Structure and Properties of Amino Acids Peptides Proteins

Structure and Properties of Amino Acids, Peptides, Proteins and Enzymes 1

Aminoacids L-alanine D-alanine Enantiomers = non superimposable mirror images

Stereochemical Notation Fischer: L (D) natural alanine Cahn-Ingold-Prelog (C. I. P. ): S (R)

Michael H. Engel, Macko, S. A. , Isotopic evidence for extraterrestrial non-racemic amino acids in the Murchison meteorite, Nature, vol. 389, 1º settembre 1997, pp. 265– 268, DOI: 10. 1038/38460. George Cooper, Kimmich, Novelle; Belisle, Warren; Sarinana, Josh; Brabham, Katrina; Garrel, Laurence, Carbonaceous meteorites as a source of sugarrelated organic compounds for the early Earth, Nature, vol. 414, 20 dicembre 2001, pp. 879– 883, DOI: 10. 1038/414879 a. Zita Martins et al. , Extraterrestrial nucleobases in the Murchison meteorite, Earth and Planetary Science Letters, vol. 270, 1– 2, 2008, pp. 130– 136, DOI: 10. 1016/j. epsl. 2008. 03. 026. Di User: Basilicofresco - Derivative work from Image: Murchison meteorite. jpg, CC BY-SA 3. 0, https: //commons. wikimedia. org/w/index. php? curid=4301968

Acids Neutral Glycine GLY G Triptophan TRP W Aspartic Ac. ASP D Alanine ALA A Serine SER S Glutammic Ac. GLU E Valine VAL V Threonine THR T Leucine LEU L Cysteine CYS C Isoleucine ILE I Methionine MET M Arginine ARG R Asparagine ASN N Lysine LYS K Phenylalanine PHE F Bases Glutammine GLN Q Tyrosine TYR Y Histidine HIS H Proline PRO P

Non Proteinogenic a. a. L-Dopa (anti-Parkinson’s) Kainic Acid stimulant (seaweed) Non proteinogenic a. a. are occasionally found in proteins replaces Azetidin 2 -carboxylic acid Pro Norleucine Met

Post-traslational Modifications C, N-terminal Side chains Lys Asp, Glu

Post-traslational Modifications Ser, Thr Cys Arg citrulline ornithine

Peptides A dipeptide: phenylalanine Phe-Ala FA N-terminal Trans peptide bonds C-terminal A tripeptide: phenylalanylserine Phe-Ala-Ser FAS

The Peptide Bond Amide resonance planar (sp 2) C, N, O restricted rotations

cis-trans Peptide Bonds trans amides are generally more stable (less hindered) w trans w = 180° the proline case cis w = 0°

Conformations of Peptides Ramachandran Plot b-sheet a-helix (left-handed) a-helix (right-handed)

Conformations of Peptides b-sheet a-helix antiparallel

Secondary Structure of Proteins α-helix β-sheet

Secondary Structure of Proteins α-helix β-sheet

Secondary Structure of Proteins

Conformations of Peptides b-turn

Secondary Structure of Proteins Antiparallel b Sheets Helices and Parallel b Sheets

Chou-Fasman Rule a-helix Glu Ala Leu His Met Gln Trp Val Phe Lys Ile Asp Thr Ser Arg Cys Asn Tyr Pro Gly promote (helicogenic) neutral inhibit 4 helicogenic aa in a sequence of 6 initiate a a-helix b-sheet Met Val Ile Cys Tyr Phe Gln Leu Thr Trp Ala Arg Gly Asp Lys Ser His Asn Pro Glu promote neutral inhibit 3 promoters in a sequence of 5 initiate a b sheet. 4 inhibitors terminate a b sheet

Tertiary Structure Collagen: LINEAR Haemoglobin: GLOBULAR

Hiv-protease complexed with a substrate