Proteomic analysis of acetylation in thermophilic Geobacillus kaustophilus

Recent analysis of prokaryotic N^ε‐lysine‐acetylated proteins highlights the posttranslational regulation of a broad spectrum of cellular proteins. However, the exact role of acetylation remains unclear due to a lack of acetylated proteome data in prokaryotes. Here, we present the N^ε‐lysine‐acetylated proteome of gram‐positive thermophilic Geobacillus kaustophilus. Affinity enrichment using acetyl‐lysine‐specific antibodies followed by LC‐MS/MS analysis revealed 253 acetylated peptides representing 114 proteins. These acetylated proteins include not only common orthologs from mesophilic Bacillus counterparts, but also unique G. kaustophilus proteins, indicating that lysine acetylation is pronounced in thermophilic bacteria. These data complement current knowledge of the bacterial acetylproteome and provide an expanded platform for better understanding of the function of acetylation in cellular metabolism.     

Adding l-lysine derivatives to the genetic code of mammalian cells with engineered pyrrolysyl-tRNA synthetases

We report a method for site-specifically incorporating l-lysine derivatives into proteins in mammalian cells, based on the expression of the pyrrolysyl-tRNA synthetase (PylRS)-tRNA^Pyl pair from Methanosarcina mazei. Different types of external promoters were tested for the expression of tRNA^Pyl in Chinese hamster ovary cells. When tRNA^Pyl was expressed from a gene cluster under the control of the U6 promoter, the wild-type PylRS-tRNA^Pyl pair facilitated the most efficient incorporation of a pyrrolysine analog, N^ε-tert-butyloxycarbonyl-l-lysine (Boc-lysine), into proteins at the amber position. This PylRS-tRNA^Pyl system yielded the Boc-lysine-containing protein in an amount accounting for 1% of the total protein in human embryonic kidney (HEK) 293 cells. We also created a PylRS variant specific to N^ε-benzyloxycarbonyl-l-lysine, to incorporate this long, bulky, non-natural lysine derivative into proteins in HEK293. The recently reported variant specific to N^ε-acetyllysine was also expressed, resulting in the genetic encoding of this naturally-occurring lysine modification in mammalian cells.     

Nε-Modified lysine containing inhibitors for SIRT1 and SIRT2

Sirtuins catalyze the NAD⁺ dependent deacetylation of N^ε-acetyl lysine residues to nicotinamide, O′-acetyl-ADP-ribose (OAADPR) and N^ε-deacetylated lysine. Here, an easy-to-synthesize Ac-Ala-Lys-Ala sequence has been used as a probe for the screening of novel N^ε-modified lysine containing inhibitors against SIRT1 and SIRT2. N^ε-Selenoacetyl and N^ε-isothiovaleryl were the most potent moieties found in this study, comparable to the widely studied N^ε-thioacetyl group. The N^ε-3,3-dimethylacryl and N^ε-isovaleryl moieties gave significant inhibition in comparison to the N^ε-acetyl group present in the substrates. In addition, the studied N^ε-alkanoyl, N^ε-α,β-unsaturated carbonyl and N^ε-aroyl moieties showed that the acetyl binding pocket can accept rather large groups, but is sensitive to even small changes in electronic and steric properties of the N^ε-modification. These results are applicable for further screening of N^ε-acetyl analogues.     

The combined effect of acetylation and glycation on the chaperone and anti-apoptotic functions of human α-crystallin

