Sulfur-containing Side Chains Research Articles

Empowering canonical biochemicals with cross-linked novelty: Recursions in applications of protein cross-links.

Diversity in the biochemical workhorses of the cell-that is, proteins-is achieved by the innumerable permutations offered primarily by the 20 canonical L-amino acids prevalent in all biological systems. Yet, proteins are known to additionally undergo unusual modifications for specialized functions. Of the various post-translational modifications known to occur in proteins, the recently identified non-disulfide cross-links are unique, residue-specific covalent modifications that confer additional structural stability and unique functional characteristics to these biomolecules. We review an exclusive class of amino acid cross-links encompassing aromatic and sulfur-containing side chains, which not only confer superior biochemical characteristics to the protein but also possess additional spectroscopic features that can be exploited as novel chromophores. Studies of their in vivo reaction mechanism have facilitated their specialized in vitro applications in hydrogels and protein anchoring in monolayer chips. Furthering the discovery of unique canonical cross-links through new chemical, structural, and bioinformatics tools will catalyze the development of protein-specific hyperstable nanostructures, superfoods, and biotherapeutics.

Plant Glucosinolate Content and Host-Plant Preference and Suitability in the Small White Butterfly (Lepidoptera: Pieridae) and Comparison with Another Specialist Lepidopteran.

Glucosinolates are used in host-plant recognition by insects specialized on Brassicaceae, such as Pieris rapae L. (Lepidoptera: Pieridae). This research investigated the association between P. rapae oviposition and larval survival and host-plant glucosinolate content using 17 plant species in which glucosinolate content had previously been determined. Two-choice oviposition tests (comparing each plant species to Arabidopsis thaliana L.) and larval survival experiments showed that indolic glucosinolate content had a positive effect on oviposition preference and larval survival in P. rapae. In the host plants tested, the effects of indolic glucosinolates on oviposition preference and of glucosinolate complexity index and aliphatic glucosinolates without sulfur-containing side chains on total oviposition were smaller on P. rapae than on Plutella xylostella L. (Lepidoptera: Plutellidae), another lepidopteran specialized on glucosinolate-containing plants. This study suggests that high indolic glucosinolate content could make crop plants more susceptible to both P. rapae and P. xylostella, but this effect seems to be greater for P. xylostella. Additionally, as some differences in oviposition and larval survival between P. rapae and P. xylostella occurred in some individual plants, it cannot be concluded that bottom-up factors are always similar in these two specialist insects.

Bacterial Alkyl-4-quinolones: Discovery, Structural Diversity and Biological Properties.

The alkyl-4-quinolones (AQs) are a class of metabolites produced primarily by members of the Pseudomonas and Burkholderia genera, consisting of a 4-quinolone core substituted by a range of pendant groups, most commonly at the C-2 position. The history of this class of compounds dates back to the 1940s, when a range of alkylquinolones with notable antibiotic properties were first isolated from Pseudomonas aeruginosa. More recently, it was discovered that an alkylquinolone derivative, the Pseudomonas Quinolone Signal (PQS) plays a key role in bacterial communication and quorum sensing in Pseudomonas aeruginosa. Many of the best-studied examples contain simple hydrocarbon side-chains, but more recent studies have revealed a wide range of structurally diverse examples from multiple bacterial genera, including those with aromatic, isoprenoid, or sulfur-containing side-chains. In addition to their well-known antimicrobial properties, alkylquinolones have been reported with antimalarial, antifungal, antialgal, and antioxidant properties. Here we review the structural diversity and biological activity of these intriguing metabolites.

Refractive index changes in polyacrylates bearing alkyl sulfur groups through the sulfur oxidation reaction

Four polyacrylates with sulfur-containing side chains were prepared to examine the changes in refractive index (RI) induced by sulfur oxidation. Linear alkyl sulfides and alicyclic sulfides, such as 1,3-dithiolane and 1,4-dithiane, were introduced to impart large RIs to polyacrylates. Oxidation of the sulfur polymers by O3 and m-chloroperoxybenzoic acid led to the formation of the corresponding sulfoxide and sulfone polymers, respectively. Sulfur oxidation occurred completely, which was highlighted by the oxidized polymer exhibiting a refractive index comparable to a polymer that was synthesized using a sulfone monomer. The RI of the linear sulfur polymer increased and decreased due to the formation of sulfoxide and sulfone polymers, respectively. The Abbe number of the polymer with a linear sulfide side chain was 33.4, which increased to 48.7 after oxidation.

