Design and synthesis of photochemically controllable restriction endonuclease BamHI by manipulating the salt-bridge network in the dimer interface

The strategy for the design of photochemically controllable enzymes by manipulating the dimer interface is described. Employing a restriction endonuclease BamHI, the selective incorporation of amino acids having a photoremovable 6-nitroveratryl group into the specific position (Lys132) in the dimer interface of the BamHI mutant (H133A) was performed. The activity of the photofunctionalized BamHI mutant was significantly suppressed, and the following photoirradiation induced the recovery of the activity. In addition, uncaging of the 6-nitroveratryl group introduced to Lys132 did not seriously reduce the catalytic activity and affinity for the substrate. These results indicate that the activity of the enzyme can be effectively regulated by caging and uncaging of the specific amino acid in the dimer interface using the photoremovable group.     

Photochemical regulation of the activity of an endonuclease BamHI using an azobenzene moiety incorporated site-selectively into the dimer interface

Endonuclease BamHI mutants having an azophenylalanine residue in the dimer interface (azoAla-BamHI) were synthesized; while the activity was almost suppressed using trans-azoAla-BamHI, the cis-isomer generated with photoirradiation recovered its intrinsic activity.     

A thermodynamic investigation into the binding properties of DNA functionalized gold nanoparticle probes and molecular fluorophore probes

We report the first quantitative analysis of the oligonucleotide binding thermodynamics for DNA functionalized gold nanoparticle probes and compare our findings to molecular fluorophore probes on a sequence-for-sequence basis. With proper design, nanoparticle probes show significantly increased binding over molecular fluorophore probes under identical conditions. This is significant because probe binding strength directly influences detection sensitivity limits.     

Calculation of intermolecular interactions in the benzene dimer using coupled-cluster and local electron correlation methods

Potential energy curves for the parallel-displaced, T-shaped and sandwich structures of the benzene dimer are computed with density fitted local second-order M?ller-Plesset perturbation theory (DF-LMP2) as well as with the spin-component scaled (SCS) variant of DF-LMP2. While DF-LMP2 strongly overestimates the dispersion interaction, in common with canonical MP2, the DF-SCS-LMP2 interaction energies are in excellent agreement with the best available literature values along the entire potential energy curves. The DF-SCS-LMP2 dissociation energies for the three structures are also compared with new complete basis set estimates of the interaction energies obtained from accurate coupled cluster (CCSD(T)) and DF-SCS-MP2 calculations. Since LMP2 is essentially free of basis set superposition errors, counterpoise corrections are not required. As a result, DF-SCS-LMP2 is computationally inexpensive and represents an attractive method for the study of larger pi-stacked systems such as truncated sections of DNA.     

Detection and characterization of methionine oxidation in peptides by collision-induced dissociation and electron capture dissociation

Electron capture dissociation (ECD) and collision-induced dissociation (CID), the two complementary fragmentation techniques, are demonstrated to be effective in the detection and localization of the methionine sulfoxide [Met(O)] residues in peptides using Fourier transform ion cyclotron resonance (FTICR) mass spectrometry. The presence of Met(O) can be easily recognized in the low-energy CID spectrum showing the characteristic loss of methanesulfenic acid (CH(3)SOH, 64 Da) from the side chain of Met(O). The position of Met(O) can then be localized by ECD which is capable of providing extensive peptide backbone fragmentation without detaching the labile Met(O) side chain. We studied CID and ECD of several Met(O)-containing peptides that included the 44-residue human growth hormone-releasing factor (GRF) and the human atrial natriuretic peptide (ANP). The distinction and complementarity of the two fragmentation techniques were particularly remarkable in their effects on ANP, a disulfide bond-containing peptide. While the predominant fragmentation pathway in CID of ANP was the loss of CH(3)SOH (64 Da) from the molecular ion, ECD of ANP resulted in many sequence-informative products, including those from cleavages within the disulfide-bonded cyclic structure, to allow for the direct localization of Met(O) without the typical procedures for disulfide bond reduction followed by [bond]SH alkylation.     

