pH‐Dependent Nitrotyrosine Formation in Ribonuclease A is Enhanced in the Presence of Polyethylene Glycol (PEG)

Protein nitration can occur as a result of peroxynitrite‐mediated oxidative stress. Excess production of peroxynitrite (PN) within the cellular medium can cause oxidative damage to biomolecules. The in vitro nitration of Ribonuclease A (RNase A) results in nitrotyrosine (NT) formation with a strong dependence on the pH of the medium. In order to mimic the cellular environment in this study, PN‐mediated RNase A nitration has been carried out in a crowded medium. The degree of nitration is higher at pH 7.4 (physiological pH) compared to pH 6.0 (tumor cell pH). The extent of nitration increases significantly when PN is added to RNase A in the presence of crowding agents PEG 400 and PEG 6000. PEG has been found to stabilize PN over a prolonged period, thereby increasing the degree of nitration. NT formation in RNase A also results in a significant loss in enzymatic activity.     

Ion‐Mobility Mass Spectrometry for the Rapid Determination of the Topology of Interlocked and Knotted Molecules

A rapid screening method based on traveling‐wave ion‐mobility spectrometry (TWIMS) combined with tandem mass spectrometry provides insight into the topology of interlocked and knotted molecules, even when they exist in complex mixtures, such as interconverting dynamic combinatorial libraries. A TWIMS characterization of structure‐indicative fragments generated by collision‐induced dissociation (CID) together with a floppiness parameter defined based on parent‐ and fragment‐ion arrival times provide a straightforward topology identification. To demonstrate its broad applicability, this approach is applied here to six Hopf and two Solomon links, a trefoil knot, and a [3]catenate.     

Syntheses,characterization, X-ray crystal structures and emission properties of copper(II), zinc(II) and cadmium(II) complexes of pyridyl–pyrazole derived Schiff base ligand – Metal selective ligand binding modes

The varying coordination modes of the title ligand, L [5-methyl-1-(pyridin-2-yl)-N′-[pyridin-2-ylmethylidene]pyrazole-3-carbohydrazide] towards the different metal centers is reported by preparation and characterization of Cu(II), Zn(II) and Cd(II) complexes, [Cu(L)NO₃.H₂O](NO₃) (1) [Zn(L)₂](ClO₄)₂·2DMF (2) and [Cd(L)(I)₂] (3) respectively. In 1, the neutral ligand serves as tetradentate 4 N donor where both pyridine and pyrazole nitrogen atoms of pyridyl–pyrazole part are coordinatively active, leaving the carbonyl oxygen of the carbohydrazide part inactive. The same pyridine and pyrazole N atoms remain abstained from the coordination process towards the Zn(II) and Cd(II) metal centers. For 2 and 3 the ligand behaves as a tridentate NNO donor where the two nitrogen atoms come from azomethine, pyridine of pyridine-2-carbaldehyde parts and O from carbonyl oxygen atoms (carbohydrazide part). The complex 1 and 2 are distorted octahedral while complex 3 adopts distorted square pyramidal geometry. All the complexes are X-ray crystallographically characterized.     

Approaching exponential growth with a self-replicating peptide

Self-replicating peptide systems hold great promise for a wide range of technological applications, as well as to address fundamental questions pertaining to the molecular origins of life. The development of self-replicating compounds capable of high efficiency, however, has remained elusive. Here we disclose a successful strategy whereby modulation of coiled-coil stability results in remarkable catalytic efficiency for self-replication. By shortening the peptide to the minimum length necessary for coiled-coil formation a highly efficient self-replicating system was obtained due to very low background reaction rates, bringing the efficiency close to naturally occurring enzymes.     

Two helium atoms inside fullerenes: probing the internal magnetic field in C60(6-) and C70(6-)

A 3He NMR resonance of C606- containing He is assigned to He2@C606-, thus showing that C60 can also accommodate two helium atoms. The ratio of the di-helium compound relative to the mono- is 1:200, 10 times lower than the equivalent counterpart of C70. The 3He NMR chemical shift of He2@C606- is 0.093 ppm downfield from the already known resonance of He@C606-. In the reduced endohedral mono- and di-helium C70, the 3He NMR chemical shift of He2@C706- is 0.154 ppm upfield from the peak of He@C706-.     

