Carboxylic Acid Side Chain Research Articles

Protein kinase CK2: a newcomer in the ‘druggable kinome’

The acronym CK2 (derived from the misnomer 'casein kinase' 2) denotes one of the most pleiotropic members of the eukaryotic protein kinase superfamily, characterized by an acidic consensus sequence in which a carboxylic acid (or pre-phosphorylated) side chain at position n+3 relative to the target serine/threonine residue plays a crucial role. The latest repertoire of CK2 substrates includes approx. 300 proteins, but the analysis of available phosphopeptide databases from different sources suggests that CK2 alone may be responsible for the generation of a much larger proportion (10-20%) of the eukaryotic phosphoproteome. Although for the time being CK2 is not included among protein kinases whose inhibitors are in clinical practice or in advanced clinical trials, evidence is accumulating that elevated CK2 constitutive activity co-operates to induce a number of pathological conditions, including cancer, infectious diseases, neurodegeneration and cardiovascular pathologies. The development and usage of cell-permeant, selective inhibitors discloses a scenario whereby CK2 plays a global anti-apoptotic role, which under special circumstances may lead to untimely and pathogenic cell survival.

Cytotoxic Macrolides from a New Species of the Deep-Water Marine Sponge Leiodermatium

Chemical investigation of a new species of the deep-water marine sponge Leiodermatium, collected by manned submersible at a depth of 740 feet in Palau, resulted in the isolation of two cytotoxic macrolides, leiodolides A (1) and B (2). The leiodolides represent the first members of a new class of 19-membered ring macrolides, incorporating several unique functional groups including a conjugated oxazole ring, a bromine substituent, and an alpha-hydroxy-alpha-methyl carboxylic acid side-chain terminus. The structures of these new metabolites were established by spectroscopic analysis, chemical modification, and degradation. The relative and absolute stereochemistries at most chiral centers were assigned on detailed interpretation of spectroscopic data, coupled with chemical degradation and application of the modified Mosher ester method. Leiodolide A showed significant cytotoxicity (average GI(50) = 2.0 microM) in the National Cancer Institute's 60 cell line panel with enhanced activity against HL-60 leukemia and OVCAR-3 ovarian cancer cell lines.

Total synthesis of (+/-)-mitorubrinic acid.

[reaction: see text] (+/-)-Mitorubrinic acid, a member of the azaphilone family of natural products, has been constructed in 12 steps. Key aspects of the synthesis include elaboration and oxidative dearomatization of an isocoumarin intermediate to provide the azaphilone nucleus with a disubstituted, unsaturated carboxylic acid side chain.

The effect of temperature on bacterial degradation of EDTA in pH-auxostat

The effect of temperature on the maximum specific growth rate and the cell yield was studied during cultivation of two bacterial strains (LPM-4 and Pseudomonas sp. LPM-410) on EDTA under unlimited cell growth conditions in a pH-auxostat. Both strains displayed linear dependence of reciprocal biomass yield against reciprocal specific growth rate, from which the values of rate of substrate expenditure for cell maintenance and the “maximum” yield (i.e., hypothetical yield without cell maintenance processes) were estimated. Analysis of the maximum yield values based on mass–energy balance theory suggested that oxidation of the carboxylic acid side chains of EDTA by a monooxygenase had zero or low energetic efficiency. An Arrhenius equation with different values of Arrhenius parameters within different temperature ranges gave a good fit with the temperature dependence of both growth rate and biomass yield. Specific growth rates of both strains showed a more pronounced temperature dependence than did the cell yields. A possible kinetic mechanism was suggested which might be responsible for the modes of the temperature dependences of specific growth rate and yield that were found. The mechanism is based on a hypothetical key substance governing the metabolic flows, which is formed in a zero-order reaction and destroyed in a first-order reaction, both rate constants depending on temperature according to the Arrhenius law.

