Hydrophobic interactions in a cyanobacterial plastocyanin-cytochrome f complex.

The complex of the photosynthetic redox partners plastocyanin and cytochrome f from the thermophilic cyanobacterium, Phormidium laminosum, was investigated by nuclear magnetic resonance (NMR). Chemical-shift perturbation analysis of amide proton and nitrogen nuclei implicates the hydrophobic patch and, to a lesser extent, the "eastern face" of plastocyanin in the complex interface. Intermolecular pseudocontact shifts observed in the complex of cadmium-substituted plastocyanin and ferric cytochrome f specifically define the site of interaction to be between the hydrophobic patch of plastocyanin and the heme region of cytochrome f. Rigid-body structure calculations using NMR-derived restraints demonstrate that plastocyanin is oriented in a "head-on" fashion, with the long axis of the molecule perpendicular to the heme plane. Remarkably, the structure and affinity of the complex are independent of ionic strength, indicating that there is little electrostatic interaction. Lowering the pH results in limited reorganization of the complex interface, while the binding affinity is unaffected. Therefore, protonation of the exposed copper ligand, His92, plays only a minor role in the complex. In contrast to other electron-transfer complexes, the plastocyanin-cytochrome f complex from P. laminosum is predominantly controlled by hydrophobic interactions. These findings are discussed in the context of the previously characterized angiosperm complex.     

Synthesis and characterization of dimensionally ordered semiconductor nanowires within mesoporous silica.

Semiconductor nanowires of silicon have been synthesized within the pores of mesoporous silica using a novel supercritical fluid solution-phase approach. Mesoporous silica, formed by the hydrolysis of tetramethoxysilane (TMOS) in the presence of a triblock copolymer surfactant, was employed for the nucleation and growth of quantum-confined nanowires. The filling of the silica mesopores with crystalline silicon and the anchoring of these nanowires to the sides of the pores were confirmed by several techniques including electron microscopy, powder X-ray diffraction, 29Si magic angle spinning nuclear magnetic resonance, infrared spectroscopy, and X-ray fluorescence. Effectively, the silica matrix provides a means of producing a high density of stable, well-ordered arrays of semiconductor nanowires in a low dielectric medium. The ordered arrays of silicon nanowires also exhibited discrete electronic and photoluminescence transitions that could be exploited in a number of applications, including nanodevices and interconnects.     

Measurements of niobium absorption spectra in plasmas with nearly full M-shell configurations

A systematic study has been carried out on the changes in the L-shell absorption structure of niobium as a result of changing the population of the n = 3 shell from full to having vacancies in the 3d level. The niobium spectra were measured in the 2–3 keV frequency range, which spanned the 2p-nd transitions where 3 ≤ n ≤ 11. In addition to the detailed structure in these arrays the data also show 2s-4p and 2p-4s transitions and the bound-free L edge. The frequencies and widths of transition arrays, transmission between arrays, and the absorption due to the bound-free edge, can be seen in the data. The sample conditions were found from a combination of two-dimensional radiation-hydrodynamics calculations using the AWE NYM code and flux measurements using X-ray diodes, measurements of 1s-2p absorption spectra in aluminium and mixed aluminium/niobium samples. The electron temperature error, inferred from the modelling, is ±2 eV, with a density error of 30%. The data were recorded over the temperature range from 28 to 45 eV and show marked changes in the spectra over this range.The data were compared to spectra predicted by the AWE CASSANDRA [B.J.B. Crowley, J.W.O. Harris, J. Quant. Spectrosc. Radiat. Transfer 71 (2000) p. 257] opacity code. The calculated spectra were able to reproduce the measurements reasonably well. However, there are some differences in line positions that cannot be accounted for by gradients and there are differences in the array structure in the prediction and the measurements, with additional structure predicted but not seen in the measurements. There is also lower transmission on the blue side of the 2p-3d transition arrays compared to prediction.     

Protein allostery at the solid-liquid interface: endoglucanase attachment to cellulose affects glucan clenching in the binding cleft

At phase boundaries, physical activities of enzymes such as substrate complexation play critical roles in driving biocatalysis. A prominent example is the cellulase cocktails secreted by fungi and bacteria for deconstructing crystalline cellulose in biomass into soluble sugars. At interfaces, molecular mechanisms of the physical steps in biocatalysis remain elusive due to the difficulties of characterizing protein action with high temporal and spatial resolution. Here, we focus on endoglucanase I (Cel7B) from the fungus Trichoderma reesei that hydrolyzes glycosidic bonds on cellulose randomly. We employ all-atom molecular dynamics (MD) simulations to elucidate the interactions of the catalytic domain (CD) of Cel7B with a cellulose microfibril before and after complexing a glucan chain in the binding cleft. The calculated mechanical coupling networks in Cel7B-glucan and Cel7B-microfibril complexes reveal a previously unresolved allosteric coupling at the solid-liquid interface: attachment of the Cel7B CD to the cellulose surface affects glucan chain clenching in the binding cleft. Alternative loop segments of the Cel7B CD were found to affix to intact or defective surface structures on the microfibril, depending on the complexation state. From a multiple sequence alignment, residues in surface-affixing segments show strong conservation, highlighting the functional importance of the physical activities that they facilitate. Surface-affixing residues also demonstrate significant sequence correlation with active-site residues, revealing the functional connection between complexation and hydrolysis. Analysis of the Cel7B CD exemplifies that the mechanical coupling networks calculated from atomistic MD simulations can be used to capture the conservation and correlation in sequence alignment.     

