Different actions of salt and pyrophosphate on protein extraction from myofibrils reveal the mechanism controlling myosin dissociation

BACKGROUND

Myosin is the major functional protein in muscle foods for water retention, protein binding/gelation and fat holding/emulsification. To maximize its functionality, myosin needs to be released from thick filaments. Understanding of the mechanism controlling myosin extraction will help improve quality traits of meat products.

RESULTS

The data obtained show that actomyosin binding is the rate-limiting constraint for myosin release in rigor condition. Magnesium pyrophosphate (MgPPi) increased myosin extraction by weakening actomyosin interaction and maximized myosin extraction at 0.4 mol L(-1) NaCl, which was not attained at 1.0 mol L(-1) NaCl in the absence of PPi. Interaction between myosin rod domains is another critical constraint for myosin extraction, which is, rather than PPi, salt dependent. Further, our data suggest that MyBP-C (myosin binding protein C) and M-line might not be of significance in the process of NaCl-induced myosin extraction, though further study was needed.

CONCLUSION

Our study provides new insight into the mechanism that controls myosin extraction from intact sarcomere, which could be applied to maximize myosin function and to improve meat quality in practice.

Label-Free Pyrophosphate Recognition with Functionalized Asymmetric Nanopores

The label-free detection of pyrophosphate (PPi) anions with a nanofluidic sensing device based on asymmetric nanopores is demonstrated. The pore surface is functionalized with zinc complexes based on two di(2-picolyl)amine [bis(DPA)] moieties using carbodiimide coupling chemistry. The complexation of zinc (Zn(2+) ) ion is achieved by exposing the modified pore to a solution of zinc chloride to form bis(Zn(2+) -DPA) complexes. The chemical functionalization is demonstrated by recording the changes in the observed current-voltage (I-V) curves before and after pore modification. The bis(Zn(2+) -DPA) complexes on the pore walls serve as recognition sites for pyrophosphate anion. The experimental results show that the proposed nanofluidic sensor has the ability to sense picomolar concentrations of PPi anion in the surrounding environment. On the contrary, it does not respond to other phosphate anions, including monohydrogen phosphate, dihydrogen phosphate, adenosine monophosphate, adenosine diphosphate, and adenosine triphosphate. The experimental results are described theoretically by using a model based on the Poisson-Nernst-Planck equations.

DNA-inorganic hybrid nanovaccine for cancer immunotherapy

Cancer evolves to evade or compromise the surveillance of the immune system, and cancer immunotherapy aims to harness the immune system in order to inhibit cancer development. Unmethylated CpG dinucleotide-containing oligonucleotides (CpG), a class of potent adjuvants that activate the toll-like receptor 9 (TLR9) located in the endolysosome of many antigen-presenting cells (APCs), are promising for cancer immunotherapy. However, clinical application of synthetic CpG confronts many challenges such as suboptimal delivery into APCs, unfavorable pharmacokinetics caused by limited biostability and short in vivo half-life, and side effects associated with leaking of CpG into the systemic circulation. Here we present DNA-inorganic hybrid nanovaccines (hNVs) for efficient uptake into APCs, prolonged tumor retention, and potent immunostimulation and cancer immunotherapy. hNVs were self-assembled from concatemer CpG analogs and magnesium pyrophosphate (Mg2PPi). Mg2PPi renders hNVs resistant to nuclease degradation and thermal denaturation, both of which are demanding characteristics for effective vaccination and the storage and transportation of vaccines. Fluorophore-labeled hNVs were tracked to be efficiently internalized into the endolysosomes of APCs, where Mg2PPi was dissolved in an acidic environment and thus CpG analogs were exposed to hNVs. Internalized hNVs in APCs led to (1) elevated secretion of proinflammatory factors, and (2) elevated expression of co-stimulatory factors. Compared with molecular CpG, hNVs dramatically prolonged the tissue retention of CpG analogs and reduced splenomegaly, a common side effect of CpG. In a melanoma mouse model, two injections of hNVs significantly inhibited the tumor growth and outperformed the molecular CpG. These results suggest hNVs are promising for cancer immunotherapy.

