Structural Basis for Substrate Recognition by the Ankyrin Repeat Domain of Human DHHC17 Palmitoyltransferase
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Verardi, Raffaello↗
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Thermo-physical and structural studies of sodium zinc borovanadate glasses in the region of high concentration of modifier oxides
Highlights: ► Highly modified sodium zinc borovanadate glasses. ► Structural model for borovanadate glasses. ► Network forming tendency of ZnO in borovanadate glasses. ► Fragility can be limited to NBO concentration in borovanadate glasses. -- Abstract: This paper reports investigation of Na{sub 2}O and ZnO modified borovanadate glasses in the highly modified regime of compositions. These glasses have been prepared by microwave route. Ultraviolet (UV) and visible, infrared (IR), Magic Angle Spinning Nuclear Magnetic Resonance (MAS NMR) and Electron Paramagnetic Resonance (EPR) spectroscopies have been used to characterize the speciation in the glasses. Together with the variation of properties such as molar volume and glass transition temperatures, spectroscopic data indicate that at high levels of modification, ZnO tends to behave like network former. It is proposed that the observed variation of all the properties can be reasonably well understood with a structural model. The model considers that the modification and speciation in glasses are strongly determined by the hierarchy of group electronegativities. Further, it is proposed that the width of the transitions of glasses obtained under same condition reflects the fragility of the glasses. An empirical expression has been suggested to quantify fragility on the basis of width of the transition regions.
36 MATERIALS SCIENCE↗
Structural adaptation of oxygen tolerance in 4-hydroxybutyrl-CoA dehydratase, a key enzyme of archaeal carbon fixation
Abstract Autotrophic microorganisms that convert inorganic carbon into organic matter were key players in the evolution of life on Earth. As the early atmosphere became oxygenated, microorganisms needed to develop mechanisms for oxygen protection, especially those relying on enzymes containing oxygen-sensitive metal clusters (e.g., Fe-S). Here we investigated how 4-hydroxybutyryl-CoA dehydratase (4HBD) - the key enzyme of the 3-hydroxypropionate/4-hydroxybutyrate (HP/HB) cycle for CO 2 -fixation - adapted as conditions shifted from anoxic to oxic. 4HBD is found in both anaerobic bacteria and aerobic ammonia-oxidizing archaea (AOA). The oxygen-sensitive bacterial 4HBD and oxygen-tolerant archaeal 4HBD share 59 % amino acid identity. To examine the structural basis of oxygen tolerance in archaeal 4HBD, we determined the atomic resolution structure of the enzyme. Two tunnels providing access to the canonical [4Fe-4S] cluster in oxygen-sensitive bacterial 4HBD were closed with four conserved mutations found in all aerobic AOA and other archaea. Further biochemical experiments and molecular dynamics simulations support our findings that restricting access to the active site is the key to oxygen tolerance, explaining how active site evolution drove a major evolutionary transition. Significance statement Autotrophy (primary production) was the first life strategy on Earth. Before photosynthesis (using solar energy to fix carbon dioxide), life relied on chemical reactions for energy. These chemosynthetic reactions are present in all domains of life, including archaea possessing the most energy-efficient carbon fixation pathway - the 3-hydroxypropionate/4-hydroxybutyrate cycle. This efficiency results from enzyme modifications, including enhanced enzyme stability and catalysis of multiple reactions. We reveal the first structure of aerobic 4-hydroxybutyryl-CoA dehydratase (4HBD) from ammonia-oxidizing archaea. These archaea are among the most abundant organisms on the planet, and their 4HBD active site evolved oxygen tolerance to support aerobic metabolism. This modification can provide further insight into enzyme evolution on early earth, as photosynthesis developed and began oxygenating the atmosphere.
DeMirci, Hasan (ORCID:0000000291355397)↗
Plasma-Generated OH Radical Production for Analyzing Three-Dimensional Structure in Protein Therapeutics
Protein three-dimensional structure dynamically changes in solution depending on the presence of ligands and interacting proteins. Methods for detecting these changes in protein conformation include ‘protein footprinting,’ using mass spectrometry. We describe herein a new technique, PLIMB (Plasma Induced Modification of Biomolecules), that generates µs bursts of hydroxyl radicals from water, to measure changes in protein structure via altered solvent accessibility of amino acid side chains. PLIMB was first benchmarked with model compounds, and then applied to a biological problem, i.e., ligand (EGF) induced changes in the conformation of the external (ecto) domain of Epidermal Growth Factor Receptor (EGFR). Regions in which oxidation decreased upon adding EGF fall along the dimerization interface, consistent with models derived from crystal structures. Furthermore these results demonstrate that plasma-generated hydroxyl radicals from water can be used to map protein conformational changes, and provide a readily accessible means of studying protein structure in solution.
