The proteolytic activity of insulin‐degrading enzyme: a mass spectrometry study

The prominent role that insulin‐degrading enzyme (IDE) has on amyloidogenic peptides degradation has recently boosted a lot of attention toward this enzyme. Although many substrates are known to be degraded by IDE, little is known about the changes in the proteolytic activity of the enzyme upon modification of environmental factors. In a previous work we have already shown the great potentiality of atmospheric pressure/laser desorption ionization‐mass spectrometry (AP/MALDI‐MS) for studying the interaction between IDE and insulin. Here, the activity of IDE was investigated regarding cleavage sites' preferentiality upon modification of environmental factors by AP/MALDI‐MS. The roles that IDE/insulin concentration ratio, reaction time, adenosine 5′‐triphosphate (ATP) and metal ions (Zn and Cu) have on the insulin cleavage pattern produced by IDE are investigated and a plausible interpretation involving the proteolytic action of the different IDE oligomeric forms is proposed. Copyright © 2009 John Wiley & Sons, Ltd.     

Modeling the effect of external electric field and current on the stochastic dynamics of ATPase nano-biomolecular motors

The rotary motion of the F₀ part of the F₀F₁-ATPase motor that synthesizes the ATP molecules used by the intracellular stepping motors, such as kinesins, is modeled within a stochastically fluctuating medium via the application of the Langevin dynamics wherein the random intramembrane fluctuations are represented by a white noise. We have investigated the influence of an applied electric field and an applied electric current on this rotary motion, and the subsequent production rate of the ATP molecules. It is seen that the application of a field, or a current, changes both the elastic behavior of the cell membrane and the transmembrane potential. These changes in turn transform the dynamics of the F₀ part of the motor. We have found that at low fields, the role of transmembrane potential becomes significant in the production rate of the ATP molecules, whereas at high fields the changes induced in the surface tension of the membrane also contribute to the production rate of the ATP.     

钯与腺苷5′-三磷酸—邻菲啰啉混配合物稳定矹牟舛

用pH电位法测定了在40%(V/V)二(口恶)烷-水介质中(Ⅰ=0.1,25±0.1℃)Pd(Ⅱ)与腺苷5＇-三磷酸(ATP)的二元配合物Pd(ATP)~(2-)和Pd(Ⅱ)-ATP-邻菲啰啉(Phen)的三元混配合物Pd(Phen)(ATP)~(2-)的稳定常数,其值分别为lgK_((Pd(ATP))~Pd)~(2-)=5.19和lgK_((Pd(Phen)(ATP)~(Pd(Phen))~(2-)-=5.42.比较了两种配合物的稳定性,其差值(?)lgK=0.23,比预期的统计值(?)lgK_(?)=-0.6为大.混配合物稳定性的增加可归因于π-酸和π-碱间的合作效应和配体分子间的堆积作用的贡献.     

Monitoring of metabolic profiling and water status of Hayward kiwifruits by nuclear magnetic resonance

The metabolic profiling of kiwifruit (Actinidia deliciosa, Hayward cultivar) aqueous extracts and the water status of entire kiwifruits were monitored over the season (June-December) using nuclear magnetic resonance (NMR) methodologies. The metabolic profiling of aqueous kiwifruit extracts was investigated by means of high field NMR spectroscopy. A large number of water-soluble metabolites were assigned by means of 1D and 2D NMR experiments. The change in the metabolic profiles monitored over the season allowed the kiwifruit development to be investigated. Specific temporal trends of aminoacids, sugars, organic acids and other metabolites were observed.The water status of kiwifruits was monitored directly on the intact fruit measuring the T₂ spin-spin relaxation time by means of a portable unilateral NMR instrument, fully non-invasive. Again, clear trends of the relaxation time were observed during the monitoring period.The results show that the monitoring of the metabolic profiling and the monitoring of the water status are two complementary means suitable to have a complete view of the investigated fruit.     

Beyond labels: A review of the application of quantum dots as integrated components of assays, bioprobes, and biosensors utilizing optical transduction

A comprehensive review of the development of assays, bioprobes, and biosensors using quantum dots (QDs) as integrated components is presented. In contrast to a QD that is selectively introduced as a label, an integrated QD is one that is present in a system throughout a bioanalysis, and simultaneously has a role in transduction and as a scaffold for biorecognition. Through a diverse array of coatings and bioconjugation strategies, it is possible to use QDs as a scaffold for biorecognition events. The modulation of QD luminescence provides the opportunity for the transduction of these events via fluorescence resonance energy transfer (FRET), bioluminescence resonance energy transfer (BRET), charge transfer quenching, and electrochemiluminescence (ECL). An overview of the basic concepts and principles underlying the use of QDs with each of these transduction methods is provided, along with many examples of their application in biological sensing. The latter include: the detection of small molecules using enzyme-linked methods, or using aptamers as affinity probes; the detection of proteins via immunoassays or aptamers; nucleic acid hybridization assays; and assays for protease or nuclease activity. Strategies for multiplexed detection are highlighted among these examples. Although the majority of developments to date have been in vitro, QD-based methods for ex vivo biological sensing are emerging. Some special attention is given to the development of solid-phase assays, which offer certain advantages over their solution-phase counterparts.     