Chiral Dicarboxamide Scaffolds Containing a Sulfiliminyl Moiety as Potential Ryanodine Receptor Activators

To search for new environmentally benign insecticides with high activity, low toxicity, and low residue, novel chiral configurations introduced into dicarboxamide scaffolds containing N-cyano sulfiliminyl moieties were first studied. Four series of phthalamides with sulfur-containing side chains were designed, synthesized, and evaluated against oriental armyworm (Pseudaletia separata Walker) and diamondback moth (Plutella xylostella (L.)) for their insecticidal activities. All structures were characterized by (1)H NMR, (13)C NMR, and HRMS (or elemental analysis), and their configurations were confirmed by optical polarimetry. The biological assessment indicated that some title compounds exhibited significant insecticidal activities. For oriental armyworm, these stereoisomers exerted different impacts on biological activity following the sequence (Sc, Ss) ≥ (Sc, Rs) ≫ (Rc, Ss) > (Rc, Rs), and carbon chirality influenced the activities more strongly than sulfur. Compounds Ia and IIa reached as high an activity as commercial flubendiamide, with LC50 values of 0.0504 and 0.0699 mg L(-1), respectively, lower than that of flubendiamide (0.1230 mg L(-1)). For diamondback moth, the sequence of activity was (Sc, Ss) > (Sc, Rs), and the sulfur chirality influenced the activities more greatly than carbon. Compound IIe exhibited even higher activity than flubendiamide, whereas Ie and Ic,d reached the activity of the latter. The results indicated that the improvement of insecticidal activity probably required a coordination of both carbon and sulfur chirality. Comparative molecular field analysis calculation indicated that stereoisomers with Sc configurations containing strong electron-withdrawing groups such as as CN are important in maintaining the high activity. The chiral scaffolds containing the N-cyano sulfiliminyl moiety are also essential for high larvicidal activity. Some title compounds could be considered as potential candidates for ryanodine receptor activators.

Synthesis and electrochemical studies of disubstituted ferrocene/dipeptide conjugates with sulfur-containing side chains

A series of 1,1′-disubstituted ferrocenoyl peptides incorporating dipeptide sidearms has been synthesized and studied electrochemically. The target peptides include ferrocene as an electrochemical reporter, sulfur-containing amino acids ( l-methionine, S-methyl- l-cysteine, S-trityl- l-cysteine, S-benzhydryl- l-cysteine) as metal binding agents, and amino acids with non-polar side chains ( l-alanine, l-valine, l-phenylalanine) as spacers between reporter and metal binding groups. Ferrocene/dipeptide conjugates were prepared using solution phase peptide synthesis methods employing a BOC-protecting group strategy and HBTU- ( O-(benzotriazol-1-yl)- N, N, N′, N′-tetramethyluronium hexafluorophosphate) mediated peptide coupling. The electrochemical properties of these 1,1′-substituted ferrocenoyl peptides have been characterized using cyclic voltammetry. All exhibit fully reversible one electron oxidation steps; forward sweep half wave peaks ( E F), reverse sweep half wave peaks ( E R), peak separations (Δ E P) and half wave potentials ( E 1/2) are reported. Finally, towards the goal of utilizing ferrocenoyl peptides to detect heavy metals in solution, the response of these ferrocene/dipeptide conjugates to metal cations (zinc(II), mercury(II), cadmium(II), lead(II), silver(I)) has been examined. Monitoring changes in the potential of the Fe(II)/Fe(III) redox couple to follow peptide/metal interactions, we have probed the influence of the spacer unit between the redox reporter and the metal-binding amino acid, and shown that these systems respond to mercury(II) more strongly than to other heavy metal ions.

