Integrative Chemical Biology Approaches for Identification and Characterization of “Erasers” for Fatty‐Acid‐Acylated Lysine Residues within Proteins

Acylation of proteins with fatty acids is important for the regulation of membrane association, trafficking, subcellular localization, and activity of many cellular proteins. While significant progress has been made in our understanding of the two major forms of protein acylation with fatty acids, N‐myristoylation and S‐palmitoylation, studies of the acylation of lysine residues, within proteins, with fatty acids have lagged behind. Demonstrated here is the use of integrative chemical biology approaches to examine human sirtuins as de‐fatty‐acid acylases in vitro and in cells. Photo‐crosslinking chemistry is used to investigate enzymes which recognize fatty‐acid acylated lysine. Human Sirt2 was identified as a robust lysine de‐fatty‐acid acylase in vitro. The results also show that Sirt2 can regulate the acylation of lysine residues, of proteins, with fatty acids within cells.     

Lysine‐directed staining of proteins for MS‐based analyses

Visualization of proteins and MS‐based analyses are elemental tasks in modern biochemistry. Nevertheless, reports about covalent protein dyes and their suitability for subsequent MS experiments remain scarce. In a recent work, we demonstrated that covalent prestaining of proteins with Uniblue A drastically speeds up proteomic workflows. The present study introduces dabsyl chloride as another truly MS‐compatible protein stain. Remarkably, although Uniblue A and dabsyl chloride employ different nucleophilic reaction mechanisms, both are highly specific for lysine residues. The predictable peptide modifications allow easy integration into state‐of‐the‐art bioinformatic workflows. Further, lysine‐directed derivatizations with hydrophobic reagents such as dabsyl chloride complement the cysteine‐directed ALiPHAT strategy for increasing the sensitivity of peptide identifications.     

2‐Oxazoline Formation for Selective Chemical Labeling of 5‐Hydroxylysine

Hydroxylation of lysine, one of posttranslational modifications of proteins, generates 5‐hydroxylysine (Koh) and plays a crucial role in regulating protein functions in cellular activity. We have developed a chemical labeling method of Koh. The 1,2‐aminoalcohol moiety of Koh in synthetic peptide sequences was trapped by an alkyne‐containing benzimidate to form a 2‐oxazoline ring. An additional ammonia treatment process removed the undesirable amidine residue formed between benzimidate and lysine. During the ammonia treatment, the oxazoline residue formed at Koh mainly remained intact, and the ring opening to the amide form was observed for only part of oxazoline, indicating that the chemical labeling is amino acid selective. Azide‐substituted biotin or fluorescent dye was attached to the peptide through Huisgen cycloaddition at Koh and converted into an alkyne‐labeled oxazoline form. The Koh‐labeling assay could provide a platform to enhance proteomic research of lysine hydroxylation.     

Syntheses of donor acceptor biobased photocurable water‐soluble resins based on poly‐l‐lysine

We report a new kind of coating using UV waterborne technique with a biobased poly(amino acid) resin. Firstly we performed the thermal polycondensation of l ‐lysine during 15 h at 150 °C to synthesize water‐soluble oligomers of poly‐l ‐lysine (PLL) with 5–6 monomer units. These oligomers were then transformed in mild conditions to give photocurable water‐soluble resins. We grafted on the poly‐l ‐lysine backbone, allyl and maleamic acid functional groups, with a grafting rate close to 65% thanks to allyl glycidyl ether and maleic anhydride respectively. The influence of the reaction time and the reagents ratio on the grafting rate was investigated. Hence, the donor/acceptor photopolymerization of the mixture of allyl ether‐poly‐l ‐lysine (PLL‐g‐AE) with maleamic acid‐poly‐l ‐lysine (PLL‐g‐MA) in aqueous solution gave yellow transparent films. The degree of conversion and other kinetic parameters have been studied and detailed. This work contributes to the development of materials based on renewable resources and cleaner processes. It opens a new pathway to both fundamental and applied‐driven research. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2015 , 53, 955–963     

Construction of L‐Lysine Sensor by Layer‐by‐Layer Adsorption of L‐Lysine 6‐Dehydrogenase and Ferrocene‐Labeled High Molecular Weight Coenzyme Derivative on Gold Electrode

