Twofold Sites Research Articles

Consequences of asymmetric mutational pressure for the dynamic of linear B-cell epitopes repertoire of influenza a virus neuraminidase rearrangement

Full-length nucleotide sequences of avian influenza A virus neuraminidase coding region (20,631 sequences) were analyzed and compared with those isolated from viruses infecting human and swine (63,750 sequences). If in fourfold degenerate sites there is asymmetric A-bias that may be more or less asymmetric depending on the type of neuraminidase and the host, than in twofold degenerate sites from third codon positions there is a strong asymmetric U-bias in coding regions of N4, N5, and N8 isolated from viruses infecting birds, as well as in those of N1 and N2 isolated from viruses infecting human, swine, and birds, while in coding regions of N9 isolated from birds, there is surprisingly strong C-bias, and in sequences of N3, N6, and N7 the usage of C is quite close to the level of U. Revealed stabilization of both U and C in twofold degenerate sites is the evidence of frequent changes in mutational pressure direction. Asymmetric mutational pressure was one of the sources of amino acid replacements that resulted in an equal percentage of sites with appeared and disappeared linear B-cell epitopes in N1, N2, N4, and N5 (33.62–35.33% vs. 32.41–36.45%, respectively), and controlled by the immune pressure it resulted in a stronger tendency to disappear for B-cell epitopes of N3, N6, N7, N8, and N9 of avian viruses (8.74–28.77% vs. 28.96–38.89%). The lack of correlation between nucleotide usages in fourfold and twofold degenerate sites for three nucleotides, except U, is a strong evidence of mutational pressure theory.

Cellular and Structural Characterization of VP1 and VP2 Knockout Mutants of AAV3B Serotype and Implications for AAV Manufacturing.

AAV virion biology is still lacking a complete understanding of the role that the various structural subunits (VP1, 2, and 3) play in virus assembly, infectivity, and therapeutic delivery for clinical indications. In this study, we focus on the less studied adeno-associated virus AAV3B and generate a collection of AAV plasmid substrates that assemble virion particles deficient specifically in VP1, VP2, or VP1 and 2 structural subunits. Using a collection of biological and structural assays, we observed that virions devoid of VP1, VP2, or VP1 and 2 efficiently assembled virion particles, indistinguishable by cryoelectron microscopy (cryo-EM) from that of wild type (WT), but unique in virion transduction (WT > VP2 > VP1 > VP1 and 2 mutants). We also observed that the missing structural subunit was mostly compensated by additional VP3 protomers in the formed virion particle. Using cryo-EM analysis, virions fell into three classes, namely full, empty, and partially filled, based on comparison of density values within the capsid. Further, we characterize virions described as "broken" or "disassembled" particles, and provide structural information that supports the particle dissolution occurring through the two-fold symmetry sites. Finally, we highlight the unique value of employing cryo-EM as an essential tool for release criteria with respect to AAV manufacturing.

Ab initio investigation of the role of the d-states on the adsorption and activation properties of CO2 on 3d, 4d, and 5d transition-metal clusters.

We report a theoretical investigation of the adsorption and activation properties of CO2 on eight-atom 3d, 4d, and 5d transition-metal (TM) clusters based on density functional theory calculations. From our results and analyses, in the lowest energy configurations, CO2 binds via a chemisorption mechanism on Fe, Co, Ni, Ru, Rh, Pd, Os, Ir, and Pt (adsorption energy from -0.49eV on Pt up to -1.40eV on Os), where CO2 breaks its linearity and adopts an angular configuration due to the charge transfer from the clusters toward the C atom in the adsorbed CO2. In contrast, it binds via physisorption on Cu, Ag, and Au and maintains its linearity due to a negligible charge transfer toward CO2 and has a small adsorption energy (from -0.17eV on Cu up to -0.18eV on Ag). There is an energetic preference for twofold bridge TM sites, which favors binding of C with two TM atoms, which enhances the charge transfer ten times than on the top TM sites (onefold). We identified that the strength of the CO2-TM8 interaction increases when the energy values of the highest occupied molecular orbital (HOMO) of the TM8 are closer to the energy values of the lowest unoccupied molecular orbital of CO2, which contributes to maximize the charge transfer toward the molecule. Beyond the energy position of the HOMO states, the delocalization of 5d orbitals plays an important role in the adsorption strength in TM, especially for the iron group, e.g., the adsorption energies are -1.08eV (Fe, 3d), -1.19eV (Ru, 4d), and -1.40eV (Os, 5d).