Insights into properties of activated carbons prepared from different raw precursors by pyrophosphoric acid activation

Low-cost activated carbons (ACs) were prepared from four kinds of solid wastes: petroleum coke, Enteromorpha prolifera, lignin from papermaking black liquid and hair, by pyrophosphoric acid (H4P2O7) activation. Thermo-gravimetric analysis of the pyrolysis of H4P2O7-precursor mixtures implied that H4P2O7 had different influences on the pyrolysis behavior of the four raw materials. N2 adsorption/desorption isotherms, scanning electron microscopy, Fourier transform infrared spectroscopy and adsorption capacities for dyes were used to characterize the prepared activated carbons. AC derived from E. prolifera exhibited the highest surface area (1094m(2)/g) and maximum monolayer adsorption capacity for malachite green (1250mg/g). Kinetic studies showed that the experimental data were in agreement with the pseudo-second-order model. The adsorption isotherms were well described by the Langmuir isotherm model, indicating the adsorption of dye onto the ACs proceeded by monolayers.

Roles of MPBQ-MT in Promoting α/γ-Tocopherol Production and Photosynthesis under High Light in Lettuce

2-methyl-6-phytyl-1, 4-benzoquinol methyltransferase (MPBQ-MT) is a vital enzyme catalyzing a key methylation step in both α/γ-tocopherol and plastoquinone biosynthetic pathway. In this study, the gene encoding MPBQ-MT was isolated from lettuce (Lactuca sativa) by rapid amplification of cDNA ends (RACE), named LsMT. Overexpression of LsMT in lettuce brought about a significant increase of α- and γ-tocopherol contents with a reduction of phylloquinone (vitamin K1) content, suggesting a competition for a common substrate phytyl diphosphate (PDP) between the two biosynthetic pathways. Besides, overexpression of LsMT significantly increased plastoquinone (PQ) level. The increase of tocopherol and plastoquinone levels by LsMT overexpression conduced to the improvement of plants' tolerance and photosynthesis under high light stress, by directing excessive light energy toward photosynthetic production rather than toward generation of more photooxidative damage. These findings suggest that the role and function of MPBQ-MT can be further explored for enhancing vitamin E value, strengthening photosynthesis and phototolerance under high light in plants.

Ionically Cross-Linked Polymer Networks for the Multiple-Month Release of Small Molecules

Long-term (multiple-week or -month) release of small, water-soluble molecules from hydrogels remains a significant pharmaceutical challenge, which is typically overcome at the expense of more-complicated drug carrier designs. Such approaches are payload-specific and include covalent conjugation of drugs to base materials or incorporation of micro- and nanoparticles. As a simpler alternative, here we report a mild and simple method for achieving multiple-month release of small molecules from gel-like polymer networks. Densely cross-linked matrices were prepared through ionotropic gelation of poly(allylamine hydrochloride) (PAH) with either pyrophosphate (PPi) or tripolyphosphate (TPP), all of which are commonly available commercial molecules. The loading of model small molecules (Fast Green FCF and Rhodamine B dyes) within these polymer networks increases with the payload/network binding strength and with the PAH and payload concentrations used during encapsulation. Once loaded into the PAH/PPi and PAH/TPP ionic networks, only a few percent of the payload is released over multiple months. This extended release is achieved regardless of the payload/network binding strength and likely reflects the small hydrodynamic mesh size within the gel-like matrices. Furthermore, the PAH/TPP networks show promising in vitro cytocompatibility with model cells (human dermal fibroblasts), though slight cytotoxic effects were exhibited by the PAH/PPi networks. Taken together, the above findings suggest that PAH/PPi and (especially) PAH/TPP networks might be attractive materials for the multiple-month delivery of drugs and other active molecules (e.g., fragrances or disinfectants).

