Fast, long-range electron-transfer reactions of a "blue" copper protein coupled non-covalently to an electrode through a stilbenyl thiolate monolayer

A self-assembled monolayer (SAM), formed by the insitu saponification of a stilbenyl thioacetate on a gold electrode, yields fast electron transfer (ET)(the exchange rate at zero driving force exceeds 1600 s-1) with adsorbed molecules of the blue copper protein, azurin, over a distance exceeding 15 angstroms .     

The NMR spectra of porphyrins-25: Meso-substituent effects in neutral and protonated porphyrins

The meso (methine) substituent chemical shifts (SCS) of a range of common functional groups have been obtained both for the neutral porphyrin molecule, and for the corresponding dications, in substituted octaethylporphyrin (OEP), etioporphyrin-I, and pyrroetioporphyrin-XV derivatives. The SCS are discussed in terms of both ring current variations and specific effects at the neighboring betasubstituents and the meso-proton opposite the perturbing substituent, using a ring current model to quantify the former. In the neutral molecules, meso substitution in OEP (Me, NO₂, CN, CHO) causes a 10% decrease in the macrocyclic ring current, and marked anisotropic shifts at the beta-positions flanking the meso function. The meso-NH₂ group introduces a much larger decrease (ca 35%) in the main ring current, due to conjugation of the amino group with the porphyrin π-system. In the porphyrin dications, SCS are much larger and there is some evidence of a concomitant decrease in the ring current of the adjacent pyrrole subunits. The meso-NMe₂; substituent at the γ-meso-position in pyrroetioporphyrin-XV has only small SCS in the neutral molecule, but a large shift (similar to that of NH₂) in the dication, due to the different orientation of the substituent with respect to the porphyrin plane in each case. The meso-OH substituent in the oxophlorin from etioporphyrin-I behaves as a conjugated OH group in the dication. The anomalous position of the meso-proton opposite to the perturbing substituent is noteworthy, and this could be due to electronic (resonance) effects, or to some protonation at this position.     

Wavelet compression of three-dimensional time-lapse biological image data.

The use of multifocal-plane, time-lapse recordings of living specimens has allowed investigators to visualize dynamic events both within ensembles of cells and individual cells. Recordings of such four-dimensional (4D) data from digital optical sectioning microscopy produce very large data sets. We describe a wavelet-based data compression algorithm that capitalizes on the inherent redunancies within multidimensional data to achieve higher compression levels than can be obtained from single images. The algorithm will permit remote users to roam through large 4D data sets using communication channels of modest bandwidth at high speed. This will allow animation to be used as a powerful aid to visualizing dynamic changes in three-dimensional structures.     

Pyrrolo[2,1-c][1,4]benzoxazepines. 2. Synthesis of 5-phenyl derivatives

A series of 5-phenylpyrrolo[2,1-c][1,4]benzoxazepines with basic substituents at the 11-position has been synthesized utilizing a nucleophilic aromatic fluoride displacement-cyclization. Piperidinyl derivatives were prepared by Vilsmeier formylation of the key 1-[(2-fluorophenyl)phenylmethyl]pyrrole ( 4 ) followed by addition of a piperidinyl Grignard reagent and cyclization of the resulting carbinol. A (dimethylamino)methyl derivative was prepared via an analogous cyclization of α-(dimethylamino)methyl-1-[(2-fluorophenyl)phenyl-methyl]-1H-pyrrole-2-methanol ( 10 ), obtained by the Hoeben-Hoesch acylation of 4 with chloroacetonitrile, addition of dimethylamine to the resulting α-chloroketone 8 , and reduction of the α-(dimethylamino)ketone 9 with sodium borohydride to give 10 .     

Spectral Features of Canthaxanthin in HCP2. A QM/MM Approach

The increased interest in sequencing cyanobacterial genomes has allowed the identification of new homologs to both the N-terminal domain (NTD) and C-terminal domain (CTD) of the Orange Carotenoid Protein (OCP). The N-terminal domain homologs are known as Helical Carotenoid Proteins (HCPs). Although some of these paralogs have been reported to act as singlet oxygen quenchers, their distinct functional roles remain unclear. One of these paralogs (HCP2) exclusively binds canthaxanthin (CAN) and its crystal structure has been recently characterized. Its absorption spectrum is significantly red-shifted, in comparison to the protein in solution, due to a dimerization where the two carotenoids are closely placed, favoring an electronic coupling interaction. Both the crystal and solution spectra are red-shifted by more than 50 nm when compared to canthaxanthin in solution. Using molecular dynamics (MD) and quantum mechanical/molecular mechanical (QM/MM) studies of HCP2, we aim to simulate these shifts as well as obtain insight into the environmental and coupling effects of carotenoid–protein interactions.     