59 BASIC BIOLOGICAL SCIENCES↗
Inelasticity and Nanostructured Dislocation Deformation of Aluminum–Silicon Alloy with a Supermodified Eutectic Structure
Young’s modulus and the logarithmic decrement of oscillations at a frequency of ~100 kHz as well as the subgrain size and residual stresses in the strontium modified alloy of aluminum with 15 wt % silicon have been studied. The alloy was obtained with a solidification rate of 1 mm/s at the shifted eutectic point. The dependence of inelastic dislocation deformation on the applied oscillating stress has been obtained and analyzed. The effect of strontium modification on the microstrain diagram can be accounted for by transformation of the lamellar fiber structure of eutectic silicon into a superfine fiber structure.
77 NANOSCIENCE AND NANOTECHNOLOGY↗
Critical heat flux on micro-structured zircaloy surfaces for flow boiling of water at low pressures
The influence of surface structure on critical heat flux for flow boiling of water was investigated for Zircaloy tubes in a vertical annular test section. The objectives were to find suitable surface modification processes for Zircaloy tubes and to test their critical heat flux performance in comparison to the smooth tube. Surface structures with micro-channels, porous layer, oxidized layer, and elevations in micro- and nano-scale were produced on a section of a Zircaloy cladding tube. These modified tubes were tested in an internally heated vertical annulus with a heated length of 326 mm and an inner and outer diameter of 9.5 and 18 mm. The experiments were performed with mass fluxes of 250 and 400 kg/(m{sup 2}s), outlet pressures between 120 and 300 kPa, and constant inlet subcooling enthalpy of 167 kJ/kg. Only a small influence of modified surface structures on critical heat flux was observed for the pressure of 120 kPa in the present test section geometry. However, with increasing pressure the critical heat flux could increase up to 29% using the surface structured tubes with micro-channels, porous and oxidized layers. Capillary effects and increased nucleation site density are assumed to improve the critical heat flux performance. (authors)
22 GENERAL STUDIES OF NUCLEAR REACTORS↗
Library Screening, In Vivo Confirmation, and Structural and Bioinformatic Analysis of Pentapeptide Sequences as Substrates for Protein Farnesyltransferase
Protein farnesylation is a post-translational modification where a 15-carbon farnesyl isoprenoid is appended to the C-terminal end of a protein by farnesyltransferase (FTase). This process often causes proteins to associate with the membrane and participate in signal transduction pathways. The most common substrates of FTase are proteins that have C-terminal tetrapeptide CaaX box sequences where the cysteine is the site of modification. However, recent work has shown that five amino acid sequences can also be recognized, including the pentapeptides CMIIM and CSLMQ. In this work, peptide libraries were initially used to systematically vary the residues in those two parental sequences using an assay based on Matrix Assisted Laser Desorption Ionization–Mass Spectrometry (MALDI-MS). In addition, 192 pentapeptide sequences from the human proteome were screened using that assay to discover additional extended CaaaX-box motifs. Selected hits from that screening effort were rescreened using an in vivo yeast reporter protein assay. The X-ray crystal structure of CMIIM bound to FTase was also solved, showing that the C-terminal tripeptide of that sequence interacted with the enzyme in a similar manner as the C-terminal tripeptide of CVVM, suggesting that the tripeptide comprises a common structural element for substrate recognition in both tetrapeptide and pentapeptide sequences. Molecular dynamics simulation of CMIIM bound to FTase further shed light on the molecular interactions involved, showing that a putative catalytically competent Zn(II)-thiolate species was able to form. Bioinformatic predictions of tetrapeptide (CaaX-box) reactivity correlated well with the reactivity of pentapeptides obtained from in vivo analysis, reinforcing the importance of the C-terminal tripeptide motif. This analysis provides a structural framework for understanding the reactivity of extended CaaaX-box motifs and a method that may be useful for predicting the reactivity of additional FTase substrates bearing CaaaX-box sequences.