Rensselaer heavy ion beam probe diagnostic methods and techniques

The operating principles, measurement capabilities, hardware, and data analysis techniques of heavy ion beam probe diagnostics as used by the Rensselaer Plasma Dynamics Lab are reviewed. The topics that are addressed include; trajectory calculations of the ion beams; how the diagnostic measures plasma density, electron temperature, electric potential, and magnetic vector potential; the energy analyzer used to detect the beam, other hardware used in the experiments, and the basic techniques used in fluctuation studies and related diagnostic issues     

Mechanistic Insights into Catalytic Ethanol Steam Reforming Using Isotope‐Labeled Reactants

The low‐temperature ethanol steam reforming (ESR) reaction mechanism over a supported Rh/Pt catalyst has been investigated using isotope‐labeled EtOH and H₂O. Through strategic isotope labeling, all nonhydrogen atoms were distinct from one another, and allowed an unprecedented level of understanding of the dominant reaction pathways. All combinations of isotope‐ and non‐isotope‐labeled atoms were detected in the products, thus there are multiple pathways involved in H₂, CO, CO₂, CH₄, C₂H₄, and C₂H₆ product formation. Both the recombination of C species on the surface of the catalyst and preservation of the C?C bond within ethanol are responsible for C₂ product formation. Ethylene is not detected until conversion drops below 100 % at t=1.25 h. Also, quantitatively, 57 % of the observed ethylene is formed directly through ethanol dehydration. Finally there is clear evidence to show that oxygen in the SiO₂‐ZrO₂ support constitutes 10 % of the CO formed during the reaction.     

Pi-interaction tuning of the active site properties of metalloproteins

The influence of pi-interactions with a His ligand have been investigated in a family of copper-containing redox metalloproteins. The Met16Phe and Met16Trp pseudoazurin, and Leu12Phe spinach and Leu14Phe Phormidium laminosum plastocyanin variants possess active-site pi-contacts between the introduced residue and His81 and His87/92 respectively. The striking overlap of the side chain of Phe16 in the Met16Phe variant and that of Met16 in wild type pseudoazurin identifies that this position provides an important second coordination sphere interaction in both cases. His-ligand protonation and dissociation from Cu(I) occurs in the wild type proteins resulting in diminished redox activity, providing a [H(+)]-driven switch for regulating electron transfer. The introduced pi-interaction has opposing effects on the pKa for the His ligand in pseudoazurin and plastocyanin due to subtle differences in the pi-contact, stabilizing the coordinated form of pseudoazurin whereas in plastocyanin protonation and dissociation is favored. Replacement of Pro36, a residue that has been suggested to facilitate structural changes upon His ligand protonation, with a Gly, has little effect on the pKa of His87 in spinach plastocyanin. The mutations at Met16 have a significant influence on the reduction potential of pseudoazurin. Electron self-exchange is enhanced, whereas association with the physiological partner, nitrite reductase, is only affected by the Met16Phe mutation, but kcat is halved in both the Met16Phe and Met16Trp variants. Protonation of the His ligand is the feature most affected by the introduction of a pi-interaction.     

Ring-modified analogues and molecular dynamics studies to probe the requirements for fungicidal activities of malayamycin A and its N-nucleoside variants

The importance of functional group orientations and the integrity of the bicyclic perhydrofuran core of malayamycin A and two equally active N-nucleoside analogues as fungicides were investigated. Two analogues 10 and 11, representing a THP-truncated and a bicyclic aza-variant, were synthesized and found to be inactive. Molecular dynamics studies on malayamycin A and analogues were performed to highlight the importance of properly orientating the urea and methyl ether groups.     

Segregated Protein–Cucurbit[7]uril Crystalline Architectures via Modulatory Peptide Tectons

One approach to protein assembly involves water-soluble supramolecular receptors that act like glues. Bionanoarchitectures directed by these scaffolds are often system-specific, with few studies investigating their customization. Herein, the modulation of cucurbituril-mediated protein assemblies through the inclusion of peptide tectons is described. Three peptides of varying length and structural order were N-terminally appended to RSL, a β-propeller building block. Each fusion protein was incorporated into crystalline architectures mediated by cucurbit[7]uril ( Q7 ). A trimeric coiled-coil served as a spacer within a Q7 -directed sheet assembly of RSL, giving rise to a layered material of varying porosity. Within the spacer layers, the coiled-coils were dynamic. This result prompted consideration of intrinsically disordered peptides (IDPs) as modulatory tectons. Similar to the coiled-coil, a mussel adhesion peptide (Mefp) also acted as a spacer between protein– Q7 sheets. In contrast, the fusion of a nucleoporin peptide (Nup) to RSL did not recapitulate the sheet assembly. Instead, a Q7 -directed cage was adopted, within which disordered Nup peptides were partially “captured” by Q7 receptors. IDP capture occurred by macrocycle recognition of an intrapeptide Phe-Gly motif in which the benzyl group was encapsulated by Q7 . The modularity of these protein–cucurbituril architectures adds a new dimension to macrocycle-mediated protein assembly. Segregated protein crystals, with alternating layers of high and low porosity, could provide a basis for new types of materials.