally defined as low energy side-chain conformations. q Rotamers are knowledge-based. They are derived from statistical analysis of sidechain conformations in known protein structures through clustering observed conformations or by dividing torsion angle space into bins and determining an average conformation in each bin qrotamer libraries: collections of rotamers for each residue type. In general, rotamer libraries contain information about both the conformation and the frequency of a certain conformation. There are several different types of rotamer libraies.

Side Chain Rotamers http://www.cgl.ucsf.edu/chimera/docs/contributedsoftware/rotamers/rotamers.html

Modified Amino Acids Found in Proteins

Reversible Modifications of Amino Acids

Other Uncommon Amino Acids They are not encoded within the genetic code and not incorporated into proteins. They are intermediates in the biosynthesis of arginine and in the urea cycle.

Titration of Glycine Cation à Zwitterion à Anion At acidic ph, the carboxyl group is protonated and the amino acid is in the cationic form. At neutral ph, the carboxyl group is deprotonated but the amino group is protonated. The net charge is zero; such ions are called Zwitterions. At alkaline ph, the amino group is neutral NH 2 and the amino acid is in the anionic form.

Titration Curves for Glutamate PI: isoelectric point Net charge is 0. PI for glutamate: 3.22

Titration Curves for Histidine

Amino Acid Sidechain pka Values Residue pk a values: CT: 3.8 (R-CO 2 H) Asp: 4.0 (R-CO 2 H) Glu: 4.4 (R-CO 2 H) His: 6.5 (imidazole) NT: 8.0 (R-NH 3+ ) Cys: 8.5 (R-SH) Tyr: 10.0 (Ph-OH) Lys: 10.0 (R-NH 3+ ) Arg: 12.0 (guanidinium) The model pka for a particular amino acid residue is determined for the case when the titratable group is completely accessible to the solvent and minimally perturbed by the surrounding environment.

From: Protein Sci. 2006 May; 15(5): 1214 1218.

Effect of the Chemical Environment on pka a-carboxy group is much more acidic than that in carboxylic acids a-amino group is slightly less basic than in amines

Levels of Structure in Proteins Primary structure = the complete set of covalent bonds within a protein

Polypeptides Linear arrangement of n amino acid residues linked by peptide bonds. Polymers composed of two, three, a few, and many amino acid residues are called as dipeptides, tripeptides, oligopeptides and polypeptides. Proteins are molecules that consist of one or more polypeptide chains.

Formation of a Peptide Amino Acid 1 Amino Acid 2 Peptide bond Note: this chemistry will not work as drawn!

Formation of a Peptide Amino Acid 1 Amino Acid 2 Note: this chemistry will not work as drawn! Peptide bond Why is this important to biology? Peptide bond is the amide linkage that is formed between two amino acids, which results in (net) release of a molecule of water (H 2 O). The four atoms in the brown box form a rigid planar unit and, as we will see next, there is no rotation around the C-N bond.

FYI: Nucleophilic Attack Reactions The electronegative nucleophile attacks the electropositive center

FYI: Nucleophilic Attack Reactions Reality is more complicated b/c OH - is a horrible leaving group

A quick aside + +.... + + A horrible leaving group + + A viable leaving group

A Pentapeptide Numbering (and naming) starts from the amino terminus

The Peptide Bond The peptide bond has a partial double bond character, estimated at 40% under typical conditions. It is this fact that makes the peptide bond planar and rigid.

Disulfide Bond and Insulin

Disulfide Bond in Ribonuclease