On the kinematics of protein folding

We offer simple solutions to three kinematic problems that occur in the folding of proteins. We show how to construct suitably local elementary Monte Carlo moves, how to close a loop, and how to fold a loop without breaking the bond that closes it.     

Forming architectured paper by printing a starch patterned grid: a new low-cost approach for lightweighting packaging

To meet the environmental challenges, the use of plastic packaging must be drastically reduced. Paper-based solutions may be a credible alternative provided that their production cost is reduced. One way may be to improve the paper stiffness to weight ratio. In this work, a simple and low-cost approach is proposed, which consists in printing a patterned grid of starch at the paper surface by using a widespread printing process. With only a small quantity of starch (7 g/m²), the bending stiffness of a packaging paper of 60 g/m² was multiplied by more than a factor three. This improvement originates from the permanent 3D shape the paper unexpectedly took after printing. The printed lines formed “valleys” whereas the unprinted zones were raised, forming “mountains”. Drying shrinkage of the starch is assumed to play a major role, in particular by inducing local buckling of the unprinted zones. In addition, the resulting 3D shape could be interestingly tuned by adjusting the grid pattern. Even if a better understanding is necessary to be able to well control the phenomena, this approach appears relevant to form “architectured” papers with improved bending resistance to weight ratio.

     

Bridging photochemistry and photomechanics with NMR crystallography: the molecular basis for the macroscopic expansion of an anthracene ester nanorod

Crystals composed of photoreactive molecules represent a new class of photomechanical materials with the potential to generate large forces on fast timescales. An example is the photodimerization of 9-tert-butyl-anthracene ester (9TBAE) in molecular crystal nanorods that leads to an average elongation of 8%. Previous work showed that this expansion results from the formation of a metastable crystalline product. In this article, it is shown how a novel combination of ensemble oriented-crystal solid-state NMR, X-ray diffraction, and first principles computational modeling can be used to establish the absolute unit cell orientations relative to the shape change, revealing the atomic-resolution mechanism for the photomechanical response and enabling the construction of a model that predicts an elongation of 7.4%, in good agreement with the experimental value. According to this model, the nanorod expansion does not result from an overall change in the volume of the unit cell, but rather from an anisotropic rearrangement of the molecular contents. The ability to understand quantitatively how molecular-level photochemistry generates mechanical displacements allows us to predict that the expansion could be tuned from +9% to −9.5% by controlling the initial orientation of the unit cell with respect to the nanorod axis. This application of NMR-assisted crystallography provides a new tool capable of tying the atomic-level structural rearrangement of the reacting molecular species to the mechanical response of a nanostructured sample.

NMR crystallography establishes absolute unit-cell orientations relative to the shape change, revealing the atomic-resolution mechanism for the nanorod''s photomechanical response.     

Small molecules targeting the NEDD8·NAE protein–protein interaction

Ubiquitination is a major controller of protein homeostasis in cells. Some ubiquitination pathways are modulated by a NEDDylation cascade, that also features E1 – 3 enzymes. The E1 enzyme in the NEDDylation cascade involves a protein–protein interaction (PPI) between NEDD8 (similar to ubiquitin) and NAE (NEDD8 Activating Enzyme). A small molecule inhibitor of the ATP binding site in NAE is in clinical trials. We hypothesized a similar effect could be induced by disrupting the NEDD8·NAE PPI, though, to the best of our knowledge, no small molecules have been reported to disrupt this to date. In the research described here, Exploring Key Orientations (EKO) was used to evaluate several chemotype designs for their potential to disrupt NEDD8·NAE; specifically, for their biases towards orientation of side-chains in similar ways to protein segments at the interface. One chemotype design was selected, and a targeted library of 24 compounds was made around this theme via solid phase synthesis. An entry level hit for disrupting NEDD8·NAE was identified from this library on the basis of its ability to bind NAE (K_i of 6.4 ± 0.3 μM from fluorescence polarization), inhibit NEDDylation, suppress formation of the corresponding E1 – 3 complexes as monitored by cell-based immunoblotting, and cytotoxicity to K562 leukemia cells via early stage apoptosis. The cell-based immunoblot assay also showed the compound caused NEDD8 to accumulate in cells, presumably due to inhibition of the downstream pathways involving the E1 enzyme. The affinity and cellular activities of the hit compound are modest, but is interesting as first in class for this mode of inhibition of NEDDylation, and as another illustration of the way EKO can be used to evaluate user-defined chemotypes as potential inhibitors of PPIs.

Discovery of the first NEDDylation inhibitor, that targets the NEDD8·NAE protein–protein interaction, was acheived using the Exploring Key Orientations (EKO) approach.