59 BASIC BIOLOGICAL SCIENCES↗
Neutron spin structure with polarized deuterons and spectator proton tagging at EIC
The neutron's deep-inelastic structure functions provide essential information for the flavor separation of the nucleon parton densities, the nucleon spin decomposition, and precision studies of QCD phenomena in the flavor-singlet and nonsinglet sectors. Thus, traditional inclusive measurements on nuclear targets are limited by dilution from scattering on protons, Fermi motion and binding effects, final-state interactions, and nuclear shadowing at x << 0.1. An Electron-Ion Collider (EIC) would enable next-generation measurements of neutron structure with polarized deuteron beams and detection of forward-moving spectator protons over a wide range of recoil momenta (0 < pR << several 100 MeV in the nucleus rest frame). The free neutron structure functions could be obtained by extrapolating the measured recoil momentum distributions to the on-shell point. The method eliminates nuclear modifications and can be applied to polarized scattering, as well as to semi-inclusive and exclusive final states. We review the prospects for neutron structure measurements with spectator tagging at EIC, the status of R&D efforts, and the accelerator and detector requirements.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
Polarized light ions and spectator nucleon tagging at EIC
The neutron's deep-inelastic structure functions provide essential information for the flavor separation of the nucleon parton densities, the nucleon spin decomposition, and precision studies of QCD phenomena in the flavor-singlet and nonsinglet sectors. Traditional inclusive measurements on nuclear targets are limited by dilution from scattering on protons, Fermi motion and binding effects, final-state interactions, and nuclear shadowing at x ll 0.1. An Electron-Ion Collider (EIC) would enable next-generation measurements of neutron structure with polarized deuteron beams and detection of forward-moving spectator protons over a wide range of recoil momenta (0 < p(R) < several 100MeV in the nucleus rest frame). The free neutron structure functions could be obtained by extrapolating the measured recoil momentum distributions to the on-shell point. The method eliminates nuclear modifications and can be applied to polarized scattering, as well as to semi-inclusive and exclusive final states. We review the prospects for neutron structure measurements with spectator tagging at EIC, the status of R&D efforts, and the accelerator and detector requirements.
Guzey, Vadim↗
Crystal structures of nitrato-(2-[2-(1-pyridine-2-ylethylidene)hydrazine]-1,3-benzothiazolo) aquacopper and chloro-(2-[2-phenyl(pyridine-2-ylethylidene)hydrazine]-1,3-benzothiazolo) copper
Two crystal modifications of nitrato-(2-[2-(1-pyridine-2-ylethylidene)hydrazine]-1,3-benzothiazolo) aquacopper (I and II) and two modifications of chloro-(2-[2-phenyl(pyridine-2-ylethylidene)hydrazine]-1,3-benzothiazolo) copper (III and IV) have been synthesized and studied by X-ray diffraction. In structures I and II, the copper atoms coordinate a monodeprotonated molecule of the organic ligand, nitrate ions, and a water molecule. In crystals of I, the complexes are monomeric, whereas complexes II are linked via nitrate ions to form polymeric chains. In both structures the coordination polyhedron of the copper atom can be described as a distorted tetragonal bipyramid—(4 + 1 + 1) in I and (4 + 2) in II. These coordination polyherdra have different compositions. In structures III and IV, the metal atoms coordinate a monodeprotonated (2-[2-phenyl(pyridine-2-ylethylidene)hydrazine]-1,3-benzothiazole molecule and chloride ions. In III the complex-forming ion has square-planar coordination geometry, whereas structure IV consists of centrosymmetric dimers with two bridging chlorine atoms. It was found that nitrato-(2-[2-(1-pyridine-2-ylethylidene)hydrazine]-1,3-benzothiazolo) aquacopper possesses antitumor activity.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Structural basis of undecaprenyl phosphate glycosylation leading to polymyxin resistance in Gram-negative bacteria
In Gram-negative bacteria, the enzymatic modification of Lipid A with aminoarabinose (L-Ara4N) leads to resistance against polymyxin antibiotics and cationic antimicrobial peptides. ArnC, an integral membrane glycosyltransferase, attaches a formylated form of aminoarabinose to the lipid undecaprenyl phosphate, enabling its association with the bacterial inner membrane. Here, we present cryo-electron microscopy structures of ArnC from S. enterica in apo and nucleotide-bound conformations. These structures reveal a conformational transition that takes place upon binding of the partial donor substrate. Using coarse-grained and atomistic simulations, we provide insights into substrate coordination before and during catalysis, and we propose a catalytic mechanism that may operate on all similar metal-dependent polyprenyl phosphate glycosyltransferases. The reported structures provide a new target for drug design aiming to combat polymyxin resistance.