N^ε-acetylation occurs on select lysine residues in α-crystallin of the human lens and alters its chaperone function. In this study, we investigated the effect of N^ε-acetylation on advanced glycation end product (AGE) formation and consequences of the combined N^ε-acetylation and AGE formation on the function of α-crystallin. Immunoprecipitation experiments revealed that N^ε-acetylation of lysine residues and AGE formation co-occurs in both αA- and αB-crystallin of the human lens. Prior acetylation of αA- and αB-crystallin with acetic anhydride (Ac₂O) before glycation with methylglyoxal (MGO) resulted in significant inhibition of the synthesis of two AGEs, hydroimidazolone (HI) and argpyrimidine. Similarly, synthesis of ascorbate-derived AGEs, pentosidine and N^ε-carboxymethyl lysine (CML), was inhibited in both proteins by prior acetylation. In all cases, inhibition of AGE synthesis was positively related to the degree of acetylation. While prior acetylation further increased the chaperone activity of MGO-glycated αA-crystallin, it inhibited the loss of chaperone activity by ascorbate-glycation in both proteins. BioPORTER-mediated transfer of αA- and αB-crystallin into CHO cells resulted in significant protection against hyperthermia-induced apoptosis. This effect was enhanced in acetylated and MGO-modified αA- and αB-crystallin. Caspase-3 activity was reduced in α-crystallin transferred cells. Glycation of acetylated proteins with either MGO or ascorbate produced no significant change in the anti-apoptotic function. Collectively, these data demonstrate that lysine acetylation and AGE formation can occur concurrently in α-crystallin of human lens, and that lysine acetylation improves anti-apoptotic function of α-crystallin and prevents ascorbate-mediated loss of chaperone function.     

Digestibility of Acetylated and Succinylated Proteins by Pepsin-Pancreatin and Some Intracellular Peptidases

The molecular sizes of hydrolysates of acetylated and succinylated caseins by pepsin-pancreatin were examined by gel filtration on Sephadex G-15. There were more large peptides (average residual number > 15) in the hydrolysates of the acylated caseins than there were in the hydrolysate of unmodified casein. In these large peptides from the acylated caseins the contents of N^ε-acyl-lysines were high. The digestibility of N^ε-acetyl and N^ε-succinyl lysine bonds in peptides by aminopeptidases [(EC 3.4.11.1) and (EC 3.4.11.2)] and watermelon carboxypeptidase [model enzyme of cathepsin A (EC 3.4.16.1)] was examined using digest of acylated caseins by pepsin, trypsin and α-chymotrypsin and some synthetic peptides. All peptidases released either N^ε-acetyl or N^ε-succinyl-lysine from peptides.

The hydrolytic processes of acetylated and succinylated proteins before and after intestinal absorption are discussed.     

Potent inhibitors of human matriptase‐1 based on the scaffold of sunflower trypsin inhibitor

Sunflower trypsin inhibitor‐1 (SFTI‐1), a bicyclic tetradecapeptide, has become a versatile tool as a scaffold for the development of the inhibitors of therapeutically relevant serine proteases, among them matriptase and kallikreins. Herein, we report the rational design of potent monocyclic and bicyclic inhibitors of human matriptase‐1. We found that the presence of positive charge and lack of bulky residues at the peptide N‐terminus is required for the maintenance of inhibitory activity. Replacement of the N‐terminal glycine residue by lysine allowed for the chemical conjugation with a fluorophor via the ε‐amino group without significant loss of inhibitory activity. Head‐to‐tail and side‐chain‐to‐tail cyclization resulted in potent inhibitors with comparable activities against matriptase‐1. The most potent synthetic bicyclic inhibitor found in this study (K_i = 2.6 nM at pH 7.6) is a truncated version of SFTI‐1 (cyclo‐KRCTKSIPPRCH) lacking a C‐terminal proline and aspartate residue. It combines an internal disulfide bond with a peptide macrocycle that is formed through side‐chain‐to‐tail cyclization of the ε‐amino group of an N‐terminal lysine and a C‐terminal proline. Copyright © 2014 European Peptide Society and John Wiley & Sons, Ltd.     

Study on the interaction between human serum albumin and a novel bioactive acridine derivative using optical spectroscopy