A ferrocene‐labeled high molecular weight coenzyme derivative (PEI‐Fc‐NAD) and a thermostable NAD‐dependent L ‐lysine 6‐dehydrogenase (LysDH) from thermophile Geobacillus stearothermophilus were used to fabricate a reagentless L ‐lysine sensor. Both LysDH and PEI‐Fc‐NAD were immobilized on the surface of a gold electrode by consecutive layer‐by‐layer adsorption (LBL) technique. By the simple LBL method, the reagentless L ‐lysine sensor, with co‐immobilization of the mediator, coenzyme, and enzyme was obtained, which exhibited current response to L ‐lysine without the addition of native coenzyme to the analysis system. The amperometric response of the sensor was dependent on the applied potential, bilayer number of PEI‐Fc‐NAD/LysDH, and substrate concentration. A linear current response, proportional to L ‐lysine concentration in the range of 1–120 mM was observed. The response of the sensor to L ‐lysine was decreased by 30% from the original activity after one month storage.     

A Versatile Approach for Site‐Specific Lysine Acylation in Proteins

Using amber suppression in coordination with a mutant pyrrolysyl‐tRNA synthetase‐tRNA^Pyl pair, azidonorleucine is genetically encoded in E. coli . Its genetic incorporation followed by traceless Staudinger ligation with a phosphinothioester allows the convenient synthesis of a protein with a site‐specifically installed lysine acylation. By simply changing the phosphinothioester identity, any lysine acylation type could be introduced. Using this approach, we demonstrated that both lysine acetylation and lysine succinylation can be installed selectively in ubiquitin and synthesized histone H3 with succinylation at its K4 position (H3K4su). Using an H3K4su‐H4 tetramer as a substrate, we further confirmed that Sirt5 is an active histone desuccinylase. Lysine succinylation is a recently identified post‐translational modification. The reported technique makes it possible to explicate regulatory functions of this modification in proteins.     

Hydroxamic Acid‐Piperidine Conjugate is an Activated Catalyst for Lysine Acetylation under Physiological Conditions

Lysine acylation of proteins is an essential chemical reaction for posttranslational modification and as a means of protein modification in various applications. N,N‐Dimethyl‐4‐aminopyridine (DMAP) derivatives are widely‐used catalysts for lysine acylation of proteins; however, the DMAP moiety mostly exists in a protonated, and thus deactivated, form under physiological conditions due to its basicity. An alternative catalytic motif furnishing higher acylation activity would further broaden the possible applications of chemical lysine acylation. We herein report that the hydroxamic acid‐piperidine conjugate Ph‐HXA is a more active catalytic motif for lysine acetylation than DMAP under physiological conditions. In contrast to DMAP, the hydroxamic acid moiety is mostly deprotonated under aqueous neutral pH, resulting in a higher concentration of the activated form. The Ph‐HXA catalyst is also more tolerant of deactivation by a high concentration of glutathione than DMAP. Therefore, Ph‐HXA might be a suitable catalytic motif for target protein‐selective and site‐selective acetylation in cells.     

Enzyme‐Responsive Intracellular‐Controlled Release Using Silica Mesoporous Nanoparticles Capped with ε‐Poly‐L‐lysine

The synthesis and characterization of two new capped silica mesoporous nanoparticles for controlled delivery purposes are described. Capped hybrid systems consist of MCM‐41 nanoparticles functionalized on the outer surface with polymer ε‐poly‐L ‐lysine by two different anchoring strategies. In both cases, nanoparticles were loaded with model dye molecule [Ru(bipy)₃]²⁺. An anchoring strategy involved the random formation of urea bonds by the treatment of propyl isocyanate‐functionalized MCM‐41 nanoparticles with the lysine amino groups located on the ε‐poly‐L ‐lysine backbone (solid Ru‐rLys‐S1 ). The second strategy involved a specific attachment through the carboxyl terminus of the polypeptide with azidopropyl‐functionalized MCM‐41 nanoparticles (solid Ru‐tLys‐S1 ). Once synthesized, both nanoparticles showed a nearly zero cargo release in water due to the coverage of the nanoparticle surface by polymer ε‐poly‐L ‐lysine. In contrast, a remarkable payload delivery was observed in the presence of proteases due to the hydrolysis of the polymer’s amide bonds. Once chemically characterized, studies of the viability and the lysosomal enzyme‐controlled release of the dye in intracellular media were carried out. Finally, the possibility of using these materials as drug‐delivery systems was tested by preparing the corresponding ε‐poly‐L ‐lysine capped mesoporous silica nanoparticles loaded with cytotoxic drug camptothecin (CPT), CPT‐rLys‐S1 and CPT‐tLys‐S1 . Cellular uptake and cell‐death induction were studied. The efficiency of both nanoparticles as new potential platforms for cancer treatment was demonstrated.     