Ashraf, Khuram U. [Rutgers University, Newark, NJ ↗
The Structure and Immune Regulatory Implications of the Ubiquitin-Like Tandem Domain Within an Avian 2’-5’ Oligoadenylate Synthetase-Like Protein
Post-translational modification of host and viral proteins by ubiquitin and ubiquitin-like proteins plays a key role in a host’s ability to mount an effective immune response. Avian species lack a ubiquitin-like protein found in mammals and other non-avian reptiles; interferon stimulated gene product 15 (ISG15). ISG15 serves as a messenger molecule and can be conjugated to both host and viral proteins leading them to be stabilized, degraded, or sequestered. Structurally, ISG15 is comprised of a tandem ubiquitin-like domain (Ubl), which serves as the motif for post-translational modification. The 2’-5’ oligoadenylate synthetase-like proteins (OASL) also encode two Ubl domains in series near its C-terminus which binds OASL to retinoic acid inducible gene-I (RIG-I). This protein-protein interaction increases the sensitivity of RIG-I and results in an enhanced production of type 1 interferons and a robust immune response. Unlike human and other mammalian OASL homologues, avian OASLs terminate their tandem Ubl domains with the same LRLRGG motif found in ubiquitin and ISG15, a motif required for their conjugation to proteins. Chickens, however, lack RIG-I, raising the question of structural and functional characteristics of chicken OASL (chOASL). By investigating chOASL, the evolutionary history of viruses with deubiquitinases can be explored and drivers of species specificity for these viruses may be uncovered. Here we show that the chOASL tandem Ubl domains shares structural characteristics with mammalian ISG15, and that chOASL can oligomerize and conjugate to itself. In addition, the ISG15-like features of avian OASLs and how they impact interactions with viral deubiquitinases and deISGylases are explored.
59 BASIC BIOLOGICAL SCIENCES↗
Predicting peak spectral sensitivities of vertebrate cone visual pigments using atomistic molecular simulations
Vision is the dominant sensory modality in many organisms for foraging, predator avoidance, and social behaviors including mate selection. Vertebrate visual perception is initiated when light strikes rod and cone photoreceptors within the neural retina of the eye. Sensitivity to individual colors, i.e., peak spectral sensitivities (λ max ) of visual pigments, are a function of the type of chromophore and the amino acid sequence of the associated opsin protein in the photoreceptors. Large differences in peak spectral sensitivities can result from minor differences in amino acid sequence of cone opsins. To determine how minor sequence differences could result in large spectral shifts we selected a spectrally-diverse group of 14 teleost Rh2 cone opsins for which sequences and λ max are experimentally known. Classical molecular dynamics simulations were carried out after embedding chromophore-associated homology structures within explicit bilayers and water. These simulations revealed structural features of visual pigments, particularly within the chromophore, that contributed to diverged spectral sensitivities. Statistical tests performed on all the observed structural parameters associated with the chromophore revealed that a two-term, first-order regression model was sufficient to accurately predict λ max over a range of 452–528 nm. The approach was accurate, efficient and simple in that site-by-site molecular modifications or complex quantum mechanics models were not required to predict λ max . These studies identify structural features associated with the chromophore that may explain diverged spectral sensitivities, and provide a platform for future, functionally predictive opsin modeling.
59 BASIC BIOLOGICAL SCIENCES↗
Predicting chemically-induced skin reactions. Part II: QSAR models of skin permeability and the relationships between skin permeability and skin sensitization
Skin permeability is widely considered to be mechanistically implicated in chemically-induced skin sensitization. Although many chemicals have been identified as skin sensitizers, there have been very few reports analyzing the relationships between molecular structure and skin permeability of sensitizers and non-sensitizers. The goals of this study were to: (i) compile, curate, and integrate the largest publicly available dataset of chemicals studied for their skin permeability; (ii) develop and rigorously validate QSAR models to predict skin permeability; and (iii) explore the complex relationships between skin sensitization and skin permeability. Based on the largest publicly available dataset compiled in this study, we found no overall correlation between skin permeability and skin sensitization. In addition, cross-species correlation coefficient between human and rodent permeability data was found to be as low as R{sup 2} = 0.44. Human skin permeability models based on the random forest method have been developed and validated using OECD-compliant QSAR modeling workflow. Their external accuracy was high (Q{sup 2}{sub ext} = 0.73 for 63% of external compounds inside the applicability domain). The extended analysis using both experimentally-measured and QSAR-imputed data still confirmed the absence of any overall concordance between skin permeability and skin sensitization. This observation suggests that chemical modifications that affect skin permeability should not be presumed a priori to modulate the sensitization potential of chemicals. The models reported herein as well as those developed in the companion paper on skin sensitization suggest that it may be possible to rationally design compounds with the desired high skin permeability but low sensitization potential. - Highlights: • It was compiled the largest publicly-available skin permeability dataset. • Predictive QSAR models were developed for skin permeability. • No concordance between skin sensitization and skin permeability has been found. • Structural rules for optimizing sensitization and penetration were established.
