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At least 307 records · Page 17

Mirror dark sector solution of the Hubble tension with time-varying fine-structure constant

Here we explore a model introduced by Cyr-Racine et al. that resolves the Hubble tension by invoking a “mirror world” dark sector with energy density a fixed fraction of the “ordinary” sector of Λ+ cold dark matter. Although it reconciles cosmic microwave background and large-scale structure observations with local measurements of the Hubble constant, H 0 , the model requires a value of the primordial helium mass fraction, Y p = 0.170 ± 0.025, that is discrepant with observations and with the predictions of big bang nucleosynthesis. We consider a variant of the model with standard helium mass fraction but with the value of the electromagnetic fine-structure constant, α, slightly different during photon decoupling from its present value. If α at that epoch is lower than its current value by Δα ≃ -2 x 10 -5 , then we can achieve the same Hubble tension resolution as in the work by Cyr-Racine et al. but with consistent helium abundance. As an example of such time evolution of α, we consider a toy model of an ultralight scalar field, with mass m < 4 x 10 -29 eV, coupled to electromagnetism, which evolves after photon decoupling at redshift z ≃ 10 3 , and that with appropriate coupling appears to be consistent with late-time constraints on α variation and the weak equivalence principle.

79 ASTRONOMY AND ASTROPHYSICS↗

Wrapped fivebranes redux

The near-horizon region of Neveu-Schwarz fivebranes provides interesting examples of gauge/gravity duality. We revisit the structure of wrapped and/or intersecting fivebranes using the tools of null-gauged WZW models in worldsheet string theory, revealing the effective geometry of the fivebrane throat in a variety of examples. Variant gaugings yield linear dilaton fivebrane throats with AdS 3 caps, providing a wealth of information about the near-BPS structure of the corresponding spacetime CFT duals.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

The impact of long-range dispersal on gene surfing

Range expansions lead to distinctive patterns of genetic variation in populations, even in the absence of selection. These patterns and their genetic consequences have been well studied for populations advancing through successive short-ranged migration events. However, most populations harbor some degree of long-range dispersal, experiencing rare yet consequential migration events over arbitrarily long distances. Although dispersal is known to strongly affect spatial genetic structure during range expansions, the resulting patterns and their impact on neutral diversity remain poorly understood. Here, we systematically study the consequences of long-range dispersal on patterns of neutral variation during range expansion in a class of dispersal models which spans the extremes of local (effectively short-ranged) and global (effectively well-mixed) migration. We find that sufficiently long-ranged dispersal leaves behind a mosaic of monoallelic patches, whose number and size are highly sensitive to the distribution of dispersal distances. We develop a coarse-grained model which connects statistical features of these spatial patterns to the evolution of neutral diversity during the range expansion. We show that growth mechanisms that appear qualitatively similar can engender vastly different outcomes for diversity: Depending on the tail of the dispersal distance distribution, diversity can be either preserved (i.e., many variants survive) or lost (i.e., one variant dominates) at long times. Our results highlight the impact of spatial and migratory structure on genetic variation during processes as varied as range expansions, species invasions, epidemics, and the spread of beneficial mutations in established populations.

59 BASIC BIOLOGICAL SCIENCES↗

Molecular recognition requires dimerization of a VHH antibody

Camelid heavy-chain-only antibodies are a unique class of antibody that possesses only a single variable domain (termed VHH) for antigen recognition. Despite their apparent canonical mechanism of target recognition, where a single VHH domain binds a single target, an anti-caffeine VHH has been observed to possess 2:1 stoichiometry. Here, the structure of the anti-caffeine VHH/caffeine complex enabled the generation and biophysical analysis of variants that were used to better understand the role of VHH homodimerization in caffeine recognition. VHH interface mutants and caffeine analogs, which were examined to probe the mechanism of caffeine binding, suggested caffeine recognition is only possible with the VHH dimer species. Correspondingly, in the absence of caffeine, the anti-caffeine VHH was found to form a dimer with a dimerization constant comparable to that observed with VH:VL domains in conventional antibody systems, which was most stable near physiological temperature. While the VHH:VHH dimer structure (at 1.13 Å resolution) is reminiscent of conventional VH:VL heterodimers, the homodimeric VHH possesses a smaller angle of domain interaction, as well as a larger amount of apolar surface area burial. To test the general hypothesis that the short complementarity-determining region-3 (CDR3) may help drive VHH:VHH homodimerization, an anti-picloram VHH domain containing a short CDR3 was generated and characterized, which revealed it also existed as dimer species in solution. These results suggest homodimer-driven recognition may represent a more common method of VHH ligand recognition, opening opportunities for novel VHH homodimer affinity reagents and helping to guide their use in chemically induced dimerization applications.

