7. DIPOLE ORIGIN OF PEPTIDE BOND PLANE NOT ALL CONFORMATIONS POSSIBLE PREFERED CONFORMATIONS
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10. the alpha-helix: repeating i,i+4 h-bonds 2 1 3 4 5 7 8 9 6 10 11 12 right-handed helical region of phi-psi space hydrogen bond
11. The -helix, with i,i+4 h-bonds, is not the only way to have local hydrogen bonding of the backbone to itself. The 3 10 helix has hydrogen bonds between residues i and i+3 The helix has hydrogen bonds between residues i and i+5. For a number of reasons almost all helices in proteins are -helices--include backbone, side chain steric issues, van der Waals contacts, H-bond geometry -helix 3 10 helix helix these are poly-Ala, so the gray balls on the outside are -carbons from the side chains
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16. Principal types of secondary structure found in proteins Repeating ( ) values -63 o -42 o -57 o -30 o -119 o +113 o -139 o +135 o -helix (1 5) (right-handed) helix (1 4) Parallel -sheet Antiparallel -sheet
17. STRUCTURES IN ACTION GCN4 “leucine zipper” (green) bound as a dimer (two copies of the polypeptide) to target DNA The GCN4 dimer is formed through hydrophobic interactions between leucines (red) in the two polypeptide chains Leu Leu
19. Do Small Peptides have Conformation Yes & No. S-Peptide Ribonuclease A – Helical structure in solution Use of Helix Inducing Solvents – TFE and N-Propanol
24. BIOLOGY OF PEPTIDES RIBOSOMAL PROTEINS NON-RIBOSOMAL PEPTIDES SPECIFIC ENZYMES PROTEOLYTICALY PROCESSED DEGRADED TO AA (Antibiotics, phytochelatins) (Enzymes) MHC Peptides
25. CHEMICAL METHOD –PEPTIDE SYNTHESIS STAGE 1: ASSEMBLE AA ON POLYMER SUPPORT (R – PROTECTED) NON-REACTIVE STAGE 2: CLEAVE THE SYNTHESIZED PEPTIDE a) CLEAVAGE OF CHAIN b) DE-PROTECT SIDE CHAIN STAGE 3: PURIFY CRUDE PEPTIDES – HPLC STAGE 4: STORAGE – LYOPHILIZE, SPEEDVAC, ETC STAGE 5: SEQUENCE, MALDI-TOF
26. SOLID-PHASE PEPTIDE SYNTHESIS (SPPS) STAGE 1: a) Attach N-terminal + Side Chain Protected to Polymer Support (Activation of C & Coupling to Support) b) Deprotection (N-term ) c) Coupling Next AA (Protected) d) Deprotection (N-term) Continued ….
29. Conformational Trap of product – ambient conditions, easy Isolation, and Purification of Products Applications 1. Ability to Incorporate Non-Natural aminoacids or synthesize Man-made peptides or proteins of therapeutic interest Semisynthetic Insulin, Hemoglobin, and IL-10 Sortases – Glycoprotein synthesis Laboratory reagents :- Protein with reporter groups, Kinases or Phosphotases with Pmp(phosphonomethylene phenylalanine )