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At least 595 records · Page 33

Structure-function analysis of ribonucleotide bypass by B family DNA replicases

Ribonucleotides are frequently incorporated into DNA during replication, they are normally removed, and failure to remove them results in replication stress. This stress correlates with DNA polymerase (Pol) stalling during bypass of ribonucleotides in DNA templates. Here we demonstrate that stalling by yeast replicative Pols δ and ε increases as the number of consecutive template ribonucleotides increases from one to four. The homologous bacteriophage RB69 Pol also stalls during ribonucleotide bypass, with a pattern most similar to that of Pol ε. Crystal structures of an exonuclease-deficient variant of RB69 Pol corresponding to multiple steps in single ribonucleotide bypass reveal that increased stalling is associated with displacement of Tyr391 and an unpreferred C2´-endo conformation for the ribose. Even less efficient bypass of two consecutive ribonucleotides in DNA correlates with similar movements of Tyr391 and displacement of one of the ribonucleotides along with the primer-strand DNA backbone. These structure–function studies have implications for cellular signaling by ribonucleotides, and they may be relevant to replication stress in cells defective in ribonucleotide excision repair, including humans suffering from autoimmune disease associated with RNase H2 defects.

Clausen, Anders R.↗

Exposing structural variations in SARS-CoV-2 evolution

The mutation of SARS-CoV-2 influences viral function as residue replacements affect both physiochemical properties and folding conformations. Although a large amount of data on SARS-CoV-2 is available, the investigation of how viral functions change in response to mutations is hampered by a lack of effective structural analysis. Here, we exploit the advances of protein structure fingerprint technology to study the folding conformational changes induced by mutations. With integration of both protein sequences and folding conformations, the structures are aligned for SARS-CoV to SARS-CoV-2, including Alpha variant (lineage B.1.1.7) and Delta variant (lineage B.1.617.2). The results showed that the virus evolution with change in mutational positions and physicochemical properties increased the affinity between spike protein and ACE2, which plays a critical role in coronavirus entry into human cells. Additionally, these structural variations impact vaccine effectiveness and drug function over the course of SARS-CoV-2 evolution. The analysis of structural variations revealed how the coronavirus has gradually evolved in both structure and function and how the SARS-CoV-2 variants have contributed to more severe acute disease worldwide.

59 BASIC BIOLOGICAL SCIENCES↗

Crystal structure, mutational analysis and RNA-dependent ATPase activity of the yeast DEAD-box pre-mRNA splicing factor Prp28

Yeast Prp28 is a DEAD-box pre-mRNA splicing factor implicated in displacing U1 snRNP from the 5' splice site. Here we report that the 588-aa Prp28 protein consists of a trypsin-sensitive 126-aa N-terminal segment (of which aa 1–89 are dispensable for Prp28 function in vivo ) fused to a trypsin-resistant C-terminal catalytic domain. Purified recombinant Prp28 and Prp28-(127–588) have an intrinsic RNA-dependent ATPase activity, albeit with a low turnover number. The crystal structure of Prp28-(127–588) comprises two RecA-like domains splayed widely apart. AMPPNP•Mg 2+ is engaged by the proximal domain, with proper and specific contacts from Phe194 and Gln201 (Q motif) to the adenine nucleobase. The triphosphate moiety of AMPPNP•Mg 2+ is not poised for catalysis in the open domain conformation. Guided by the Prp28•AMPPNP structure, and that of the Drosophila Vasa•AMPPNP•Mg 2+ •RNA complex, we targeted 20 positions in Prp28 for alanine scanning. ATP-site components Asp341 and Glu342 (motif II) and Arg527 and Arg530 (motif VI) and RNA-site constituent Arg476 (motif Va) are essential for Prp28 activity in vivo . Synthetic lethality of double-alanine mutations highlighted functionally redundant contacts in the ATP-binding (Phe194-Gln201, Gln201-Asp502) and RNA-binding (Arg264-Arg320) sites. As a result, overexpression of defective ATP-site mutants, but not defective RNA-site mutants, elicited severe dominant-negative growth defects.