Molecular Dynamics Assisted Mechanistic Study of Isoniazid-Resistance against Mycobacterium tuberculosis InhA

Examination of InhA mutants I16T, I21V, I47T, S94A, and I95P showed that direct and water mediated H-bond interactions between NADH and binding site residues reduced drastically. It allowed conformational flexibility to NADH, particularly at the pyrophosphate region, leading to weakening of its binding at dinucleotide binding site. The highly scattered distribution of pyrophosphate dihedral angles and chi1 side chain dihedral angles of corresponding active site residues therein confirmed weak bonding between InhA and NADH. The average direct and water mediated bridged H-bond interactions between NADH and mutants were observed weaker as compared to wild type. Further, estimated NADH binding free energy in mutants supported the observed weakening of InhA-NADH interactions. Similarly, per residue contribution to NADH binding was also found little less as compared to corresponding residues in wild type. This investigation clearly depicted and supported the effect of mutations on NADH binding and can be accounted for isoniazid resistance as suggested by previous biochemical and mutagenic studies. Further, structural analysis of InhA provided the crucial points to enhance the NADH binding affinity towards InhA mutants in the presence of direct InhA inhibitors to combat isoniazid drug resistance. This combination could be a potential alternative for treatment of drug resistant tuberculosis.

A Jump-from-Cavity Pyrophosphate Ion Release Assisted by a Key Lysine Residue in T7 RNA Polymerase Transcription Elongation

Pyrophosphate ion (PPi) release during transcription elongation is a signature step in each nucleotide addition cycle. The kinetics and energetics of the process as well as how it proceeds with substantial conformational changes of the polymerase complex determine the mechano-chemical coupling mechanism of the transcription elongation. Here we investigated detailed dynamics of the PPi release process in a single-subunit RNA polymerase (RNAP) from bacteriophage T7, implementing all-atom molecular dynamics (MD) simulations. We obtained a jump-from-cavity kinetic model of the PPi release utilizing extensive nanosecond MD simulations. We found that the PPi release in T7 RNAP is initiated by the PPi dissociation from two catalytic aspartic acids, followed by a comparatively slow jump-from-cavity activation process. Combining with a number of microsecond long MD simulations, we also found that the activation process is hindered by charged residue associations as well as by local steric and hydrogen bond interactions. On the other hand, the activation is greatly assisted by a highly flexible lysine residue Lys472 that swings its side chain to pull PPi out. The mechanism can apply in general to single subunit RNA and DNA polymerases with similar molecular structures and conserved key residues. Remarkably, the flexible lysine or arginine residue appears to be a universal module that assists the PPi release even in multi-subunit RNAPs with charge facilitated hopping mechanisms. We also noticed that the PPi release is not tightly coupled to opening motions of an O-helix on the fingers domain of T7 RNAP according to the microsecond MD simulations. Our study thus supports the Brownian ratchet scenario of the mechano-chemical coupling in the transcription elongation of the single-subunit polymerase.

Negative Feedbacks by Isoprenoids on a Mevalonate Kinase Expressed in the Corpora Allata of Mosquitoes

Background

Juvenile hormones (JH) regulate development and reproductive maturation in insects. JHs are synthesized through the mevalonate pathway (MVAP), an ancient metabolic pathway present in the three domains of life. Mevalonate kinase (MVK) is a key enzyme in the MVAP. MVK catalyzes the synthesis of phosphomevalonate (PM) by transferring the γ-phosphoryl group from ATP to the C₅ hydroxyl oxygen of mevalonic acid (MA). Despite the importance of MVKs, these enzymes have been poorly characterized in insects.

Results

We functionally characterized an Aedes aegypti MVK (AaMVK) expressed in the corpora allata (CA) of the mosquito. AaMVK displayed its activity in the presence of metal cofactors. Different nucleotides were used by AaMVK as phosphoryl donors. In the presence of Mg²⁺, the enzyme has higher affinity for MA than ATP. The activity of AaMVK was regulated by feedback inhibition from long-chain isoprenoids, such as geranyl diphosphate (GPP) and farnesyl diphosphate (FPP).