60 APPLIED LIFE SCIENCES↗
Comparative Study on the Charge-Ordered and Mixed-Valence Phases of LuFe{sub 2}O{sub 4} via First-Principles Calculations
The first-principles density functional theory calculations have been used to investigate the relation between magnetic and structural properties of LuFe{sub 2}O{sub 4} for both the charge-ordered (CO) and the mixed-valence (MV) phases and also to compare the electronic properties for both phases. The computed structural parameters of rhombohedral and monoclinic systems are found to be in good agreement with experimental findings. An analysis of the magnetic properties is provided considering nonmagnetic, ferromagnetic, antiferromagnetic, and ferrimagnetic model orderings. In agreement with experimental results, CO modification of LuFe{sub 2}O{sub 4} is predicted to be ferrimagnetic. The GGA + U electronic structures show a semiconducting behavior of CO phase while a metallic character for MV LuFe{sub 2}O{sub 4} phase.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Modification of electron states in CdTe absorber due to a buffer layer in CdTe/CdS solar cells
By application of the ac admittance spectroscopy method, the defect state energy distributions were determined in CdTe incorporated in thin film solar cell structures concluded on ZnO, ZnSe, and ZnS buffer layers. Together with the Mott-Schottky analysis, the results revealed a strong modification of the defect density of states and the concentration of the uncompensated acceptors as influenced by the choice of the buffer layer. In the solar cells formed on ZnSe and ZnS, the Fermi level and the energy position of the dominant deep trap levels were observed to shift closer to the midgap of CdTe, suggesting the mid-gap states may act as recombination centers and impact the open-circuit voltage and the fill factor of the solar cells. For the deeper states, the broadening parameter was observed to increase, indicating fluctuations of the charge on a microscopic scale. Such changes can be attributed to the grain-boundary strain and the modification of the charge trapped at the grain-boundary interface states in polycrystalline CdTe.
36 MATERIALS SCIENCE↗
GlcNAc-1-P-transferase–tunicamycin complex structure reveals basis for inhibition of N-glycosylation
N-linked glycosylation is a predominant post-translational modification of protein in eukaryotes, and its dysregulation is the etiology of several human disorders. The enzyme UDP-N-acetylglucosamine:dolichyl-phosphate N-acetylglucosaminephosphotransferase (GlcNAc-1-P-transferase or GPT) catalyzes the first and committed step of N-linked glycosylation in the endoplasmic reticulum membrane, and it is the target of the natural product tunicamycin. Tunicamycin has potent antibacterial activity, inhibiting the bacterial cell wall synthesis enzyme MraY, but its usefulness as an antibiotic is limited by off-target inhibition of human GPT. Our understanding of how tunicamycin inhibits N-linked glycosylation and efforts to selectively target MraY are hampered by a lack of structural information. Here we present crystal structures of human GPT in complex with tunicamycin. In conclusion, structural and functional analyses reveal the difference between GPT and MraY in their mechanisms of inhibition by tunicamycin. Here, we demonstrate that this difference could be exploited to design MraY-specific inhibitors as potential antibiotics.
59 BASIC BIOLOGICAL SCIENCES↗
Electron-ion plasma modification of Al-based alloys
The paper reports on the study where we analyzed the surface structure and strength properties of coated Al alloys modified by electron-ion plasma treatment. The Al alloys were deposited with a thin (≈0.5 μm) TiCu film coating (TiCu-Al system) and with a hard TiCuN coating (TiCuN–AlSi system) on a TRIO vacuum setup in the plasma of low-pressure arc discharges. The temperature fields and phase transformations in the film–substrate system were estimated by numerical simulation in a wide range of electron energy densities (5–30 J/cm{sup 2}) and pulse durations (50–200 μs). The calculations allowed us to determine the threshold energy density and pulse duration at which the surface structure of the irradiated Al-based systems is transformed in a single-phase state (solid or liquid) and in a two-phase state (solid plus liquid). The elemental composition, defect structure, phase state, and lattice state in the modified surface layers were examined by optical, scanning, and transmission electron microscopy, and by X-ray diffraction analysis. The mechanical characteristics of the modified layers were studied by measuring the hardness and Young’s modulus. The tribological properties of the modified layers were analyzed by measuring the wear resistance and friction coefficient. It is shown that melting and subsequent high-rate crystallization of the TiCu–Al system makes possible a multiphase Al-based surface structure with the following characteristics: crystallite size ranging within micrometer, microhardness of more than 3 times that in the specimen bulk, and wear resistance ≈1.8 times higher compared to the initial material. Electron beam irradiation of the TiCuN–AlSi system allows fusion of the coating into the substrate, thus increasing the wear resistance of the material ≈2.2 times at a surface hardness of ∼14 GPa.
36 MATERIALS SCIENCE↗