Natural and artificial light-harvesting systems utilizing the functions of carotenoids

Carotenoids are essential pigments in natural photosynthesis. They absorb in the blue–green region of the solar spectrum and transfer the absorbed energy to (bacterio-)chlorophylls, and so expand the wavelength range of light that is able to drive photosynthesis. This process is an example of singlet–singlet energy transfer and so carotenoids serve to enhance the overall efficiency of photosynthetic light reactions. Carotenoids also act to protect photosynthetic organisms from the harmful effects of excess exposure to light. In this case, triplet–triplet energy transfer from (bacterio-)chlorophyll to carotenoid plays a key role in this photoprotective reaction. In the light-harvesting pigment–protein complexes from purple photosynthetic bacteria and chlorophytes, carotenoids have an additional role, namely the structural stabilization of those complexes. In this article we review what is currently known about how carotenoids discharge these functions. The molecular architecture of photosynthetic systems will be outlined to provide a basis from which to describe the photochemistry of carotenoids, which underlies most of their important functions in photosynthesis. Then, the possibility to utilize the functions of carotenoids in artificial photosynthetic light-harvesting systems will be discussed. Some examples of the model systems are introduced.     

Systematic investigation of sequence and structural motifs that recognize ATP

Interaction between ATP, a multifunctional and ubiquitous nucleotide, and proteins initializes phosphorylation, polypeptide synthesis and ATP hydrolysis which supplies energy for metabolism. However, current knowledge concerning the mechanisms through which ATP is recognized by proteins is incomplete, scattered, and inaccurate. We systemically investigate sequence and structural motifs of proteins that recognize ATP. We identified three novel motifs and refined the known p-loop and class II aminoacyl-tRNA synthetase motifs. The five motifs define five distinct ATP–protein interaction modes which concern over 5% of known protein structures. We demonstrate that although these motifs share a common GXG tripeptide they recognize ATP through different functional groups. The p-loop motif recognizes ATP through phosphates, class II aminoacyl-tRNA synthetase motif targets adenosine and the other three motifs recognize both phosphates and adenosine. We show that some motifs are shared by different enzyme types. Statistical tests demonstrate that the five sequence motifs are significantly associated with the nucleotide binding proteins. Large-scale test on PDB reveals that about 98% of proteins that include one of the structural motifs are confirmed to bind ATP.     

Interactions of DNA with graphene and sensing applications of graphene field-effect transistor devices: A review

Graphene field-effect transistors (GFET) have emerged as powerful detection platforms enabled by the advent of chemical vapor deposition (CVD) production of the unique atomically thin 2D material on a large scale. DNA aptamers, short target-specific oligonucleotides, are excellent sensor moieties for GFETs due to their strong affinity to graphene, relatively short chain-length, selectivity, and a high degree of analyte variability. However, the interaction between DNA and graphene is not fully understood, leading to questions about the structure of surface-bound DNA, including the morphology of DNA nanostructures and the nature of the electronic response seen from analyte binding. This review critically evaluates recent insights into the nature of the DNA graphene interaction and its affect on sensor viability for DNA, small molecules, and proteins with respect to previously established sensing methods. We first discuss the sorption of DNA to graphene to introduce the interactions and forces acting in DNA based GFET devices and how these forces can potentially affect the performance of increasingly popular DNA aptamers and even future DNA nanostructures as sensor substrates. Next, we discuss the novel use of GFETs to detect DNA and the underlying electronic phenomena that are typically used as benchmarks for characterizing the analyte response of these devices. Finally, we address the use of DNA aptamers to increase the selectivity of GFET sensors for small molecules and proteins and compare them with other, state of the art, detection methods.     

肌球蛋白中金属离子与ATP相互作用及其催化ATP水解的研究进展

生物体内细胞在氧化物质的过程中释放出的大量自由能,这些能量先形成高能磷酸化合物三磷酸腺苷（adenosine 5′-triphosphate,ATP）,当ATP水解为ADP（二磷酸腺苷,adenosine 5′-diphosphate）和无机磷酸时.     

Rational design of an inhibitor of dethiobiotin synthetase; interaction of 6-hydroxypyrimindin-4(3H)-one with the adenine base binding site

Modelling of the H-bonding interactions involved in the binding of the adenine base component of ATP to E. coli dethiobiotin synthetase (DTBS) suggested that 6-hydroxypyrimidin-4(3H)-one (6-HP4) should selectively bind to this site in the enzyme. Kinetic studies show that 6-HP4 is a competitive inhibitor of DTBS and x-ray crystallography shows that 6-HP4 binds specifically in the purine base binding site of the enzyme.