Protonation-mediated structural flexibility in the F conjugation regulatory protein, TraM

TraM is essential for F plasmid-mediated bacterial conjugation, where it binds to the plasmid DNA near the origin of transfer, and recognizes a component of the transmembrane DNA transfer complex, TraD. Here we report the 1.40 A crystal structure of the TraM core tetramer (TraM58-127). TraM58-127 is a compact eight-helical bundle, in which the N-terminal helices from each protomer interact to form a central, parallel four-stranded coiled-coil, whereas each C-terminal helix packs in an antiparallel arrangement around the outside of the structure. Four protonated glutamic acid residues (Glu88) are packed in a hydrogen-bonded arrangement within the central four-helix bundle. Mutational and biophysical analyses indicate that this protonated state is in equilibrium with a deprotonated tetrameric form characterized by a lower helical content at physiological pH and temperature. Comparison of TraM to its Glu88 mutants predicted to stabilize the helical structure suggests that the protonated state is the active form for binding TraD in conjugation.

Involvement of a Putative [Fe-S]-cluster-binding Protein in the Biogenesis of Quinohemoprotein Amine Dehydrogenase

Quinohemoprotein amine dehydrogenase (QHNDH) of Paracoccus denitrificans contains a peptidyl quinone cofactor, cysteine tryptophylquinone, as well as intrapeptidyl thioether cross-links between Cys and Asp/Glu residues within the smallestgamma-subunit of the alphabetagamma heterotrimeric protein. A putative [Fe-S]-cluster-binding protein (ORF2 protein) encoded between the structural genes for the alpha- and gamma-subunits of QHNDH in the n-butylamine-utilizing operon likely belongs to a Radical SAM (S-Ado-Met) superfamily that includes many proteins involved in vitamin biosynthesis and enzyme activation. In this study the role of ORF2 protein in the biogenesis of QHNDH has been explored. Although the wild-type strain of Paracoccus denitrificans produced an active, mature enzyme upon induction with n-butylamine, a mutant strain in which the ORF2 gene had been mostly deleted, neither grew in the n-butylamine medium nor showed QHNDH activity. When the mutant strain was transformed with an expression plasmid for the ORF2 protein, n-butylamine-dependent bacterial growth and QHNDH activity were restored. Site-specific mutations in the putative [Fe-S]-cluster or SAM binding motifs in the ORF2 protein failed to support bacterial growth. The alpha- and beta-subunits were both detected in the periplasm of the mutant strain, whereas the gamma-subunit polypeptide was accumulated in the cytoplasm and stained negatively for redox-cycling quinone staining. Matrix-assisted laser desorption ionization time-of-flight mass spectrometric analysis revealed that the gamma-subunit isolated from the mutant strain had not undergone posttranslational modification. These results unequivocally show that the putative [Fe-S]-cluster- and SAM-binding ORF2 protein is necessary for the posttranslational processing of gamma-subunit, most likely participating in the formation of the intrapeptidyl thioether cross-links.

Indole Diterpenoid Synthetic Studies. The Total Synthesis of (+)-Nodulisporic Acid F

[structure: see text] A stereocontrolled total synthesis of (+)-nodulisporic acid F, the simplest member of a family of novel ectoparasiticidal agents, has been achieved. Highlights of the effective modular synthetic strategy include anionic union of a tricyclic lactone with o-toluidine via our 2-substituted indole synthetic protocol, an optimized C-ring construction protocol, and a late-stage installation of the alpha,beta-unsaturated carboxylic acid side chain via the B-alkyl Suzuki-Miyaura cross-coupling tactic.

Enhancement of Transcriptional Activity of DNA Complexes by Amphoteric PEG Derivative

A water-soluble PEG derivative having both amino and carboxylic acid side chains (PEG-AC) was synthesized and explored for its transcription- and transfection-enhancing activity. PEG-AC could be deposited onto the surface of DNA/polycation complexes to form a ternary complex with slightly negative surface potential. PEG-AC-coating on the plasmid/PEI complexes obviously enhanced their transcriptional activity, and 31-fold higher consumption of UTP was observed. Amphoteric PEG-AC would loosen the tightly compacted DNA/PEI complex and facilitate the approach of transcriptional factors. PEG-AC also evidently improved the transgene expression level on the cultured CHO cells.