The interaction of a novel bioactive agent N‐{[N‐(2‐dimethylamino) ethyl] acridine‐4‐carboxamide}‐α‐alanine [N‐(ACR‐4‐CA)‐α‐ALA] with human serum albumin (HSA) was investigated by fluorescence spectroscopy, UV–vis absorption and circular dichroism spectrophotometric techniques under simulative physiological conditions. The fluorescence quenching of HSA by addition of N‐(ACR‐4‐CA)‐α‐ALA is due to static quenching and hydrogen bonding. Moreover, hydrophobic interactions play a role in the binding of N‐(ACR‐4‐CA)‐α‐ALA to HSA as well. The number of binding sites, n, and the binding constant values, K_A, were noted to be 0.88 and 3.4 × 10⁴ L mol^?1 for N‐(ACR‐4‐CA)‐α‐ALA at 293 K. The binding distances and the energy transfer efficiency between N‐(ACR‐4‐CA)‐α‐ALA and protein were determined. The negative value of enthalpy change and positive value of entropy change in the present study indicated that both hydrogen bonding and hydrophobic forces played a major role in the binding of N‐(ACR‐4‐CA)‐α‐ALA to HSA. Copyright © 2010 John Wiley & Sons, Ltd.     

Bimolecular fluorescence quenching reactions of the biologically active coumarin composite 2‐acetyl‐3H‐benzo[f]chromen‐3‐one in different solvents

A study on fluorescence quenching was carried out for the coumarin derivative 2‐acetyl‐3H‐benzo[f]chromen‐3‐one (2AHBC) with aniline at room temperature. Efficient fluorescence quenching was observed and Stern–Volmer (S–V) plots showed upward curves from linearity in all solvents of different polarities. For the solute 2AHBC, ground state complex formation does not hold in our study. The kinetic distance (r) value was found to be greater than the encounter distance (R) and indicated that the quenching reaction was held within the sphere of action. Diffusion‐limited reactions were found to be more prominent in high polarity solvents, namely dimethyl sulfoxide (DMSO), DMF, ACN, methanol, ethanol, propanol and DCM. The relationships between quenching constant (K_SV) and dielectric constants (ε) of the different solvents were studied.     

Protonation and quaternization of 1, N6-ethenoadenosine: What are the species responsible for the fluorescence of 1, N6-ethenoadenosine?

Methylation of 1,N⁶-ethenoadenosine (εAdo) gives a mixture of N1- and N9-quaternized methyl-3-β-D -ribofuranosylimidazo[2,1-i] purinium salts (m¹εAdo⁺ and m⁹εAdo⁺, respectively). The ratio of the two forms of the protonated εAdo [H¹εAdo⁺]/[H⁹εAdo⁺] has been estimated to be approximately 0.10 by comparing the uv absorption spectra of the protonated species of εAdo and the two nontautomerizable model compounds. In relation to a study on the protonation effect on the fluorescence of εAdo, we have now determined the effect of quaternization on the fluorescence spectra at 293 and 77 K. We have found that m¹εAdo⁺ and m⁹εAdo⁺ are both fluorescent, and the high degree of coincidence between the fluorescence spectra of εAdo and m¹εAdo⁺ at pH 7 is noted. The m¹εAdo⁺ singlet form is a more efficient fluorescer than the m⁹εAdo⁺ ion at room temperature (quantum yields of 0.43 and 0.11, respectively). All the results which are presented in this paper are consistent with the picture that there exist more than one species responsible for the fluorescence of εAdo, depending on the environment of the molecule in aqueous solution (temperature and pH of solvent).     

Building blocks for the synthesis of post‐translationally modified glycated peptides and proteins

Growing interest in synthetic peptides carrying post‐traslational modifications, in general, and the Amadori modification in particular, raises the need for specific building blocks that can be used in stepwise peptide synthesis. Herein, we report the synthesis of N^α‐Fmoc‐Lys‐OH derivatives containing N^ε‐1‐deoxyfructopyranosyl moiety. Copyright © 2008 European Peptide Society and John Wiley & Sons, Ltd.     

Synthesis of stable isotope-labelled monolysyl advanced glycation endproducts

Advanced Glycation Endproducts (AGEs) are modified amino acids that form on proteins and are known to be implicated in the pathogenesis of diabetes and related diseases. Ready access to synthetic stable isotope-labelled AGEs allows for quantitative mass spectrometry studies to be undertaken, providing key insights into the roles AGEs play in the progression of such diseases. However, the majority of current syntheses of these compounds suffer from poor yields and lengthy procedures and are not suitable for the purposes required here. Here, we report robust syntheses of stable isotope-labelled monolysyl AGEs, N^ε-(carboxymethyl)lysine, N^ε-(carboxyethyl)lysine and pyrraline, that provide straightforward access to these compounds for quantitative amino acid analysis. This work will facilitate future investigations with these compounds and lead to a better understanding of the roles they play in diabetes and related diseases.     

