Beta-sheet preferences from first principles

The natural amino acids have different preferences of occurring in specific types of secondary protein structure. Simulations are performed on periodic model beta-sheets of 14 different amino acids, at the level of density functional theory, employing the generalized gradient approximation. We find that the statistically observed beta-sheet propensities correlate very well with the calculated binding energies. Analysis of the calculations shows that the beta-sheet propensities are determined by the local flexibility of the individual polypeptide strands.     

Using light to bioactivate surfaces: A new way of creating oriented, active immunobiosensors

Ultraviolet light can be used to immobilize biomolecules onto thiol reactive surfaces in order to, e.g., make biosensors. The mechanism involves light-induced formation of free, reactive thiol groups in disulphide containing molecules. This technology allows for the creation of arrays of biomolecules with a high degree of reproducibility, circumventing the need for often expensive nano/micro-dispensing technologies. The ultimate size of the immobilized spots is defined by the focal area of the UV beam. Light-induced immobilization has the added benefit that the immobilized molecules will be spatially oriented and covalently bound to the surface. In this paper, we demonstrate the utility of a sensor array created with the new sensor technology when integrated into a microfluidic system. Protein arrays made using light-induced immobilization showed successful antigen/antibody binding in a flow cell allowing the visualisation of real time binding and enzyme activity. This new technology is ideal for the creation of protein/DNA microarrays, can replace present micro-dispensing arraying technologies and is ideal as a molecular imprinting technology.     

Determination of formaldehyde in frozen fish with formaldehyde dehydrogenase using a flow injection system with an incorporated gel-filtration chromatography column

A flow injection analysis (FIA) system for determination of formaldehyde in frozen fish products is described. The system provides a rapid and selective determination of formaldehyde in aqueous fish extracts by the combination of a deproteinization procedure and a stopped-flow enzymatic approach in a FIA system. The FIA system is furnished with a gel-filtration chromatography column for on-line removal of the proteins from the extract before the enzymatic analysis is performed. Compared with the standard methods for determination of formaldehyde in fish products the present method is much faster and less affected by interferences. The limit of detection for the proposed method is 2.5 mg/l of formaldehyde. The sampling frequency is about 10 determinations per hour.     

Biophysical Properties of Phenyl Succinic Acid Derivatised Hyaluronic Acid

Modification of hyaluronic acid (HA) with aryl succinic anhydrides results in new biomedical properties of HA as compared to non-modified HA, such as more efficient skin penetration, stronger binding to the skin, and the ability to blend with hydrophobic materials. In the present study, hyaluronic acid has been derivatised with the anhydride form of phenyl succinic acid (PheSA). The fluorescence of PheSA was efficiently quenched by the HA matrix. HA also acted as a singlet oxygen scavenger. Fluorescence lifetime(s) of PheSA in solution and when attached to the HA matrix has been monitored with ps resolved streak camera technology. Structural and fluorescence properties changes induced on HA-PheSA due to the presence of singlet oxygen were monitored using static light scattering (SLS), steady state fluorescence and ps time resolved fluorescence studies. SLS studies provided insight into the depolymerisation kinetics of PheSA derivatised HA matrix in the presence of singlet oxygen. Time resolved fluorescence studies grave insight into the dynamics of the reaction mechanisms induced on HA-PheSA by singlet oxygen. These studies provided insight into the medical relevance of PheSA derivatised HA: its capacity of scavenging singlet oxygen and of quenching PheSA fluorescence. These studies revealed that HA-PheSA is a strong quencher of electronic excited state PheSA and acts as a scavenger of singlet oxygen, thus medical applications of this derivatised form of HA may protect tissues and organs, such as skin, against reactive oxygen species damage.     

Novel retinylidene iminium salts for defining opsin shifts: synthesis and intrinsic chromophoric properties

Retinal Schiff bases serve as chromophores in many photoactive proteins that carry out functions such as signalling and light-induced ion translocation. The retinal Schiff base can be found as neutral or protonated, as all-trans, 11-cis or 13-cis isomers and can adopt different conformations in the protein binding pocket. Here we present the synthesis and characterisation of isomeric retinylidene iminium salts as mimics blocked towards isomerisation at the C11 position and conformationally restrained. The intrinsic chromophoric properties are elucidated by gas phase absorption studies. These studies reveal a small blue-shift in the S0-->S1 absorption for the 11-locked derivative as compared to the unlocked one. The gas phase absorption spectra of all the cationic mimics so far investigated show almost no absorption in the blue region. This observation stresses the importance of protein interactions for colour tuning, which allows the human eye to perceive blue light.     