Selection for Cheaper Amino Acids Drives Nucleotide Usage at the Start of Translation in Eukaryotic Genes

Coding regions have complex interactions among multiple selective forces, which are manifested as biases in nucleotide composition. Previous studies have revealed a decreasing GC gradient from the 5′-end to 3′-end of coding regions in various organisms. We confirmed that this gradient is universal in eukaryotic genes, but the decrease only starts from the ∼ 25th codon. This trend is mostly found in nonsynonymous (ns) sites at which the GC gradient is universal across the eukaryotic genome. Increased GC contents at ns sites result in cheaper amino acids, indicating a universal selection for energy efficiency toward the N-termini of encoded proteins. Within a genome, the decreasing GC gradient is intensified from lowly to highly expressed genes (more and more protein products), further supporting this hypothesis. This reveals a conserved selective constraint for cheaper amino acids at the translation start that drives the increased GC contents at ns sites. Elevated GC contents can facilitate transcription but result in a more stable local secondary structure around the start codon and subsequently impede translation initiation. Conversely, the GC gradients at four-fold and two-fold synonymous sites vary across species. They could decrease or increase, suggesting different constraints acting at the GC contents of different codon sites in different species. This study reveals that the overall GC contents at the translation start are consequences of complex interactions among several major biological processes that shape the nucleotide sequences, especially efficient energy usage.

Modeling single-atom reactivity

Surface Chemistry Noble metals often perform best for demanding reactions such as oxygen reduction, an effect often explained by the position of their d-band. One way to minimize the cost of noble metals is to disperse them as single atoms. To model the reactivity of supported single atoms, Hulva et al. evaporated different transition metals such as nickel, silver, and iridium on an Fe3O4(001) support. Single atoms adsorbed in the same twofold site between underlying rows of surface iron atoms. In studies of CO adsorption as a proxy for reactivity, the d-band was strongly affected by the charge transfer to the support and CO-induced structural changes. These effects can weaken the adsorption energy compared with the expected values based on electronic structure alone. Science , this issue p. [375][1] [1]: /lookup/doi/10.1126/science.abe5757

Unraveling CO adsorption on model single-atom catalysts.

Understanding how the local environment of a "single-atom" catalyst affects stability and reactivity remains a challenge. We present an in-depth study of copper1, silver1, gold1, nickel1, palladium1, platinum1, rhodium1, and iridium1 species on Fe3O4(001), a model support in which all metals occupy the same twofold-coordinated adsorption site upon deposition at room temperature. Surface science techniques revealed that CO adsorption strength at single metal sites differs from the respective metal surfaces and supported clusters. Charge transfer into the support modifies the d-states of the metal atom and the strength of the metal-CO bond. These effects could strengthen the bond (as for Ag1-CO) or weaken it (as for Ni1-CO), but CO-induced structural distortions reduce adsorption energies from those expected on the basis of electronic structure alone. The extent of the relaxations depends on the local geometry and could be predicted by analogy to coordination chemistry.

Adsorption and diffusion of sulfur on the (111), (100), (110), and (211) surfaces of FCC metals: Density functional theory calculations.