Real-time kinetic method to monitor isopeptidase activity of transglutaminase 2 on protein substrate

Transglutaminase 2 (TG2) is a ubiquitously expressed multifunctional protein with Ca²⁺-dependent transamidase activity forming protease-resistant N^ε-(γ-glutamyl) lysine crosslinks between proteins. It can also function as an isopeptidase cleaving the previously formed crosslinks. The biological significance of this activity has not been revealed yet, mainly because of the lack of a protein-based method for its characterization. Here we report the development of a novel kinetic method for measuring isopeptidase activity of human TG2 by monitoring decrease in the fluorescence polarization of a protein substrate previously formed by crosslinking fluorescently labeled glutamine donor FLpepT26 to S100A4 at a specific lysine residue. The developed method could be applied to test mutant enzymes and compounds that influence isopeptidase activity of TG2.     

Study on the synthesis of sulfonamide derivatives and their interaction with bovine serum albumin

Three sulfonamide derivatives (SAD) were first synthesized from p‐hydroxybenzoic acid and sulfonamides (sulfadimidine, sulfamethoxazole and sulfachloropyridazine sodium) and were characterized by elemental analysis, ¹H NMR and MS. The interaction between bovine serum albumin (BSA) and SAD was studied using UV/vis absorption spectroscopy, fluorescence spectroscopy, time‐resolved fluorescence spectroscopy and circular dichroism spectra under imitated physiological conditions. The experimental results indicated that SAD effectively quenched the intrinsic fluorescence of BSA via a static quenching process. The thermodynamic parameters showed that hydrogen bonding and van der Waal's forces were the predominant intermolecular forces between BSA and two SADs [4‐((4‐(N‐(4,6‐dimethylpyrimidin‐2‐yl)sulfamoyl)phenyl)carbamoyl)phenyl acetate and 4‐((4‐(N‐(5‐methylisoxazol‐3‐yl)sulfamoyl)phenyl)carbamoyl)phenyl acetate], but hydrophobic forces played a major role in the binding process of BSA and 4‐((4‐(N‐(6‐chloropyridazin‐3‐yl)sulfamoyl)phenyl) carbamoyl)phenyl acetate. In addition, the effect of SAD on the conformation of BSA was investigated using synchronous fluorescence spectroscopy and circular dichroism spectra. Molecular modeling results showed that SAD was situated in subdomain IIA of BSA. Copyright © 2014 John Wiley & Sons, Ltd.     

Mechanism of tyrosine hydroxylase activation by phosphorylation

It was found that the fluorescence of 1,N⁶-ethenoadenosine triphosphate (ε-ATP) bound to myosin subfragment-1 (S-1) is resistant to quenching by acrylamide, while free ε-ATP is effectively quenched. Thus in the presence of acrylamide the bound ε-ATP is still highly fluorescent, while free ε-ATP is much less fluorescent. The Stern-Volmer constants of bound and free ε-ATP are 6.83 and 57.86 M^?1, respectively. Therefore it is easy to distinguish spectro-scopically the nucleotide-ligated S-1 from nucleotide-free S-1. Moreover acrylamide does not alter the S-1-Mg²⁺-ε-ATPase behavior.     

Growing a gasdermin pore in membranes of pyroptotic cells

Inflammasome‐activated caspase‐1, caspase‐11, caspase‐4, and caspase‐5 cleave GSDMD to unleash its N‐terminal gasdermin‐N domain (GSDMD^Nterm) that perforates the plasma membrane to execute pyroptosis and stimulate inflammation. The mechanism underlying GSDMD^Nterm pore formation is unclear. Mulvihill et al use high‐resolution atomic force microscopy (AFM) to analyze the dynamic pore formation process of GSDMD^Nterm. GSDMD^Nterm protomers are inserted into the lipid membrane to assemble arc‐ or slit‐shaped oligomers that can incorporate additional protomers and grow into large and stable ring‐shaped oligomers to form pores.     