Conclusions

AaMVK exhibited efficient inhibition by GPP and FPP (Ki less than 1 μM), and none by isopentenyl pyrophosphate (IPP) and dimethyl allyl pyrophosphate (DPPM). These results suggest that GPP and FPP might act as physiological inhibitors in the synthesis of isoprenoids in the CA of mosquitoes. Changing MVK activity can alter the flux of precursors and therefore regulate juvenile hormone biosynthesis.

Gas-Phase Partial Oxidation of Lignin to Carboxylic Acids over Vanadium Pyrophosphate and Aluminum-Vanadium-Molybdenum

Lignin is a complex polymer that is a potential feedstock for aromatic compounds and carboxylic acids by cleaving the β-O-4 and 5-5' linkages. In this work, a syringe pump atomizes an alkaline solution of lignin into a catalytic fluidized bed operating above 600 K. The vanadium heterogeneous catalysts convert all the lignin into carboxylic acids (up to 25 % selectivity), coke, carbon oxides, and hydrogen. Aluminum-vanadium-molybdenum mostly produced lactic acid (together with formic acid, acrylic acid, and maleic anhydride), whereas the vanadium pyrophosphate catalyst produced more maleic anhydride.

ABTS as an Electron Shuttle to Enhance the Oxidation Kinetics of Substituted Phenols by Aqueous Permanganate

In this study, it was, interestingly, found that 2,2'-azino-bis(3-ethylbenzothiazoline)-6-sulfonate (ABTS), a widely used electron shuttle, could greatly accelerate the oxidation of substituted phenols by potassium permanganate (Mn(VII)) in aqueous solutions at pH 5-9. This was attributed to the fact that these substituted phenols could be readily oxidized by the stable radical cation (ABTS(•+)), which was quickly produced from the oxidation of ABTS by Mn(VII). The reaction of Mn(VII) with ABTS exhibited second-order kinetics, with stoichiometries of ∼5:1 at pH 5-6 and ∼3:1 at pH 7-9, and the rate constants varied negligibly from pH 5 to 9 (k = (9.44 ± 0.21) × 10(4) M(-1) s(-1)). Comparatively, the reaction of ABTS(•+) with phenol showed biphasic kinetics. The second-order rate constants for the reactions of ABTS(•+) with substituted phenols obtained in the initial phase were strongly affected by pH, and they were several orders of magnitude higher than those for the reactions of Mn(VII) with substituted phenols at each pH. Good Hammett-type correlations were found for the reactions of ABTS(•+) with undissociated (log(k) = 2.82-4.31σ) and dissociated phenols (log(k) = 7.29-5.90σ). The stoichiometries of (2.2 ± 0.06):1 (ABTS(•+) in excess) and (1.38 ± 0.18):1 (phenol in excess) were achieved in the reaction of ABTS(•+) with phenol, but they exhibited no pH dependency.

Remobilization of Phytol from Chlorophyll Degradation Is Essential for Tocopherol Synthesis and Growth of Arabidopsis

Phytol from chlorophyll degradation can be phosphorylated to phytyl-phosphate and phytyl-diphosphate, the substrate for tocopherol (vitamin E) synthesis. A candidate for the phytyl-phosphate kinase from Arabidopsis thaliana (At1g78620) was identified via a phylogeny-based approach. This gene was designated VITAMIN E DEFICIENT6 (VTE6) because the leaves of the Arabidopsis vte6 mutants are tocopherol deficient. The vte6 mutant plants are incapable of photoautotrophic growth. Phytol and phytyl-phosphate accumulate, and the phytyl-diphosphate content is strongly decreased in vte6 leaves. Phytol feeding and enzyme assays with Arabidopsis and recombinant Escherichia coli cells demonstrated that VTE6 has phytyl-P kinase activity. Overexpression of VTE6 resulted in increased phytyl-diphosphate and tocopherol contents in seeds, indicating that VTE6 encodes phytyl-phosphate kinase. The severe growth retardation of vte6 mutants was partially rescued by introducing the phytol kinase mutation vte5. Double mutant plants (vte5 vte6) are tocopherol deficient and contain more chlorophyll, but reduced amounts of phytol and phytyl-phosphate compared with vte6 mutants, suggesting that phytol or phytyl-phosphate are detrimental to plant growth. Therefore, VTE6 represents the missing phytyl-phosphate kinase, linking phytol release from chlorophyll with tocopherol synthesis. Moreover, tocopherol synthesis in leaves depends on phytol derived from chlorophyll, not on de novo synthesis of phytyl-diphosphate from geranylgeranyl-diphosphate.

