Probing the role of interfacial waters in protein–DNA recognition using a hybrid implicit/explicit solvation model

When proteins bind to their DNA target sites, ordered water molecules are often present at the protein–DNA interface bridging protein and DNA through hydrogen bonds. What is the role of these ordered interfacial waters? Are they important determinants of the specificity of DNA sequence recognition, or do they act in binding in a primarily nonspecific manner, by improving packing of the interface, shielding unfavorable electrostatic interactions, and solvating unsatisfied polar groups that are inaccessible to bulk solvent? When modeling details of structure and binding preferences, can fully implicit solvent models be fruitfully applied to protein–DNA interfaces, or must the individualistic properties of these interfacial waters be accounted for? To address these questions, we have developed a hybrid implicit/explicit solvation model that specifically accounts for the locations and orientations of small numbers of DNA‐bound water molecules, while treating the majority of the solvent implicitly. Comparing the performance of this model with that of its fully implicit counterpart, we find that explicit treatment of interfacial waters results in a modest but significant improvement in protein side‐chain placement and DNA sequence recovery. Base‐by‐base comparison of the performance of the two models highlights DNA sequence positions whose recognition may be dependent on interfacial water. Our study offers large‐scale statistical evidence for the role of ordered water for protein–DNA recognition, together with detailed examination of several well‐characterized systems. In addition, our approach provides a template for modeling explicit water molecules at interfaces that should be extensible to other systems. Proteins 2013; 81:1318–1329. © 2013 Wiley Periodicals, Inc.     

Benthic foraminifera across the Cretaceous–Tertiary (K–T) boundary: a review

The response of the Earth’s biota to global change is of fundamental interest to paleontologists, but patterns of change in paleontologic data are also of interest to a wider spectrum of Earth scientists in that those patterns are of great significance in constraining hypotheses that attempt to explain physical changes in the Earth’s environment. The Cretaceous–Tertiary (K–T) boundary is a case in point. Some paleontologists have criticized the bolide impact hypothesis, not because they deny the impact but because the proposed effects of that impact do not always conform to the available paleontological data. Benthic foraminifera are of particular interest in this context because it has been suggested for over 20 years that shallow-water benthic foraminifera were affected more severely than deep-water benthic foraminifera by events at the K–T boundary. This observation adds to the fact of planktonic foraminiferal extinction and indicates that K–T boundary environmental effects were largely restricted to shallow waters. In this paper I review all published works on smaller benthic foraminifera at the K–T boundary and conclude the following. (1) Shallow-water benthic foraminifera were not more severely affected than deeper dwelling species. True extinction, as opposed to local extinction and/or mass mortality, is generally quite low no matter what the water depth. (2) The data are not sufficient in quality, quantity and geographic range to conclude that there is a latitudinal pattern of extinction. (3) In general, biotic changes (such as they are) begin before the boundary in shallow and intermediate depth waters and at the boundary in deep water. Disagreements about the placement of the boundary and the presence, absence and duration of hiatuses hinder more precise conclusions. (4) There appears to be preferential survivorship of epifaunal species into the early Danian with a short interval dominated by infaunal taxa in the earliest Danian. This pattern can best be explained by short-lived input of increased amounts of organic matter at the boundary followed by a sudden collapse of primary productivity and, hence, major reduction or cessation of organic flux to the seafloor. In summary, based on the current dataset, smaller benthic foraminifera, no matter whether they lived in shallow or deep waters, high or low latitudes, or infaunal or epifaunal microhabitats, survived the environmental events across the K–T boundary quite well. Mass extinction does not characterize this group of organisms at this time.     