Study on the structural changes of bovine serum albumin with effects on polydatin binding by a multitechnique approach

Polydatin is a traditional Chinese medicine which shows effective biological activity as antimicrobial and antiviral agent. The secondary structure changes of bovine serum albumin (BSA) were investigated by the methods of Fourier transform infrared spectroscopy (FT-IR), circular dichroism (CD) and Raman spectroscopy. The experimental results indicated that polydatin changed the secondary structure of BSA. The presence of polydatin decreased α-helix content of BSA. The conformations of disulfide bridges and the microenvironment of Tyr, Trp residues were also changed.     

Approach to equilibrium after dilution of a monomer/dimer mixture. Measurement of the rate constant for dissociation of trityl dimer by stopped-flow methods

A general expression is derived for the approach to a new equilibrium when a monomer/dimer solution is diluted by a factor of n. The error introduced by a simple exponential treatment is analyzed. The response of a trityl monomer/dimer equilibrium to dilution by a factor of two in a stopped-flow apparatus has been used to measure the rate constant k₁₁. The results fall on the same Eyring plot with those obtained at lower temperatures, by another method, in the early 1930's by Ziegler and co-workers. © John Wiley & Sons, Inc.      

Diffusion of uncharged probe reveals structural changes in polyacids initiated by their neutralization: poly(acrylic acids)

The diffusion studies of the uncharged probe (1,1'-ferrocenedimethanol) have been successfully applied for the evaluation of the changes in the three-dimensional structure of poly(acrylic acids) of various molecular weights (ranging from 2000 to 4,000,000 g/mol) during their neutralization with a strong base. The qualitative picture of the macromolecule arrangement during the titration of the polyacids has been obtained from the conductometric measurements. The characteristic changes in the poly(acrylic acid) conductivity are practically the same for all polyacids examined and are in a very good agreement with the predictions of our theoretical model of the polyelectrolyte conductance. The transformation of the polyelectrolyte solution into the gel-like or gel phase has been investigated more quantitatively by tracing the changes in the diffusion coefficient of the uncharged probe redox system. The probe diffusivities, D, were determined using steady-state voltammetry at microelectrodes for a wide range of neutralization degree, alpha, of the polyacids tested. The dependencies of D versus alpha are of similar shape for all poly(acrylic acids). The first parts of the dependencies reflect a rapid increase in D (up to neutralization degree of either 45% for the lowest molecular-weight poly(acrylic acid) or 75-80% for other polyacids). They are followed by the parts of a slight drop in the diffusion coefficient. The changes in the probe diffusivity become stronger as the molecular weight of poly(acrylic acid) increases. The maximum probe diffusion coefficients are greater than the initial values in the pure polyacid solutions by 14, 24, 19, 30, and 28% for poly(acrylic acid) of molecular weights of 2000, 450,000, 1,250,000, 3,000,000, and 4,000,000 g/mol, respectively. The variation in the probe diffusion coefficient qualitatively follows the line of the changes in the macroscopic viscosity of the polyelectrolyte system. This is in contrast to the predictions of the Stokes-Einstein relation and, therefore, suggests that the changes in the probe diffusion rate are mainly due to the structural changes in the polyacrylate medium and the macromolecular rearrangements induced by the chemical, acid-base reaction. By adapting the obstruction model for diffusion in homogeneous gels, the transport characteristics of the probe were converted into the structural characteristics of the polyelectrolytic systems. It has been found that the most ordered structure of the polyelectrolyte, or in other words the most permeable structure, is obtained when poly(acrylic acid) is neutralized at 75-80%.     

Catalytic water dissociation using hyperbranched aliphatic polyester (Boltorn series) as the interface of a bipolar membrane

The effect of hyperbranched aliphatic polyester (Boltorn series) on the water dissociation in bipolar membranes was firstly investigated in this paper. The bipolar membranes were prepared by immersing the anion exchange layer in a hyperbranched aliphatic polyester solution and then coating on the layer a polyphenylene oxide (SPPO) solution. The SEM observations proved the existence of hyperbranched aliphatic polyester at the membrane intermediate layer. The adsorption amount was evaluated by the oxygen content via XPS. The junction thickness of the prepared bipolar membrane was determined by electrochemical impedance spectroscopy (EIS), and the membrane performances were evaluated by current-voltage curves. The results showed that the amount and generation of Boltorn series, and temperature all affected I-V behaviors of the fabricated bipolar membranes, and the former two played the critical role. These effects were explained on the basis of the water dissociation theory and the characteristics of hyperbranched aliphatic polyester.     