Crystallization and X-ray diffraction analysis of a putative bacterial class I labdane-related diterpene synthase

Labdane-related diterpenoids are natural products with potential pharmaceutical applications that are rarely found in bacteria. Here, a putative class I labdane-related diterpene synthase (LrdC) identified by genome mining in a streptomycete was successfully crystallized using the microbatch method. Crystals of the LrdC enzyme were obtained in a holo form with its natural cofactor Mg(2+) (LrdC-Mg(2+)) and in complex with inorganic pyrophosphate (PPi) (LrdC-Mg(2+)-PPi). Crystals of native LrdC-Mg(2+) diffracted to 2.50 Å resolution and belonged to the trigonal space group P3221, with unit-cell parameters a = b = 107.1, c = 89.2 Å. Crystals of the LrdC-Mg(2+)-PPi complex grown in the same conditions as the native enzyme with PEG 8000 diffracted to 2.36 Å resolution and also belonged to the trigonal space group P3221. Crystals of the LrdC-Mg(2+)-PPi complex grown in a second crystallization condition with PEG 3350 diffracted to 2.57 Å resolution and belonged to the monoclinic space group P21, with unit-cell parameters a = 49.9, b = 104.1, c = 66.5 Å, β = 111.4°. The structure was determined by the single-wavelength anomalous dispersion (SAD) technique using the osmium signal from a potassium hexachloroosmate (IV) derivative.

Potter BV. Synthetic tools for studying the chemical biology of InsP8

To synthesise stabilised mimics of InsP8, the most phosphorylated inositol phosphate signalling molecule in Nature, we replaced its two diphosphate (PP) groups with either phosphonoacetate (PA) or methylenebisphosphonate (PCP) groups. Utility of the PA and PCP analogues was verified by structural and biochemical analyses of their interactions with enzymes of InsP8 metabolism.

[Laboratory evaluation and field trial of activation indigenous microbial displacements in the reservoirs after polymer flooding]

Most main oilfields in China have already entered a "double high" development stage (high water cut, high recovery degree). To further enhance oil recovery in reservoirs after polymer flooding (RAPFs), an efficient activator formulation for promoting metabolism of endogenous microorganism was studied by aerogenic experiments, physical simulation experiments, electron microscopy scanning and pyrophosphate sequencing. Results show that the activator could activate the endogenous microorganisms in the injected water and make the pressurized gas reach 2 MPa after 60 d static culture of the activator in a high pressure vessel. The oil recovery efficiency of natural core physical simulation flooding can be improved by more than 3.0% (OOIP) in RAPFs when injected 0.35 PV activator with 1.8% mass concentration, and a lot of growth and reproduction of activated endogenous microorganism in the core was observed by electron microscopy scanning. Field trial with 1 injector and 4 producers was carried out in the east of south II block of Sa Nan in December 2011. By monitoring four effective production wells, changes of carbon isotope δ13C (PDB) content of methane and carbon dioxide were -45 per thousand to -54 per thousand and 7 per thousand to 12 per thousand. Compared with east II of Sa Nan block, the oil amount increased by 35.9%, water cut stabled at 94%. The incremental oil was 5 957 t during the three and a half years, which provides an alternative approach for further improving oil recovery in similar reservoirs.

