The substrate binding domains of human SIAH E3 ubiquitin ligases are now crystal clear
Not Available
Zhang, Qi↗
SEARCH · Engineering Papers
Results for “SUBSTRATES”
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Dynamic Conformational States Dictate Selectivity toward the Native Substrate in a Substrate-Permissive Acyltransferase
Hydroxycinnamoyl-CoA:shikimate hydroxycinnamoyltransferase (HCT) is an essential acyltransferase that mediates flux through plant phenylpropanoid metabolism by catalyzing a reaction between p-coumaroyl-CoA and shikimate, yet it also exhibits broad substrate permissiveness in vitro. How do enzymes like HCT avoid functional derailment by cellular metabolites that qualify as non-native substrates? Here, we combine X-ray crystallography and molecular dynamics to reveal distinct dynamic modes of HCT under native and non-native catalysis. We find that essential electrostatic and hydrogen-bonding interactions between the ligand and active site residues, permitted by active site plasticity, are elicited more effectively by shikimate than by other non-native substrates. This work provides a structural basis for how dynamic conformational states of HCT favor native over non-native catalysis by reducing the number of futile encounters between the enzyme and shikimate.
59 BASIC BIOLOGICAL SCIENCES↗
Enhancing Oxygen Reduction Performance of Pt Monolayer Catalysts by Pd(111) Nanosheets on WNi Substrates
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99 GENERAL AND MISCELLANEOUS↗
Lateral optical confinement of channeled-substrate-planar lasers with GaAs/AlGaAs substrates
A physical explanation of the lateral guiding mechanism in channeled-substrate-planar (CSP) lasers based on the amount of wavefront tilt of the transverse field outside the channel region is presented. Because of this inherent wavefront tilt, all CSP lasers will have a very slight asymmetry in their transverse far-field pattern. The nature of the guiding mechanism does not require light absorption by the substrate. Design curves showing the complex lateral effective index step as a function of n-clad thickness with the active layer as a parameter are also presented. Depending on the specific layer compositions and thicknesses, the CSP guiding mechanism can provide a positive lateral index step for substrates with mole fractions of AlAs ranging from 0 to higher than 0.2.
Evans, Gary A.↗
Methods for both coating a substrate with aluminum oxide and infusing the substrate with elemental aluminum
Methods of aluminizing the surface of a metal substrate. The methods of the present invention do not require establishment of a vacuum or a reducing atmosphere, as is typically necessary. Accordingly, aluminization can occur in the presence of oxygen, which greatly simplifies and reduces processing costs by allowing deposition of the aluminum coating to be performed, for example, in air. Embodiments of the present invention can be characterized by applying a slurry that includes a binder and powder granules containing aluminum to the metal substrate surface. Then, in a combined step, a portion of the aluminum is diffused into the substrate and a portion of the aluminum is oxidized by heating the slurry to a temperature greater than the melting point of the aluminum in an oxygen-containing atmosphere.
36 MATERIALS SCIENCE↗
Wide bandgap, strain-balanced quantum well tunnel junctions on InP substrates
In this work, the electrical performance of strain-balanced quantum well tunnel junctions with varying designs is presented. Strain-balanced quantum well tunnel junctions comprising compressively strained InAlAs wells and tensile-strained InAlAs barriers were grown on InP substrates using solid-source molecular beam epitaxy. The use of InAlAs enables InP-based tunnel junction devices to be produced using wide bandgap layers, enabling high electrical performance with low absorption. The impact of well and barrier thickness on the electrical performance was investigated, in addition to the impact of Si and Be doping concentration. Finally, the impact of an InGaAs quantum well at the junction interface is presented, enabling a peak tunnel current density of 47.6 A/cm{sup 2} to be realized.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Inversion of substrate stereoselectivity of horse liver alcohol dehydrogenase by substitutions of Ser-48 and Phe-93
Not Available
Kim, Keehyuk (ORCID:000000023905663X)↗
Activity-induced migration of viscous droplets on a solid substrate
Active matter exploits motion to induce changes in shape and conformation via external input. Here, in this paper, we establish theoretically that viscous liquid droplets containing magnetic nanoparticles with frozen-in magnetic moments, sitting on a solid substrate and surrounded by an ambient gas phase, can deform and migrate under the influence of a magnetic torque. The effect arises because the collective rotation of the magnetic nanoparticles at the liquid–gas interface tilts the droplet away from a symmetric configuration, breaks the reflection symmetry with respect to the centre axis, and leads to a left–right asymmetry of the contact angles. A sufficiently strong magnetic torque leads the contact angles to overcome hysteresis effects leading the droplet to migrate. We develop a general framework to explain how symmetry-breaking affects droplet migration. Thus previous results of droplet spreading and migration can be recovered as special cases. Such droplets can be employed as agents in active surfaces and can move against gravity, chemical and thermal gradients, providing a mechanism that could be utilized by both industry and medicine.
