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Protein Sequences

Protein Sequences. The Genetic Code. The natural extension of the genetic code…. Overall amino acid structure Amino acid stereochemistry Amino acid sidechain structure & classification ‘ Non-standard ’ amino acids Amino acid ionization Formation of the peptide bond Disulfide bonds

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Protein Sequences

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  1. Protein Sequences

  2. The Genetic Code

  3. The natural extension of the genetic code…

  4. Overall amino acid structure • Amino acid stereochemistry • Amino acid sidechain structure & classification • ‘Non-standard’ amino acids • Amino acid ionization • Formation of the peptide bond • Disulfide bonds • Comparing protein sequences to describe evolutionary processes.

  5. Q: How many amino acids are there? a b g

  6. The twenty alpha-amino acids that are encoded by the genetic code share the generic structure… a

  7. Atom nomenclature within amino acids (as used within the PDB) O N CA C CB CG2 OG1

  8. CE CD CG CB CA C O, OXT z 7 N NZ

  9. 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 B-factor (aka Temp factor) Atom number Chain ID Residue number X-coordinate Y-coordinate Z-coordinate Occupancy Atom type Atom name Residue name Record name

  10. Atom nomenclature within amino acids (as used within the PDB) • The alpha carbon (CA) is immediately adjacent the most oxidized carbon (which is the CO2- in amino acids) • All the other heavy nuclei are named according to the Greek alphabet. • -Put otherwise, LYS can be described by: CA, CB, CG, CD, CE, and NZ. Lys • To Do: Learn how to name the atoms of all amino acids. • Hint: look at any generic PDB file to get a list of atom types. Arg

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

  12. 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.

  13. Overall amino acid structure • Amino acid stereochemistry • Amino acid sidechain structure & classification • ‘Non-standard’ amino acids • Amino acid ionization • Formation of the peptide bond • Disulfide bonds • Comparing protein sequences to describe evolutionary processes.

  14. Fischer projection

  15. Overall amino acid structure • Amino acid stereochemistry • Amino acid sidechain structure & classification • ‘Non-standard’ amino acids • Amino acid ionization • Formation of the peptide bond • Disulfide bonds • Comparing protein sequences to describe evolutionary processes.

  16. Hydrophobic: Amino acids are those with side chains that do not like to reside in an aqueous environment. Hence, these amino acids buried within the hydrophobic core of the protein. • Aliphatic: Hydrophobic group that contains only carbon or hydrogen atoms. • Aromatic: A side chain is considered aromatic when it contains an aromatic ring system. • Polar: Polar amino acids are those with side-chains that prefer to reside in an aqueous environment and hence can be generally found exposed on the surface of a protein. Terminologies

  17. It’s actually a bit more complicated…

  18. Twenty Amino acids TYR: Amphipathic GLY: Unclassifiable Hydrophobic (non polar) Polar HINT: You should definitely know this!!! Aliphatic (ALA, VAL, LEU, ILE, MET, PRO) Aromatic (PHE, TRP) Polar Neutral Charged -SH Basic -OH Amide Acidic (HIS, LYS,ARG) (ASN, GLN) (CYS) (ASP, GLU) (THR, SER)

  19. Overall amino acid structure • Amino acid stereochemistry • Amino acid sidechain structure & classification • ‘Non-standard’ amino acids • Amino acid ionization • Formation of the peptide bond • Disulfide bonds • Comparing protein sequences to describe evolutionary processes.

  20. Not uncommon amino acids in biochemistry, but they are not encoded within the genetic code (meaning not incorporated into proteins)…

  21. Overall amino acid structure • Amino acid stereochemistry • Amino acid sidechain structure & classification • ‘Non-standard’ amino acids • Amino acid ionization • Formation of the peptide bond • Disulfide bonds • Comparing protein sequences to describe evolutionary processes.

  22. Overall amino acid structure • Amino acid stereochemistry • Amino acid sidechain structure & classification • ‘Non-standard’ amino acids • Amino acid ionization • Formation of the peptide bond • Disulfide bonds • Comparing protein sequences to describe evolutionary processes.

  23. Primary structure = the complete set of covalent bonds within a protein

  24. 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. Polypeptides

  25. Q: why is the pentapeptide SGYAL different than LAYGS?

  26. Amino Acid 1 Amino Acid 2 Amino acid to Dipeptide Note: this chemistry will not work as drawn! Peptide bond Peptide bond is the amide linkage that is formed between two amino acids, which results in (net) release of a molecule of water (H2O). The four atoms in the yellow box form a rigid planar unit and, as we will see next, there is no rotation around the C-N bond.

  27. The peptide bond has a partial double bond character, estimated at 40% under typical conditions.It is this fact that makes the peptide bondplanarandrigid.

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

  29. Overall amino acid structure • Amino acid stereochemistry • Amino acid sidechain structure & classification • ‘Non-standard’ amino acids • Amino acid ionization • Formation of the peptide bond • Disulfide bonds • Comparing protein sequences to describe evolutionary processes.

  30. -- The primary structure is a complete description of the covalent bond network within a protein. -- This is almost(!) completely described by the sequence of amino acids. -- If you know that the protein is AVG…, you can look up the structures of A, V and G, plus what you know about peptide bonding allows you to complete the covalent bond structure. -- So, when does the primary structure not fully describe the covalent bond network? -- BTW, this is a HUGE pet peeve of mine…there is no such thing as a primary sequence, despite its rather common usage (including in journal article titles…UGG!). A primary sequence implies a secondary sequence, which is nonsense. While there is of course primary, secondary, tertiary and quaternary structures, there is only the “sequence”.

  31. Overall amino acid structure • Amino acid stereochemistry • Amino acid sidechain structure & classification • ‘Non-standard’ amino acids • Amino acid ionization • Formation of the peptide bond • Disulfide bonds • Comparing protein sequences to describe evolutionary processes.

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