Detection of fragmented genomic DNA by PCR-free piezoelectric sensing using a denaturation approach

Label-free and real-time DNA sequence detection in PCR-amplified DNA samples can now be achieved by different approaches. On the contrary, only few works have been reported dealing with direct sequence detection in nonamplified genomic DNA. Here, a piezoelectric biosensor for direct detection of sequences in nonamplified genomic DNA is described. The system relies on real-time and label-free detection of the hybridization reaction between an immobilized probe and the complementary sequence in solution. The DNA probe is immobilized on the sensing surface (10 MHz quartz crystals), while the complementary sequence is present in the genomic DNA, previously fragmented with restriction enzymes.     

Detection of DNA hybridization by various spectroscopic methods using the copper tetraphenylporphyrin complex as a probe

We are presenting new and highly sensitive hybridization assays. They are based on various spectroscopic methods including resonance light scattering, circular dichroism, ultraviolet spectra and fluorescence spectra, as well as atomic force microscopy, and relies on the interaction of the Cu(II), Ni(II), Mg(II), Co(II), Cd(II), and Zn(II) complexes, respectively, of tetraphenylporphyrin (TPP) with double-strand DNA (dsDNA) and single strand DNA (ssDNA). The interaction results in amplified resonance light scattering (RLS) signals and enables the detection of hybridization without the need for labeling DNA. The RLS signals are strongest in case of the Cu (II)-TPP complex which therefore was selected as the probe. The technique is simple, robust, accurate, and can be completed in less than one hour.

Detection of beryllium in digested autopsy tissues by inductively coupled plasma mass spectrometry using a high matrix interface configuration

This article describes a robust methodology using the combination of instrumental design (high matrix interface—HMI), sample dilution and internal standardization for the quantification of beryllium (Be) in various digested autopsy tissues using inductively coupled plasma mass spectrometry. The applicability of rhodium as a proper internal standard for Be was demonstrated in three types of biological matrices (i.e., femur, hair, lung tissues). Using HMI, it was possible to achieve instrumental detection limits and sensitivity of 0.6 ng L⁻¹ and 157 cps L ng⁻¹, respectively. Resilience to high salt matrices of the HMI setup was also highlighted using bone mimicking solution ([Ca²⁺] = 26 to 1,400 mg L⁻¹), providing a 14-fold increase in tolerance and a 2.7-fold decrease in method detection limit compared to optimized experimental conditions obtained without the HMI configuration. Precision of the methodology to detect low levels of Be in autopsy samples was demonstrated using hair and blood certified reference materials. Be concentration ranging from 0.015 to 255 μg kg⁻¹ in autopsy samples obtained from the U.S. Transuranium and Uranium Registries were measured using the methodology presented.     

Maxwell displacement current allows to study structural changes of gramicidin A in monolayers at the air-water interface

We applied methods of measurement Maxwell displacement current (MDC) pressure-area isotherms and dipole potential for analysis of the properties of gramicidin A (gA) and mixed gA/DMPC monolayers at an air-water interface. The MDC method allowed us to observe the kinetics of formation of secondary structure of gA in monolayers at an air-water interface. We showed, that secondary structure starts to form at rather low area per molecule at which gA monolayers are in gaseous state. Changes of the MDC during compression can be attributed to the reorientation of dipole moments in a gA double helix at area 7 nm(2)/molecule, followed by the formation of intertwined double helix of gA. The properties of gA in mixed monolayers depend on the molar fraction of gA/DMPC. At higher molar fractions of gA (around 0.5) the shape of the changes of dipole moment of mixed monolayer was similar to that for pure gA. The analysis of excess free energy in a gel (18( ) degrees C) and in a liquid-crystalline phase (28( ) degrees C) allowed us to show influence of the monolayer structural state on the interaction between gA and the phospholipids. In a gel state and at the gA/DMPC molar ratio below 0.17 the aggregates of gA were formed, while above this molar ratio gA interacts favorably with DMPC. In contrast, for DMPC in a liquid-crystalline state aggregation of gA was observed for all molar fractions studied. The effect of formation ordered structures between gA and DMPC is more pronounced at low temperatures.     

