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Room temperature crystallography of human acetylcholinesterase bound to a substrate analogue 4K-TMA: Towards a neutron structure
Acetylcholinesterase (AChE) catalyzes hydrolysis of acetylcholine thereby terminating cholinergic nerve impulses for efficient neurotransmission. Human AChE (hAChE) is a target of nerve agent and pesticide organophosphorus compounds that covalently attach to the catalytic Ser203 residue. Reactivation of inhibited hAChE can be achieved with nucleophilic antidotes, such as oximes. Understanding structural and electrostatic (i.e. protonation states) determinants of the catalytic and reactivation processes is crucial to improve design of oxime reactivators. Here we report X-ray structures of hAChE conjugated with a reversible covalent inhibitor 4K-TMA (4K-TMA:hAChE) at 2.8 Å resolution and of 4K-TMA:hAChE conjugate with oxime reactivator methoxime, MMB4 (4K-TMA:hAChE:MMB4) at 2.6 Å resolution, both at physiologically relevant room temperature, as well as cryo-crystallographic structure of 4K-TMA:hAChE at 2.4 Å resolution. 4K-TMA acts as a substrate analogue reacting with the hydroxyl of Ser203 and generating a reversible tetrahedral hemiketal intermediate that closely resembles the first tetrahedral intermediate state during hAChE-catalyzed acetylcholine hydrolysis. Structural comparisons of room temperature with cryo-crystallographic structures of 4K-TMA:hAChE and published mAChE complexes with 4K-TMA, as well as the effect of MMB4 binding to the peripheral anionic site (PAS) of the 4K-TMA:hAChE complex, revealed only discrete, minor differences. The active center geometry of AChE, already highly evolved for the efficient catalysis, was thus indicative of only minor conformational adjustments to accommodate the tetrahedral intermediate in the hydrolysis of the neurotransmitter acetylcholine (ACh). To map protonation states in the hAChE active site gorge we collected 3.5 Å neutron diffraction data paving the way for obtaining higher resolution datasets that will be needed to determine locations of individual hydrogen atoms.
Elevated [CO2] changes soil organic matter composition and substrate diversity in an arid ecosystem
Little is known about how rising atmospheric [CO2] will impact long-term plant biomass or the dynamics of soil organic matter (SOM) in arid ecosystems. Evans et al. (1) reported higher soil organic carbon (SOC) and total nitrogen (N) concentrations following 10 years exposure to elevated atmospheric [CO2] at the Nevada Desert Free-Air-Carbon dioxide-Enrichment (FACE) Facility (NDFF). In this study, we investigated potential mechanisms that resulted in increased SOC and total N accumulation and SOM stabilization using high resolution mass spectrometry. Samples were collected from soil profiles to 1 m in depth with a 0.2 m increment under the dominant evergreen shrub Larrea tridentata. The differences in the molecular composition and diversity of SOM were more evident in surface soils and declined with depth, and were consistent with higher SOC and total N concentrations under elevated than ambient [CO2]. Our molecular analysis also suggested increased root exudation and/or microbial necromass from stabilization of labile C and N contributed to SOM and N stocks. Increased microbial activity and metabolism under elevated [CO2] compared to ambient treatments suggest that elevated [CO2] altered microbial carbon use patterns, reflecting changes in the quality and quantity of SOC inputs. We found that plant-derived compounds were primary substrates for microbial activity under elevated [CO2] and microbial products were the main constituents of stabilized SOM. Our results suggest that arid ecosystems are a potential large C sink under elevated [CO2], given the extensive coverage of the land surface, and that labile compounds are transformed to stable SOM via microbial processes. Arid systems are limited by water, and thus may have a different C storage potential under changing climates than other ecosystems that are limited by nitrogen or phosphorus.
One of the Substrate Waters for O 2 Formation in Photosystem II Is Provided by the Water-Splitting Mn 4 CaO 5 Cluster’s Ca 2+ Ion
During the catalytic step immediately prior to O–O bond formation in Photosystem II, a water molecule deprotonates and moves next to the water-splitting Mn 4 CaO 5 cluster’s O5 oxo bridge. Considerable evidence identifies O5 as one of the two substrate waters that ultimately form O 2 . The relocated oxygen, known as O6 or Ox, may be the second. It is currently debated whether O6 or Ox originates as the Mn-bound water denoted W2 or as the Ca 2+ -bound water denoted W3. To distinguish between these two possibilities, we analyzed the D–O–D bending mode of the water molecule that deprotonates/relocates to become O6/Ox. Here, we show that this D–O–D bending mode is not altered by the D1-S169A mutation. Previously, we showed that this D–O–D bending mode is altered substantially when Sr 2+ is substituted for Ca 2+ . Because Sr 2+ /Ca 2+ substitution alters this D–O–D bending mode but the D1-S169A mutation does not, we conclude that the water-derived oxygen that relocates and becomes O6/Ox derives from the Ca 2+ -bound W3. This conclusion provides an important constraint for proposed mechanisms of O–O bond formation in Photosystem II.