We have studied the adsorption and diffusion of sulfur at the low-coverage regime of 0.25 ML on the (111), (100), (110), and (211) surfaces of Ni, Cu, Rh, Pd, Ag, Ir, Pt, and Au using density functional theory calculations. Sulfur adsorbed preferentially on three-fold or four-fold high-coordination sites over most of the studied surfaces. On the Ir(110), Pt(110), and Au(110) surfaces, sulfur is more stable on the two-fold sites. Calculations of the minimum energy diffusion pathway show that the energy barrier for the surface diffusion of sulfur depends on the orientation and nature of the metal surfaces. On the (100), sulfur shows the highest diffusion energy, ranging from 0.47 eV in Au(100) to 1.22 eV in Pd(100). In the (110) surface, the diffusion of sulfur is along the channel for Ni, Cu, Rh, Pd, and Ag, and across the channel for Ir, Pt, and Au. In the case of the (211) surfaces, the diffusion is preferentially along the terrace or step-edge sites. Our work provides data for the adsorption of sulfur on many surfaces not previously reported. The present work is a reference point for future computational studies of sulfur and sulfur-containing molecules absorbed on face center cubic metal surfaces.

Crystal structure of a silver-, cobalt- and iron-based phosphate with an alluaudite-like structure: Ag1.655Co1.64Fe1.36(PO4)3.

The new silver-, cobalt- and iron-based phosphate, silver cobalt iron tris(ortho-phosphate), Ag1.655Co1.64Fe1.36(PO4)3, was synthesized by solid-state reactions. Its structure is isotypic to that of Na2Co2Fe(PO4)3, and belongs to the alluaudite family, with a partial cationic disorder, the AgI atoms being located on an inversion centre and twofold rotation axis sites (Wyckoff positions 4a and 4e), with partial occupancies of 0.885 (2) and 0.7688 (19), respectively. One of the two P atoms in the asymmetric unit completely fills one 4e site while the Co and Fe atoms fill another 4e site, with partial occupancies of 0.86 (5) and 0.14 (5), respectively. The remaining Co2+ and Fe3+ cations are distributed on a general position, 8f, in a 0.39 (4):0.61 (4) ratio. All O atoms and the other P atoms are in general positions. The structure is built up from zigzag chains of edge-sharing [MO6] (M = Fe/Co) octa-hedra stacked parallel to [101]. These chains are linked together through PO4 tetra-hedra, forming polyhedral sheets perpendicular to [010]. The resulting framework displays two types of channels running along [001], in which the AgI atoms (coordination number eight) are located.

Role of valence states of adsorbates in inelastic electron tunneling spectroscopy: A study of nitric oxide on Cu(110) and Cu(001)

We studied nitric oxide (NO) molecules on Cu(110) and Cu(001) surfaces with low-temperature scanning tunneling microscopy (STM) and density functional theory (DFT). NO monomers on the surfaces are characterized by STM images reflecting $2{\ensuremath{\pi}}^{*}$ resonance states located at the Fermi level. NO is bonded vertically to the twofold short-bridge site on Cu(110) and to the fourfold hollow site on Cu(001). When NO molecules form dimers on the surfaces, the valence orbitals are modified due to the covalent bonding. We measured inelastic electron tunneling spectroscopy (IETS) for both NO monomers and dimers on the two surfaces, and detected characteristic structures assigned to frustrated rotation and translation modes by density functional theory simulations. Considering symmetries of valence orbitals and vibrational modes, we explain the intensity of the observed IETS signals in a qualitative manner.

Nature of gap states in GeSbTe phase change memory materials

We have calculated the states associated with valence alternation pair defects in a Te-rich amorphous GeTe random network. Two-fold Te sites and four-fold Ge sites are found to introduce states that are resonant with the valence and conduction bands, respectively. The system has a band gap, but these defect states are in the same energy range as those found by modulated photocurrent experiments. The absence of electron spin resonance signals is still not explained.