59 BASIC BIOLOGICAL SCIENCES↗

Structure-function analysis of the FCRL5–IgG1 Fc complex reveals an unappreciated pathway for B cell modulation by Fc-attenuated IgG

The Fc region of therapeutic IgG antibodies is often engineered to remove or “silence” Fc effector functions, but it remains unclear whether these mutations eliminate all Fc-mediated effector activity. Human Fc receptor-like 5 (FCRL5/FcRH5) is a low-affinity IgG Fc receptor expressed on B cells and is an actively pursued antibody target in multiple myeloma. Here, we show that common Fc function-silencing mutations do not impair FCRL5-mediated activity and therefore attenuate, rather than eliminate, Fc effector function. The crystal structure of the FCRL5-IgG1 Fc complex, solved at 3.4 Å resolution, revealed that FCRL5 binds IgG1 Fc in a 1:1 complex through a binding mode distinct from that of classical Fcγ receptors, explaining why mutations that attenuate Fc effector function spare FCRL5 binding. Fc-engineered antibodies that selectively engage FCRL5 inhibited B cell receptor-induced Ca 2+ flux in FCRL5-expressing B cells. These findings demonstrate that Fc-attenuated therapeutic IgG retains the ability to engage FCRL5, identifying an unappreciated pathway for B cell modulation.

Herpers, Bart M. [Department of Biomedical Enginee↗

[Ni(cod) 2 ][Al(OR F ) 4 ], a Source for Naked Nickel(I) Chemistry

Abstract The straightforward synthesis of the cationic, purely organometallic Ni I salt [Ni(cod) 2 ] + [Al(OR F ) 4 ] − was realized through a reaction between [Ni(cod) 2 ] and Ag[Al(OR F ) 4 ] (cod=1,5‐cyclooctadiene). Crystal‐structure analysis and EPR, XANES, and cyclic voltammetry studies confirmed the presence of a homoleptic Ni I olefin complex. Weak interactions between the metal center, the ligands, and the anion provide a good starting material for further cationic Ni I complexes.

Schwab, Miriam M.↗

Structure, Morphology, and Assembly Behavior of Kafirin

Prolamins from grains have attracted intensive attention in recent years due to their potential in satisfying the demand for environmentally friendly (biodegradable), abundantly available (sustainable), and cost-effective biomaterials. However, for kafirin, the prolamin from sorghum, its composition, structure, morphology, and self-assembly behaviors have not been fully characterized. In this paper, kafirin was extracted from the whole sorghum grain and found to contain 68, 14, 6, and 12% of α-, β-, and γ-fractions and cross-linked kafirin, respectively. Freeze-dried kafirin contained ~49% α-helix in the solid state. When dissolved in 65% (v/v) isopropanol, 60% (v/v) tert-butanol, and 85% (v/v) ethanol aqueous solvents, the relative α-helix content in kafirin increased with the decrease of solvent polarity. Structural analysis using small-angle X-ray scattering (SAXS) indicated that kafirin (2 mg/mL) took stretched and extended conformations with dimensions of 118 × 15 × 15 and 100 × 11 × 11 Å in 60% tert-butanol and 65% isopropanol, respectively. More elongated conformation of individual kafirin with high-order assembly was observed in 85% ethanol. Protein aggregation occurred as protein concentration increased in its good solvent. The morphology of kafirin assemblies captured by atomic force microscopy (AFM) revealed that kafirin protein took uniform particle morphology at low concentration, and disk-like or rod-like structures resulting from solvent evaporation induced particle interactions emerged at high concentrations. These results suggest that both protein concentration and solvent polarity can effectively regulate kafirin assemblies from thick rod-like to slim rod-like structures, a convenient way to tune the fibrillation of prolamin-based biomaterials.

60 APPLIED LIFE SCIENCES↗

Structure-Based Analysis of the Interaction between the Simian Virus 40 T-Antigen Origin Binding Domain and Single-Stranded DNA

The origin-binding domain (OBD) of simian virus 40 (SV40) large T-antigen (T-Ag) is essential for many of T-Ag's interactions with DNA. Nevertheless, many important issues related to DNA binding, for example, how single-stranded DNA (ssDNA) transits along the T-Ag OBD, have yet to be established. Therefore, X-ray crystallography was used to determine the costructure of the T-Ag OBD bound to DNA substrates such as the single-stranded region of a forked oligonucleotide. A second structure of the T-Ag OBD crystallized in the presence of poly(dT){sub 12} is also reported. To test the conclusions derived from these structures, residues identified as being involved in binding to ssDNA by crystallography or by an earlier nuclear magnetic resonance study were mutated, and their binding to DNA was characterized via fluorescence anisotropy. In addition, these mutations were introduced into full-length T-Ag, and these mutants were tested for their ability to support replication. When considered in terms of additional homology-based sequence alignments, our studies refine our understanding of how the T-Ag OBDs encoded by the polyomavirus family interact with ssDNA, a critical step during the initiation of DNA replication.