Density Functional Theory Study of the Adsorption and Dissociation of Copper(I) Acetamidinates on Ni(110): The Effect of the Substrate
In order to assess the role of a metal substrates on the thermal chemistry of adsorbed acetamidinate metalorganic compounds, we have studied the surface chemistry of copper(I)–N,N'-dimethylacetamidinate on Ni(110) using density functional theory and contrasted it with similar calculations we previously carried out on Cu(110). At low coverages, it was found that, in its most stable configuration, the molecular adsorption of copper(I)–N,N'-dimethylacetamidinate dimers occurs with the Cu atoms occupying surface hollow sites. In this work, the ligands reorient away from those metal centers, and the N atoms develop new direct bonds with surface Ni atoms. However, this configuration is not stable and decomposes by losing both ligands to the surface. In the final state, the two ligands bind via their N atoms to Ni sites one lattice space away from the sites where the Cu atoms remain, with their molecular planes perpendicular to that of the surface. This is in contrast with what happens in the case of adsorption on Cu(110), where the Cu atoms from the metalorganic complex still occupy hollow sites but where only one of the ligands breaks away and binds directly to the surface; the other remains on top of the two Cu ions. In terms of the energetics of adsorption and decomposition, the reactions on Ni(110) are much more exothermic than on Cu(110). Further analysis of the distribution of charge within the adsorbates shows a minor reduction of the Cu atoms of the dimer upon interaction with the surface; full reduction to metallic copper is complete only when both ligands have fully migrated to their new Ni surface sites.
Phase transition and energy storage behavior of antiferroelectric PLZT thin films epitaxially deposited on SRO buffered STO single crystal substrates [Phase transition and energy storage behavior of antiferroelectric PLZT thin films epitaxially deposited on SRO buffered STO single crystal substrates]
Thin films of 300-nm-thick (Pb 0.98 , La 0.02 )(Zr 0.95 , Ti 0.05 )O 3 (PLZT) were epitaxially deposited on (100), (110), and (111) SrTiO3 single crystal substrates by pulsed laser deposition. X-ray diffraction line and reciprocal space mapping (RSM) scans were used to determine the crystal structure. Tetragonal ((001) PLZT) and monoclinic MA ((O 1 1 ) and (111) PLZT) structures were found, which influenced the stored energy density. Electric field induced antiferroelectric to ferroelectric (AFE—>FE) phase transitions were found to have a large reversible energy density of up to 30J/cm 3 . With increasing temperature, an AFE to relaxor ferroelectric (AFE—>RFE) transition was found. The RFE phase exhibited lower energy loss, and an improved energy storage efficiency. Here, the results are discussed from the perspective of crystal structure, dielectric phase transitions, and energy storage characteristics.
The structure of the RCAN1:CN complex explains the inhibition of and substrate recruitment by calcineurin
Regulator of calcineurin 1 (RCAN1) is an endogenous inhibitor of the Ser/Thr phosphatase calcineurin (CN). It has been shown that excessive inhibition of CN is a critical factor for Down syndrome and Alzheimer’s disease. Here, we determined RCAN1’s mode of action. Using a combination of structural, biophysical, and biochemical studies, we show that RCAN1 inhibits CN via multiple routes: first, by blocking essential substrate recruitment sites and, second, by blocking the CN active site using two distinct mechanisms. We also show that phosphorylation either inhibits RCAN1-CN assembly or converts RCAN1 into a weak inhibitor, which can be reversed by CN via dephosphorylation. This highlights the interplay between posttranslational modifications in regulating CN activity. Last, this work advances our understanding of how active site inhibition of CN can be achieved in a highly specific manner. Together, these data provide the necessary road map for targeting multiple neurological disorders.
Substrate deformation regulates DRM2-mediated DNA methylation in plants
DRM2 induces substrate deformation to underlie its methylation preference for CHH DNA in plants.
The effect of grooves in amorphous substrates on the orientation of metal deposits. I - Carbon substrates
The graphoepitaxial alignment of vapor-deposited discrete metal crystallites is investigated in the nucleation and growth stages and during annealing by in situ UHV/TEM techniques. Various stages of nucleation, growth and coalescence of vapor deposits of Au, Ag, Pb, Sn, and Bi on amorphous, topographically structured C substrates are analyzed by advanced dark-field techniques to detect preferred local orientations. It is found that the topography-induced orientation of metal crystallites depends strongly on their mobility and their respective tendency to develop pronounced crystallographic shapes. Lowering of the average surface free energies and increasing the crystallographic surface energy anisotropies cause generally improved graphoepitaxial alignments.
Graphene layer formation at low substrate temperature on a metal and carbon based substrate
A system and method for forming graphene layers on a substrate. The system and methods include direct growth of graphene on diamond and low temperature growth of graphene using a solid carbon source.
Substrate matters: Coupled phonon modes of a spherical particle on a substrate probed with EELS
Using vibrational electron energy loss spectroscopy (vib-EELS) combined with numerical modeling, we investigate the physical mechanisms governing the phonon coupling between a spherical particle sustaining multipolar surface phonon modes and an underlying thin film. Depending upon their dielectric composition, a variety of hybrid phonon modes arise in the EEL spectrum due to the interaction between polarization charges in the particle and film. Mirror charge effects and phonon mode hybridization are the active mechanisms acting on dielectric and metallic-type films, respectively. Furthermore, processes beyond dipole-dipole interactions are required to describe the sphere-film coupling.
A structural and kinetic survey of GH5_4 endoglucanases reveals determinants of broad substrate spec
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Role of substrate thermal conductivity and vapor pressure in dropwise condensation
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