Modeling the effects of lowland stream restoration projects on stream–subsurface water exchange

The relative effect of individual elements of restoration projects on stream–subsurface water exchange was studied by identifying elements that were most effective in increasing downwelling stream water (DSW) into subsurface environments using groundwater flow modeling. Several restoration projects studied in lowland streams involved riffle-pool construction, lateral gravel bar construction and channel re-meandering. Simulations using a homogeneous field of mean hydraulic conductivity that removed heterogeneity showed a large decline in DSW in the four restoration projects studied, suggesting that use of coarse sediments in construction initially increases stream–subsurface water exchange, but the effects may not persist in streams where fine sediments clog streambeds. In two riffle-pool construction projects studied, modification of the channel gradient showed a greater effect on DSW than the alteration of substrate texture. In the gravel bar construction site, modeling results indicated that the construction of a riffle-pool sequence along the bar had a greater effect than the construction of the gravel bar itself. In contrast in the channel re-meandering site, the combination of a greater sinuosity and a lower hydraulic head along the small riffles resulted in re-meandering having a greater effect than the associated riffle-pool construction. A simulation in which the floodplain sediments of low saturated hydraulic conductivity at the re-meandered site were replaced with sandy gravels increased DSW by 10 times. This modeling suggests that the addition of coarse sediments in combination with re-meandering would be required to significantly enhance stream–subsurface water exchange in reaches with fine-grained floodplain sediments. Designing the size and type of morphologic features constructed in restoration projects is somewhat flexible, and the use of modeling to simulate stream–groundwater interactions may help to enhance the hydrologic link with a stream and the subsurface environment in restored stream reaches.     

Cutinase purification on poly(ethylene glycol)–hydroxypropyl starch aqueous two-phase systems

The partition behaviour of cutinase on poly(ethylene glycol) (PEG)–hydroxypropyl starch aqueous two-phase systems was characterized. The effect of molecular mass of PEG, the pH of the system and tie-line length on cutinase partition coefficient and cutinase yield to the top phase was investigated for systems prepared with a purified hydroxypropyl starch (Reppal PES 100) and a crude one (HPS). The effect of the presence of different salts, such as sodium chloride, sodium sulphate and ammonium sulphate, on cutinase partition was also studied. The results lead to the conclusion that aqueous two-phase systems composed of PEG and hydroxypropyl starch are not efficient in the purification of cutinase. In the majority of cases, the partition coefficients were very close to 1, with pH being the factor which affects most cutinase partition. Partition coefficients were significantly improved when salts were added to the systems. For PEG 4000–Reppal PES 100 [at pH 4.0; 0.5 M (NH₄)₂SO₄], the partition coefficient for cutinase was 3.7, while a value of 12 was obtained for PEG 4000–HPS (at pH 4.0; 1 M NaCl). An isoelectric point (pI) of 7.8 was confirmed for cutinase by constructing a cross partition graphic from the results obtained in the experiments with different salts.     

Effect of sorbitol addition on the physicochemical characteristics of starch–fatty acid systems

Aqueous maize starch dispersions (20%) were heated at 100 °C, in the presence of myristic, palmitic or stearic acid potassium salts as well as of sorbitol added at concentrations up to 60% (dry starch). Flow behaviour measurements at 100 °C indicated that interactions took place between the starch–fatty acid systems and sorbitol resulting in viscosity increase which was more pronounced as the sorbitol content increased. Water solubility measurements showed that a major part of sorbitol was easily extracted by excess water whereas sorption experiments revealed that the moisture uptake rate was proportional to sorbitol content of the starch systems examined. Thermomechanical studies indicated that the starch–fatty acid samples containing sorbitol up to 40% exhibited antiplasticizing behaviour. Scanning electron microscopy studies revealed that at sorbitol concentrations over 30%, free sorbitol crystals were formed on the surface of starch–fatty acid samples, whereas the percentage crystallinity as well as the crystallite size of samples were proportional to sorbitol content.     