First Principles Ab Initio Study of CO2 Adsorption on the Kaolinite (001) Surface

AbstractThe capture and storage of carbon dioxide (CO2) have considerable potential for mitigating climate change. Adsorption is one of the most popular methods for the storage of CO2. The adsorption of CO2 molecules on the hydroxylated (001) surface of kaolinite was investigated using density-functional theory within the generalized gradient approximation and a supercell approach. The coverage dependence of the adsorption structures and energetics was studied systematically for a wide range of coverage, Θ [from 0.11 to 1.0 monolayers (ML)], and adsorption sites. The CO2 was adsorbed on the two-fold bridge-x (see the text for a definition) and the one-fold top-x sites in the bent, recumbent configuration, and on the three-fold hollow-z, two-fold bridge-z site, and the one-fold top-z sites in the vertical configuration. The surface-adsorbed binding site of CO2 was strongest at the bridge-x site and weakest at the top-z site. The adsorption energy increased with coverage, thus indicating the greater stability of surface adsorption and a tendency to form CO2 islands (clusters) with increasing coverage. The other properties of the CO2/kaolinite (001) system, including the different charge distribution, the lattice relaxation, and the electronic density of states, were also studied and are discussed in detail.

Adsorption and diffusion of Pb(II) on the kaolinite(001) surface: A density-functional theory study

The adsorption and diffusion of Pb(II) atom on the hydroxylated (001) surface of kaolinite were investigated using density-functional theory within the generalized gradient approximation and a supercell approach. The coverage dependence of the adsorption structures and energetics was systematically studied for a wide range of coverage Θ [from 0.11 to 1.0 monolayers (ML)] and adsorption sites. The most stable among all possible adsorption sites was the two-fold bridge site followed by the one-fold top site, and the adsorption energy increased with the coverage, thus indicating the higher stability of surface adsorption and a tendency to the formation of Pb(II) islands (clusters) with increasing coverage. Moreover, the energy barrier for diffusion of Pb(II) atom between the one-fold top and the two-fold bridge adsorption sites on kaolinite(001) surface was 0.23 (0.31) eV, implying that the Pb(II) atom is prone to diffusing on kaolinite(001) surface. The other properties of the Pb(II)/kaolinite(001) system including the different charge distribution, the lattice relaxation, and the electronic density of states were also studied and discussed in detail.

Copper scandium zirconium phosphate: occupancy of theM1 andM2 sites in the temperature range 100–300 K

The title compound, with nominal formula Cu(2)ScZr(PO(4))(3), has a beige coloration and displays fast Cu(+) cation conduction at elevated temperatures. It adopts a NASICON-type structure in the space group R3c. The examined crystal was an obverse-reverse twin with approximately equal twin components. The [Sc(III)Zr(IV)(PO(4))(3)](2-) framework is composed of corner-sharing Sc/ZrO(6) octahedra and PO(4) tetrahedra. The Sc and Zr atoms are disordered on one atomic site on a crystallographic threefold axis. The P atom of the phosphate group lies on a crystallographic twofold axis. Nonframework Cu(+) cations occupy three positions. Two of the Cu(+) positions generate an approximately circular distribution around a site of 3 symmetry, referred to as the M1 site in the NASICON-type structure. The other Cu(+) position is situated close to the twofold symmetric M2 site, displaced into a position with a distorted square-based pyramidal coordination geometry. The structure has been determined at 100, 200 and 300 K. Changes in the refined site-occupancy factors of the Cu(+) positions suggest increased mobility of Cu(+) around the circular orbit close to the M1 site at room temperature, but no movement into or out of the M2 site. Free refinement of the Cu site-occupancy factors suggests that the formula of the crystal is Cu(1.92(1))ScZr(PO(4))(3), which is consistent with the low-level presence of Cu(2+) exclusively in the M2 site.