Absorption studies of neutral retinal Schiff base chromophores

The neutral retinal Schiff base is connected to opsin in UV sensing pigments and in the blue-shifted meta-II signaling state of the rhodopsin photocycle. We have designed and synthesized two model systems for this neutral chromophore and have measured their gas-phase absorption spectra in the electrostatic storage ring ELISA with a photofragmentation technique. By comparison to the absorption spectrum of the protonated retinal Schiff base in vacuo, we found that the blue shift caused by deprotonation of the Schiff base is more than 200 nm. The absorption properties of the UV absorbing proteins are thus largely determined by the intrinsic properties of the chromophore. The effect of approaching a positive charge to the Schiff base was also studied, as well as the susceptibility of the protonated and unprotonated chromophores to experience spectral shifts in different solvents.     

Substrates and Cyclic Peptide Inhibitors of the Oligonucleotide-Activated Sirtuin 7**

The sirtuins are NAD⁺-dependent lysine deacylases, comprising seven isoforms (SIRT1–7) in humans, which are involved in the regulation of a plethora of biological processes, including gene expression and metabolism. The sirtuins share a common hydrolytic mechanism but display preferences for different ϵ-N-acyllysine substrates. SIRT7 deacetylates targets in nuclei and nucleoli but remains one of the lesser studied of the seven isoforms, in part due to a lack of chemical tools to specifically probe SIRT7 activity. Here we expressed SIRT7 and, using small-angle X-ray scattering, reveal SIRT7 to be a monomeric enzyme with a low degree of globular flexibility in solution. We developed a fluorogenic assay for investigation of the substrate preferences of SIRT7 and to evaluate compounds that modulate its activity. We report several mechanism-based SIRT7 inhibitors as well as de novo cyclic peptide inhibitors selected from mRNA-display library screening that exhibit selectivity for SIRT7 over other sirtuin isoforms, stabilize SIRT7 in cells, and cause an increase in the acetylation of H3 K18.     

Gas-phase spectroscopy of protonated 3-OH kynurenine and argpyrimidine. comparison of experimental results to theoretical modeling

The aging process of the human lens is associated with accumulation of chromophores and fluorophores that impair visual function. In the present study, we examined the photodissociation of 3-OH-kynurenine and argpyrimidine. Furthermore, absorption spectra obtained in gas phase using an electrostatic ion storage ring were studied as gas phase absorption have been shown to be more similar to the in vivo condition than absorption spectra obtained in the liquid phase. Experimental results were compared to theoretical modeling using the multistate, multireference perturbation theory approach combined with advanced molecular modeling tools to account for the solvent effects and to provide direct support for band assignments. Absorption maxima were determined both experimentally and theoretically and significant differences between the two chromophores were found. In particular, 3-OH-kynurenine demonstrated a blue-shift of more than 130 nm in the aqueous phase compared to the gas-phase due to the existence of different 3-OH-kynurenine conformers, which are stable under different conditions and originate from the interplay between intra- and intermolecular interactions. Photodissociation of argpyrimidine and 3-OH-kynurenine was observed in vacuum thus confirming the results previously obtained in liquid phase demonstrating that the photodestruction takes place in both media.     

Determination of shikimate in crude plant extracts by micellar electrokinetic capillary chromatography

A method based on micellar electrokinetic capillary chromatography (MECC) has been developed for the determination of shikimate in water and crude plant extracts. The analytes are separated in a cholate-taurine buffer by MECC at pH 7.3 and measured by direct UV detection at 206 nm. Shikimate showed linearity up to 12.5 mM, with a squared correlation coefficient (r(2)) of 0.9997. The method has concentration limit of detection (cLOD) and concentration limit of quantification (cLOQ) at 24.4 and 67.8 microM, respectively, corresponding to detection in the femtomol range. The number of theoretical plates (N) was estimated to 245,000 for the optimized system using a capillary with an effective length of 560 mm. The method was tested on plant samples by measuring the shikimate content in leaves of rapeseed plants grown in hydroponic solutions containing the herbicide glyphosate, a well-known inhibitor of the shikimate pathway. In crude extracts of these plants, shikimate was found to accumulate in the leaves, confirming earlier reports of shikimate as a potential biomarker for glyphosate treatment. The method now developed was also able to detect shikimate-3-phosphate, but this compound was not accumulated in glyphosate inhibited plants as found for shikimate.