Acute modulation of myocardial function by angiotensin 1–7

Angiotensin 1–7 is a bioactive heptapeptide of the renin–angiotensin system. Its cardiovascular actions have recently acquired growing relevance, mainly due to its counter-regulatory actions in the angiotensin cascade. The aim of the present study was to evaluate the actions of angiotensin 1–7 on myocardial function. Increasing concentrations of angiotensin 1–7 (10⁻⁹ to 10⁻⁵ M) were added to rabbit right papillary muscles: (1) in baseline conditions with intact endocardial endothelium (EE); (2) after selective removal of the EE with Triton X-100 (1 s, 0.01%); (3) with intact EE in the presence of the Mas receptor antagonist A-779, the AT₁ receptor antagonist ZD-7155, the AT₂ receptor antagonist PD-123,319 or the nitric oxide synthesis inhibitor NG-nitro-l-arginine (l-NA). Concerning the effects on contractility, we observed a significant decrease on active tension, dT/dt_max, peak shortening and dL/dt_max of −10.5 ± 3.6%, −8.0 ± 3.0%, −5.3 ± 2.6% and −5.7 ± 2.3%, respectively. There was no change on relaxation parameters, namely dT/dt_min or dL/dt_min. Time to half relaxation was significantly decreased. The presence of ZD-7155 or PD-123,319 did not change these effects. However, angiotensin 1–7 effects on myocardial properties were abolished after selective EE removal and in the presence of A-779 or l-NA. In conclusion, in this animal species, angiotensin 1–7 through its binding to Mas receptor induces a negative inotropic effect modulated by the EE and nitric oxide and independent of AT₁ or AT₂ receptors activation. As the effects described in the present work were influenced by the endocardial endothelium, they may be disrupted in situations associated to endothelial dysfunction, as in heart failure or myocardial ischemia.     

Modeling of α(1–4) chain arrangements in α(1–4)(1–6) glucans: The action and outcome of β-amylase and Pseudomonas stutzeri amylase on an α(1–4)(1–6) glucan model

Simulated enzymic debranching of a β-limit dextrin model, prepared from a computed construct made by random extension and branching, and given the CCL value of w-maize amylopectin (and equal amounts of external chains with ECL values of 2 and 3) has been related to experimental chromatograms of the debranched β-limit dextrin of the amylopectin. The profile was similar to those from gel chromatograms and IEC-PAD chromatography.The equivalent lengths in glucosyl units of grid-links (g-links) of internal and external chains in constructs were calculated from the ICL and ECL values of amylopectin and models produced from the constructs with the appropriate lengths for internal and external chains. These derived models were subjected to simulated hydrolysis by Pseudomonas stutzeri amylase and the products compared with those of the experimental distribution from w-maize amylopectin. With the model the amounts of maltotetraose and maltodextrins released were similar to the experimental values but the distribution of branched maltodextrins was quite different. Unlike w-maize amylopectin – a polymer with the cluster structure – which has given a profile of molecular sizes of maltodextrins with low amounts of single and small numbers of internal chains and with a peak at a M_W of about 14,000 (13 chains), in the model the proportion of maltodextrin with one internal chain was high and as d.p. increased the amounts decreased exponentially. This would be expected if the distribution of internal chains in the core was random. It is suggested that in the core of a model prepared from a construct made with alternating probabilities of extension – one in which this probability is high relative to branching, and a second in which it is low – may give clusters of branched maltodextrins with short internal chains which are joined by longer chains; more closely approximating the distribution of internal chains of different lengths in amylopectin.An arrangement for amylopectin molecules in the starch granule has been proposed. In this, they have a wafer-like, discoidal shape, composed of the amorphous zone overlain with the double helical, crystalline region. The flat macromolecules are concentrically layered with the former on the inside and the latter oriented to the outside of the granule.     