Poly(L‐lysine)‐Induced Aggregation of Single‐Strand Oligo‐DNA‐Modified Gold Nanoparticles

Single‐strand oligo‐DNA‐modified Au nanoparticles (AuNPs) undergo aggregation in the presence of poly(L ‐lysine) (PLL), which is attributed to the interactions between the oligo‐DNA and PLL. These interactions between the oligo‐DNA and PLL were identified to be electrostatic when the lysine residues of PLL were positively charged and to be hydrogen bonding when the residues were deprotonated. The aggregation was promoted with an increase in the pH value at a pH level lower than the pK_a value of PLL (pK_a≈10.0) due to the gradual deprotonation of the lysine residues and thus suppressed electrostatic interactions between the positively charged lysine residues of PLL and the negatively charged backbone phosphate groups of the oligo‐DNA. At pH levels higher than the pK_a value of PLL, the aggregation was identified to be dominated by the hydrogen bonds between the bases of the oligo‐DNA and the deprotonated lysine residues of PLL. This study prompts the possibility that the spectral, and thus color, change of AuNPs upon aggregation can be used as a probe to follow the interactions between oligo‐DNA and polypeptides.     

Synthesis and ring‐opening (co)polymerization of L‐lysine N‐carboxyanhydrides containing labile side‐chain protective groups

This contribution describes the synthesis and ring‐opening (co)polymerization of several L ‐lysine N‐carboxyanhydrides (NCAs) that contain labile protective groups at the ?‐NH₂ position. Four of the following L ‐lysine NCAs were investigated: N^?‐trifluoroacetyl‐L ‐lysine N‐carboxyanhydride, N^?‐(tert‐butoxycarbonyl)‐L ‐lysine N‐carboxyanhydride, N^?‐(9‐fluorenylmethoxycarbonyl)‐L ‐lysine N‐carboxyanhydride, and N^?‐(6‐nitroveratryloxycarbonyl)‐L ‐lysine N‐carboxyanhydride. In contrast to the harsh conditions that are required for acidolysis of benzyl carbamate moieties, which are usually used to protect the ?‐NH₂ position of L ‐lysine during NCA polymerization, the protective groups of the L ‐lysine NCAs presented here can be removed under mildly acidic or basic conditions or by photolysis. As a consequence, these monomers may allow access to novel peptide hybrid materials that cannot be prepared from ?‐benzyloxycarbonyl‐L ‐lysine N‐carboxyanhydride (Z‐Lys NCA) because of side reactions that accompany the removal of the Z groups. By copolymerization of these L ‐lysine NCAs with labile protective groups, either with each other or with γ‐benzyl‐L ‐glutamate N‐carboxyanhydride or Z‐Lys NCA, orthogonally side‐chain‐protected copolypeptides with number‐average degrees of polymerization ≤20 were obtained. Such copolypeptides, which contain different side‐chain protective groups that can be removed independently, are interesting for the synthesis of complex polypeptide architectures or can be used as scaffolds for the preparation of synthetic antigens or protein mimetics. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 41: 1167–1187, 2003     

Enzyme‐Mediated,Site‐Specific Protein Coupling Strategies for Surface‐Based Binding Assays