Transition Metal−Peptide Binding Studied by Metal-Catalyzed Oxidation Reactions and Mass Spectrometry

We have identified conditions that allow metal-catalyzed oxidation (MCO) reactions and mass spectrometry (MS) to correctly identify binding sites of first-row transition metal ions to model peptides. This work extends the applicability of the MCO/MS method to metals other than Cu(II). When the appropriate reducing agent (ascorbate, 10 mM) and oxidizing agent concentrations (1 mM persulfate, atmospheric O2, or both) are used, metal-bound amino acids can be sufficiently and specifically oxidized for clear identification by MS. The MCO reactions with Mn(II), Fe(II), Co(II), and Ni(II) occur to lesser extents than with Cu(II), but oxidation is still extensive enough to allow easy identification of the metal-bound residues. With the exception of aspartic acid, the known metal-binding amino acids of angiotensin I and bacitracin A are oxidized, while no oxidation is observed at nonbinding residues. Failure to oxidize aspartic acid is likely due to the relatively slow reactivity of its carboxylic acid side chain with reactive oxygen species, suggesting that the current MCO/MS protocol is transparent to such acidic residues. Overall, this study indicates that, just as is possible for Cu(II), the MCO/MS method should be suitable for determining the Mn(II)-, Fe(II)-, Co(II)-, and Ni(II)-binding sites of metalloproteins.

Avidin and streptavidin ligands based on the glycoluril bicyclic system

Glycoluril derivatives with a carboxylic acid side chain have been synthesized and shown to bind to both avidin and streptavidin. Introduction of a valerate side chain in glycoluril led to an increased binding to both proteins only when the valerate group was bound to a N atom and with the proper stereochemistry [(+)-enantiomer]. On the other hand, introduction of the valerate side chain either on the bridgehead carbon or on the N atom with the opposite stereochemistry [(-)-enantiomer] led to a decrease in binding constant compared with unsubstituted glycoluril. Direct spectrophotometric competitive titration of each protein with a racemic ligand allowed measurement of the enantioselectivity of the ligand-protein complexation, together with the binding constant of the two enantiomers. In the case of the N-substituted glycoluril, the extension of the side chain by one methylene group, from valerate to caproate, led to an increase in the binding constant to both proteins. Docking studies using AutoDock 3.05 have been performed in order to predict the binding modes of these ligands to streptavidin. The effect of the stereochemistry and the position of the side chain on the binding constant to streptavidin is discussed in view of the predicted binding modes.

Mutations in the Central Cavity and Periplasmic Domain Affect Efflux Activity of the Resistance-Nodulation-Division Pump EmhB from Pseudomonas fluorescens cLP6a

The EmhABC efflux system in Pseudomonas fluorescens cLP6a is homologous to the multidrug and solvent efflux systems belonging to the resistance-nodulation-division (RND) family and is responsible for polycyclic aromatic hydrocarbon transport, antibiotic resistance, and toluene efflux. To gain a better understanding of substrate transport in RND efflux pumps, the EmhB pump was subjected to mutational analysis. Mutagenesis of amino acids within the central cavity of the predicted three-dimensional structure of EmhB showed selective activity towards antibiotic substrates. An A384P/A385Y double mutant showed increased susceptibility toward rhodamine 6G compared to the wild type, and F386A and N99A single mutants showed increased susceptibility to dequalinium compared to the wild type. As well, the carboxylic acid side chain of D101, located in the central cavity region, was found to be essential for polycyclic aromatic hydrocarbon transport and resistance to all antibiotic substrates of EmhB. Phenylalanine residues located within the periplasmic pore domain were also targeted for mutagenesis, and the F325A and F281A mutations significantly impaired efflux activity for all EmhB substrates. One mutation (A206S) in the outer membrane protein docking domain increased antibiotic resistance and toluene tolerance, demonstrating the important role of this domain in transport activity. These data demonstrate the roles of the central cavity and periplasmic domains in the function of the RND efflux pump EmhB.

A Tailoring Activity Is Responsible for Generating Polyene Amide Derivatives in Streptomyces diastaticus var. 108

We recently characterized rimocidin B (3b) and CE-108B (4b) as two polyene amides with improved pharmacological properties, produced by genetically modified Streptomyces diastaticus var. 108. In this work, genetic and biochemical analysis of the producer strain show that the two amides are derived from the parental polyenes rimocidin (3a) and CE-108 (4a) by a post-PKS modification of the free side chain carboxylic acid. This modification is mediated by an amidotransferase activity operating after the biosynthesis of rimocidin (3a) and CE-108 (4a) are completed. Two polyenes, intermediates of the biosynthetic pathway of rimocidin (3a) and CE-108 (4a), were also isolated and shown to have some improved pharmacological properties compared with the final products.