Experimental and computational studies of strain–conduction velocity relationships in cardiac tissue

Velocity of electrical conduction in cardiac tissue is a function of mechanical strain. Although strain-modulated velocity is a well established finding in experimental cardiology, its underlying mechanisms are not well understood. In this work, we summarized potential factors contributing to strain–velocity relationships and reviewed related experimental and computational studies. We presented results from our experimental studies on rabbit papillary muscle, which supported a biphasic relationship of strain and velocity under uni-axial straining conditions. In the low strain range, the strain–velocity relationship was positive. Conduction velocity peaked with 0.59 m/s at 100% strain corresponding to maximal force development. In the high strain range, the relationship was negative. Conduction was reversibly blocked at 118±1.8% strain. Reversible block occurred also in the presence of streptomycin. Furthermore, our studies revealed a moderate hysteresis of conduction velocity, which was reduced by streptomycin. We reconstructed several features of the strain–velocity relationship in a computational study with a myocyte strand. The modeling included strain-modulation of intracellular conductivity and stretch-activated cation non-selective ion channels. The computational study supported our hypotheses, that the positive strain–velocity relationship at low strain is caused by strain-modulation of intracellular conductivity and the negative relationship at high strain results from activity of stretch-activated channels. Conduction block was not reconstructed in our computational studies. We concluded this work by sketching a hypothesis for strain-modulation of conduction and conduction block in papillary muscle. We suggest that this hypothesis can also explain uni-axially measured strain–conduction velocity relationships in other types of cardiac tissue, but apparently necessitates adjustments to reconstruct pressure or volume related changes of velocity in atria and ventricles.     

Computational design of second‐site suppressor mutations at protein–protein interfaces

The importance of a protein–protein interaction to a signaling pathway can be established by showing that amino acid mutations that weaken the interaction disrupt signaling, and that additional mutations that rescue the interaction recover signaling. Identifying rescue mutations, often referred to as second‐site suppressor mutations, controls against scenarios in which the initial deleterious mutation inactivates the protein or disrupts alternative protein–protein interactions. Here, we test a structure‐based protocol for identifying second‐site suppressor mutations that is based on a strategy previously described by Kortemme and Baker. The molecular modeling software Rosetta is used to scan an interface for point mutations that are predicted to weaken binding but can be rescued by mutations on the partner protein. The protocol typically identifies three types of specificity switches: knob‐in‐to‐hole redesigns, switching hydrophobic interactions to hydrogen bond interactions, and replacing polar interactions with nonpolar interactions. Computational predictions were tested with two separate protein complexes; the G‐protein Gα_i1 bound to the RGS14 GoLoco motif, and UbcH7 bound to the ubiquitin ligase E6AP. Eight designs were experimentally tested. Swapping a buried hydrophobic residue with a polar residue dramatically weakened binding affinities. In none of these cases were we able to identify compensating mutations that returned binding to wild‐type affinity, highlighting the challenges inherent in designing buried hydrogen bond networks. The strongest specificity switches were a knob‐in‐to‐hole design (20‐fold) and the replacement of a charge–charge interaction with nonpolar interactions (55‐fold). In two cases, specificity was further tuned by including mutations distant from the initial design. Proteins 2010. © 2009 Wiley‐Liss, Inc.     

Improved purification of the membrane-bound hydrogenase–sulfur-reductase complex from thermophilic archaea using ε-aminocaproic acid-containing chromatography buffers

A hydrogenase–sulfur reductase (SR) complex was purified from membrane preparations of the extremely thermophilic, acidophilic archaeon Acidianus ambivalens using a combination of sucrose density gradient centrifugation and column chromatography (FPLC). All chromatographic steps were performed in the presence of 0.5% ε-aminocaproic acid resulting in the elution of the SR complex as a sharp peak. In contrast, chromatography using buffers without ε-aminocaproic acid, or in the presence of detergents, were not successful. The purified A. ambivalens SR complex consisted of at least four subunits with relative molecular masses of 110 000, 66 000, 39 000 and 29 000, respectively. A similar procedure was applied to purify the membrane-bound hydrogenase from Thermoproteus neutrophilus, a non-related extremely thermophilic but neutrophilic archaeon, which consisted of only two subunits with relative molecular masses of 66 000 and 39 000, respectively.     