Theoretical and experimental studies of hydrogen adsorption and desorption on Ir surfaces

We report adsorption and desorption of hydrogen on planar Ir(210) and faceted Ir(210), consisting of nanoscale {311} and (110) facets, by means of temperature programmed desorption (TPD) and density functional theory (DFT) in combination with the ab initio atomistic thermodynamics approach. TPD spectra show that only one H2 peak is seen from planar Ir(210) at all coverages whereas a single H2 peak is observed at around 440 K (F1) at fractional monolayer (ML) coverage and an additional H2 peak appears at around 360 K (F2) at 1 ML coverage on faceted Ir(210), implying structure sensitivity in recombination and desorption of hydrogen on faceted Ir(210) versus planar Ir(210), but no evidence is found for size effects in recombination and desorption of hydrogen on faceted Ir(210) for average facet sizes of 5-14 nm. Calculations indicate that H prefers to bind at the two-fold short-bridge sites of the Ir surfaces. In addition, we studied the stability of the Ir surfaces in the presence of hydrogen at different H coverages through surface free energy plots as a function of the chemical potential, which is also converted to a temperature scale. Moreover, the calculations revealed the origin of the two TPD peaks of H2 from faceted Ir(210): F1 from desorption of H2 on {311} facets while F2 from desorption of H2 on (110) facets.

The Structure of Benzoquinone Chemisorbed on Pd(111): Simulation of EC-STM Images and HREELS Spectra by Density Functional Theory

Earlier studies on the chemisorption of hydroquinone (H2Q) on well-defined Pd(111) surfaces based on electrochemistry, high-resolution electron energy loss spectroscopy, and in situ scanning tunneling microscopy revealed that H2Q undergoes oxidative chemisorption to generate an adlayer of benzoquinone oriented flat, albeit with a slight tilt. Certain structural details, however, such as the actual adsorbate structure and the surface coordination site could not be unambiguously confirmed solely from the experimental measurements. Density functional theory was thus employed not only to calculate the total adsorption energies of the likely configurations but also to simulate their respective vibrational spectra. The results suggest that: (1) the flat-adsorbed quinone ring is centered on a bridge site in which the C2 axis that points along the para-oxygen atoms is rotated 30° from the [110] direction of the Pd(111) substrate; (2) the p-oxygen atoms are located above twofold sites; and (3) quinonoid ring is slightly puckered with the C–H bonds tilted away from the surface, at an angle of approximately 20°.

A blueprint for a mutationist theory of replicative strand asymmetries formation.

In the present review, we summarized current knowledge on replicative strand asymmetries in prokaryotic genomes. A cornerstone for the creation of a theory of their formation has been overviewed. According to our recent works, the probability of nonsense mutation caused by replication-associated mutational pressure is higher for genes from lagging strands than for genes from leading strands of both bacterial and archaeal genomes. Lower density of open reading frames in lagging strands can be explained by faster rates of nonsense mutations in genes situated on them. According to the asymmetries in nucleotide usage in fourfold and twofold degenerate sites, the direction of replication-associated mutational pressure for genes from lagging strands is usually the same as the direction of transcription-associated mutational pressure. It means that lagging strands should accumulate more 8-oxo-G, uracil and 5-formyl-uracil, respectively. In our opinion, consequences of cytosine deamination (C to T transitions) do not lead to the decrease of cytosine usage in genes from lagging strands because of the consequences of thymine oxidation (T to C transitions), while guanine oxidation (causing G to T transversions) makes the main contribution into the decrease of guanine usage in fourfold degenerate sites of genes from lagging strands. Nucleotide usage asymmetries and bias in density of coding regions can be found in archaeal genomes, although, the percent of “inversed” asymmetries is much higher for them than for bacterial genomes. “Homogenized” and “inversed” replicative strand asymmetries in archaeal genomes can be used as retrospective indexes for detection of OriC translocations and large inversions.

Density functional theory study of the adsorption of oxygen atoms on gold (111), (100) and (211) surfaces

The interaction of an oxygen atom with various gold surfaces was examined computationally using density functional theory. The relative binding energies for a range of possible adatom locations on each surface were obtained. The results demonstrated the relative importance of low-coordinated gold atoms to bind oxygen for a particular surface and a preference for three-fold adatom coordination over the two-fold and single-coordination sites. Pseudo-potential energy curves were obtained by following the calculated energy as a function of surface position. These general results provide a reference for the interaction of oxygen atoms with gold nanoparticles that may project faces similar to the surfaces studied here.

