Kevin Burgess, May 3, 2017 1 Peptides And Proteins from chapter(s) in the recommended text A. Introduction B. omenclature And Conventions by amide bonds. on the left, right. 2 -terminal C-terminal triglycine amine, acid. ammonium and a C-terminal carboxylate. trans (based on the peptide polyamide backbone alkenes. local conformations like f (the -Ca dihedral w because of amide Cα Cβ φ ψ ω Cβ Cα φ ψ ω trans cis
Kevin Burgess, May 3, 2017 2 C. Primary tructures sequence of amino sequence of similarity fold into similar shapes. Elucidation f Primary Peptide tructure Via The Edman Degradation primary structure C + 2 C 2 Me C 2 Me C -Ala-e-Me C 2 Me Cl protonate and cyclize 2 C 2 Me amino acid _-e-me_ initial cyclization product rearranged cyclized product Chromatographic analysis does require It is possible. It is not
Kevin Burgess, May 3, 2017 3 2 first thiohydantoin second thiohydantion third thiohydantoin Elucidation f Primary tructure Via Enzymatic Cleavage And Mass pectroscopy mass spectrometry so proteases at predictable sites within of a chain. Positions of cleavage vary fragment 1: -Pro-Ala-Pro-Gly-Arg- fragment 2: fragment 3: -Trp-Ala-is-Gln-Met-Val-Lys- -is-lys- fragment 4: -Pro-Trp-Pro-er-Tyr-Thr-Ala-
Kevin Burgess, May 3, 2017 4 Chymotrypsin fragment 1: -Pro-Ala-Pro-Gly-Arg-Trp- fragment 2: fragment 3: fragment 4: -Ala-is-Gln-Met-Val-Lys-is-Lys-Pro-Trp- -Pro-er-Tyr- -Thr-Ala- Elastase fragment 1: fragment 2: fragment 3: fragment 4: -Pro-Ala- -Pro-Gly- -Arg-Trp-Ala- -is-gln-met-val-lys-is-lys-pro-trp-pro-er-tyr-thr-ala- Elucidation f Primary tructure Via Cyanogen Bromide Cleavage And Mass pectroscopy methionine methionine Cg atom iminolactone produced Br 2 Br-C 2 cyclization Ac-Met-Ala- 2 sulfonium salt
Kevin Burgess, May 3, 2017 5 2 hydrolysis 2 2 iminolactone lactone Ala- 2 -Pro-Ala-Met-Val-Lys-Met-Lys- 2 BrC -Pro-Ala + -Val-Lys + -Lys- 2 -Pro-Ala-Pro-Gly-Arg-Trp-Ala-is-Gln-Met-Val-Lys-is-Lys-Pro-Trp-Pro-er-Tyr-Thr-Ala- + BrC -Pro-Ala-Pro-Gly-Arg-Trp-Ala-is-Gln + -Val-Lys-is-Lys-Pro-Trp-Pro-er-Tyr-Thr-Ala-
Kevin Burgess, May 3, 2017 6 D. econdary tructures hydrogen bonding between residues shielding of hydrophobic residues from aqueous surroundings entropy gains placing hydrophilic residues at the core placing hydrophilic residues at the periphery ionic interactions between charged side-chains stacking of aromatic rings packing of one chain against another increased temperature overlap of orbitals containing C lone pairs with other C p* orbitals addition of high concentrations of guanidine hydrochloride secondary structure. primary structures. are called helices. right handed the -terminus. most common 3.6 amino acid Pro is rarely in collagen. in the same directions. in opposite directions. the strand loops back on itself. b-turns, while g-turns antiparallel b-sheets. Different protein, a! a b-strand b sheet-turn-sheet c parallel b-sheet d antiparallel b-sheet
Kevin Burgess, May 3, 2017 7 1 3 2 4 sheet turn sheet helix 1 2 3 4
Kevin Burgess, May 3, 2017 8 6 7 5 8 helix sheet turn helix 5 6 7 8 E. Tertiary And Quaternary tructures these protein units usually are not covalently
Kevin Burgess, May 3, 2017 9 F. Constraints n Peptide And Protein tructures do not fold cyclo(-val-rn-leu-d-e-pro-) 2 gramicidin 2 2 2 2 L-rn D-rn Cys residues. oxidizing agents. BC t Bu I 2 BC t Bu BC-Cys-Cys- t Bu BC-Cys-Cys- t Bu
Kevin Burgess, May 3, 2017 10 actually following should be shown with one letter codes where: Cys = C Tyr = Y Ile = I Gln = Q Asn = Pro = P Leu = L: Gly = G -Cys-Tyr-Ile-Gln-Asn-Cys-Pro-Leu-Gly- 2 Ac-Cys-Ala-Cys-Ala-Cys-Ala-Cys- Ac-Cys-Ala-Cys-Ala-Cys-Ala-Cys- Ac-Cys-Ala-Cys-Ala-Cys-Ala-Cys- Ac-Cys-Ala-Cys-Ala-Cys-Ala-Cys- It is necessary could be done