59 BASIC BIOLOGICAL SCIENCES↗

Formic Acid Electrooxidation on Pt or Pd Monolayer on Transition-Metal Single Crystals: A First-Principles Structure Sensitivity Analysis

Here, we present a density functional theory analysis of trends for the electrooxidation of formic acid (FAO) on a single Pt or Pd monolayer supported on the close-packed (111) facet of transition metals (Pt*/M or Pd*/M): Au, Ag, Cu, Pt, Pd, Ir, and Rh, the close-packed (0001) facet of Os, Ru, and Re, and the open (100) facet of Au, Ag, Pt, Pd, Ir, and Rh. We show that the deposition of Pt or Pd pseudomorphic monolayers on these single crystals modifies the electronic structure of the Pt or Pd monolayer. Specifically, we found a direct correlation between the d-band center of the Pt and Pd monolayer and the free energy of adsorbed CO*, the latter being a reactivity descriptor for FAO. Together with the free energy of adsorbed OH* as a second reactivity descriptor, we depict the thermochemistry of the reaction network as phase diagrams showing calculated free energies across regions of rate-determining steps. We found that FAO is structure-sensitive on most surfaces studied. Pt*/Au(111) is predicted to be the most active among all Pt*/M(111/0001) surfaces studied, despite binding CO*, the strongest among the close-packed facets. This is the case because of its superiority in activating water to OH*, thus removing CO* at lower potentials than other surfaces. On similar grounds, Pt*/Pd(100), Pd*/Re(0001), Pd*/Au(111), Pd*/Ag(111), and Pd*/Pt(111) are predicted to show higher FAO activity than the corresponding monometallic Pt and Pd surfaces.

(100) facets↗

Structural insights into the metabolism of 2-chlorodibenzofuran by an evolved biphenyl dioxygenase

The biphenyl dioxygenase of Burkholderia xenovorans LB400 (BphAE{sub LB400}) is a Rieske-type oxygenase that catalyzes the stereospecific oxygenation of many heterocyclic aromatics including dibenzofuran. In a previous work, we evolved BphAE{sub LB400} and obtained BphAE{sub RR41}. This variant metabolizes dibenzofuran and 2-chlorodibenzofuran more efficiently than BphAE{sub LB400}. However, the regiospecificity of BphAE{sub RR41} toward these substrates differs. Dibenzofuran is metabolized principally through a lateral dioxygenation whereas 2-chlorodibenzofuran is metabolized principally through an angular dioxygenation. In order to explain this difference, we examined the crystal structures of both substrate-bound forms of BphAE{sub RR41} obtained under anaerobic conditions. This structure analysis, in combination with biochemical data for a Ser283Gly mutant provided evidences that the substrate is compelled to move after oxygen-binding in BphAE{sub RR41}:dibenzofuran. In BphAE{sub RR41}:2-chlorodibenzofuran, the chlorine atom is close to the side chain of Ser283. This contact is missing in the BphAE{sub RR41}:dibenzofuran, and strong enough in the BphAE{sub RR41}:2-chlorodibenzofuran to help prevent substrate movement during the catalytic reaction.

59 BASIC BIOLOGICAL SCIENCES↗

Preparation and reactivity of macrocyclic rhodium(III) alkyl complexes

We found that the macrocyclic rhodium(II) complexes LRh(H 2 O) 2+ (L = L 1 = cyclam and L 2 = meso-Me-6-cyclam) react with alkyl hydroperoxides RC(CH 3 ) 2 OOH to generate the corresponding rhodium(III) alkyls L(H 2 O)RhR 2+ (R = CH 3 , C 2 H 5 , PhCH 2 ). Methyl and benzyl complexes can also be prepared by bimolecular group transfer from alkyl cobaloximes (dmgH) 2 (H 2 O) CoR and (dmgBF 2 ) 2 (H 2 O) CoR (R = CH 3 , PhCH 2 ) to LRh(H 2 O) 2+ . Moreover, the new complexes were characterized by solution NMR and by crystal structure analysis. They exhibit great stability in aqueous solution at room temperature, but undergo efficient Rh-C bond cleavage upon photolysis.

