Abstract
Developments in chemical protein synthesis have enabled the generation of tailor-made proteins including incorporation of many types of modifications into proteins, enhancing our ability to control site-specificity of protein posttranslational modifications (PTMs), modify protein backbones and introduce photocrosslinking probes. For PDZ (postsynaptic density protein, disks large, zonula occludens) protein domains, expressed protein ligation (EPL) has been employed to introduce analogs of cognate amino acids, amide-to-ester bond mutations, and phosphorylations in the study of PDZ domain-mediated protein-protein interactions (PPIs). Here, we present protocols for EPL of PDZ domains focusing on phosphorylation and amide-to-ester modifications in the PDZ domain proteins.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Merrifield RB (1963) Solid-phase peptide synthesis. I. The synthesis of a tetrapeptide. J Am Chem Soc 85:2149–2154
Palomo JM (2014) Solid-phase peptide synthesis: an overview focused on the preparation of biologically relevant peptides. RSC Adv 4:32658–32672
Behrendt R, White P, Offer J (2016) Advances in Fmoc solid-phase peptide synthesis. J Pept Sci 22:4–27
Wöhr T, Mutter M (1995) Pseudo-prolines in peptide synthesis: direct insertion of serine and threonine derived oxazolidines in dipeptides. Tetrahedron Lett 36:3847–3848
Spare LK, Laude V, Harman DG, Aldrich-Wright JR, Gordon CP (2018) An optimised approach for continuous-flow solid-phase peptide synthesis utilising a rudimentary flow reactor. React Chem Eng 3:875–882
Varela Y, Vanegas Murcia M, Patarroyo M (2018) Synthetic evaluation of standard and microwave-assisted solid-phase peptide synthesis of a long chimeric peptide derived from four plasmodium falciparum proteins. Molecules 23:2877
Dawson PE, Kent SB (2000) Synthesis of native proteins by chemical ligation. Annu Rev Biochem 69:923–960
Conibear AC, Watson EE, Payne RJ, Becker CF (2018) Native chemical ligation in protein synthesis and semi-synthesis. Chem Soc Rev 47:9046–9068
Johnson EC, Kent SB (2006) Insights into the mechanism and catalysis of the native chemical ligation reaction. J Am Chem Soc 128:6640–6646
Li J, Li Y, He Q, Li Y, Li H, Liu L (2014) One-pot native chemical ligation of peptide hydrazides enables total synthesis of modified histones. Org Biomol Chem 12:5435–5441
Thompson RE, Liu X, Alonso-García N, Pereira PJB, Jolliffe KA, Payne RJ (2014) Trifluoroethanethiol: an additive for efficient one-pot peptide ligation- desulfurization chemistry. J Am Chem Soc 136:8161–8164
Huang YC, Chen CC, Gao S, Wang YH, Xiao H, Wang F, Li YM (2016) Synthesis of l-and d-ubiquitin by one-pot ligation and metal-free desulfurization. Chem Eur J 22:7623–7628
Ghassemian A, Wang CIA, Yau MK, Reid RC, Lewis RJ, Fairlie DP, Durek T (2013) Efficient chemical synthesis of human complement protein C3a. Chem Commun 49:2356–2358
Torbeev VY, Kent SB (2007) Convergent chemical synthesis and crystal structure of a 203 amino acid “covalent dimer” HIV-1 protease enzyme molecule. Angew Chem Int Ed 46:1667–1670
Durek T, Becker CF (2005) Protein semi-synthesis: new proteins for functional and structural studies. J Biomed Eng 22:153–172
Blanco-Canosa JB, Nardone B, Albericio F, Dawson PE (2015) Chemical protein synthesis using a second-generation N-acylurea linker for the preparation of peptide-thioester precursors. J Am Chem Soc 13:7197–7209
Huang YC, Chen CC, Li SJ, Gao S, Shi J, Li YM (2014) Facile synthesis of C-terminal peptide hydrazide and thioester of NY-ESO-1 (A39-A68) from an Fmoc-hydrazine 2-chlorotrityl chloride resin. Tetrahedron Lett 70:2951–2955
Muir TW, Sondhi D, Cole PA (1998) Expressed protein ligation: a general method for protein engineering. Proc Natl Acad Sci U S A 95:6705–6710
Haase C, Rohde H, Seitz O (2008) Native chemical ligation at valine. Angew Chem Int Ed 47:6807–6810
Sato K, Kitakaze K, Nakamura T, Naruse N, Aihara K, Shigenaga A, Otaka A (2015) The total chemical synthesis of the monoglycosylated GM2 ganglioside activator using a novel cysteine surrogate. Chem Commun 51:9946–9948
Harpaz Z, Siman P, Kumar KA, Brik A (2010) Protein synthesis assisted by native chemical ligation at leucine. Chembiochem 11:1232–1235
Han J, Luby-Phelps K, Das B, Shu X, Xia Y, Mosteller RD, Broek D (1998) Role of substrates and products of PI 3-kinase in regulating activation of Rac-related guanosine triphosphatases by Vav. Science 279:558–560
Wan Q, Danishefsky SJ (2007) Free-radical-based, specific desulfurization of cysteine: a powerful advance in the synthesis of polypeptides and glycopolypeptides. Angew Chem Int Ed 46:9248–9252
Pedersen SW, Moran GE, Sereikaitė V, Haugaard-Kedström LM, Strømgaard K (2016) Importance of a conserved Lys/Arg residue for ligand/PDZ domain interactions as examined by protein semisynthesis. Chembiochem 17:1936–1944
Eildal JN, Hultqvist G, Balle T, Stuhr-Hansen N, Padrah S, Gianni S, Jemth P (2013) Probing the role of backbone hydrogen bonds in protein–peptide interactions by amide-to-ester mutations. J Am Chem Soc 135:12998–13007
Pedersen SW, Albertsen L, Moran GE, Levesque B, Pedersen SB, Bartels L, Strømgaard K (2017) Site-specific phosphorylation of PSD-95 PDZ domains reveals fine-tuned regulation of protein-protein interactions. ACS Chem Biol 12:2313–2323
Haj-Yahya M, Lashuel HA (2018) Protein semisynthesis provides access to tau disease-associated post-translational modifications (PTMs) and paves the way to deciphering the tau PTM code in health and diseased states. J Am Chem Soc 140:6611–6621
Chin JW, Cropp TA, Anderson JC, Mukherji M, Zhang Z, Schultz PG (2003) An expanded eukaryotic genetic code. Science 301:964–967
Eissler S, Kley M, Bächle D, Loidl G, Meier T, Samson D (2017) Substitution determination of Fmoc-substituted resins at different wavelengths. J Pept Sci 23:757–762
Applied Biosystems (1998) Cleavage, deprotection, and isolation of peptides after Fmoc synthesis. Tech Bull 1–12
Schnölzer M, Alewood P, Jones A, Alewood D, Kent SB (2007) In situ neutralization in Boc-chemistry solid-phase peptide synthesis. Int J Pept Res Ther 13:31–44
Jensen KJ (2013) Solid-phase peptide synthesis: an introduction. Peptide synthesis and applications. Methods Mol Biol 1047:1–21
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2021 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Kossmann, C., Ma, S., Clemmensen, L.S., Strømgaard, K. (2021). Chemical Synthesis of PDZ Domains. In: Borg, JP. (eds) PDZ Mediated Interactions. Methods in Molecular Biology, vol 2256. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1166-1_12
Download citation
DOI: https://doi.org/10.1007/978-1-0716-1166-1_12
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-1165-4
Online ISBN: 978-1-0716-1166-1
eBook Packages: Springer Protocols