A New Type of Peroxisomal Acyl-Coenzyme A Synthetase from Arabidopsis thaliana Has the Catalytic Capacity to Activate Biosynthetic Precursors of Jasmonic Acid

Arabidopsis thaliana contains a large number of genes that encode carboxylic acid-activating enzymes, including nine long-chain fatty acyl-CoA synthetases, four 4-coumarate:CoA ligases (4CL), and 25 4CL-like proteins of unknown biochemical function. Because of their high structural and sequence similarity with bona fide 4CLs and their highly hydrophobic putative substrate-binding pockets, the 4CL-like proteins At4g05160 and At5g63380 were selected for detailed analysis. Following heterologous expression, the purified proteins were subjected to a large scale screen to identify their preferred in vitro substrates. This study uncovered a significant activity of At4g05160 with medium-chain fatty acids, medium-chain fatty acids carrying a phenyl substitution, long-chain fatty acids, as well as the jasmonic acid precursors 12-oxo-phytodienoic acid and 3-oxo-2-(2'-pentenyl)-cyclopentane-1-hexanoic acid. The closest homolog of At4g05160, namely At5g63380, showed high activity with long-chain fatty acids and 12-oxo-phytodienoic acid, the latter representing the most efficiently converted substrate. By using fluorescent-tagged variants, we demonstrated that both 4CL-like proteins are targeted to leaf peroxisomes. Collectively, these data demonstrate that At4g05160 and At5g63380 have the capacity to contribute to jasmonic acid biosynthesis by initiating the beta-oxidative chain shortening of its precursors.

The P450cam G248E Mutant Covalently Binds Its Prosthetic Heme Group

Previous studies on mammalian peroxidases and cytochrome P450 family 4 enzymes have shown that a carboxylic group positioned close to a methyl group of the prosthetic heme is required for the formation of a covalent link between a protein carboxylic acid side chain and the heme. To determine whether there are additional requirements for covalent bond formation in the P450 enzymes, a glutamic acid or an aspartic acid has been introduced into P450(cam) close to the heme 5-methyl group. Spectroscopic and kinetic studies of the resulting G248E and G248D mutants suggest that the carboxylate group coordinates with the heme iron atom, as reported for a comparable P450(BM3) mutant [Girvan, H. M., Marshall, K. R., Lawson, R. J., Leys, D., Joyce, M. G., Clarkson, J., Smith, W. E., Cheesman, M. R., and Munro, A. W. (2004) J. Biol. Chem. 279, 23274-23286]. The two P450(cam) mutants have low catalytic activity, but in contrast to the P450(BM3) mutant, incubation of the G248E (but not G248D) mutant with camphor, putidaredoxin, putidaredoxin reductase, and NADH results in partial covalent binding of the heme to the protein. No covalent attachment is observed in the absence of camphor or any of the other reaction components. Pronase digestion of the G248E P450(cam) mutant after covalent attachment of the heme releases 5-hydroxyheme, establishing that the heme is covalently attached through its 5-methyl group as predicted by in silico modeling. The results establish that a properly positioned carboxyl group is the sole requirement for autocatalytic formation of a heme-protein link in P450 enzymes, but also show that efficient covalent binding requires placement of the carboxyl close to the methyl but in a manner that prevents strong coordination to the iron atom.

Switching of turn conformation in an aspartate anion peptide fragment by NH · · · O− hydrogen bonds