Aggarwal, A.↗
Glassy Carbon Substrate Oxidation Effects on Electrode Stability for Oxygen Evolution Reaction Catalysis Stability Benchmarking
Employing benchmarking metrics to capture the activity and stability of electrocatalysts for the oxygen evolution reaction (OER) in acid is a critical practice that enables meaningful comparison of catalyst material candidates reported throughout the literature. In this work, we find that ubiquitously used glassy carbon electrode substrates oxidize under typical OER operating conditions, forming a pacified, electrically insulating, and oxygen-rich surface layer that causes drastic loss of current density over the course of extended chronoamperometric stability tests at an anodic potential of 1.7 VRHE. We show that the experimentally observed stability of glassy carbon-based electrodes is approximately two orders of magnitude lower than that expected solely from dissolution-based catalyst intrinsic stability of Ir-based catalysts. We additionally find that glassy carbon-based electrode stability measured by chronoamperometric holds is greatly impacted by catalyst loading, with high catalyst loadings improving the stability of the overall electrode via a protective effect on the glassy carbon substrate. Altogether, our investigation highlights that glassy carbon is not electrochemically inert under OER conditions on the timescale of common stability tests, which can cause electrodes to exhibit performance losses that do not reflect the intrinsic stability of the actual catalyst material being investigated. In light of our findings, we underscore the usefulness of metrics, such as the S-number, to reflect intrinsic catalyst material stability.
25 ENERGY STORAGE↗
Characterizing substrate–surface interactions on alumina-supported metal catalysts by dynamic nuclear polarization-enhanced double-resonance NMR spectroscopy [Characterizing substrate-surface interactions on alumina supported metal catalysts by DNP-enhanced double-resonance NMR spectroscopy]
The characterization of nanometer-scale interactions between carbon-containing substrates and alumina surfaces is of paramount importance to industrial and academic catalysis applications, but it is also very challenging. Here, we demonstrate that dynamic nuclear polarization surface-enhanced NMR spectroscopy (DNP SENS) allows the unambiguous description of the coordination geometries and conformations of the substrates at the alumina surface through high-resolution measurements of 13 C– 27 Al distances. We apply this new technique to elucidate the molecular-level geometry of 13 C-enriched methionine and natural abundance poly(vinyl alcohol) adsorbed on γ-Al 2 O 3 -supported Pd catalysts, and we support these results with element-specific X-ray absorption near-edge measurements. Furthermore, this work clearly demonstrates a surprising bimodal coordination of methionine at the Pd–Al 2 O 3 interface.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Structure of photosystem II and substrate binding at room temperature
Light-induced oxidation of water by photosystem II (PS II) in plants, algae and cyanobacteria has generated most of the dioxygen in the atmosphere. PS II, a membrane-bound multi-subunit pigment protein complex, couples the one-electron photochemistry at the reaction centre with the four-electron redox chemistry of water oxidation at the Mn 4 CaO 5 cluster in the oxygen-evolving complex (OEC). Under illumination, the OEC cycles through five intermediate S-states (S 0 to S 4), in which S 1 is the dark-stable state and S 3 is the last semi-stable state before O-O bond formation and O 2 evolution. A detailed understanding of the O-O bond formation mechanism remains a challenge, and will require elucidation of both the structures of the OEC in the different S-states and