Are free radicals involved in IspH catalysis? An EPR and crystallographic investigation

The [4Fe-4S] protein IspH in the methylerythritol phosphate isoprenoid biosynthesis pathway is an important anti-infective drug target, but its mechanism of action is still the subject of debate. Here, by using electron paramagnetic resonance (EPR) spectroscopy and (2)H, (17)O, and (57)Fe isotopic labeling, we have characterized and assigned two key reaction intermediates in IspH catalysis. The results are consistent with the bioorganometallic mechanism proposed earlier, and the mechanism is proposed to have similarities to that of ferredoxin, thioredoxin reductase, in that one electron is transferred to the [4Fe-4S](2+) cluster, which then performs a formal two-electron reduction of its substrate, generating an oxidized high potential iron-sulfur protein (HiPIP)-like intermediate. The two paramagnetic reaction intermediates observed correspond to the two intermediates proposed in the bioorganometallic mechanism: the early π-complex in which the substrate's 3-CH(2)OH group has rotated away from the reduced iron-sulfur cluster, and the next, η(3)-allyl complex formed after dehydroxylation. No free radical intermediates are observed, and the two paramagnetic intermediates observed do not fit in a Birch reduction-like or ferraoxetane mechanism. Additionally, we show by using EPR spectroscopy and X-ray crystallography that two substrate analogues (4 and 5) follow the same reaction mechanism.     

A molecular "phase ordering" phase transition leading to a modulated aperiodic composite in n-heptane/urea

n-Heptane/urea is an aperiodic inclusion compound in which the ratio of host and guest repeats along the channel axis is very close to unity and is found to have a constant value (0.981) from 280 K to 90 K. Below 280 K, two phase transitions are observed. The first (T(c1) = 145 K) is a ferroelastic phase transition that generates superstructure reflections for the host while leaving the guest with 1D order. The second (T(c2) = 130 K) is a "phase ordering" transition to a four-dimensional structure (P2(1)11(0βγ)) with pronounced host-guest intermodulation and a temperature dependent phase shift between guests in adjacent channels.     

The use of sigmoid pH gradients in free-flow isoelectric focusing of human endothelial cell proteins

Prefractionation of proteins enhances the resolution of proteome analysis of whole cells. Free-flow electrophoresis (FFE) provides a useful step in various prefractionation protocols, since matrix-free isoelectric focusing (FF-IEF) performed in this machine enables the enrichment of large, easily absorbable, sensitive proteins. The impact of the FFE on the success of a proteome analysis depends on the quality of the FF-IEF separation procedure. Therefore, attempts are continuously being made to improve FF-IEF. Here, we applied sigmoid pH gradients to the prefractionation of endothelial cell proteins. Small steps of pH incline between neighboring FFE fractions were established in pH ranges, in which the proteins of interest have their pIs. With the help of this advanced technology, we separated vimentin and cytoplasmic actin as well as triosephosphate isomerase and glyceraldehyde phosphate dehydrogenase preparatively, and found a pI of 5.9 ± 0.2 for nonmuscle myosin.     

A practical preparation of aryl β-ketophosphonates

The condensation of alkyl phosphonates with aryl esters to give β-ketophosphonates may be carried out at elevated temperatures mediated by LiHMDS under Barbier type conditions. The reaction is scalable, does not require specialized cryogenic equipment, and is general for all aryl and heteroaryl esters examined.     

Biotin–Avidin as a Protease‐Responsive Cap System for Controlled Guest Release from Colloidal Mesoporous Silica

Tell your guests when it's time to go : When avidin caps are attached to biotinylated colloidal mesoporous silica, the four subunits of the protein avidin can each bind to a biotin moiety attached to the surface (see picture). The resulting material is a promising candidate for the design of smart detergents or drug‐delivery systems. The caps can be opened to release guest molecules by controlled enzymatic hydrolysis of the protein.

     

Decarboxylative Grob‐Type Fragmentations in the Synthesis of Trisubstituted Z Olefins: Application to Peloruside A,Discodermolide, and Epothilone D

Discriminating elimination : A new method for the synthesis of methyl‐branched trisubstituted Z olefins, a structural motif in many polyketides with anticancer activity, relies on an ^?OH‐induced decarboxylative Grob‐type fragmentation (see scheme; Ms=mesyl). The starting materials are β‐mesyloxy lactones with a quaternary α center, which are prepared by aldol reactions in a diastereo‐ and enantioselective manner.

     

Development of versatile and silver-free protocols for gold(I) catalysis

The use of a versatile N‐heterocyclic carbene (NHC) gold(I) hydroxide precatalyst, [Au(OH)(IPr)], (IPr=N,N′‐bis(2,6‐diisopropylphenyl)imidazol‐2‐ylidene) permits the in situ generation of the [Au(IPr)]⁺ ion by simple addition of a Brønsted acid. This cationic entity is believed to be the active species in numerous catalytic reactions. ¹H NMR studies in several solvent media of the in situ generation of this [Au(IPr)]⁺ ion also reveal the formation of a dinuclear gold hydroxide intermediate [{Au(IPr)}₂(μ‐OH)], which is fully characterized and was tested in gold(I) catalysis.     

Engineering of an enantioselective tyrosine aminomutase by mutation of a single active site residue in phenylalanine aminomutase

By replacing a single active-site residue Cys107 with Ser in phenylalanine aminomutase (PAM), the enzyme gained tyrosine aminomutase (TAM) activity while retaining PAM activity and high enantioselectivity. This engineered enantioselective TAM also catalyzed formation of β-tyrosine from p-coumaric acid and may prove to be useful for the synthesis of enantiopure β-tyrosine and its derivatives.     

Design of multiplex calibrant plasmids, their use in GMO detection and the limit of their applicability for quantitative purposes owing to competition effects

Five double-target multiplex plasmids to be used as calibrants for GMO quantification were constructed. They were composed of two modified targets associated in tandem in the same plasmid : (1) a part of the soybean lectin gene and (2) a part of the transgenic construction of the GTS40-3-2 event. Modifications were performed in such a way that each target could be amplified with the same primers as those for the original target from which they were derived but such that each was specifically detected with an appropriate probe. Sequence modifications were done to keep the parameters of the new target as similar as possible to those of its original sequence. The plasmids were designed to be used either in separate reactions or in multiplex reactions. Evidence is given that with each of the five different plasmids used in separate wells as a calibrant for a different copy number, a calibration curve can be built. When the targets were amplified together (in multiplex) and at different concentrations inside the same well, the calibration curves showed that there was a competition effect between the targets and this limits the range of copy numbers for calibration over a maximum of 2 orders of magnitude. Another possible application of multiplex plasmids is discussed.     

Limits of miniaturization: assessing ITP performance in sub-micron and nanochannels

The feasibility of isotachophoresis in channels of sub micrometer and nanometer dimension is investigated. A sample injection volume of 0.4 pL is focused and separated in a 330 nm deep channel. The sample consists of a biomatrix containing the fluorescently-labeled amino acids glutamate and phenylalanine, 20 attomoles of each. Isotachophoretic focusing is successfully demonstrated in a 50 nm deep channel. Separation of the two amino acids in the 50 nm deep channel however, could not be performed as the maximum applicable voltage was insufficient. This limit is imposed by bubble formation that we contribute to cavitation as a result of the mismatch in electro-osmotic flow, so called electrocavitation. This represents an unexpected limit on the miniaturization of ITP. Nonetheless, we report the smallest isotachophoretic separation and focusing experiment to date, both in terms of controlled sample injection volume and channel height.