Utilization of inorganic carbon in the edible cyanobacterium Ge-Xian-Mi (Nostoc) and its role in alleviating photo-inhibition

The present work investigated the inorganic carbon (C_i) uptake, fluorescence quenching and photo‐inhibition of the edible cyanobacterium Ge‐Xian‐Mi (Nostoc) to obtain an insight into the role of CO₂ concentrating mechanism (CCM) operation in alleviating photo‐inhibition. Ge‐Xian‐Mi used HCO₃^– in addition to CO₂ for its photosynthesis and oxygen evolution was greater than the theoretical rates of CO₂ production derived from uncatalysed dehydration of HCO₃^–. Multiple transporters for CO₂ and HCO₃^– operated in air‐grown Ge‐Xian‐Mi. Na⁺‐dependent HCO₃^– transport was the primary mode of active C_i uptake and contributed 53–62% of net photosynthetic activity at 250 µmol L^?1 KHCO₃ and pH 8.0. However, the CO₂‐uptake systems and Na⁺‐independent HCO₃^– transport played minor roles in Ge‐Xian‐Mi and supported, respectively, 39 and 8% of net photosynthetic activity. The steady‐state fluorescence decreased and the photochemical quenching increased in response to the transport‐mediated accumulation of intracellular C_i. Inorganic carbon transport was a major factor in facilitating quenching during the initial stage and the initial rate of fluorescence quenching in the presence of iodoacetamide, an inhibitor of CO₂ fixation, was 88% of control. Both the initial rate and extent of fluorescence quenching increased with increasing external dissolved inorganic carbon (DIC) and saturated at higher than 200 µmol L^?1 HCO₃^–. The operation of the CCM in Ge‐Xian‐Mi served as a means of diminishing photodynamic damage by dissipating excess light energy and higher external DIC in the range of 100–10000 µmol L^?1 KHCO₃ was associated with more severe photo‐inhibition under strong irradiance.     

Development,validation of a GC–MS method for the simultaneous measurement of amino acids,their PTM metabolites and AGEs in human urine,and application to the bi-ethnic ASOS study with special emphasis to lysine

A gas chromatography-mass spectrometry (GC–MS) method was developed and validated in relevant concentration ranges for the simultaneous measurement of l-lysine (Lys, L) and its N^ε- and N^α-methylated (M), N^ε- and N^α-acetylated (Ac), N^ε-carboxymethylated (CM) and N^ε-carboxyethylated (CE) metabolites in human urine. Analyzed Lys metabolites were the post-translational modification (PTM) products N^ε-mono-, di- and trimethyllsine, N^ε-MML, N^ε-DML, N^ε-TML, respectively, N^α-ML, N^ε-AcL, N^α-AcL, and its advanced glycation end-products (AGEs) N^ε-CML, N^ε-CM-[2,4,4-²H₃]Lys (d₃-CML), N^ε-CEL and furosine. AGEs of arginine (Arg) and cysteine (Cys) were also analyzed. De novo synthesized trideutero-methyl esters (R-COOCD₃) from unlabelled amino acids and derivatives were used as internal standards. Native urine samples (10 µL aliquots) were evaporated to dryness under a stream of nitrogen. Analytes were esterified using 2 M HCl in methanol (60 min, 80 °C) and subsequently amidated by pentafluoropropionic anhydride in ethyl acetate (30 min, 65 °C). The generated methyl ester-pentafluoropropionyl (Me-PFP) derivatives were reconstituted in borate buffer and extracted immediately with toluene. GC–MS analyses were performed by split-less injection of 1-µL aliquots, oven-programmed separation and negative-ion chemical ionization (NICI). Mass spectra were generated in the scan mode (range, m/z 50–1000). Quantification was performed in the selected-ion monitoring (SIM) mode using a dwell time of 50 or 100 ms for each ion. The GC–MS method was suitable for the measurement of Lys and all of its metabolites, except for the quaternary ammonium cation N^ε-TML. The Me-PFP derivatives of Lys, Arg and Cys and its metabolites eluted in the retention time window of 9 to 14 min. The derivatization of N^ε-CML, d₃-CML and N^ε-CEL was accompanied by partial N^ε-decarboxylation and formation of the Me-PFP Lys derivative. The lowest derivatization yield was observed for N^ε-DML, indicating a major role of the N^ε-DML group in Lys derivatization. The GC–MS method enables precise (relative standard deviation, RSD?<?20%) and accurate (bias,?<?±?20%) simultaneous measurement of 33 analytes in human urine in relevant concentration ranges. We used the method to measure the urinary excretion rates of Lys and its PTM metabolites and AGEs in healthy black (n?=?39) and white (n?=?41) boys of the Arterial Stiffness in Offspring Study (ASOS). No remarkable differences were found indicating no ethnic-related differences in PTM metabolites and AGEs except for N^ε-monomethyllysine and S-(2-carboxymethylcysteine).