Investigation of the Ligand-binding Mechanism of Methionine Sulfoxide Reductase A of E.coli

The rise of free oxygen in the atmosphere over 2.5 billion years ago made it possible for large land-based plants and animals to thrive. But oxygen, and the energy it provides, comes at great cost. Aerobic metabolism generates highly reactive intermediates and by-products in the form of hydroxyl radicals, superoxide anions and hydrogen peroxide. Within the cell, these reactive oxygen species attack biological macromolecules, producing covalent modifications that can affect both function and structure. One amino acid residue in proteins that is particularly sensitive to oxidation is the sulfur-containing side chain of methionine. Fortunately, methionine oxidation can be reversed by the actions of peptide methionine sulfoxide reductase (MsrA), which reduces methionine sulfoxide back to methionine and restores function to damaged proteins. We have used multiple spectroscopic techniques to investigate the mechanism by which MsrA recognizes and binds to a wide range of oxidized substrates in need of repair. Substrates studied include proteins, peptides and the non-steroidal anti-inflammatory drug Sulindac. Competition experiments with the fluorescent reporter ANS suggest the existence of weak, but specific, hydrophobic interactions between MsrA and unstructured and/or hydrophobic ligands.

Mercury binding by ferrocenoyl peptides with sulfur-containing side chains: Electrochemical, spectroscopic and structural studies

Ferrocenoyl peptides incorporating amino acids derived from either l-methionine, l-cysteine or dl-homocysteine have been synthesised and investigated as agents for heavy metal binding and detection. Heavy metal–peptide interactions have been characterised using cyclic voltammetry to follow changes in the potential of the Fe(II)/Fe(III) redox couple, revealing that these systems interact with mercury(II) ions more strongly than with other thiophilic heavy metals such as cadmium(II), silver(I) and lead(II). Proton NMR experiments have demonstrated 1:1 peptide:mercury binding and enabled quantitative characterisation of this binding interaction. Crystal structures for two of these ferrocenoyl peptide derivatives have been elucidated, revealing that these compounds adopt a P-1,3′ open solid state conformation in the absence of mercury; this arrangement precludes intramolecular hydrogen bonding between chains, while extensive intermolecular hydrogen bonding is evident. The particular affinity of these systems for mercury(II) opens the possibility of incorporating them in new, biologically inspired sensors for detecting this toxic pollutant.

A new approach to the synthesis of strained cyclic systems: II. Mass spectrometric study of 2-dialkylamino-3-phenylthiophenes and their structural isomers, iminothietanes and iminocyclobutenes

Triads of isomeric N-alkyl-N-methyl-3-phenylthiophen-2-amines, N-methyl-3-alkyl-4-methylidene-3-phenylthietan-2-imines, and N-methyl-4-alkylsulfanyl-2-phenylcyclobut-2-en-1-imines (Alk = Me, Et, Bu) were synthesized from 1,3-dilithio-3-phenylpropyne, methyl isothiocyanate, and alkyl halides, and their fragmentation under electron impact was studied. Primary decomposition of the molecular ions of 2-aminothiophenes is determined by the localization of a radical cation center on the nitrogen atom, and it follows a path typical of alkyl(aryl)amines with elimination of hydrogen atom or methyl or propyl radical from the α-carbon atom in the N-alkyl substituent. Fragmentation of the iminothietanes involves cleavage of the four-membered ring in half to give neutral MeNCS molecule and 1-alkyl-1-phenylallene radical cation. Alkylsulfanyl(imino)-cyclobutenes undergo cleavage at the sulfur-containing side chain according to general relations holding in the fragmentation of alkyl sulfides.

Ferrocenoyl peptides with sulfur-containing side chains: synthesis, solid state and solution structures

The synthesis and full characterization of a number of amino acid and dipeptide derivatives with sulfur-containing side chains derived from ferrocene carboxylic acid and ferrocene-1,1′-dicarboxylic acid is presented. In particular, compounds Fc-CO-(Aaa) n -OMe ( 4) and Fe[C 5H 4-CO-(Aaa) n -OMe] 2 ( 3) with (Aaa) n = Cys(Bzl) ( a), Cys(Bzl)-Cys(Bzl) ( b), Cys( p-OMe-Bzl) ( c), Cys( p-OMe-Bzl)-Cys( p-OMe-Bzl) ( d), Met ( e), and Met-Met ( f) were prepared. Also, the free acid derivatives Fe[C 5H 4-CO-Met-OH] 2 ( 6e) and Fc-CO-Met-OH ( 7e) were prepared and characterized. The solid state structures of 3a, 4b, and 4e were determined by single crystal X-ray diffraction. Compound 3a shows a 1,3′ substitution pattern on the Cp rings in the solid state. Structures in solution were determined by NMR, IR and CD spectroscopy, with particular emphasis on the question of hydrogen bonding and helical chirality of the metallocene. As an example, the full assignment for the Cp signals in the disubstituted derivative 3a was achieved by simulation of the 1H NMR signals from the cyclopentadienyl ring in combination with 2D-NOESY spectra. In solution, 3a has the known 1,2′ substitution pattern, which is stabilized by intramolecular hydrogen bonds.