Amino-functionalized green fluorescent carbon dots as surface energy transfer biosensors for hyaluronidase

Amino-functionalized fluorescent carbon dots have been prepared by hydrothermal treatment of glucosamine with excess pyrophosphate. The produced carbon dots showed stabilized green emission fluorescence at various excitation wavelengths and pH environments. Herein, we demonstrate the surface energy transfer between the amino-functionalized carbon dots and negatively charged hyaluronate stabilized gold nanoparticles. Hyaluronidase can degrade hyaluronate and break down the hyaluronate stabilized gold nanoparticles to inhibit the surface energy transfer. The developed fluorescent carbon dot/gold nanoparticle system can be utilized as a biosensor for sensitive and selective detection of hyaluronidase by two modes which include fluorescence measurements and colorimetric analysis.

Enhanced photoelectrocatalytic decomposition of copper cyanide complexes and simultaneous recovery of copper with a Bi2MoO6 electrode under visible light by EDTA/K4P2O7

Simultaneous photoelectrocatalytic (PEC) oxidation of cyanides and recovery of copper in a PEC reactor with a Bi(2)MoO(6) photoanode was investigated at alkaline conditions under visible light irradiation. The surface variation of the Bi(2)MoO(6) photoanode and titanium cathode was characterized. The Cu mass distribution onto the anode, in the solution, and onto the cathode was fully investigated. In the individual PEC oxidation of copper cyanides, the formation of a black copper oxide on the anode occurred. By keeping the initial cyanide concentration at 0.01 mM, the effect of EDTA/K(4)P(2)O(7) was examined at different molar ratios of EDTA/K(4)P(2)O(7) to cyanide. It was indicated that the oxidation of cyanides increased and simultaneous copper electrodeposition with zero value onto the cathode was feasible at pH 11. Under the optimal conditions, the total cyanide concentration was lowered from 250 to 5.0 mg/L, and the Cu recovery efficiency deposited onto the cathode was higher than 90%. Cyanate was the only product. The role of the photogenerated hole in the oxidation of cyanide ions was confirmed.

Development of optically transparent water oxidation catalysts using manganese pyrophosphate compounds

One challenge in artificial photosynthetic systems is the development of active oxygen evolution catalysts composed of abundant elements. The oxygen evolution activities of manganese pyrophosphate compounds were examined in electrochemical and photochemical experiments. Electrocatalysis using calcium-manganese pyrophosphate exhibited good catalytic ability under neutral pH and an oxygen evolution reaction was driven with a small overpotential (η<100 mV). UV-vis diffuse reflectance measurements revealed that manganese pyrophosphates exhibit weak absorption in the visible light region while commonly used oxygen evolution catalysts exhibit intense absorption. Therefore, the efficient light absorption of a photocatalyst was retained even after surface modification with a manganese pyrophosphate, and photochemical oxygen evolution was achieved by using magnesium ferrite modified with manganese pyrophosphate nanoparticles under the illumination of visible light at wavelength of over 420 nm.

[Effects of superphosphate addition on NH3 and greenhouse gas emissions during vegetable waste composting]

To study the effects of superphosphate (SP) on the NH, and greenhouse gas emissions, vegetable waste composting was performed for 27 days using 6 different treatments. In addition to the controls, five vegetable waste mixtures (0.77 m3 each) were treated with different amounts of the SP additive, namely, 5%, 10%, 15%, 20% and 25%. The ammonia volatilization loss and greenhouse gas emissions were measured during composting. Results indicated that the SP additive significantly decreased the ammonia volatilization and greenhouse gas emissions during vegetable waste composting. The additive reduced the total NH3 emission by 4.0% to 16.7%. The total greenhouse gas emissions (CO2-eq) of all treatments with SP additives were decreased by 10.2% to 20.8%, as compared with the controls. The NH3 emission during vegetable waste composting had the highest contribution to the greenhouse effect caused by the four different gases. The amount of NH3 (CO2-eq) from each treatment ranged from 59.90 kg . t-1 to 81.58 kg . t-1; NH3(CO2-eq) accounted for 69% to 77% of the total emissions from the four gases. Therefore, SP is a cost-effective phosphorus-based fertilizer that can be used as an additive during vegetable waste composting to reduce the NH3 and greenhouse gas emissions as well as to improve the value of compost as a fertilizer.

