Functionalization of poly-SNS-anchored carboxylic acid with Lys and PAMAM: surface modifications for biomolecule immobilization/stabilization and bio-sensing applications

Poly(2-(2,5-di(thiophen-2-yl)-1H-pyrrol-1-yl) (SNS) acetic acid) was electrochemically deposited on graphite electrodes and functionalized with lysine (Lys) amino acid and poly(amidoamine) derivatives (PAMAM?G2 and PAMAM?G4) to investigate their matrix properties for biosensor applications. Glucose oxidase (GOx) was immobilized onto the modified surface as the model enzyme. X-Ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM) were used to report the surface properties of the matrices in each step of the biosensor construction. The biosensors were characterized in terms of their operational and storage stabilities and the kinetic parameters (K and I(max)). Three new glucose biosensors revealed good stability, featuring low detection limits (19.0 μM, 3.47 μM and 2.93 μM for lysine-, PAMAM?G2- and PAMAM?G4-functionalized electrodes, respectively) and prolonged the shelf lives (4, 5, and 6 weeks for Lys-, PAMAM?G2- and PAMAM?G4-modified electrodes, respectively). The proposed biosensors were tested for glucose detection on real human blood serum samples.     

Organoruthenium-catalyzed chemical protein synthesis to elucidate the functions of epigenetic modifications on heterochromatin factors

The application of organometallic compounds for protein science has received attention. Recently, total chemical protein synthesis using transition metal complexes has been developed to produce various proteins bearing site-specific posttranslational modifications (PTMs). However, in general, significant amounts of metal complexes were required to achieve chemical reactions of proteins bearing a large number of nucleophilic functional groups. Moreover, syntheses of medium-size proteins (>20 kDa) were plagued by time-consuming procedures due to cumbersome purification and isolation steps, which prevented access to variously decorated proteins. Here, we report a one-pot multiple peptide ligation strategy assisted by an air-tolerant organoruthenium catalyst that showed more than 50-fold activity over previous palladium complexes, leading to rapid and quantitative deprotection on a protein with a catalytic amount (20 mol%) of the metal complex even in the presence of excess thiol moieties. Utilizing the organoruthenium catalyst, heterochromatin factors above 20 kDa, such as linker histone H1.2 and heterochromatin protein 1α (HP1α), bearing site-specific PTMs including phosphorylation, ubiquitination, citrullination, and acetylation have been synthesized. The biochemical assays using synthetic proteins revealed that the citrullination at R53 in H1.2 resulted in the reduced electrostatic interaction with DNA and the reduced binding affinity to nucleosomes. Furthermore, we identified a key phosphorylation region in HP1α to control its DNA-binding ability. The ruthenium chemistry developed here will facilitate the preparation of a variety of biologically and medically significant proteins containing PTMs and non-natural amino acids.

Chemical protein synthesis assisted by an organoruthenium catalyst streamlined the production of heterochromatin factors bearing various patterns of epigenetic modifications, and their biological significance was elucidated.     

Interatomic magnetizability: a QTAIM-based approach toward deciphering magnetic aromaticity

Interatomic magnetizability provides insight into the extent of electronic current density between two adjacent atomic basins. By studying a number of well-known aromatic, nonaromatic, and antiaromatic molecules, it is demonstrated that interatomic magnetizability (bond magnetizability) not only is able to verify the exact nature of aromaticity/antiaromaticity among different molecules, but also can distinguish the correct aromaticity order among sets of aromatic/antiaromatic molecules. The interatomic magnetizability is a direct measure of the current flux between two adjacent atomic basins and is the first QTAIM-derived index that evaluates aromaticity based on a response property, that is, magnetizability. Bond magnetizability is easy to compute, straightforward to interpret, and can be employed to evaluate the pure π- or σ-orbital contributions to magnetic aromaticity.     