A CASE STUDY OF HYDRODYNAMIC AND MORPHOLOGICAL MODELING OF A RE-MIGRATING INLET

The present paper tackles morphological modeling of a rare case of a re-migrating inlet to be used as the basis of a fishery port site selection study. The Tang inlet, located on the south-eastern shores of Iran, has so far been experiencing a cyclic migration with a return period of approximately a decade. In order to grasp the essence of the morphological behavior of the inlet, a two-fold site monitoring campaign was performed, consisting of a shoreline evolution study using aerial & satellite imagery for the outside of the bay as well as a sedimentation pattern comparison based on past hydrographical survey results for the inside of the bay utilizing ArcGIS software. Subsequently, numerical modeling of the inlet comprising of nearshore wave transformation, tidal regime of the bay, one-line coastline evolution and two-dimensional sediment transport within the bay was carried out utilizing MIKE 21 package. Ebb channel switching from a westerly to an easterly orientation is deemed to occur due to self-suffocation as a result of the presence of an existing offshore rock formation, as well as the salient making potential of the rock system. On the other hand, the closure of the east-facing channel is mainly attributed to diffraction currents due to Monsoon southerly waves helped by sedimentation load from inside the bay system due to floods & ebb currents.

Hydrido-Ruthenium Cluster Complexes as Models for Reactive Surface Hydrogen Species of Ruthenium Nanoparticles. Solid-State 2H NMR and Quantum Chemical Calculations

The (2)H quadrupolar interaction is a sensitive tool for the characterization of deuterium-metal binding states. In the present study, experimental solid-state (2)H MAS NMR techniques are used in the investigations of two ruthenium clusters, D(4)Ru(4)(CO)(12) (1) and D(2)Ru(6)(CO)(18) (2), which serve as model compounds for typical two-fold, three-fold, and octahedral coordination sites on metal surfaces. By line-shape analysis of the (2)H MAS NMR measurements of sample 1, a quadrupolar coupling constant of 67 +/- 1 kHz, an asymmetry parameter of 0.67 +/- 0.1, and an isotropic chemical shift of -17.4 ppm are obtained. In addition to the neutral complex, sample 2 includes two ionic clusters, identified as anionic [DRu(6)(CO)(18)](-) (2(-)) and cationic [D(3)Ru(6)(CO)(18)](+) (2(+)). By virtue of the very weak quadrupolar interaction (<2 kHz) and the strong low-field shift (+16.8 ppm) of 2(-), it is shown that the deuteron is located in the symmetry center of the octahedron spanned by the six ruthenium atoms. For the cationic 2(+), the quadrupolar interaction is similar to that of the neutral 2. Quantum chemical DFT calculations at different model structures for these ruthenium clusters were arranged in order to help in the interpretation of the experimental results. It is shown that the (2)H nuclear quadrupolar interaction is a sensitive tool for distinguishing the binding state of the deuterons to the transition metal. Combining the data from the polynuclear complexes with the data from mononuclear complexes, a molecular ruler for quadrupolar interactions is created. This ruler now permits the solid-state NMR spectroscopic characterization of deuterium adsorbed on the surfaces of catalytically active metal nanoparticles.

1,1′-Methylenedipyridinium dichloride monohydrate

In the crystal structure of the title salt, C11H12N2 2+·2Cl−·H2O, the dication adopts a butterfly shape [dihedral angle between rings = 69.0 (1)°] with the water mol­ecule lying in the V-shaped cavity. Each O—H bond of the water molecule lies parallel to an aromatic ring and forms an O—H⋯Cl inter­action to a chloride anion. The methyl­ene C atom in the dication and the water O atoms lie on special positions of twofold site symmetry.