Covalent surface immobilization of proteins for binding assays is typically performed non‐specifically via lysine residues. However, receptors that either have lysines near their binding pockets, or whose presence at the sensor surface is electrostatically disfavoured, can be hard to probe. To overcome these limitations and to improve the homogeneity of surface functionalization, we adapted and optimized three different enzymatic coupling strategies (4′‐phosphopantetheinyl transferase, sortase A, and asparaginyl endopeptidase) for biolayer interferometry surface modification. All of these enzymes can be used to site‐specifically and covalently ligate proteins of interest via short recognition sequences. The enzymes function under mild conditions and thus immobilization does not affect the receptors’ functionality. We successfully employed this enzymatic surface functionalization approach to study the binding kinetics of two different receptor–ligand pairs.     

Preparing to read the ubiquitin code: a middle‐out strategy for characterization of all lysine‐linked diubiquitins

Multiple studies demonstrate that ubiquitination of proteins codes for regulation of cell differentiation, apoptosis, endocytosis and many other cellular functions. There is great interest in and considerable effort being given to defining the relationships between the structures of polyubiquitin modifications and the fates of the modified proteins. Does each ubiquitin modification achieve a specific effect, much like phosphorylation, or is ubiquitin like glycosylation, where there is heterogeneity and redundancy in the signal? The sensitive analytical tools needed to address such questions readily are not yet mature. To lay the foundation for mass spectrometry (MS)‐based studies of the ubiquitin code, we have assembled seven isomeric diubiquitins with all‐native sequences and isopeptide linkages. Using these compounds as standards enables the development and testing of a new MS‐based strategy tailored specifically to characterize the number and sites of isopeptide linkages in polyubiquitin chains. Here, we report the use of Asp‐selective acid cleavage, separation by reverse phase high‐performance liquid chromatography and characterization by tandem MS to distinguish and characterize all seven isomeric lysine‐linked ubiquitin dimers. Copyright © 2014 John Wiley & Sons, Ltd.     

Ways of selective polycondensation of L‐lysine towards linear α‐ and ε‐poly‐L‐lysine

Polylysines (PL) are highly interesting polymers due to their biocompatibility and their high number of reactive amino groups. So far it was not possible to synthesize them directly from L ‐lysine. Here, we describe two different synthesis routes to selectively polymerize lysine in one batch without the use of protection groups. Applying 1‐ethyl‐3‐(3‐dimethylaminopropyl) carbodiimide as activating agent for the polycondensation of L ‐lysine in water gave selectively linear ε‐PLL. In contrast to this, the polymerization of L ‐lysine in chloroform in the presence of dicyclohexyl carbodiimide and 18‐crown‐6 ether selectively afforded pure α‐PLL. We also assessed the capability of polylysine derivatization by polymer analog reactions with acetic anhydride, methyl iodide and 2,4,6‐trinitrobenzenesulfonic acid. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 5053–5063, 2008     

A Highly Selective Amperometric Hydrogen Peroxide Sensor Based on Silicomolybdate‐Doped‐Glutaraldehyde‐Cross‐Linked Poly‐L‐Lysine Film Modified Glassy Carbon Electrode

Silicomolybdate‐doped‐glutaraldehyde‐cross‐linked poly‐L ‐lysine (PLL‐GA‐SiMo) film modified glassy carbon electrode was prepared by means of electrostatically trapping the silicomolybdate anion in the cationic film. The PLL‐GA‐SiMo film was stable and the charge transport through the film was fast. The modified electrode shows excellent electrocatalytic activity towards hydrogen peroxide reduction with significant reduction of overpotential, however, not responded to potential interferrents such as dopamine, ascorbic acid and uric acid. This unique feature of PLL‐GA‐SiMo modified electrode allowed for the development of a highly selective method for the determination of H₂O₂ in the presence of interferents.     