Cysteine/cystine couple is a newly recognized node in the circuitry for biologic redox signaling and control.

Redox mechanisms function in control of gene expression, cell proliferation, and apoptosis, but the circuitry for redox signaling remains unclear. Cysteine and methionine are the only amino acids in proteins that undergo reversible oxidation/reduction under biologic conditions and, as such, provide a means for control of protein activity, protein-protein interaction, protein trafficking, and protein-DNA interaction. Hydrogen peroxide and other reactive oxygen species (ROS) provide a mechanism to oxidize signaling proteins. However, oxidation of sulfur-containing side chains of cysteine and methionine by ROS can result in oxidation states of sulfur (e.g., sulfinate, sulfonate, sulfone) that are not reducible under biologic conditions. Thus, mechanisms for oxidation that protect against over-oxidation of these susceptible residues and prevent irreversible loss of activity would be advantageous. The present study shows that the steady-state redox potential of the cysteine/cystine couple (Eh = -145 mV) in cells is sufficiently oxidized (>90 mV) relative to the GSH/GSSG (-250 mV) and thioredoxin (Trx1, -280 mV) redox couples for the cysteine/cystine couple to function as an oxidant in redox switching. Consequently, the cysteine/cystine couple provides a means to oxidize proteins without direct involvement of more potent oxidants. A circuitry model incorporating cysteine as a redox node, along with Trx1 and GSH, reveals how selective interactions between the different thiol/disulfide couples and reactive protein thiols could differentially regulate metabolic functions. Moreover, inclusion of cysteine/cystine as a signaling node distinct from GSH and Trx1 significantly expands the redox range over which protein thiol/disulfide couples may operate to control physiologically relevant processes.

First-second shell interactions in metal binding sites in proteins: a PDB survey and DFT/CDM calculations.

The role of the second shell in the process of metal binding and selectivity in metalloproteins has been elucidated by combining Protein Data Bank (PDB) surveys of Mg, Mn, Ca, and Zn binding sites with density functional theory/continuum dielectric methods (DFT/CDM). Peptide backbone groups were found to be the most common second-shell ligand in Mg, Mn, Ca, and Zn binding sites, followed (in decreasing order) by Asp/Glu, Lys/Arg, Asn/Gln, and Ser/Thr side chains. Aromatic oxygen- or nitrogen-containing side chains (Tyr, His, and Trp) and sulfur-containing side chains (Cys and Met) are seldom found in the second coordination layer. The backbone and Asn/Gln side chain are ubiquitous in the metal second coordination layer as their carbonyl oxygen and amide hydrogen can act as a hydrogen-bond acceptor and donor, respectively, and can therefore partner practically every first-shell ligand. The second most common outer-shell ligand, Asp/Glu, predominantly hydrogen bonds to a metal-bound water or Zn-bound histidine and polarizes the H-O or H-N bond. In certain cases, a second-shell Asp/Glu could affect the protonation state of the metal ligand. It could also energetically stabilize a positively charged metal complex more than a neutral ligand such as the backbone and Asn/Gln side chain. As for the first shell, the second shell is predicted to contribute to the metal selectivity of the binding site by discriminating between metal cations of different ionic radii and coordination geometries. The first-shell-second-shell interaction energies decay rapidly with increasing solvent exposure of the metal binding site. They are less favorable but are of the same order of magnitude as compared to the respective metal-first-shell interaction energies. Altogether, the results indicate that the structure and properties of the second shell are dictated by those of the first layer. The outer shell is apparently designed to stabilize/protect the inner-shell and complement/enhance its properties.