60 APPLIED LIFE SCIENCES↗

Driving rapid atomic order in MnAl via low-magnitude magnetic field annealing

Application of a mild (60 mT), uniform magnetic field during short-term thermal treatment of kinetically retained, atomically disordered (paramagnetic) ε-MnAl was found to deliver a significant ~50 % increase in the formation of L1 0 atomically ordered (ferromagnetic) τ-MnAl product phase, compared to that produced by conventional (i.e., zero-field) annealing under identical thermal conditions. The magnetic field, applied in a passive closed-circuit configuration during annealing, induced significant changes in the structural, magnetic, and phase evolution of the material. Computational results based on electronic structure calculations demonstrate that the effective magnetic susceptibility of τ-MnAl is sensitive to the orientation, rather than the magnitude, of an applied magnetic field in the vicinity of the Curie temperature. The uniaxial magnetocrystalline anisotropy of the L1 0 structure is proposed to act as a filter for selective propagation of the population of τ-MnAl variants that are favorably aligned with the applied field. In this manner, crystallographic “gridlock” is alleviated that would otherwise arise from the coexistence of multiple, energetically equivalent τ-phase variants within the parent ε-phase matrix. These results confirm that static, low-magnitude magnetic field annealing is able to accelerate L1 0 atomic ordering in the MnAl system and likely can exert similar influences in relevant magnetic systems, facilitating efficient tailoring of structure-sensitive magnetic properties for the manufacture of magnetic materials.

36 MATERIALS SCIENCE↗

Growth and Characterization of Epitaxial FeWO 4 Thin Films with Controlled Oxygen Stoichiometry

Here, we report the growth of single-phase epitaxial FeWO 4 thin films, using plasma-assisted molecular beam epitaxy, and investigate structural, optical, and electronic properties. The FeWO 4 films grow in (100) orientation on c-plane sapphire (0001) substrates and exhibit 3 rotational twin variants where FeWO 4 [001] is aligned to sapphire [100] equivalent in-plane directions. X-ray diffraction measurements indicate that the epitaxial FeWO 4 (100) structure is optimized when 80-100 W of rf power is applied to an atomic oxygen source during growth, yielding films with minimal strain and impurity phases or other orientations. In films grown with 120 W of rf power, FeWO 4 crystallites develop inhomogeneous and homogeneous strains and are potentially contaminated with Fe 3+ oxide phase impurities. In films grown with 60 W of rf power, FeWO 4 crystallites do not form fully epitaxial layers. X-ray photoelectron spectroscopy indicates that the structural changes are correlated with the Fe 3+ /Fe 2+ oxidation state ratio increasing from 0.6-1.4 with rf power from 60-120 W. X-ray fluorescence spectroscopy indicates that the Fe/W composition ratio is also increasing from 1.1-1.8 with rf power from 60-120 W. Ultraviolet and visible optical absorption spectra indicate a 1.8 ± 0.1 eV band gap with an additional interband absorption feature at 3.1 ± 0.1 eV in the 80-100 W films, with similar onsets observed in the 60 W films. In the 120 W films, the higher lying transition is shifted to 2.7 ± 0.1 eV due to the Fe 3+ enrichment. Electrical resistivity decreases over 2 orders of magnitude with oxidation from 10 4 -10 5 Ω cm in 60 W films to 120 ± 10 Ω cm in 120 W films. Thermopower measurements show p-type to n-type conductivity conversion when oxidation states shift from Fe 2+ majority in the 100 W films to Fe 3+ majority in the 120 W films. We conclude that electron polaron hopping driven by Fe 3+ is a dominant transport mechanism and a source of n-type conductivity in overoxidized FeWO 4 films.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Vacancy-mediated complex phase selection in high entropy alloys