Enzyme‐Mediated,Site‐Specific Protein Coupling Strategies for Surface‐Based Binding Assays

Covalent surface immobilization of proteins for binding assays is typically performed non‐specifically via lysine residues. However, receptors that either have lysines near their binding pockets, or whose presence at the sensor surface is electrostatically disfavoured, can be hard to probe. To overcome these limitations and to improve the homogeneity of surface functionalization, we adapted and optimized three different enzymatic coupling strategies (4′‐phosphopantetheinyl transferase, sortase A, and asparaginyl endopeptidase) for biolayer interferometry surface modification. All of these enzymes can be used to site‐specifically and covalently ligate proteins of interest via short recognition sequences. The enzymes function under mild conditions and thus immobilization does not affect the receptors’ functionality. We successfully employed this enzymatic surface functionalization approach to study the binding kinetics of two different receptor–ligand pairs.     

DNA‐Catalyzed Lysine Side Chain Modification

Catalyzing the covalent modification of aliphatic amino groups, such as the lysine (Lys) side chain, by nucleic acids has been challenging to achieve. Such catalysis will be valuable, for example, for the practical preparation of Lys‐modified proteins. We previously reported the DNA‐catalyzed modification of the tyrosine and serine hydroxy side chains, but Lys modification has been elusive. Herein, we show that increasing the reactivity of the electrophilic reaction partner by using 5′‐phosphorimidazolide (5′‐Imp) rather than 5′‐triphosphate (5′‐ppp) enables the DNA‐catalyzed modification of Lys in a DNA‐anchored peptide substrate. The DNA‐catalyzed reaction of Lys with 5′‐Imp is observed in an architecture in which the nucleophile and electrophile are not preorganized. In contrast, previous efforts showed that catalysis was not observed when Lys and 5′‐ppp were used in a preorganized arrangement. Therefore, substrate reactivity is more important than preorganization in this context. These findings will assist ongoing efforts to identify DNA catalysts for reactions of protein substrates at lysine side chains.     

Pyrylium‐based dye and charge tagging in proteomics

The pyrylium group is a selective reagent for ε‐amino groups in proteins. In particular, for fluorescence labeling, a number of advantages over traditional N‐hydroxysuccinimidyl ester chemistry were recognized such as the rapid prestaining procedure. Here, we have investigated the labeling reaction for the fluorogenic pyrylium dye Py‐1 using liquid chromatography coupled to MS with the aim of determining its specificity and possible side products. Peptides containing no, one, and two lysine residue and a choice of no or one cysteine residue were labeled with Py‐1 at yields > 30%. Gas phase fragmentation proved both labeling of lysine residues as well as that of the N‐terminus also in peptides that contained a lysine residue. Evidence for cysteine labeling was not found, but several other products were detected such as the results of rearrangements with adjacent acidic amino acids. Apart from the use as a fluorogenic label, Py‐1 recommends itself for N‐terminal charge tagging as alternative to the commonly used quaternary ammonium salts. Predominantly a‐ and b‐type ion series were observed for N‐terminally labeled peptides. Further applications include chromophore tagging since the labeled product is not only fluorescent but also colored red.     

Synthesis of poly(L‐lysine)‐graft‐polyesters through Michael addition and their self‐assemblies in aqueous solutions

A series of poly(L ‐lysine)s grafted with aliphatic polyesters, poly(L ‐lysine)‐graft‐poly(L ‐lactide) (PLy‐g‐PLLA) and poly(L ‐lysine)‐graft‐poly(?‐caprolactone) (PLy‐ g‐PCL), were synthesized through the Michael addition of poly(L ‐lysine) and maleimido‐terminated poly(L ‐lactide) or poly(?‐caprolactone). The graft density of the polyesters could be adjusted by the variation of the feed ratio of poly(L ‐lysine) to the maleimido‐terminated polyesters. IR spectra of PLy‐g‐PCL showed that the graft copolymers adopted an α‐helix conformation in the solid state. Differential scanning calorimetry measurements of the two kinds of graft copolymers indicated that the glass transition temperature of PLy‐g‐PLLA and the melting temperature of PLy‐g‐PCL increased with the increasing graft density of the polyesters on the backbone of poly(L ‐lysine). Circular dichroism analysis of PLy‐g‐PCL in water demonstrated that the graft copolymer existed in a random‐coil conformation at pH 6 and as an α‐helix at pH 9. In addition, PLy‐g‐PCL was found to form micelles to vesicles in an aqueous medium with the increasing graft density of poly(?‐caprolactone). © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 1889–1898, 2007