the binding of the two substrate waters to the catalytic site. Here we report the use of femtosecond pulses from an X-ray free electron laser (XFEL) to obtain damage-free, room temperature structures of dark-adapted (S 1), two-flash illuminated (2F; S 3 -enriched), and ammonia-bound two-flash illuminated (2F-NH 3; S 3 -enriched) PS II. Although the recent 1.95 Å resolution structure of PS II at cryogenic temperature using an XFEL provided a damage-free view of the S 1 state, measurements at room temperature are required to study the structural landscape of proteins under functional conditions, and also for in situ advancement of the S-states. To investigate the water-binding site(s), ammonia, a water analogue, has been used as a marker, as it binds to the Mn 4 CaO 5 cluster in the S 2 and S 3 states. Since the ammonia-bound OEC is active, the ammonia-binding Mn site is not a substrate water site. This approach, together with a comparison of the native dark and 2F states, is used to discriminate between proposed O-O bond formation mechanisms.
Young, Iris D.↗
Tuning two-dimensional phase formation through epitaxial strain and growth conditions: silica and silicate on Ni x Pd 1−x (111) alloy substrates
The combined experimental and theoretical results demonstrate the manipulation of 2D VDW silica and 2D Ni silicate through growth conditions, and the determination of the maximum epitaxial strain imparted to the 2D system through alloy substrate.
Zhou, Chao↗
Kinetic characterization of Vibrio cholerae ApbE: Substrate specificity and regulatory mechanisms
ApbE is a member of a novel family of flavin transferases that incorporates flavin mononucleotide (FMN) to subunits of diverse respiratory complexes, which fulfill important homeostatic functions. In this work a detailed characterization of Vibrio cholerae ApbE physiologic activity, substrate specificity and pH dependency was carried out. The data obtained show novel characteristics of the regulation and function of this family. For instance, our experiments indicate that divalent cations are essential for ApbE function, and that the selectivity depends largely on size and the coordination sphere of the cation. Our data also show that ApbE regulation by pH, ADP and potassium is an important mechanism that enhances the adaptation, survival and colonization of V. cholerae in the small intestine. Moreover, studies of the pH-dependency of the activity show that the reaction is favored under alkaline conditions, with a pKa of 8.4. These studies, together with sequence and structure analysis allowed us to identify His257, which is absolutely conserved in the family, as a candidate for the residue whose deprotonation controls the activity. Remarkably, the mutant H257G abolished the flavin transfer activity, strongly indicating that this residue plays an important role in the catalytic mechanism of ApbE.
59 BASIC BIOLOGICAL SCIENCES↗
Isolating GaSb membranes grown metamorphically on GaAs substrates using highly selective substrate removal etch processes
The etch rates of NH 4 OH:H 2 O 2 and C 6 H 8 O 7 :H 2 O 2 for GaAs and GaSb have been investigated to develop a selective etch for GaAs substrates and to isolate GaSb epilayers grown on GaAs. The NH 4 OH:H 2 O 2 solution has a greater etch rate differential for the GaSb/GaAs material system than C 6 H 8 O 7 :H 2 O 2 solution. The selectivity of NH 4 OH:H 2 O 2 for GaAs/GaSb under optimized etch conditions has been observed to be as high as 11471 ± 1691 whereas that of C 6 H 8 O 7 :H 2 O 2 has been measured up to 143 ± 2. The etch contrast has been verified by isolating 2 μm thick GaSb epi-layers that were grown on GaAs substrates. GaSb membranes were tested and characterized with high-resolution X-Ray diffraction (HR-XRD) and atomic force microscopy (AFM).
36 MATERIALS SCIENCE↗