Phase selection in Ti-Zr-Hf-Al high-entropy alloys was investigated by in-situ high-energy x-ray diffraction, single-crystal x-ray diffraction, and KKR-CPA electronic-structure methods that address disorder and vacancies, predicting formation enthalpy and chemical short-range order (SRO). Samples with varying Al content were synthesized, characterized, and computationally assessed to ascertain the composition-dependent phase selection, as increased Al content often acts as a stabilizer of a body-centered-cubic structure. Equiatomic TiZrHfAl was especially interesting due to its observed bcc superstructure – a variant of γ-brass with 4 vacancies per cell (not 2 as in γ-brass). We highlight how vacancy ordering mediates selection of this variant of γ-brass, which is driven by vacancy-atom SRO that dramatically suppress all atomic SRO. As vacancies are inherent in processing refractory systems, we expect that similar discoveries await in other high entropy alloys or in revisiting older experimental data.

36 MATERIALS SCIENCE↗

An active site loop toggles between conformations to control antibiotic hydrolysis and inhibition potency for CTX-M β-lactamase drug-resistance enzymes

Abstract β-lactamases inactivate β-lactam antibiotics leading to drug resistance. Consequently, inhibitors of β-lactamases can combat this resistance, and the β-lactamase inhibitory protein (BLIP) is a naturally occurring inhibitor. The widespread CTX-M-14 and CTX-M-15 β-lactamases have an 83% sequence identity. In this study, we show that BLIP weakly inhibits CTX-M-14 but potently inhibits CTX-M-15. The structure of the BLIP/CTX-M-15 complex reveals that binding is associated with a conformational change of an active site loop of β-lactamase. Surprisingly, the loop structure in the complex is similar to that in a drug-resistant variant (N106S) of CTX-M-14. We hypothesized that the pre-established favorable loop conformation of the N106S mutant would facilitate binding. The N106S substitution results in a ~100- and 10-fold increase in BLIP inhibition potency for CTX-M-14 and CTX-M-15, respectively. Thus, this indicates that an active site loop in β-lactamase toggles between conformations that control antibiotic hydrolysis and inhibitor susceptibility. These findings highlight the role of accessible active site conformations in controlling enzyme activity and inhibitor susceptibility as well as the influence of mutations in selectively stabilizing discrete conformations.

59 BASIC BIOLOGICAL SCIENCES↗

Application of Amber Suppression To Study the Role of Tyr M210 in Electron Transfer in Rhodobacter sphaeroides Photosynthetic Reaction Centers

The initial light-induced electron transfer (ET) steps in the bacterial photosynthetic reaction center (RC) have been extensively studied and provide a paradigm for connecting structure and function. Although RCs have local pseudo-C 2 symmetry, ET only occurs along the A branch of chromophores. Tyrosine M210 is a key symmetry-breaking residue adjacent to bacteriochlorophyll B A that bridges primary electron donor P and bacteriopheophytin acceptor H A . Here, we used amber suppression to incorporate phenylalanine variants with different electron-withdrawing/donating capabilities at position M210. X-ray data generally reveal no appreciable structural changes due to the mutations. P* decay and P + H A - formation are multi-exponential (~2-9, ~10-60, and ~100-300 ps) and temperature dependent. The 1020 nm transient-absorption band of P + B A - is barely resolved for a few variants at 295 K and for none at 77 K. The results indicate a change from two-step ET for wild-type RCs to dominance of one-step superexchange ET for the mutants. Resonance Stark spectroscopy reveals that the free energy of P + B A - changes by -57 to +66 meV among the phenylalanine variants. Because P+BA apparently lies above P* in all phenylalanine variants, the perturbations primarily affect the energy denominator for superexchange mixing. The findings deepen insight into primary ET in the bacterial RC.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Molecular basis of C-S bond cleavage in the glycyl radical enzyme isethionate sulfite-lyase