Speciation-rate dependence in species–area relationships

The general tendency for species number (S) to increase with sampled area (A) constitutes one of the most robust empirical laws of ecology, quantified by species–area relationships (SAR). In many ecosystems, SAR curves display a power-law dependence, S∝A^z. The exponent z is always less than one but shows significant variation in different ecosystems. We study the multitype voter model as one of the simplest models able to reproduce SAR similar to those observed in real ecosystems in terms of basic ecological processes such as birth, dispersal and speciation. Within the model, the species–area exponent z depends on the dimensionless speciation rate ν, even though the detailed dependence is still matter of controversy. We present extensive numerical simulations in a broad range of speciation rates from ν=10^-3 down to ν=10^-11, where the model reproduces values of the exponent observed in nature. In particular, we show that the inverse of the species–area exponent linearly depends on the logarithm of ν. Further, we compare the model outcomes with field data collected from previous studies, for which we separate the effect of the speciation rate from that of the different species lifespans. We find a good linear relationship between inverse exponents and logarithm of species lifespans. However, the slope sets bounds on the speciation rates that can hardly be justified on evolutionary basis, suggesting that additional effects should be taken into account to consistently interpret the observed exponents.     

Cell–Substrate Contact: Another Factor May Influence Transepithelial Electrical Resistance of Cell Layers Cultured on Permeable Filters

Transepithelial resistance (TER) measurement has often been used to study the paracellular transport properties of epithelia grown on permeable filters, especially the barrier function of tight junctions. However, the TER value includes another source, the resistance caused by cell–substrate contact, that may give rise to a high TER value if cell–substrate separation is small. In this study we use electric cell–substrate impedance sensing (ECIS) to measure both paracellular resistance and the average cell–substrate distance of MDCK (II), HEp-2, and WI-38 VA13 cells. Comparing ECIS data with those from TER measurements of cell layers cultured on polycarbonate filters, we can obtain the approximate extra resistance resulting from cell–substrate contact for each cell type. The value of cell–substrate resistance was also estimated by two theoretical calculations that bracket the true values. Our results demonstrate that cell–substrate contact substantially influences the TER data measured using polycarbonate filters and that the extra resistance due to cell–substrate spaces depends on both cell type and filter property.     

Adapting subject specific motor imagery EEG patterns in space–time–frequency for a brain computer interface

In this paper we propose a new technique that adaptively extracts subject specific motor imagery related EEG patterns in the space–time–frequency plane for single trial classification. The proposed approach requires no prior knowledge of reactive frequency bands, their temporal behavior or cortical locations. For a given electrode array, it finds all these parameters by constructing electrode adaptive time–frequency segmentations that are optimized for discrimination. This is accomplished first by segmenting the EEG along the time axis with Local Cosine Packets. Next the most discriminant frequency subbands are selected in each time segment with a frequency axis clustering algorithm to achieve time and frequency band adaptation individually. Finally the subject adapted features are sorted according to their discrimination power to reduce dimensionality and the top subset is used for final classification. We provide experimental results for 5 subjects of the BCI competition 2005 dataset IVa to show the superior performance of the proposed method. In particular, we demonstrate that by using a linear support vector machine as a classifier, the classification accuracy of the proposed algorithm varied between 90.5% and 99.7% and the average classification accuracy was 96%.     

Production of tailor made short chain amylose–lipid complexes using varying reaction conditions

When amylose was synthesized using potato phosphorylase in the presence of amylose complexing lipids, monodisperse populations of amylose–lipid complexes were formed. Enzyme dosage and glucose-1-phosphate (glc-1-P)/primer ratio influenced the reaction rate of the enzymic synthesis, presumably by changing the balance between amylose synthesis and amylose–lipid complexation and precipitation, and impacted the molecular weight of the complexes. Lipid characteristics affected the dissociation properties and amylose chain lengths of the amylose–lipid complexes presumably by determining the minimal amylose chain length necessary for complexation and precipitation. Tailor made short chain amylose–lipid complexes can hence be produced by choosing the appropriate reaction conditions. We propose a synthesis mechanism in which the primer is elongated until an amylose chain is obtained which is of sufficient length to complex a first lipid. Further chain extension then occurs, together with subsequent complexation until the complex becomes insoluble and precipitates.     