Probing the pH-dependent chain dynamics of poly(acrylate acid) in concentrated solution by using a cationic AIE fluorophore

We report a novel strategy to study the chain dynamics of poly(acrylic acid) (PAA) in a relative concentrated solution (1.0 g/L). The strategy is based on the fluorescent probe (DCTPE) with unique aggregation-induced emission (AIE) characteristics. Free DCTPE molecules are non-emissive in aqueous solution, but they become highly emissive when trapped in polymer coils. The fluorescence intensity is proportional to the efficiency of trapping DCTPE molecules in polymer coils. By correlation the change of fluorescence intensity with the variation of pH value (from 1.78 to 12.06), the PAA chain’s dynamics in the relatively concentrated solution have been elucidated into three processes. In the pH range from 12.06 to 6.0, PAA chains take an extended and non-folding conformation. Changing pH from 6.0 to 3.86, PAA chains are partially protonated and loosely packed polymer coils are formed. Further lowering the pH value of the solution (from 3.86 to 1.78), protonated segments dominate the PAA chains, and at the same time, the intermolecular hydrogen bonding takes effect, thus the polymer chains posses in the conformation of more compact coils.     

Aptamer based voltammetric determination of ampicillin using a single-stranded DNA binding protein and DNA functionalized gold nanoparticles

An aptamer based method is described for the electrochemical determination of ampicillin. It is based on the use of DNA aptamer, DNA functionalized gold nanoparticles (DNA-AuNPs), and single-stranded DNA binding protein (ssDNA-BP). When the aptamer hybridizes with the target DNA on the AuNPs, the ssDNA-BP is captured on the electrode surface via its specific interaction with ss-DNA. This results in a decreased electrochemical signal of the redox probe Fe(CN)₆ ^3? which is measured best at a voltage of 0.188 mV (vs. reference electrode). In the presence of ampicillin, the formation of aptamer-ampicillin conjugate blocks the further immobilization of DNA-AuNPs and ssDNA-BP, and this leads to an increased response. The method has a linear reposne that convers the 1 pM to 5 nM ampicillin concentration range, with a 0.38 pM detection limit (at an S/N ratio of 3). The assay is selective, stable and reproducible. It was applied to the determination of ampicillin in spiked milk samples where it gave recoveries ranging from 95.5 to 105.5%.

Open image in new window

Graphical abstract Schematic of a simple and sensitive electrochemical apta-biosensor for ampicillin detection. It is based on the use of gold nanoparticles (AuNPs), DNA aptamer, DNA functionalized AuNPs (DNA-AuNPs), and single-strand DNA binding protein (SSBP).

     

Mapping of two networks of residues that exhibit structural and dynamical changes upon binding in a PDZ domain protein

We describe the changes in structure and dynamics that occur in the second PDZ domain of human tyrosine phosphatase 1E upon binding the small peptide RA-GEF2 by an analysis of NMR data based on their use as ensemble-averaged restraints in molecular dynamics simulations. This approach reveals the presence of two interconnected networks of residues, the first exhibiting structural changes and the second dynamical changes upon binding, and it provides a detailed mapping of the regions of increased and decreased mobility upon binding. Analysis of the dynamical properties of the residues in these networks reveals that conformational changes are transmitted through pathways of coupled side-chain reorientations. These results illustrate how the strategy we described, in which NMR data are used in combination with molecular dynamics simulations, can be used to characterize in detail the complex organization of the changes in structure and dynamics that take place in proteins upon binding.