Biologisch-chemisches Praktikum, Teil B Peptide and protein chemistry
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1 Biologisch-chemisches Praktikum, Teil B Peptide and protein chemistry Part 2: Peptide synthesis (protease inhibitor) Protein labeling Protease inhibition assay Riboflavin analog: pk a change upon binding to protein Phytocyanin: folding, stability, non-covalent bonds 1
2 Solid-phase Peptide Synthesis Robert B. Merrifield 2
3 SPPS: Fmoc- and Boc-Strategy F TFA Fmoc Boc: 3
4 SPPS: Activators Carbodiimides: Triazoles: C DCC ATU PyBP C DIC BTU CTU CMU 4
5 ATU: eighbouring Group Effect 5
6 Proteases 6
7 Protease Inhibitors Reversible: BPTI Atazanavir Saquinavir Irreversible: PMSF E-64 7
8 Why Antipain Analog? Antipain Antipain analog Lysine is easier to couple and easier to deprotect. Methyl ester difficult to remove on resine and impossible in solution. iether of the modifications affects activity! 8
9 Urea Linker Formation Boc Boc Boc Boc Boc Boc Boc Boc C C C C C C 2 9
10 Two Compounds with the Same Mass Exact Mass: Molecular Weight: Exact Mass: Molecular Weight:
11 Trypsin Inhibition by Methyl-Antipain 0.5 D 410, AU VV = VV mmmmmm MMMMMMMM MMMMMMMM + KK ii Time, sec 11
12 Trypsin Inhibition by Methyl-Antipain: Fitting to Correct Equation 16 Trypsin inhibition by methyl-antipain R2K 0.5 mm L-BAPA, p 8.1, RT, µm trypsin 14 Rate, M/min Vo ± 0.22 E 0.56 ± Ki ± R2 = A K R2= [Me-AP R2K], M 12
13 Important!!! Please give unused synthesized inhibitor to me for purification! 13
14 Protein Labeling Purposes: Protein structure and dynamics Protein-protein and protein-ligand interactions Protein distribution, transport and fate in vivo Drug delivery Protein visualization Methods: Modification of native amino acids (mostly lysine and cysteine) Incorporation of modifieable unnatural amino acids Incorporation of pre-labeled peptides using native chemical ligation (CL) 14
15 Protein Labeling: Examples -ydroxysuccinimid (S) ester: Maleimide: Click reaction: 15
16 Thermodynamics of Protein Folding U F K ffffffffffffff = F U GG ffffffffffffff = RRRR ln KK ffffffffffffff = UU FF TT SS UU FF Bond breaking and formation Folding of peptide chain Release of structured water molecules For most globular proteins G folding = kcal/mol 16
17 Entropic Contributions to Protein Folding 17
18 Energetics and Kinetics of Folding Easy and fast Difficult and slow (or not) A.orwich. J. Clin Invest. 2002;110(9):
19 on-covalent Bonds in Protein Structure ydrophobic interactions Van der Waals interactions Ionic interactions ydrogen bonds Disruption of non-covalent bonds can: Provide information of their relative contribution to the structure Give estimate of protein s thermodynamic stabilty Allow study of protein folding kinetics/pathways 19
20 Protein Structure Disruptors (Denaturants) Chaotropic Agents a + - S C Denaturing Detergent a + S - Sodium dodecyl sulfate (SDS) 20
21 Phytocyanin Light-harvesting Antenna 21
22 Chromophore: Phycocyanobilin 22
23 Phycocyanobilin Bound to Phycocyanin C C 3 C C S Cys 23
24 Phycocyanobilin Free in Solution 24
25 Interior of Folded Proteins Provide Enviroment Very Different from Solution 25
26 pk a s of Amino Acids Differ on Protein Surface and in Protein Interior AA/Group Summary of measured amino acid pk a values in folded proteins pk a value in alanine pentapeptides Low pk a value Folded proteins igh pk a value Asp Glu is Cys Tyr Lys C-term term Grimsley, G. R., et al. (2009). Protein Sci 18(1):
27 Effects of Ligand (Substrate) Binding to Proteins Change in pk a Spectral properties Redox potentials Bond strength ucleo-/electrophilic properties Stereoselectivity 27
28 Riboflavin-binding Protein (RBP) from Chicken Egg Whites 220 amino acids Glycosilated (pos. 36 and 147) eavily phosphorilated (loop ) K d (Riboflavin) = 1.3 nm (p 6-9) Monaco,. L. (1997). EMB J 16(7):
29 Structures of Riboflavin and Its Derivatives Riboflavin Adenine Dinucleotide (FAD) Riboflavin Mononucleotide (FM) Riboflavin (vitamin B 2 ) P P
30 Spectra of Free and RBP-bound Riboflavin at Various p free bound Chenprakhon, P., et al. (2012). Journal of Chemical Education 89(6):
31 pk a Determination of Free and RBP-bound Riboflavin Fit to equation: AA oooooo = AA 1111 pppp + AA AA 1111 pppp aa 1111 pppp aa pppp Derived from: pppp = ppkk aa + log AA enderson-asselbalch equation Chenprakhon, P., et al. (2012). Journal of Chemical Education 89(6):
32 Using SciDAVis to fit pk a data AA oooooo = AA 1111 pppp + AA AA 1111 pppp aa 1111 pppp aa pppp a = 0,0899 +/- 0,00069 b = 0,127 +/- 0,00075 K = 10,01 +/- 0,045 R^2 = 0,
33 Using SciDAVis to fit pk a data Change! 33
34 eutral Red Riboflavin Analog
35 Why analog? Advantages: igher analytical wavelengths (no protein interference) Lower pk a Stronger signal Beautiful color Disadvatages: Weaker binding (2.2 µm at p 9.0) More expensive 35
36 Protein Folding in the GroEL/ES Chaperone Cage M. ayer-artl,, A. Bracher, F. U. artl. Trends in Biochem. Sciences Vol. 41, p
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