Molecular diagnosis of Menkes disease: Genotype–phenotype correlation

Menkes syndrome is an X-linked, fatal neurodegenerative disorder of copper metabolism, caused by mutations in the ATP7A gene, encoding a copper-transporting P1B-type ATPase. To date, a total of approximately 160 different mutations have been reported worldwide. The clinical phenotypes observed in these patients include progressive neuro-degeneration, connective-tissue abnormalities and peculiar hair. There is phenotypic variability. While the majority of the patients do not survive early childhood, milder cases leading to longer survival have been reported. In this review we focus on mutations, identified in patients with milder forms of Menkes disease, and discuss the possibility of establishing a genotype–phenotype correlation. The presence of small amounts of normal protein, or the presence of partly functional protein variants containing a less essential amino acid substitution or a truncation of the N- or C-terminus, might all result in a milder, atypical phenotype. A clear phenotype–genotype correlation is however difficult to establish, clearly illustrated by the presence of inter- and even intra-familial variability.     

Development and characterization of microsatellite markers in <Emphasis Type="Italic">Castanea sativa</Emphasis> (Mill.)

Thirty-three simple sequence repeat (SSR) markers were isolated andcharacterized in Castanea sativa (Mill.) from the cultivarGarrone Nero. For the identification of SSR loci, primers were designed on eachside flanking the repeat region and they were initially tested on 5 chestnutsamples using chemiluminescence detection. Twenty four loci where shown to bepolymorphic and the number of alleles detected per locus varied from 2 to 7.Fourteen loci were chosen for the analysis of 20 cultivars grown in North Italyusing the semi-automatic system ABI PRISM 377. These 14 markers showed a highlevel of genetic polymorphism with a total of 90 alleles; the number of allelesranged from 4 to 10 per locus, with an average level of 6.4. The mean expectedand observed heterozygosity were 0.724 (range: 0.649–0.835) and 0.793(range: 0.350–0.950) respectively. The estimated frequency of nullallelesshowed a positive value for 3 loci, but except for 1 locus, the values wereverylow. The total value for the probability of identity was 7.04 ×10^–11. Paternity exclusion probability was very high (0.999),sufficiently high to study pollen flow.     

Catalpol protects primary cultured cortical neurons induced by Aβ1–42 through a mitochondrial-dependent caspase pathway

It has been reported that catalpol, an iridoid glucoside, isolated from the root of Rehmannia glutinosa, protected cells from damage induced by a variety of toxic stimulus such as LPS, MPP⁺ and rotenone. Here, we further evaluated the effect of catalpol against Aβ_1–42-induced apoptosis in primary cortical neuron cultures. In the present study, the primary cortical neuron culture treated with Aβ_1–42 was severed as cell model of Alzheimer's disease (AD) in vitro. By exposure to Aβ_1–42 (5 μM) for 72 h in cultures, neuronal apoptosis occurred characterized by enhancement of activities of caspases and reactive oxygen species (ROS) as well as Bax increase, loss of mitochondrial membrane potential and cytochrome c release. Pretreatment with catalpol (0.5 mM) for 30 min prior to Aβ_1–42 treatment attenuated neuronal apoptosis not only by reversing intracellular ROS accumulation, Bax level, mitochondrial membrane potential and, cytochrome c release to some extent, but also through regulating the activity and cleavage of caspase-3 and caspase-9. Thus, catalpol protects primary cultured cortical neurons induced by Aβ_1–42 through a mitochondrial-dependent caspase pathway.     