Mapping the G-actin binding surface of cofilin using synchrotron protein footprinting.

Cofilin is an actin regulatory protein that binds to both monomeric and filamentous actin, and has filament severing activity. Although crystal structures for the monomeric forms of both G-actin and cofilin have been described, the structure of the binary cofilin-G-actin complex is not available. Synchrotron protein footprinting is used to identify specific side chain residues on the cofilin surface that are buried in the formation of the cofilin-G-actin binary complex. Exposure to synchrotron X-rays results in stable oxidative modifications of aromatic, aliphatic, and sulfur-containing side chains, with the rate of modification for a particular residue being dependent on its intrinsic reactivity and solvent accessibility. The rates of modification were monitored for a number of peptides generated by digestion of oxidized cofilin, both in isolation and in its binary complex with G-actin. After binding to G-actin takes place, a significant decrease in modification rates, indicating protection of side chain groups, is seen for cofilin peptides corresponding to residues 4-20, 10-17, 83-96, 91-105, and 106-117. A number of other peptides show no change in reactivity, and are presumed to represent regions distal to the binding site. Tandem mass spectrometry demonstrates that residues Leu 13, Pro 94, Met 99, and Leu 108 and 112 directly participate in the binding interface. These results are generally consistent with, and complementary to, the results of previous site-directed mutagenesis studies and extend our understanding of the G-actin binding surface of cofilin.

Purification and characterization of an l-amino acid deaminase used to prepare unnatural amino acids

l-Amino acid deaminase (l-AAD) from Proteus myxofaciens was cloned and over-expressed in Escherichia coli K12. This enzyme has a broad substrate specificity, working on both natural and unnatural l-amino acids. Of the 20 naturally occurring l-amino acids, l-AAD prefers amino acid substrates that have aliphatic, aromatic or sulfur-containing side chains; those with charged side chains (–CO2− or –NH3+) are poor or non-substrates. Enzyme activity was monitored using a microtiter-plate-based assay, which measures the formation of phenylpyruvic acid from l-phenylalanine. The reaction has an absolute requirement for O2, releases NH3 and does not produce H2O2. Substrate comparisons were carried out by using an O2 electrode to measure the O2 utilization rates. Studies on partially purified enzyme show a pH optimum of 7.5 with a subunit molecular weight of approximately 51 kDa. Additional purification and characterization strategies will be presented. The use of whole cells containing l-AAD will be discussed to prepare chiral pharmaceutical intermediates.

Antiestrogenic activities of 3,8-dihydroxy-6,11-dihydrobenzo[a]carbazoles with sulfur-containing side chains.

The objective of this study was to explore whether the conversion of the 2-phenylindole system into the tetracyclic benzo[a]carbazole changes the endocrine profile when the side chain structure was kept constant. Five different sulfur-containing side chains were linked to the nitrogen of the tetracycle. The biological evaluation revealed that the character of the indole derivatives remained unchanged after the conversion to the respective benzocarbzoles but the potency decreased by one order of magnitude. In vitro, all derivatives acted as pure antiestrogens without any agonist activity. They strongly inhibited the growth of estrogen-sensitive MCF-7 breast cancer cells with IC50-values in the nanomolar range. In the mouse uterine weight test, the derivatives with an aliphatic side chain were devoid of estrogenic activity and antagonized the effect of estradiol. The presence of an aromatic ring in the side chain gave rise to significant agonist activity in vivo independently of the carrier structure. All data revealed the equivalence of both carrier structures in respect to the endocrine profile but showed a decrease in potency upon the conversion of the 2-phenylindole system into the benzocarbazole structure.