36 MATERIALS SCIENCE↗

Flow-induced vibration analysis of a helical coil steam generator experiment using large eddy simulation

This paper describes a numerical study of flow-induced vibration in a helical coil steam generator experiment conducted at Argonne National Laboratory in the 1980s. In the experiment, a half-scale sector model of a steam generator helical coil tube bank was subjected to still and flowing air and water, and the vibrational characteristics were recorded. The research detailed in this document utilizes the multi-physics simulation toolkit SHARP developed at Argonne National Laboratory, in cooperation with Lawrence Livermore National Laboratory, to simulate the experiment. SHARP uses the spectral element code Nek5000 for fluid dynamics analysis and the finite element code DIABLO for structural analysis. The flow around the coil tubes is modeled in Nek5000 by using a large eddy simulation turbulence model. Transient pressure data on the tube surfaces is sampled and transferred to DIABLO for the structural simulation. The structural response is simulated in DIABLO via an implicit time-marching algorithm and a combination of continuum elements and structural shells. Tube vibration data (acceleration and frequency) are sampled and compared with the experimental data. Currently, only one-way coupling is used, which means that pressure loads from the fluid simulation are transferred to the structural simulation but the resulting structural displacements are not fed back to the fluid simulation

CFD↗

Molten salt flux synthesis and crystal structure of a new open-framework uranyl phosphate Cs{sub 3}(UO{sub 2}){sub 2}(PO{sub 4})O{sub 2}: Spectroscopic characterization and cationic mobility studies

The reaction of triuranyl diphosphate tetrahydrate precursor (UO{sub 2}){sub 3}(PO{sub 4}){sub 2}(H{sub 2}O){sub 4} with a CsI flux at 750 °C yields a yellow single crystals of new compound Cs{sub 3}(UO{sub 2}){sub 2}(PO{sub 4})O{sub 2}. The crystal structure (monoclinic, space group C2/c, a=13.6261 (13) Å, b=8.1081(8) Å, c=12.3983(12) Å, β=114.61(12)°, V=1245.41(20) Å{sup 3} with Z=4) has been solved using direct methods and Fourier difference techniques. A full-matrix least-squares refinement on the basis of F{sup 2} yielded R1=0.028 and wR2=0.071 for 79 parameters and 1352 independent reflections with I≥2σ(I) collected on a BRUKER AXS diffractometer with MoKα radiation and a charge-coupled device detector. The crystal structure is built by two independent uranium atoms in square bipyramidal coordination, connected by two opposite corners to form infinite chains {sup 1}{sub ∞}[UO{sub 5}] and by one phosphorus atom in a tetrahedral environment PO{sub 4}. The two last entities {sup 1}{sub ∞}[UO{sub 5}] and PO{sub 4} are linked by sharing corners to form a three-dimensional structure presenting different types of channels occupied by Cs{sup +} alkaline cations. Their mobility within the tunnels were studied between 280 and 800 °C and compared with other tunneled uranyl minerals. The infrared spectrum shows a good agreement with the values inferred from the single crystal structure analysis of uranyl phosphate compound. - Graphical abstract: Arrhenius plot of the electrical conductivity of tunneled compounds Cs{sub 3}U{sub 2}PO{sub 10} and CsU{sub 2}Nb{sub 2}O{sub 11.5}. Highlights: ► The reaction of (UO{sub 2}){sub 3}(PO{sub 4}){sub 2}(H{sub 2}O){sub 4} in excess of molten CsI leads to single-crystals of new tunneled compound Cs{sub 3}(UO{sub 2}){sub 2}(PO{sub 4})O{sub 2}. ► Ionic conductivity measurements and crystal structure analysis indicate a strong connection of the Cs{sup +} cations to the tunnels. ► A low symmetry in Cs{sub 3}(UO{sub 2}){sub 2}(PO{sub 4})O{sub 2} is the cause of IR activation and splitting of the bands in the IR spectrum.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structure-Function Analysis of Vaccinia Virus H7 Protein Reveals a Novel Phosphoinositide Binding Fold Essential for Poxvirus Replication