Aldehyde-terminated amorphous carbon substrates for the fabrication of biomolecule arrays

Amorphous carbon thin films are easily deposited at room temperature, readily functionalized with alkene-containing molecules through a UV photochemical reaction, and provide a robust surface capable of supporting chemical and biomolecule array fabrication. Aldehyde-terminated amorphous carbon substrates were fabricated via the attachment of a 2-(10-undecen-1-yl)-1,3-dioxolane molecule. The surfaces were then deprotected in 1.5 M HCl to yield an aldehyde-terminated surface that is readily reactive with amine containing molecules. An array of amine-modified oligonucleotides was prepared on aldehyde-terminated surfaces prepared on both amorphous carbon and on gold self-assembled monolayers, and the fluorescence background, feature signal-to-noise ratio, and hybridization densities were compared. The aldehyde-terminated amorphous carbon substrates offer inherently lower background fluorescence intensity and a greater number of hybridization-accessible sites.     

From triazines to heptazines: deciphering the local structure of amorphous nitrogen-rich carbon nitride materials

Nitrogen-rich carbon nitride (CN x , x >/= 1) network materials have been produced as disordered structures by a variety of precursor-based methods, many that involve solid-state thermolysis at or above 500 degrees C. One popular precursor building block is the triazine unit (C 3N 3), and most postulated amorphous CN x network structures are based on cross-linked triazine units. Since hydrogen is most often observed in the product, these materials are usually more appropriately described as CN x H y materials. Results from recent carbon nitride studies using larger conjugated heptazine (C 6N 7) precursors and from rigorous structural investigations of triazine to heptazine thermal conversion processes have prompted a reexamination of likely local structures present in amorphous carbon nitride networks formed by triazine thermolysis reactions. In the present study, the formation and local structure of a CN x H y material formed via the rapid and exothermic decomposition of a reactive triazine precursor, C 3N 3(NHCl) 3, was examined by byproduct gas mass spectrometry, NMR and IR spectroscopy, base hydrolysis, and crystallographic analysis. The combined results clearly indicate that the moderate-temperature ( approximately 400 degrees C) self-sustaining decomposition of trichloromelamine results in ring fragmentation and reorganization into a CN x H y product that contains predominantly larger heptazine-like structural building blocks. These results may have applicability to many other disordered carbon nitride materials that are formed via triazine thermolysis. It also provides clearer and more accurate structural guidance in the use of these carbon nitrides as photoactive materials or coordination supports for metal and nonmetal species.     

Biomimetic engineering of modular bispecific antibodies for biomolecule immobilization

Modular bispecific antibodies (BsAb's) that interact directly with a gold surface were engineered for immobilization on biosensing devices. The BsAb's consist of the variable fragments of antigold and antilysozyme antibodies connected via one of three linkers derived from naturally occurring proteins. The BsAb's were bound tightly to both the gold surface and to lysozyme, thus functioning as interface molecules between lysozyme and the gold surface without a substantial loss of antigen-binding activity. The antigen-binding capacity (the ratio of the amount of immobilized lysozyme to the amount of immobilized BsAb) on the gold surface reached 82%. An analysis of the correlation between binding capacity and linker characteristics indicated that the presence of a long, rigid linker sequence derived from a cellulase resulted in a higher antigen-binding capacity than did the presence of a long but relatively flexible glycine-rich linker. This result suggests a strategy for designing linkers suitable for BsAb-based biomolecular immobilization.     

The complete microspeciation of ovothiol A,the smallest octafarious antioxidant biomolecule

Ovothiol A, a small biomolecule with highly potent antioxidant capacity, and three newly synthesized derivatives were studied by ¹H NMR, ¹⁵N NMR, UV-pH titrations, and a customized evaluation method. The omni-interactive imidazole, amino, carboxylate, and thiolate moieties of ovothiol A are quantified in terms of 32 microscopic protonation constants, the relative concentrations of 16 microspecies, 6 pairwise interactivity parameters, and 8 protonation shifts. The highest and lowest imidazole basicities differ by a record-breaking five orders of magnitude, and the predominant thiolate protonation constant is by far the smallest known thiolate logK value. The latter provides an indication as to why ovothiol A occurs naturally under deep-water circumstances only. Since thiolate basicities are in correlation with thiol-disulfide redox potentials, the eight different, fine-tunable thiolate basicities offer versatile and highly specific antioxidant capacities within one single molecular skeleton. This work is the first complete microspeciation of a tetrabasic, nonsymmetrical natural compound.