Aspartic acid protease model peptides Z-Phe-Asp(COOH)-Thr-Gly-Ser-Ala-NHCy (1) and AdCO-Asp(COOH)-Val-Gly-NHBzl (3), and their aspartate anions (NEt4)[Z-Phe-Asp(COO-)-Thr-Gly-Ser-Ala-NHCy] (2) and (NEt4)[AdCO-Asp(COO-)-Val-Gly-NHBzl] (4), having an invariant primary sequence of the Asp-X(Thr,Ser)-Gly fragment, were synthesized and characterized by 1H-NMR, CD, and infrared (IR) spectroscopies. NMR structure analyses indicate that the Asp O(delta) atoms of the aspartate peptide 2 are intramolecularly hydrogen-bonded with Gly, Ser, Ala NH, and Ser OH, supporting the rigid beta-turn-like conformation in acetonitrile solution. The tripeptide in the aspartic acid 3 forms an inverse gamma-turn structure, which is converted to a beta-turn-like conformation because of the formation of the intramolecular NH . . . O- hydrogen bonds with the Asp O(delta) in 4. Such a conformational change is not detected between dipeptides AdCO-Asp(COOH)-Va-NHAd (5) and (NEt4)[AdCO-Asp(COO-)-Val-NHAd] (6). The pK(a) value of side-chain carboxylic acid (5.0) for 3 exhibits a lower shift (0.3 unit) from that of 5 in aqueous polyethyleneglycol lauryl ether micellar solution. NMR structure analyses for 3 in an aqueous micellar solution indicate that the preorganized turn structure, which readily forms the NH . . . O- hydrogen bonds, lowers the pK(a) value and that resulting hydrogen bonds stabilize the rigid conformation in the aspartate anion state. We found that the formation of the NH . . . O- hydrogen bonds involved in the hairpin turn is correlated with the protonation and deprotonation state of the Asp side chain in the conserved amino acid fragments.

Analysis of pH‐dependent elements in proteins: Geometry and properties of pairs of hydrogen‐bonded carboxylic acid side‐chains

A rather frequent but so far little discussed observation is that pairs of carboxylic acid side-chains in proteins can share a proton in a hydrogen bond. In the present article, quantum chemical calculations of simple model systems for carboxyl-carboxylate interactions are compared with structural observations from proteins. A detailed structural analysis of the proteins deposited in the PDB revealed that, in a subset of proteins sharing less than 90% sequence identity, 19% (314) contain at least one pair of carboxylic acids with their side-chain oxygen atoms within hydrogen-bonding distance. As the distance between those interacting oxygen atoms is frequently very short ( approximately 2.55 A), many of these carboxylic acids are suggested to share a proton in a strong hydrogen bond. When situated in an appropriate structural environment (low dielectric constant), some might even form a low barrier hydrogen bond. The quantum chemical studies show that the most frequent geometric features of carboxyl-carboxylate pairs found in proteins, and no or symmetric ligation, are also the most stable arrangements at low dielectric constants, and they also suggest at medium and low pH a higher stability than for isosteric amide-carboxylate pairs. The presence of these pairs in 119 different enzymes found in the BRENDA database is set in relation to their properties and functions. This analysis shows that pH optima of enzymes with carboxyl-carboxylate pairs are shifted to lower than average values, whereas temperature optima seem to be increased. The described structural principles can be used as guidelines for rational protein design (e.g., in order to improve pH or temperature stability).

PH-Dependent Mucoadhesion of a Poly(N-isopropylacrylamide) Copolymer Reveals Design Rules for Drug Delivery

This study investigated the mucoadhesive property of a hydrophobically modified copolymer N-isopropylacryamide and glycidylacrylamide NIPAM-N-Gly-(C18)2 (NIPAM-Gly). Prior studies demonstrated that the interfacial properties of this copolymer are pH dependent and that the chains form strong hydrogen bonds at pH < 7 via the carboxylic acid side chains of the glycine moieties. Mucin interactions with the copolymer brushes were investigated by surface plasmon resonance and by direct force measurements. Mucin adsorption was determined as a function of pH, ionic strength, and mucin concentration. It adsorbs to the copolymer strongly at pH 5, but the adsorption decreases with increasing pH. The adsorbed amount is also ionic-strength dependent, decreasing with increasing monovalent salt concentrations at all pH values investigated. When compared with similar investigations with poly(ethylene oxide), these results provide insights into both the chemical characteristics and the solution conditions that determine the mucoadhesive properties of polymers.

Synthesis and protein conjugation studies of vitamin K analogues

Two vitamin K analogues bearing a carboxylic acid side chain ( 9a and its deuterated analogue 9b) were each synthesised in six steps from commercially available menadione. Analogue 9b was conjugated to lysozyme and bovine serum albumin (BSA) using EDCI/HOBT and by prior formation of its activated succinimidyl ester 11. Quantification of the thus formed conjugates by ESMS and LC–MS revealed that the number of equivalents of the analogue used in the couplings systematically controls the number of analogues that conjugate to the protein.

