1. Protein Sequences

3. The Genetic Code

4. The natural extension of the genetic code…

5. 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 8.Comparing protein sequences to describe evolutionary processes.

6. Q: How many amino acids are there?   

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

8. Atom nomenclature within amino acids (as used within the PDB) CA CB C O N OG1CG2

9. 77 CACBCGCDCE NZ C O, OXT N

10. 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 The.pdb file format Atom numberAtom nameResidue nameChain IDResidue number X-coordinateY-coordinateZ-coordinateOccupancy B-factor (aka Temp factor) Atom type Record name

11. Lys Arg 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. -The alpha carbon (CA) is immediately adjacent the most oxidized carbon (which is the CO 2 - 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. Atom nomenclature within amino acids (as used within the PDB)

12. Numbers are used to discriminate between similar positions… CB CG OD1 ND2 CB CG ND1 CE1NE2 CD2 Here are some harder examples… CB CG CD2 CE2 CZ OH CD1 CE2 CB CG CD2 CD1 NE1 CE2 CH2 CE3 CZ2 CZ3 CB CD2 CD1 CG CB OG1CG2

13. 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.

14. 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 8.Comparing protein sequences to describe evolutionary processes.

16. Fischer projection

18. 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 8.Comparing protein sequences to describe evolutionary processes.

19. Terminologies 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.

25. It’s actually a bit more complicated…

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

27. 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 8.Comparing protein sequences to describe evolutionary processes.

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

31. 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 8.Comparing protein sequences to describe evolutionary processes.

37. 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 8.Comparing protein sequences to describe evolutionary processes.

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

39. 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.

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

41. Amino acid to Dipeptide Amino Acid 1 Amino Acid 2 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 yellow box form a rigid planar unit and, as we will see next, there is no rotation around the C-N bond. Peptide bond Note: this chemistry will not work as drawn!

42. 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.

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

44. 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 8.Comparing protein sequences to describe evolutionary processes.

45. --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”.

49. 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 8.Comparing protein sequences to describe evolutionary processes.

51. Multiple sequence alignments Given the sequences: INDUSTRY INTERESTING IMPORTANT One example of a MSA is:But is it better than: IN-DUST--RYINDU--ST-RYINTERESTING IMPOR--TANTIMPOR-T-ANT

52. Multiple sequence alignments I-N-DU-ST-RYI--NDU-ST-RY- I-NTERESTINGI--NTERESTING IMPO-R--TANTI-MPO-R--TANT IN-DUTS--RYINDU--ST-RYINTERESTING IMPOR--TANTIMPOR-T-ANT I-NDUS--T-RY-I-N--D--U-S-T-RY INT-ERES-TINGI-N-TE-RE-S-TING IMPOR--TAN--T-M-PO--RTA-NT---

53. Multiple sequence alignments Possible MSAEntire column can NOT have only gaps! I-N-DU-ST-RYI--NDU-ST-RY- I-NTERESTINGI--NTERESTING IMPO-R--TANTI-MPO-R--TANT Can NOT move residues aroundPossible IN-DUTS--RYINDU--ST-RYINTERESTING IMPOR--TANTIMPOR-T-ANT Very few matches!Too many gaps! I-NDUS--T-RY-I-N--D--U-S-T-RY INT-ERES-TINGI-N-TE-RE-S-TING IMPOR--TAN--TIM-PO--RTA-NT---

54. Which alignment pairs make the most sense? AVGTLE VLASID AVGTLE EKWVKV VS. A-VT-G-R-L-E AA-TA-Q-V-IE AVTG-RLE AATAQ-IE VS. AVWF----VLIM ALWFAMVFILIM ESQG----KTD DTQADGKCRTD VS. More similar amino acids Fewer gapsGap location makes more sense because gaps are less frequent in nonpolar regions.

55. A multiple sequence alignment: -CAPSRPLNENDDGR-QAFELIGTAVNM... -CVPGRGEMEHDD-RDQVLELFGTVVNL... -AVPKRAALQNDDGR-QGWELYGTVSAQ... -AVPTKMNCFNDDGR-QSVNLIGTVSGN... -ILPARTSMCNDDGR-QTIEMKGTPAGG... --APGK--NGHKLV--Q-FELKGTYSRT... AFAPRRIKMVNKLGR-QNFTLLGTFERT... AYRPDRCNTCNKLGR-QDVELMGTDART... -YRPEEWFGENKLGR-QSAELIGTDERS... --APL-ETYWPKLGR-QTGALAGTNSAV... --RPY-KAGWNKLGR-QSYELGGTNPYI... ---PARAKNMG---R-QSYHL--TMEWQ... Chothia & Lesk. EMBO J. 5:823- 826 (1986).

56. AN EXAMPLE MULTIPLE SEQUENCE ALIGNMENT. Conserved residues are indicated by color. Note that gaps tend to cluster together. Also gaps at the N- and C-terminal ends are more common. Why?

57. REGULAR EXPRESSIONS AND SEQUENCE LOGOS. Regular expressions provide a coarse-grain summary of an alignment segment. Sequence logos essentially due the same, but without information loss (cf. http://en.wikipedia.org/wiki/Sequence_logo).http://en.wikipedia.org/wiki/Sequence_logo

58. A PHYLOGENETIC TREE DESCRIBES AN EVOLUTIONARY PROCESS. But from a more pragmatic viewpoint, it also visually describes the similarities and dissimilarities between sequences within a multiple alignment.