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At least 1,225 records · Page 68

Rn gravity as a viable alternative to dark matter: Application to stellar dynamics

The role of f(R) gravity, as well as the other modifications of standard Einstein’s gravity, is to explain the accelerated expansion, structure formation of the Universe, and some other phenomena at extragalactic scales (such as e.g. flat rotation curves of spiral galaxies) without adding unknown forms of dark energy or dark matter. In f(R) model, the Ricci scalar in the Einstein–Hilbert action is replaced by a general function of it. Its power-law form Rn is analyzed here using observed orbits of S-stars around the Galactic Center and also their computer simulations. We review the various consequences of the Rn gravity parameters (rc, the characteristic radius, i.e. the scalelength depending on the gravitating system properties; and β, the universal constant) on stellar dynamics and investigate their constraints from the observed S-star orbits. The presented results show that these observations could put reliable constraints on the parameters of Rn gravity.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Reconfigurable modified surface layers using plasma capillaries around the neutral inclusion regime

We show both theoretically and experimentally reconfigurable properties achieved by plasma inclusions placed in modified surface layers generally used to tailor the transmission and beaming properties of electromagnetic bandgap based waveguiding structures. A proper parametrization of the plasma capillaries allows to reach the neutral inclusion regime, where the inclusions appear to be electromagnetically transparent, letting the surface mode characteristics unaltered. Varying the electron density of the plasma inclusions provoques small perturbations around this peculiar regime, and we observe significant modifications of the transmission/beaming properties. This offers a way to dynamically select the enhanced transmission frequency or to modify the radiation pattern of the structure, depending on whether the modified surface layer is placed at the entrance/exit of the waveguide.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Structural analysis of the endogenous glycoallergen Hev b 2 (endo-β-1,3-glucanase) from Hevea brasiliensis and its recognition by human basophils

This study describes the three-dimensional structure of the endogenous glycosylated allergen Hev b 2 (endo-β-1,3-glucanase), which exhibits three post-translational modifications that form a patch on the surface of the molecule that is proposed to be an allergenic IgE epitope. Endogenous glycosylated Hev b 2 (endo-β-1,3-glucanase) from Hevea brasiliensis is an important latex allergen that is recognized by IgE antibodies from patients who suffer from latex allergy. The carbohydrate moieties of Hev b 2 constitute a potentially important IgE-binding epitope that could be responsible for its cross-reactivity. Here, the structure of the endogenous isoform II of Hev b 2 that exhibits three post-translational modifications, including an N-terminal pyroglutamate and two glycosylation sites at Asn27 and at Asn314, is reported from two crystal polymorphs. These modifications form a patch on the surface of the molecule that is proposed to be one of the binding sites for IgE. A structure is also proposed for the most important N-glycan present in this protein as determined by digestion with specific enzymes. To analyze the role of the carbohydrate moieties in IgE antibody binding and in human basophil activation, the glycoallergen was enzymatically deglycosylated and evaluated. Time-lapse automated video microscopy of basophils stimulated with glycosylated Hev b 2 revealed basophil activation and degranulation. Immunological studies suggested that carbohydrates on Hev b 2 represent an allergenic IgE epitope. In addition, a dimer was found in each asymmetric unit that may reflect a regulatory mechanism of this plant defence protein.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Towards functionalized lignin and its derivatives for high-value material applications

In pursuit of low-carbon development, the production of diverse functional materials from renewable resources, especially lignocellulosic biomass, is of vital importance. Lignin is a major component of lignocellulose, and it is nature's only true high-volume aromatic polymer, which has the advantages of biodegradability, biocompatibility, and low acquisition cost. After modification by a variety of physicochemical strategies, it can be applied as an alternative to basic industrial materials, including polyurethanes, phenolic, and epoxy resins, which stands comparably to conventional synthetic polymers in terms of both performance and reduced cost. To further unlock the potential of lignin, an alluring opportunity is the exploitation of lignin for high-value materials, especially nanomaterials, that find extensive applications in energy and environment areas. This review provides a systematic summary and perspective of research that has been devoted to lignin transformation to high-value materials, ranging from industrially well-established engineering materials to the recently emerged nanomaterials that were used for energy and environment applications. Latest cutting-edge innovations on lignin modification, controlled depolymerization, and assembly during the last five years are summarized. Structure-function relationships of lignin materials in terms of their specific applications are analyzed. Furthermore, challenges and future opportunities for lignin conversion to high-value materials are also provided. We wish this review will stimulate further advances in lignin based high-value materials, and promote “waste” into “wealth”.

36 MATERIALS SCIENCE↗

Insights into the Specificity of Lysine Acetyltransferases

Reversible lysine acetylation by protein acetyltransferases is a conserved regulatory mechanism that controls diverse cellular pathways. Gcn5-related N-acetyltransferases (GNATs), named after their founding member, are found in all domains of life. GNATs are known for their role as histone acetyltransferases, but non-histone bacterial protein acetytransferases have been identified. Only structures of GNAT complexes with short histone peptide substrates are available in databases. Given the biological importance of this modification and the abundance of lysine in polypeptides, how specificity is attained for larger protein substrates is central to understanding acetyl-lysine-regulated networks. In this paper, we report the structure of a GNAT in complex with a globular protein substrate solved to 1.9 Å. GNAT binds the protein substrate with extensive surface interactions distinct from those reported for GNAT-peptide complexes. Finally, our data reveal determinants needed for the recognition of a protein substrate and provide insight into the specificity of GNATs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Crystal structures and mutagenesis of PPP-family ser/thr protein phosphatases elucidate the selectivity of cantharidin and novel norcantharidin-based inhibitors of PP5C

Cantharidin is a natural toxin and an active constituent in a traditional Chinese medicine used to treat tumors. Cantharidin acts as a semi-selective inhibitor of PPP-family ser/thr protein phosphatases. Despite sharing a common catalytic mechanism and marked structural similarity with PP1C, PP2AC and PP5C, human PP4C was found to be insensitive to the inhibitory activity of cantharidin. To explore the molecular basis for this selectivity, in this work we synthesized and tested novel C5/C6-derivatives designed from quantum-based modeling of the interactions revealed in the co-crystal structures of PP5C in complex with cantharidin. Structure–activity relationship studies and analysis of high-resolution (1.25 Å) PP5C-inhibitor co-crystal structures reveal close contacts between the inhibitor bridgehead oxygen and both a catalytic metal ion and a non-catalytic phenylalanine residue, the latter of which is substituted by tryptophan in PP4C. Quantum chemistry calculations predicted that steric clashes with the bulkier tryptophan side chain in PP4C would force all cantharidin-based inhibitors into an unfavorable binding mode, disrupting the strong coordination of active site metal ions observed in the PP5C co-crystal structures, thereby rendering PP4C insensitive to the inhibitors. This prediction was confirmed by inhibition studies employing native human PP4C. Mutation of PP5C (F446W) and PP1C (F257W), to mimic the PP4C active site, resulted in markedly suppressed sensitivity to cantharidin. These observations provide insight into the structural basis for the natural selectivity of cantharidin and provide an avenue for PP4C deselection. The novel crystal structures also provide insight into interactions that provide increased selectivity of the C5/C6 modifications for PP5C versus other PPP-family phosphatases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

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↗

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↗