847. Hyaluronic Acid as a Self-Assembled Coating of Plasmid / Polycation Complexes for Cell-Specific Gene Delivery

Top of pageAbstract As non-viral vectors for gene therapy, uncontrolled interaction of the cationic DNA/polycation complexes with the extracellular matrix or the serum proteins has been obstacle to the in vivo gene therapy. We have reported that the poly(ethylene glycol) derivatives having carboxylic acid-side chains (PEG-C) coated the DNA/polycation complexes, and protect them from these uncontrollable interactions1. Introducing the ligand into the side chains of the polymer allowed the receptor-mediated cell-specific and highly effective gene transfection2. PEG-C could be deposited onto the surface of the plasmid/ polycation complexes, and the ternary complex was formed. But common polyanions like polyacrylic acid, or heparin would decompose the complex and substitute with the plasmid releasing the free DNA molecules. Hyaluronic acid (HA) is a natural acidic mucopolysaccharide, and was found to coat the DNA/polycation complexes without decomposition. CD44, a receptor for HA, is known to be overexpressed on the various tumor cell surfaces, and HA is thus expected to form ternary complexes with plasmid and polycation, expressing the binding site to the receptors on the malignant cell surfaces. In this study, we investigated the effect of the HA-coating of the plasmid/polycation complex on the suppression of the undesired interaction with serum protein, and the gene-transfection efficiency on the CD44-presenting CHO cells. (1) Microscopic observation of the plasmid/polycation/HA ternary complex: The fluorescence microscopic images of the DAPI-DNA, fluorescein-PEI and rhodamine-HA mixture were all observed at the same position as brightening dots, indicating the formation of the ternary complexes. Albumin induced the aggregation of the plasmid/polycation binary complexes, but not the HA-coated ternary complexes, which remained to fluctuate for a long time after the albumin addition, showing the protecting effect of HA against the serum protein. The efficient binding of the fluorescence-labeled plasmid/PEI/HA ternary complex to the CHO cells was observed under the fluorescence microscopic observation. (2) Gene expression study: HA obviously enhanced the gene-expression on CHO cells mediated by HelΔ1 (a cationic amphiphilic peptide) up to 30-fold higher than those without HA. Transfection efficiency mediated by chitosan, or linear-PEI was also 3-4 times improved by HA. Such enhancing effect was, however, not observed on the CD44-negative COS-7 cells. Far excess addition of HA or the pretreatment by the polysaccharide diminished the gene-expression, indicating the receptor-mediated mechanism of the HA-coated ternary complex.

A proposed mechanism for the reductive ring opening of the cyclodiphosphate MEcPP, a crucial transformation in the new DXP/MEP pathway to isoprenoids based on modeling studies and feeding experiments.

Experimental and theoretical investigations concerning the second-to-last step of the DXP/MEP pathway in isoprenoid biosynthesis in plants are reported. The proposed intrinsic or late intermediates 4-oxo-DMAPP (12) and 4-hydroxy-DMAPP (11) were synthesized in deuterium- or tritium-labeled form according to new protocols especially adapted to work without protection of the diphosphate moiety. When the labeled compounds MEcPP (7), 11, and 12 were applied to chromoplast cultures, aldehyde 12 was not incorporated. This finding is in agreement with a mechanistic and structural model of the responsible enzyme family: a three-dimensional model of the fragment L271-A375 of the enzyme GcpE of Streptomyces coelicolor including NADPH, the Fe(4)S(4) cluster, and MEcPP (7) as ligand has been developed based on homology modeling techniques. The model has been accepted by the Protein Data Bank (entry code 1OX2). Supported by this model, semiempirical PM3 calculations were performed to analyze the likely catalysis mechanism of the reductive ring opening of MEcPP (7), hydroxyl abstraction, and formation of HMBPP (8). The mechanism is characterized by a proton transfer (presumably from a conserved arginine 286) to the substrate, accompanied by a ring opening without high energy barriers, followed by the transfer of two electrons delivered from the Fe(4)S(4) cluster, and finally proton transfer from a carboxylic acid side chain to the hydroxyl group to be removed from the ligand as water. The proposed mechanism is in agreement with all known experimental findings and the arrangement of the ligand within the enzyme. Thus, a very likely mechanism for the second to last step of the DXP/MEP pathway in isoprenoid biosynthesis in plants is presented. A principally similar mechanism is also expected for the reductive dehydroxylation of HMBPP (8) to IPP (9) and DMAPP (10) in the last step.