Serine octamers: cluster formation, reactions, and implications for biomolecule homochirality

The emergence of homochirality continues to be one of the most challenging topics associated with the origin of life. One possible scenario is that aggregates of amino acids might have been involved in a sequence of chemical events that led to chiral biomolecules in self-replicating systems, that is, to homochirogenesis. Serine is the amino acid of principal interest, since it forms "magic-number" ionic clusters composed of eight amino acid units, and the clusters have a remarkable preference for homochirality. These serine octamer clusters (Ser8) can be generated under simulated prebiotic conditions and react selectively with other biomolecules. These observations led to the hypothesis that serine reactions were responsible for the first chiral selection in nature which was then passed through chemical reactions to other amino acids, saccharides, and peptides. This Review evaluates the chemistry of Ser8 clusters and the experimental evidence that supports their possible role in homochirogenesis.     

Decrypting the TEM images for deciphering the microstructural code of complex oxides

The knowledge of the structure of the real solids is required for achieving the desired architectures in the research of new materials and/or optimizing the relationships between structure and properties. Understanding complex oxides needs accurate characterization at different length scales and the combined application of all solid-state techniques. Deciphering the relationships between all this information provides codes that allow the identification of the different structural levels, their roles and the way they interact. These step-by-step routes are illustrated through two basic mechanisms of solid-state chemistry: to determine the building units of one complex oxide in order to predict the existence of other arrangements on the one hand and to correlate complex ordering phenomena, such as those involving charges, orbitals and spins of manganese atoms in perovskite-type manganites on the other hand.     

Enhanced antifouling and anticoagulant properties of grafted biomolecule polyethersulfone membranes

Polyethersulfone (PES) has been widely used in membrane technology and used to purify water in water treatments application or as a dialyzer to purify blood in hemodialysis. In this work, PES was chemically modified by separately grafting two biomolecules, 4‐aminobenzenesulfonamide (ABS), and 4‐amino‐N‐(5‐methylisoxazol‐3‐yl)benzenesulfonamide (AMBS), on PES backbone, and these modified membranes were blended to unmodified PES, in 1:1 ratio, in order to obtain PES‐b‐PES‐ABS and PES‐b‐PES‐AMBS membranes. The first aim of this study is to measure the anticoagulant properties of the modified membrane by measuring the activated partial thromboplastin time (APTT) and prothrombin time (PT). The second aim of the study is to evaluate the antifouling properties of the modified PES membranes by examining its antimicrobial activity against two Gram‐negative bacteria, which are Pseudomonas aeruginosa (P. aeruginosa) and Escherichia coli (E. coli); two Gram‐positive bacteria, which are Bacillus subtilis (B. subtilis) and Staphylococcus aureus (S. aureus); and a fungus, which is Candida albicans (C. albicans). The results showed that grafting of ABS and AMBS improved overall the hydrophilicity properties of the modified PES membranes. PES‐b‐PES‐ABS membranes showed better anticoagulant properties with 13 seconds for PT and 38 seconds for APPT, in comparison with the control sample (pure plasma), which showed 12 seconds for PT and 30 seconds for APPT. For antimicrobial tests, both PES‐b‐PES‐ABS and PES‐b‐PES‐AMBS membranes did not show any antibacterial activity, but when zinc oxide (ZnO) nanoparticles were added to the modified PES membranes in concentrations between 3% to 5% w/w, PES‐b‐PES‐ABS‐ZnO (M‐4 and M‐5), and PES‐b‐PES‐AMBS‐ZnO (M‐8 and M‐9) nanocomposite membranes showed antibacterial activity against P. aeruginosa and S. aureus.     