Nucleophilic displacement at benzhydryl centers: asymmetric synthesis of 1,1-diarylalkyl derivatives

[reaction: see text] Activation of substituted 1,1-diarylmethanols as their corresponding toluenesulfonates and subsequent displacement with a range of carbon, nitrogen, oxygen, and sulfur nucleophiles proceeds in 81-96% yield. Enantiomerically enriched diarylmethanols 8a-c were activated and displaced with pyridine acetate enolate with complete stereochemical inversion at carbon to yield 1,1-diarylalkyl derivatives 10a-c without loss of optical purity.     

Cellulose synthesis in maize: isolation and expression analysis of the cellulose synthase (CesA) gene family

Stalk lodging in maize results in significant yield losses. We have determined that cellulose per unit length of the stalk is the primary determinant of internodal strength. An increase in cellulose concentration in the wall might allow simultaneous improvements in stalk strength and harvest index. Cellulose formation in plants can be perturbed by mutations in the genes involved in cellulose synthesis, post-synthetic cellulose alteration or deposition, N-glycosylation, and some other genes with as yet unknown functions. We have isolated 12 members of the cellulose synthase (CesA) gene family from maize. The genes involved in primary wall formation appear to have duplicated relatively independently in dicots and monocots. The deduced amino acid sequences of three of the maize genes, ZmCesA10–12, cluster with the Arabidopsis CesA sequences that have been shown to be involved in secondary wall formation. Based on their expression patterns across multiple tissues, these three genes appear to be coordinately expressed. The remaining genes show overlapping expression to varying degrees with ZmCesA1, 7, and 8 forming one group, ZmCesA3 and 5 a second group, and ZmCesA2 and 6 exhibiting independent expression of any other gene. This suggests that the varying levels of coexpression may just be incidental except in the case of ZmCesA10–12, which may interact with each other to form a functional enzyme complex. Isolation of the expressed CesA genes from maize and their association with primary or secondary wall formation has made it possible to test their respective roles in cellulose synthesis through mutational genetics or transgenic approaches. This information would be useful in improving stalk strength.     

Nanostructured Ion-Selective MCM-48 Membranes

Templated MCM-48 silica was prepared using CTAB as surfactant. The MCM-48 powders and thin films were characterized by different techniques. MCM-48 layers were deposited on macroporous α-alumina supports and silicon nitride microsieves. The water permeability of MCM-48 was compared with the permeability of conventional mesoporous γ-alumina membranes. The applicability of MCM-48 as ion-selective electric field-driven switchable interconnect for microfluidic devices was demonstrated.     

Development and optimisation of a novel genetic algorithm for studying model protein folding

Determination of the native state of a protein from its amino acid sequence is the goal of protein folding simulations, with potential applications in gene therapy and drug design. Location of the global minimum structure for a given sequence, however, is a difficult optimisation problem. In this paper, we describe the development and application of a genetic algorithm (GA) to find the lowest-energy conformations for the 2D HP lattice bead protein model. Optimisation of the parameters of our standard GA program reveals that the GA is most successful (at finding the lowest-energy conformations) for high rates of mating and mutation and relatively high elitism. We have also introduced a number of new genetic operators: a duplicate predator—which maintains population diversity by eliminating duplicate structures; brood selection—where two parent structures undergo crossover and give rise to a brood of (not just two) offspring; and a Monte Carlo based local search algorithm—to explore the neighbourhood of all members of the population. It is shown that these operators lead to significant improvements in the success and efficiency of the GA, both compared with our standard GA and with previously published GA studies for benchmark HP sequences with up to 50 beads.     

Designer ribozymes: programming the tRNA specificity into flexizyme

Fx3 is an artificial ribozyme with the ability to aminoacylate various tRNAs with phenylalanine and its nonnatural derivatives. Herein we report a simple strategy to build tRNA specificity into the generic Fx3, by appending to its 3'-end a tRNA-specific sequence (TSS), which is complementary to the acceptor stem of the cognate tRNA. This new designer ribozyme, referred to as Fx10, is able to recognize its cognate tRNA via a 10-base-pair interaction that is formed after the invasion of the tRNA acceptor stem by the TSS. We have demonstrated that Fx10 can aminoacylate its cognate tRNA with a high degree of specificity and also discriminate against the noncognate tRNAs. Because the tRNA specificity can be easily programmed into Fx10, it is a custom-made catalyst to generate nonnatural aminoacyl-tRNAs.