Biochemical and kinetic characterization of the recombinant ADP-forming acetyl coenzyme A synthetase from the amitochondriate protozoan Entamoeba histolytica

Entamoeba histolytica, an amitochondriate protozoan parasite that relies on glycolysis as a key pathway for ATP generation, has developed a unique extended PPi-dependent glycolytic pathway in which ADP-forming acetyl-coenzyme A (CoA) synthetase (ACD; acetate:CoA ligase [ADP-forming]; EC 6.2.1.13) converts acetyl-CoA to acetate to produce additional ATP and recycle CoA. We characterized the recombinant E. histolytica ACD and found that the enzyme is bidirectional, allowing it to potentially play a role in ATP production or in utilization of acetate. In the acetate-forming direction, acetyl-CoA was the preferred substrate and propionyl-CoA was used with lower efficiency. In the acetyl-CoA-forming direction, acetate was the preferred substrate, with a lower efficiency observed with propionate. The enzyme can utilize both ADP/ATP and GDP/GTP in the respective directions of the reaction. ATP and PPi were found to inhibit the acetate-forming direction of the reaction, with 50% inhibitory concentrations of 0.81 ± 0.17 mM (mean ± standard deviation) and 0.75 ± 0.20 mM, respectively, which are both in the range of their physiological concentrations. ATP and PPi displayed mixed inhibition versus each of the three substrates, acetyl-CoA, ADP, and phosphate. This is the first example of regulation of ACD enzymatic activity, and possible roles for this regulation are discussed.

A binuclear Zn(II)-Zn(II) complex from a 2-hydroxybenzohydrazide-derived Schiff base for selective detection of pyrophosphate

A hydroxybenzohydrazide-based Schiff base ligand was conveniently synthesized. Upon addition of Zn(2+) cations, the ligand exhibited a high tendency to form a binuclear structure with a 2 : 2 ligand-to-zinc ratio, which was accompanied by a large fluorescence turn-on (λem = 507 nm, ϕfl≈ 0.28). The reactivity of the zinc complex was examined using different phosphate anions, which reveals a higher response to acid pyrophosphate anions. Detailed spectroscopic studies show that the pyrophosphate response is based on the ligand displacement mechanism.

Elucidation of kinetic mechanisms of human translesion DNA polymerase κ using tryptophan mutants

To investigate the conformational dynamics of human DNA polymerase κ (hpol κ), we generated two mutants, Y50W (N-clasp region) and Y408W (linker between the thumb and little finger domains), using a Trp-null mutant (W214Y/W392H) of the hpol κ catalytic core enzyme. These mutants retained catalytic activity and similar patterns of selectivity for bypassing the DNA adduct 7,8-dihydro-8-oxo-2'-deoxyguanosine, as indicated by the results of steady-state and pre-steady-state kinetic experiments. Stopped-flow kinetic assays with hpol κ Y50W and T408W revealed a decrease in Trp fluorescence with the template G:dCTP pair but not for any mispairs. This decrease in fluorescence was not rate-limiting and is considered to be related to a conformational change necessary for correct nucleotidyl transfer. When a free 3'-hydroxyl was present on the primer, the Trp fluorescence returned to the baseline level at a rate similar to the observed kcat , suggesting that this change occurs during or after nucleotidyl transfer. However, polymerization rates (kpol ) of extended-product formation were fast, indicating that the slow fluorescence step follows phosphodiester bond formation and is rate-limiting. Pyrophosphate formation and release were fast and are likely to precede the slower relaxation step. The available kinetic data were used to fit a simplified minimal model. The extracted rate constants confirmed that the conformational change after phosphodiester bond formation was rate-limiting for hpol κ catalysis with the template G:dCTP pair.