An enhanced immobilization of BSA biomolecule on anionic hydrogels: swelling and adsorption modeling

The three-dimensional structure of hydrogels plays a leading role in several areas of applications. The hydrogels are more and more used as systems of immobilized and controlled release of biomolecules in biotechnology and bio-pharmacy industries. To improve protein adsorption capacity in poly(acrylamide) hydrogels, maleic acid co-monomer was included into the reaction mixture during hydrogel synthesis. So, hydrogels of poly(acrylamide) and its copolymers with diprotic maleic acid were prepared by copolymerization and chemical crosslinking with N,N′-methylene bis-acrylamide. Swelling behavior in distilled water, in physiological saline and in bovine serum albumin (BSA) solutions was studied. Influence of initial BSA concentration on hydrogel swelling and BSA adsorption was investigated. The high amount of maleic acid present in the hydrogels has a significant effect on the swelling behavior and BSA adsorption. Results showed that the pH sensitivity of hydrogels resulted in the high amount of adsorbed BSA. The adsorption isotherms were described by Langmuir and Freundlich models. The thermodynamic parameter (ΔG _ads ⁰ ) was determined for all obtained hydrogels. We demonstrated the favorable character and reversibility of the BSA adsorption process.     

Protein posttranslational modifications: the chemistry of proteome diversifications

The diversity of distinct covalent forms of proteins (the proteome) greatly exceeds the number of proteins predicted by DNA coding capacities owing to directed posttranslational modifications. Enzymes dedicated to such protein modifications include 500 human protein kinases, 150 protein phosphatases, and 500 proteases. The major types of protein covalent modifications, such as phosphorylation, acetylation, glycosylation, methylation, and ubiquitylation, can be classified according to the type of amino acid side chain modified, the category of the modifying enzyme, and the extent of reversibility. Chemical events such as protein splicing, green fluorescent protein maturation, and proteasome autoactivations also represent posttranslational modifications. An understanding of the scope and pattern of the many posttranslational modifications in eukaryotic cells provides insight into the function and dynamics of proteome compositions.     

Toward deciphering the code to aminergic G protein-coupled receptor drug design

The trace amine-associated receptor 1 (TAAR(1)) is a biogenic amine G protein-coupled receptor (GPCR) that is potently activated by 3-iodothyronamine (1, T(1)AM) in vitro. Compound 1 is an endogenous derivative of the thyroid hormone thyroxine which rapidly induces hypothermia, anergia, and bradycardia when administered to mice. To explore the role of TAAR(1) in mediating the effects of 1, we rationally designed and synthesized rat TAAR(1) superagonists and lead antagonists using the rotamer toggle switch model of aminergic GPCR activation. The functional activity of a ligand is proposed to be correlated to its probable interactions with the rotamer switch residues; agonists allow the rotamer switch residues to toggle to their active conformation, whereas antagonists interfere with this conformational transition. These agonist and antagonist design principles provide a conceptual model for understanding the relationship between the molecular structure of a drug and its pharmacological properties.     

Biosynthetic gene cluster of the non-ribosomally synthesized cyclodepsipeptide skyllamycin: deciphering unprecedented ways of unusual hydroxylation reactions

The cyclic depsipeptide skyllamycin A is a potent inhibitor of the platelet-derived growth factor (PDGF) signaling pathway by inhibiting binding of homodimeric PDGF BB to the PDGF β-receptor. Its structure contains a cinnamoyl side chain and shows a high amount of β-hydroxylated amino acids as well as an unusual α-hydroxyglycine moiety as a rare structural modification. The skyllamycin biosynthetic gene cluster was cloned and sequenced from Streptomyces sp. Acta 2897. Its analysis revealed the presence of open reading frames encoding proteins for fatty acid precursor biosynthesis, non-ribosomal peptide synthetases, regulators, and transporters along with other modifying enzymes. Specific in-frame mutagenesis of these tailoring enzymes resulted in the production of novel skyllamycin derivatives revealing that β-hydroxy groups in skyllamycin A are introduced by a promiscuous cytochrome P450 monooxygenase, whereas a two-component flavin-dependent monooxygenase is involved in α-hydroxylation.     

Entropic and electrostatic effects on the folding free energy of a surface-attached biomolecule: an experimental and theoretical study