     

Insights into In Vitro Binding of Parecoxib to Human Serum Albumin by Spectroscopic Methods

Herein, we report the effect of parecoxib on the structure and function of human serum albumin (HSA) by using fluorescence, circular dichroism (CD), Fourier transforms infrared (FTIR), three‐dimensional (3D) fluorescence spectroscopy, and molecular docking techniques. The Stern–Volmer quenching constants K_SV and the corresponding thermodynamic parameters ΔH, ΔG, and ΔS have been estimated by the fluorescence quenching method. The results indicated that parecoxib binds spontaneously with HSA through van der Waals forces and hydrogen bonds with binding constant of 3.45 × 10⁴ M^?1 at 298 K. It can be seen from far‐UV CD spectra that the α‐helical network of HSA is disrupted and its content decreases from 60.5% to 49.6% at drug:protein = 10:1. Protein tertiary structural alterations induced by parecoxib were also confirmed by FTIR and 3D fluorescence spectroscopy. The molecular docking study indicated that parecoxib is embedded into the hydrophobic pocket of HSA.     

Synthesis of a novel fluorescent probe based on 7‐nitrobenzo‐2‐oxa‐1,3‐diazole skeleton for the rapid determination of vitamin B12 in pharmaceuticals

A new fluorescent probe, 4‐N,N‐di(2‐hydroxyethyl)imino‐7‐nitrobenzo‐2‐oxa‐1,3‐diazole (HINBD) was synthesized in a single step with reasonably good yield. The water‐soluble HINBD emits strongly in the visible region (λ_ex = 479 nm, λ_em = 545 nm) and is stable over a wide range of pH values. It was found that vitamin B₁₂ (VB₁₂) had the ability to quench the fluorescence of HINBD, and the quenched fluorescence intensity was proportional to the concentration of VB₁₂. A method for VB₁₂ determination based on the quenching fluorescence of HINBD was thus established. Interference effects of various substances, including sugars, vitamins, amino acids, inorganic cations and some organic substances have been studied. Under optimal conditions, the linear range is 0.0–2.4 × 10^–5 mol/L. The determination limit is 8.3 × 10^–8 mol/L. The method was applied to measure VB₁₂ in pharmaceutical preparations with satisfactory results. Copyright © 2013 John Wiley & Sons, Ltd.     

Crystal structure of the PHF8 Jumonji domain, an N-methyl lysine demethylase

Crystallographic analysis of the catalytic domain of PHD finger protein 8 (PHF8), an N^ε-methyl lysine histone demethylase associated with mental retardation and cleft lip/palate, reveals a double-stranded β-helix fold with conserved Fe(II) and cosubstrate binding sites typical of the 2-oxoglutarate dependent oxygenases. The PHF8 active site is highly conserved with those of the FBXL10/11demethylases, which are also selective for the di-/mono-methylated lysine states, but differs from that of the JMJD2 demethylases which are selective for tri-/di-methylated states. The results rationalize the lack of activity for the clinically observed F279S PHF8 variant and they will help to identify inhibitors selective for specific N^ε-methyl lysine demethylase subfamilies.