Singlet oxygen's response to protein dynamics

Singlet molecular oxygen, O(2)(a(1)Δ(g)), is an intermediate in a variety of processes pertinent to the function of biological systems, including events that result in cell death. Many of these processes involve a reaction between singlet oxygen and a given protein. It is acknowledged that the behavior of a protein can change upon reaction with singlet oxygen, as a result of a structural alteration and/or a direct chemical modification of an active site. However, the converse, where one considers how the behavior of singlet oxygen can be altered by changes in protein structure, has received little attention. In this report, we use a variety of proteins to demonstrate how the rate constant for singlet oxygen removal by a protein responds to (a) protein denaturation, (b) macromolecular crowding of the protein, (c) ligand binding by the protein, and (d) polymerization of the protein. From one perspective, the data show that the kinetics of singlet oxygen removal can be used to monitor protein dynamics. Most importantly, however, the data indicate that protein structural changes that either reveal or cloak a given amino acid residue can have a measurable effect on the overall rate constant for singlet oxygen removal which, in turn, can have ramifications for singlet-oxygen-mediated intracellular events that perturb cell function.     

Membrane activity of biomimetic facially amphiphilic antibiotics

Membranes are a central feature of all biological systems, and their ability to control many cellular processes is critically important. As a result, a better understanding of how molecules bind to and select between biological membranes is an active area of research. Antimicrobial host defense peptides are known to be membrane-active and, in many cases, exhibit discrimination between prokaryotic and eukaryotic cells. The design of synthetic molecules that capture the biological activity of these natural peptides has been shown. In this report, the interaction between our biomimetic structures and different biological membranes is reported using both model vesicle and in vitro bacterial cell experiments. Compound 1 induces 12% leakage at 20 microg/mL against phosphatidylglycerol (PG)-phosphatidylethanolamine (PE) vesicles vs only 3% leakage at 200 microg/mL against phosphatidyl-L-serine (PS)-phosphatidylcholine (PC) vesicles. Similarly, a 40% reduction in fluorescence is measured in lipid movement experiments for PG-PE compared to 10% for PS-PC at 600 s. A 30 degrees C increase in the phase transition of stearoyl-oleoyl-phosphatidylserine is observed in the presence of 1. These results show that lipid composition is more important for selectivity than overall net charge. Additionally, the overall concentration of a given lipid is another important factor. An effort is made to connect model vesicle studies with in vitro data and naturally occurring lipid compositions.     

Recent methods for the determination of peroxide-based explosives

In the last few years, the need to determine peroxide-based explosives in solid samples and air samples has resulted in the development of a series of new analytical methods for triacetonetriperoxide (TATP, acetone peroxide) and hexamethylenetriperoxidediamine (HMTD). In this review, after a short introduction describing the state of the art in the field, these new analytical methods are critically discussed. Particular emphasis is placed on spectroscopic and mass spectrometric methods as well as on chromatographic techniques with selective detection schemes. The potential of these methods to analyse unknown solid samples that might contain one or more of the explosives and to analyse peroxide-based explosives in air is evaluated.     

Proton-detected scalar coupling based assignment strategies in MAS solid-state NMR spectroscopy applied to perdeuterated proteins

Assignment of proteins in MAS (magic angle spinning) solid-state NMR relies so far on correlations among heteronuclei. This strategy is based on well dispersed resonances in the ¹⁵N dimension. In many complex cases like membrane proteins or amyloid fibrils, an additional frequency dimension is desirable in order to spread the amide resonances. We show here that proton detected HNCO, HNCA, and HNCACB type experiments can successfully be implemented in the solid-state. Coherences are sufficiently long lived to allow pulse schemes of a duration greater than 70 ms before incrementation of the first indirect dimension. The achieved resolution is comparable to the resolution obtained in solution-state NMR experiments. We demonstrate the experiments using a triply labeled sample of the SH3 domain of chicken α-spectrin, which was re-crystallized in H₂O/D₂O using a ratio of 1/9. We employ paramagnetic relaxation enhancement (PRE) using EDTA chelated Cu^II to enable rapid data acquisition.     

Transformation of a [4+6] Salicylbisimine Cage to Chemically Robust Amide Cages

In recent years, interest in shape‐persistent organic cage compounds has steadily increased, not least because dynamic covalent bond formation enables such structures to be made in high to excellent yields. One often used type of dynamic bond formation is the generation of an imine bond from an aldehyde and an amine. Although the reversibility of the imine bond formation is advantageous for high yields, it is disadvantageous for the chemical stability of the compounds. Amide bonds are, in contrast to imine bonds much more robust. Shape‐persistent amide cages have so far been made by irreversible amide bond formations in multiple steps, very often accompanied by low yields. Here, we present an approach to shape‐persistent amide cages by exploiting a high‐yielding reversible cage formation in the first step, and a Pinnick oxidation as a key step to access the amide cages in just three steps. These chemically robust amide cages can be further transformed by bromination or nitration to allow post‐functionalization in high yields. The impact of the substituents on the gas sorption behavior was also investigated.     

Base-Pairing Properties of Double-Headed Nucleotides

Nucleotides that contain two nucleobases (double-headed nucleotides) have the potential to condense the information of two separate nucleotides into one. This presupposes that both bases must successfully pair with a cognate strand. Here, double-headed nucleotides that feature cytosine, guanine, thymine, adenine, hypoxanthine, and diaminopurine linked to the C2′-position of an arabinose scaffold were developed and examined in full detail. These monomeric units were efficiently prepared by convergent synthesis and incorporated into DNA oligonucleotides by means of the automated phosphoramidite method. Their pairing efficiency was assessed by UV-based melting-temperature analysis in several contexts and extensive molecular dynamics studies. Altogether, the results show that these double-headed nucleotides have a well-defined structure and invariably behave as functional dinucleotide mimics in DNA duplexes.     

SIMS of organic layers with unknown matrix parameters: Locating the interface in dual beam argon gas cluster depth profiles

Four simple methods are evaluated to determine their accuracies for establishing the interface location in secondary ion mass spectrometry intensity depth profiles of organic layers where matrix effects have not been measured. Accurate location requires the separate measurement of each ion's matrix factor. This is often not possible, and so estimates using matrix-less methods are required. Six pure organic material interfaces are measured using many secondary ions to compare their locations from the four methods with those from full evaluation with matrix terms. For different secondary ions, matrix effects cause the apparent interface positions to vary over 20 nm. The shifts in the intensity profiles on going from a layer of P into a layer of Q are in the opposite direction to that for going from Q into P, so doubling layer thickness errors. The four methods are as follows: M1, use of the median interface position in the intensity profiles for the five lightest ions for 15 ≤ m/z ≤ 150; M2, extrapolation of the position for each ion to m/z = 0 for ions with m/z ≤ 150; M3, as M2 but for m/z ≤ 300; and M4, the extreme positions for all m/z ≤ 100. Comparison with the location using matrix terms shows their ranking, from best to worst, to be M4, M3, M1, and M2 with average errors of 10%, 12%, 14%, and 17%, respectively, of the profile interface full widths at half maximum. Use of pseudo-molecular ions is very much poorer, exceeding 50%, and should be avoided.