Nanoscale lithography mediated by surface self-assembly of 16-[3,5-bis(mercaptomethyl)phenoxy]hexadecanoic acid on Au(111) investigated by scanning probe microscopy

The solution-phase self-assembly of bidentate 16-[3,5-bis(mercapto-methyl)phenoxy]hexadecanoic acid (BMPHA) on Au(111) was studied using nano-fabrication protocols with scanning probe nanolithography and immersion particle lithography. Molecularly thin films of BMPHA prepared by surface self-assembly have potential application as spatially selective layers in sensor designs. Either monolayer or bilayer films of BMPHA can be formed under ambient conditions, depending on the parameters of concentration and immersion intervals. Experiments with scanning probe-based lithography (nanoshaving and nanografting) were applied to measure the thickness of BMPHA films. The thickness of a monolayer and bilayer film of BMPHA on Au(111) were measured in situ with atomic force microscopy using n-octadecanethiol as an internal reference. Scanning probe-based nanofabrication provides a way to insert nanopatterns of a reference molecule of known dimensions within a matrix film of unknown thickness to enable a direct comparison of heights and surface morphology. Immersion particle lithography was used to prepare a periodic arrangement of nanoholes within films of BMPHA. The nanoholes could be backfilled by immersion in a SAM solution to produce nanodots of n-octadecanethiol surrounded by a film of BMPHA. Test platforms prepared by immersion particle lithography enables control of the dimensions of surface sites to construct supramolecular assemblies.

Intramolecular indicator displacement assay for anions: supramolecular sensor for glyphosate

One of the well-known strategies for anion sensing is an indicator (dye) displacement assay. However, the disadvantage of the dye displacement assays is the low sensitivity due to the excess of the dye used. To overcome this setback, we have developed an "Intramolecular Indicator Displacement Assay (IIDA)". The IIDAs comprise a receptor and a spacer with an attached anionic chromophore in a single-molecule assembly. In the resting state, the environment-sensitive anionic chromophore is bound by the receptor, while the anionic substrate competes for binding into the receptor. The photophysical properties of the dye exhibit change in fluorescence when displaced by anions, which results in cross-reactive response. To illustrate the concept, we have prepared IID sensors 1 and 2. Here, the characterization of sensors and microtiter arrays comprising the IIDA are reported. The microtiter array including IID sensors 1 and 2 is capable of recognizing biological phosphates in water. The utility of the IIDA approach is demonstrated on sensing of a phosphonate herbicide glyphosate and other biologically important anions such as pyrophosphate in the presence of interferent sodium chloride.

Site-specific labeling of proteins and peptides with trans-cyclooctene containing handles capable of tetrazine ligation

There is a growing library of functionalized non-natural substrates for the enzyme protein farnesyltransferase (PFTase). PFTase covalently attaches these functionalized non-natural substrates to proteins ending in the sequence CAAX, where C is a cysteine that becomes alkylated, A represents an aliphatic amino acid, and X is Ser, Met, Ala, or Gln. Reported substrates include a variety of functionalities that allow modified proteins to undergo subsequent bioconjugation reactions. To date the most common strategy used in this approach has been copper catalyzed azide-alkyne cycloaddition (CuAAC). While being fast and bioorthogonal CuAAC has limited use in live cell experiments due to copper's toxicity.(1) Here, we report the synthesis of trans-cyclooctene geranyl diphosphate. This substrate can be synthesized from geraniol in six steps and be enzymatically transferred to peptides and proteins that end in a CAAX sequence. Proteins and peptides site-specially modified with trans-cyclooctene geranyl diphosphate were subsequently targeted for further modification via tetrazine ligation. As tetrazine ligation is bioorthogonal, fast, and is contingent on ring strain rather than the addition of a copper catalyst, this labeling strategy should prove useful for labeling proteins where the presence of copper may hinder solubility or biological reactivity.