Phosphoinositides and phosphoinositide binding proteins play a critical role in membrane and protein trafficking in eukaryotes. Their critical role in replication of cytoplasmic viruses has just begun to be understood. Poxviruses, a family of large cytoplasmic DNA viruses, rely on the intracellular membranes to develop their envelope, and poxvirus morphogenesis requires enzymes from the cellular phosphoinositide metabolic pathway. However, the role of phosphoinositides in poxvirus replication remains unclear, and no poxvirus proteins show any homology to eukaryotic phosphoinositide binding domains. Recently, a group of poxvirus proteins, termed viral membrane assembly proteins (VMAPs), were identified as essential for poxvirus membrane biogenesis. A key component of VMAPs is the H7 protein. Here we report the crystal structure of the H7 protein from vaccinia virus. The H7 structure displays a novel fold comprised of seven α-helices and a highly curved three-stranded antiparallel β-sheet. We identified a phosphoinositide binding site in H7, comprised of basic residues on a surface patch and the flexible C-terminal tail. These residues were found to be essential for viral replication and for binding of H7 to phosphatidylinositol-3-phosphate (PI3P) and phosphatidylinositol-4-phosphate (PI4P). Our studies suggest that phosphoinositide binding by H7 plays an essential role in poxvirus membrane biogenesis.

59 BASIC BIOLOGICAL SCIENCES↗

Structure-Based Analysis of Boronic Acids as Inhibitors of Acinetobacter -Derived Cephalosporinase-7, a Unique Class C β-Lactamase

Acinetobacter baumannii is a multidrug resistant pathogen that infects more than 12 000 patients each year in the US. Much of the resistance to β-lactam antibiotics in Acinetobacter spp. is mediated by class C β-lactamases known as Acinetobacter-derived cephalosporinases (ADCs). ADCs are unaffected by clinically used β-lactam-based β-lactamase inhibitors. In this study, five boronic acid transition state analog inhibitors (BATSIs) were evaluated for inhibition of the class C cephalosporinase ADC-7. Our goal was to explore the properties of BATSIs designed to probe the R1 binding site. K i values ranged from low micromolar to subnanomolar, and circular dichroism (CD) demonstrated that each inhibitor stabilizes the β-lactamase–inhibitor complexes. Additionally, X-ray crystal structures of ADC-7 in complex with five inhibitors were determined (resolutions from 1.80 to 2.09 Å). In the ADC-7/CR192 complex, the BATSI with the lowest K i (0.45 nM) and greatest ΔT m (+9 °C), a trifluoromethyl substituent, interacts with Arg340. Arg340 is unique to ADCs and may play an important role in the inhibition of ADC-7. Here, the ADC-7/BATSI complexes determined in this study shed light into the unique recognition sites in ADC enzymes and also offer insight into further structure-based optimization of these inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗

Insights into Substrate Specificity of NlpC/P60 Cell Wall Hydrolases Containing Bacterial SH3 Domains

ABSTRACT Bacterial SH3 (SH3b) domains are commonly fused with papain-like Nlp/P60 cell wall hydrolase domains. To understand how the modular architecture of SH3b and NlpC/P60 affects the activity of the catalytic domain, three putative NlpC/P60 cell wall hydrolases were biochemically and structurally characterized. These enzymes all have γ- d -Glu-A 2 pm (A 2 pm is diaminopimelic acid) cysteine amidase (or dl -endopeptidase) activities but with different substrate specificities. One enzyme is a cell wall lysin that cleaves peptidoglycan (PG), while the other two are cell wall recycling enzymes that only cleave stem peptides with an N-terminal l -Ala. Their crystal structures revealed a highly conserved structure consisting of two SH3b domains and a C-terminal NlpC/P60 catalytic domain, despite very low sequence identity. Interestingly, loops from the first SH3b domain dock into the ends of the active site groove of the catalytic domain, remodel the substrate binding site, and modulate substrate specificity. Two amino acid differences at the domain interface alter the substrate binding specificity in favor of stem peptides in recycling enzymes, whereas the SH3b domain may extend the peptidoglycan binding surface in the cell wall lysins. Remarkably, the cell wall lysin can be converted into a recycling enzyme with a single mutation. IMPORTANCE Peptidoglycan is a meshlike polymer that envelops the bacterial plasma membrane and bestows structural integrity. Cell wall lysins and recycling enzymes are part of a set of lytic enzymes that target covalent bonds connecting the amino acid and amino sugar building blocks of the PG network. These hydrolases are involved in processes such as cell growth and division, autolysis, invasion, and PG turnover and recycling. To avoid cleavage of unintended substrates, these enzymes have very selective substrate specificities. Our biochemical and structural analysis of three modular NlpC/P60 hydrolases, one lysin, and two recycling enzymes, show that they may have evolved from a common molecular architecture, where the substrate preference is modulated by local changes. These results also suggest that new pathways for recycling PG turnover products, such as tracheal cytotoxin, may have evolved in bacteria in the human gut microbiome that involve NlpC/P60 cell wall hydrolases.