Antiestrogenic Activities of 3,8-Dihydroxy-6,11-dihydrobenzo[a]carbazoles with Sulfur-Containing Side Chains

Antiestrogenic Activities of 3,8-Dihydroxy-6,11-dihydrobenzo[a]carbazoles with Sulfur-Containing Side Chains

Correcting the Circular Dichroism Spectra of Peptides for Contributions of Absorbing Side Chains

The aromatic and sulfur-containing side chains Trp, Tyr, Phe, Cys, and Met contribute to the CD spectra of peptides and proteins in the amide region, interfering with the analysis for secondary structure. We propose a method to correct the CD spectra of peptides undergoing the helix–coil transition for contributions due to absorbing side chains using singular value decomposition. The method uses the common basis vectors obtained from an analysis of the CD spectra of related peptides without the aromatic and sulfur-containing amino acids. The common basis vectors are fitted to a portion of the CD spectrum of the peptide being corrected, in the range that is unaffected by its sidechain contributions. Then the resulting coefficients from the fitting are used along with the common basis vectors to regenerate the entire corrected spectrum. The method is illustrated for the CD spectra of the peptide sequence acetyl-Y-VAXAK-VAXAK-VAXAK-amide, where X is substituted with the 20 naturally occurring amino acids. This peptide model adopts a random-coil conformation in 2 mmsodium phosphate buffer, pH 5.5, and becomes an α helix in methanol/buffer solutions. The difference between the original and corrected spectra shows the contribution from the aromatic and sulfur-containing side chains.

Isolation and characterization of [formula omitted], a new metabolite of histidine, from normal human urine and its formation from [formula omitted]

N- Acetyl-S-[2- carboxy-1-(1 H- imidazol-4- yl)ethyl]- l-cysteine ( I), a new imidazole compound with a sulfur-containing side chain, was isolated from normal human urine by ion-exchange column chromatography, and characterized by physicochemical analyses involving 1H-NMR spectrometry, mass spectrometry and high-voltage paper electrophoresis as well as chemical synthesis. Approximately five milligrams of crystals of the compound were obtained from 450 litres of the urine. Compound I was synthesized by the addition of N- acetyl- l-cysteine to urocanic acid. The compound was also formed by incubation of S-[2- carboxy-1-(1 H- imidazol-4- yl)ethyl]- l-cysteine ( II) with acetyl-CoA in the use of rat kidney or liver homogenate as an enzyme source in a Tris buffer at pH 7.4. Rat brain and spleen homogenates were the less or no effective preparations as the enzyme source. On the other hand, little N-acetylation of a diastereomer of compound II occurred in enzymatic reactions with rat tissue homogenates. Compound I was degraded to compound II by rat kidney or liver homogenate. These results suggest that compound I is a new N-acetylated metabolite of compound II, a compound previously found in human urine, and that the acetylating enzyme recognizes stereoisomerism of asymmetric carbon atoms on the molecule of compound II. These findings support an alternative pathway of l-histidine catabolism initiated by the adduction of glutathione and/or cysteine to urocanic acid, the first catabolite of histidine.

ChemInform Abstract: Reaction Mechanisms in the Radiolysis of Peptides, Polypeptides, and Proteins

The purpose of this review is to bring together and to correlate the wide variety of experimental studies that provide information on the reaction products and reaction mechanisms involved in the radiolysis of peptides, polypeptides and proteins (including chromosomal proteins) in both aqueous and solid-state systems. The comparative radiation chemistry of these systems is developed in terms of specific reactions of the peptide main-chain and the aliphatic, aromatic-unsaturated and sulfur-containing side-chains. Information obtained with the various experimental techniques of product analysis, competition kinetics, spin-trapping, pulse radiolysis and ESR spectroscopy is included. 147 refs.

Structure-activity relationships of sparsomycin: modification at the hydroxyl group

Ten analogues of the antibiotic sparsomycin were prepared and evaluated in several in vitro tests. Nine of them carry a modification at the hydroxymethylene group of the molecules, two have a disulfide bond instead of the S(O)-CH 2-S moiety at the sulfur-containing side chain of the molecules. While the presence of the S-S group decreases the activity of the analogues in all the tests performed, the modification at the OH group has no deleterious effects on the activity when a polyphenylalanine synthesis assay is used in an Escherichia coli extract. The same modifications, however, diminish drastically the activity of the analogues when tested in a similar Saccharomyces cerevisiae extract. A polymerization system in the archaebacterium Halobacterium halobium extract behaves like the eukaryotic preparations. A discrepancy is also found between the results of the polymerization tests and those of the ‘puromycin reaction’ which is also less sensitive to the modified sparsomycin analogues. The results of cell growth inhibition tests in bacteria as well as in eukaryotic organisms agree only partially with the in vitro data.