Use of NaCl prevents aggregation of recombinant COMP–Angiopoietin-1 in Chinese hamster ovary cells

To investigate the effect of hyperosmotic medium on production and aggregation of the variant of Angiopoietin-1 (Ang1), cartilage oligomeric matrix protein (COMP)–Ang1, in recombinant Chinese hamster ovary (CHO) cells, CHO cells were cultivated in shaking flasks. NaCl and/or sorbitol were used to raise medium osmolality in the range of 300–450 mOsm/kg. The specific productivity of COMP–Ang1, q_COMP–Ang1, increased as medium osmolality increased. At NaCl-450 mOsm/kg, the q_COMP–Ang1 was 7.7-fold higher than that at NaCl-300 mOsm/kg, while, at sorbitol-450 mOsm/kg, it was 2.9-fold higher than that at sorbitol-300 mOsm/kg. This can be attributed to the increased relative mRNA level of COMP–Ang1 at NaCl-450 mOsm/kg which was approximately 2.4-fold higher than that at sorbitol-450 mOsm/kg. Western blot analysis showed that COMP–Ang1 aggregates started to occur in the late-exponential phase of cell growth. When sorbitol was used to raise the medium osmolality, a severe aggregation of COMP–Ang1 was observed. On the other hand, when NaCl was used, the aggregation of COMP–Ang1 was drastically reduced at NaCl-400 mOsm/kg. At NaCl-450 mOsm/kg, the aggregation of COMP–Ang1 was hardly observed. This suggests that environmental conditions are critical for the aggregation of COMP–Ang1. Taken together, the use of NaCl-induced hyperosmotic medium to cell culture process turns out to be an efficient strategy for enhancing COMP–Ang1 production and reducing COMP–Ang1 aggregation.     

Characterization of emodin metabolites in Raji cells by LC–APCI-MS/MS

A rapid, simple, and sensitive liquid chromatography–atmospheric pressure chemical ionization tandem mass spectrometry (LC–APCI-MS/MS) method was developed for the identification and quantification of emodin metabolites in Raji cells, using aloe-emodin as an internal standard. Analyses were performed on an LC system employing a Cosmosil 5C₁₈ AR-II column and a stepwise gradient elution with methanol–20 mM ammonium formate at a flow rate of 1.0 mL/min operating in the negative ion mode. As a result, the starting material emodin and its five metabolites were detected by analyzing extracts of Raji cells that had been cultivated in the presence of emodin. The identification of the metabolites and elucidation of their structures were performed by comparing their retention times and spectral patterns with those of synthetic samples. In addition to the major metabolite 8-O-methylemodin, four other metabolites were assigned as ω-hydroxyemodin, 3-O-methyl-ω-hydroxyemodin, 3-O-methylemodin (physcion), and chrysophanol.     

Electrochemical analysis of copper ion using a Gly–Gly–His tripeptide modified poly(3-thiopheneacetic acid) biosensor

A novel biosensor harnessing a conducting polymer functionalized with a copper ion specific peptide proved to be highly effective for electrochemical analysis of copper ions. The developed sensor comprised a transducer based on a conducting polymer (poly(3-thiopheneacetic acid)) electrode and a probe (tripeptide, Gly–Gly–His) selectively cognitive of copper ions. For functionalization of the electrode, the carboxylic group of the polymer was covalently coupled with the amine group of the tripeptide, and its structural features were confirmed by X-ray photoelectron spectroscopy (XPS) and attenuated total reflection infrared (ATR-IR) spectroscopy. The peptide modified polythiophene biosensor was used for the electrochemical analysis of various trace metal ions by square wave voltammetry. The electrode was found to be highly sensitive and selective to Cu²⁺ in the range of 0.02–20 μM with almost no cross binding to other metal ions such as Ni²⁺ and Pb²⁺. Furthermore, the developed sensor exhibited a high stability and reproducibility despite the repeated use of the sensor electrode and probe. With the advent of more diverse affinity bioprobes specific towards a broad range of analytes, the demonstrated strategy harnessing peptide modified polythiophene biosensor is likely to provide an excellent platform for the selective determination of trace amount of analytes whose detection is otherwise cumbersome.