Xu, Qingping↗

Origin of the spin reorientation transitions in (Fe 1–x Co x ) 2 B alloys

Low-temperature measurements of the magnetocrystalline anisotropy energy K in (Fe 1–x Co x ) 2 B alloys are reported, and the origin of this anisotropy is elucidated using a first-principles electronic structure analysis. The calculated concentration dependence K(x) with a maximum near x = 0.3 and a minimum near x = 0.8 is in excellent agreement with experiment. This dependence is traced down to spin-orbital selection rules and the filling of electronic bands with increasing electronic concentration. In conclusion, at the optimal Co concentration, K depends strongly on the tetragonality and doubles under a modest 3% increase of the c/a ratio, suggesting that the magnetocrystalline anisotropy can be further enhanced using epitaxial or chemical strain.

36 MATERIALS SCIENCE↗

Computational screening of dopants for photocatalytic two-electron reduction of CO 2 on anatase (101) surfaces

We have carried out first-principles calculations to explore reaction mechanisms of the 2e reduction of CO 2 to HCOOH or CO in photochemical reactions catalyzed by anatase (101) surface. Two energetically competitive reaction pathways to HCOOH were identified, which involve initial 1e (via bidentate) and 2e (via monodentate) reduction steps, respectively. The pathways of producing CO were also explored. From the electronic structure analysis, we have shown the role of the anatase surface in facilitating electron and proton transfer in CO 2 reduction. Based on the determined rate-limiting step, we have carried out screening of substitutional surface cation doping and found metallic elements that could substantially lower the reaction barriers. Finally, a simple model describing the relationship between the activation barriers and the binding energies of CO 2 - to the dopant surface site is proposed.

Environmental Molecular Sciences Laboratory↗

Analysis of structure and deformation behavior of AISI 316L tensile specimens from the second operational target module at the Spallation Neutron Source

In an earlier publication, tensile testing was performed on specimens removed from the first two operational targets of the Spallation Neutron Source (SNS). There were several anomalous features in the results. First, some specimens had very large elongations (up to 57%) while others had significantly smaller values. Second, there was a larger than the usual amount of data scatter in the elongation results. Third, the stress-strain diagrams of nominally similar specimens spanned a wide range of behavior ranging from expected irradiation-induced hardening to varying levels of force drop after yield point and indirect signs of "traveling deformation wave" behavior associated with strain-induced martensite formation. To investigate the cause(s) of such variable tensile behavior, several specimens from Target 2, spanning the range of observed tensile behavior, were chosen for detailed microstructural examination using electron backscattering analysis (EBSD). It was also shown that the steel employed in the construction of the target contained an unexpected bimodal grain size distribution, containing very large out-of-specification grains surrounded by necklaces of grains of within-specification sizes. The large grains were frequently comparable to the width of the gauge section of the tensile specimen. Moreover, the propensity to form martensite during deformation was shown to be accelerated by radiation but also to be very sensitive to the relative orientation of the grains with respect to the tensile axis. Specimens having large grains in the gauge that were most favorably oriented for production of martensite strongly exhibited the traveling deformation wave phenomenon, while those specimens with less favorably oriented grains had lesser or no degree of the wave effect, thereby accounting for the larger than expected data scatter.

316L↗