Surface-tethered biomolecules play key roles in many biological processes and biotechnologies. However, while the physical consequences of such surface attachment have seen significant theoretical study, to date this issue has seen relatively little experimental investigation. In response we present here a quantitative experimental and theoretical study of the extent to which attachment to a charged-but otherwise apparently inert-surface alters the folding free energy of a simple biomolecule. Specifically, we have measured the folding free energy of a DNA stem loop both in solution and when site-specifically attached to a negatively charged, hydroxylalkane-coated gold surface. We find that whereas surface attachment is destabilizing at low ionic strength, it becomes stabilizing at ionic strengths above ~130 mM. This behavior presumably reflects two competing mechanisms: excluded volume effects, which stabilize the folded conformation by reducing the entropy of the unfolded state, and electrostatics, which, at lower ionic strengths, destabilizes the more compact folded state via repulsion from the negatively charged surface. To test this hypothesis, we have employed existing theories of the electrostatics of surface-bound polyelectrolytes and the entropy of surface-bound polymers to model both effects. Despite lacking any fitted parameters, these theoretical models quantitatively fit our experimental results, suggesting that, for this system, current knowledge of both surface electrostatics and excluded volume effects is reasonably complete and accurate.     

157-nm Laser ablation of polymeric layers for fabrication of biomolecule microarrays

A new methodology for protein microarray fabrication is proposed based on the ablation of polymer film using laser at 157 nm (F₂). The polymer has been selected among others with the criterion of negligible protein adsorption. Improved results have been obtained by pretreatment of the polymer surface with an inert protein. The use of 157-nm laser radiation allowed very good depth control during the polymeric layer ablation process. In addition the importance of laser ablation at 157 nm is based on the fact that irradiated surfaces indicate limited chemical change due to the fact that laser ablation at 157 nm is only photochemical, thus avoiding excessive surface heating and damage. Results of protein microarray fabrication are presented to illustrate the viability of the proposed method.     

Shedding light on biomolecule conformational dynamics using fluorescence measurements of trapped ions

Biomolecule conformational change has been widely investigated in solution using several methods; however, much less experimental data about structural changes are available for completely isolated, gas-phase biomolecules. Studies of conformational change in unsolvated biomolecules are required to complement the interpretation of mass spectrometry measurements and in addition, can provide a means to directly test theoretical simulations of biomolecule structure and dynamics independent of a simulated solvent. In this Feature Article, we review our recent introduction of a fluorescence-based method for probing local conformational dynamics in unsolvated biomolecules through interactions of an attached dye with tryptophan (Trp) residues and fields originating on charge sites. Dye-derivatized biomolecule ions are formed by electrospray ionization and are trapped in a variable-temperature quadrupole ion trap in which they are irradiated with either continuous or short pulse lasers to excite fluorescence. Fluorescence is measured as a function of temperature for different charge states. Optical measurements of the dye fluorescence include average intensity changes, changes in the emission spectrum, and time-resolved measurements of the fluorescence decay. These measurements have been applied to the miniprotein, Trp-cage, polyproline peptides and to a beta-hairpin-forming peptide, and the results are presented as examples of the broad applicability and utility of these methods. Model fits to Trp-cage fluorescence data measured as a function of temperature provide quantitative information on the thermodynamics of conformational changes, which are reproduced well by molecular dynamics. Time-resolved measurements of the fluorescence decays of Trp-cage and small polyproline peptides definitively demonstrate the occurrence of fluorescence quenching by the amino acid Trp in unsolvated biomolecules.     

Pentaheptite modifications of the graphite sheet

Pentaheptites (three-coordinate tilings of the plane by pentagons and heptagons only) are classified under the chemically motivated restriction that all pentagons occur in isolated pairs and all heptagons have three heptagonal neighbors. They span a continuum between the two lattices exemplified by the boron nets in ThMoB4 (cmm) and YCrB4 (pgg), in analogy with the crossover from cubic-close-packed to hexagonal-close-packed packings in 3D. Symmetries realizable for these pentaheptite layers are three strip groups (periodic in one dimension), p1a1, p112, and p111, and five Fedorov groups (periodic in two dimensions), cmm, pgg, pg, p2, and p1. All can be constructed by simultaneous rotation of the central bonds of pyrene tilings of the graphite sheet. The unique lattice of cmm symmetry corresponds to the previously proposed pentaheptite carbon metal. Analogous pentagon-heptagon tilings on other surfaces including the torus, Klein bottle, and cylinder, face-regular tilings of pentagons and b-gons, and a full characterization of tilings involving isolated pairs and/or triples of pentagons are presented. The Kelvin paradigm of a continuum of structures arising from propagation of two original motifs has many potential applications in 2D and 3D.