Desulfonation of isethionate by the bacterial glycyl radical enzyme (GRE) isethionate sulfite-lyase (IslA) generates sulfite, a substrate for respiration that in turn produces the disease-associated metabolite hydrogen sulfide. Here, we present a 2.7 Å resolution X-ray structure of wild-type IslA from Bilophila wadsworthia with isethionate bound. In comparison with other GREs, alternate positioning of the active site β strands allows for distinct residue positions to contribute to substrate binding. These structural differences, combined with sequence variations, create a highly tailored active site for the binding of the negatively charged isethionate substrate. Through the kinetic analysis of 14 IslA variants and computational analyses, we probe the mechanism by which radical chemistry is used for C-S bond cleavage. This work further elucidates the structural basis of chemistry within the GRE superfamily and will inform structure-based inhibitor design of IsIA and thus of microbial hydrogen sulfide production.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Concept designs for NASA's Solar Electric Propulsion Technology Demonstration Mission

Multiple Solar Electric Propulsion Technology Demonstration Mission were developed to assess vehicle performance and estimated mission cost. Concepts ranged from a 10,000 kilogram spacecraft capable of delivering 4000 kilogram of payload to one of the Earth Moon Lagrange points in support of future human-crewed outposts to a 180 kilogram spacecraft capable of performing an asteroid rendezvous mission after launched to a geostationary transfer orbit as a secondary payload. Low-cost and maximum Delta-V capability variants of a spacecraft concept based on utilizing a secondary payload adapter as the primary bus structure were developed as were concepts designed to be co-manifested with another spacecraft on a single launch vehicle. Each of the Solar Electric Propulsion Technology Demonstration Mission concepts developed included an estimated spacecraft cost. These data suggest estimated spacecraft costs of $200 million - $300 million if 30 kilowatt-class solar arrays and the corresponding electric propulsion system currently under development are used as the basis for sizing the mission concept regardless of launch vehicle costs. The most affordable mission concept developed based on subscale variants of the advanced solar arrays and electric propulsion technology currently under development by the NASA Space Technology Mission Directorate has an estimated cost of $50M and could provide a Delta-V capability comparable to much larger spacecraft concepts.

solar electric propulsion↗

De Novo Design of High‐Affinity Miniprotein Binders Targeting Francisella Tularensis Virulence Factor

Abstract Francisella tularensis poses considerable public health risk due to its high infectivity and potential for bioterrorism. Francisella‐like lipoprotein (Flpp3), a key virulence factor unique to Francisella, plays critical roles in infection and immune evasion, making it a promising target for therapeutic development. However, the lack of well‐defined binding pockets and structural information on native interactions has hindered structure‐guided ligand discovery against Flpp3. Here, we used a combination of physics‐based and deep‐learning methods to design high‐affinity miniprotein binders targeting two distinct sites on Flpp3. We identified four binders for site I with binding affinities ranging between 24–110 nM. For the second site, an initial binder showed a dissociation constant ( K D ) of 81 nM, and subsequent site saturation mutagenesis yielded variants with sub‐nanomolar affinities. Circular dichroism confirmed the topology of designed miniproteins. The X‐ray crystal structure of Flpp3 in complex with a site I binder is nearly identical to the design model (Cα root‐mean‐square deviation (RMSD): 0.9 Å). These designed miniproteins provide research tools to explore the roles of Flpp3 in tularemia and should enable the development of new therapeutic candidates.

Gokce‐Alpkilic, Gizem [Molecular Engineering and S↗

Effect of Delta and Omicron Mutations on the RBD-SD1 Domain of the Spike Protein in SARS-CoV-2 and the Omicron Mutations on RBD-ACE2 Interface Complex

The receptor-binding domain (RBD) is the essential part in the Spike-protein (S-protein) of SARS-CoV-2 virus that directly binds to the human ACE2 receptor, making it a key target for many vaccines and therapies. Therefore, any mutations at this domain could affect the efficacy of these treatments as well as the viral-cell entry mechanism. We introduce ab initio DFT-based computational study that mainly focuses on two parts: (1) Mutations effects of both Delta and Omicron variants in the RBD-SD1 domain. (2) Impact of Omicron RBD mutations on the structure and properties of the RBD-ACE2 interface system. The in-depth analysis is based on the novel concept of amino acid-amino acid bond pair units (AABPU) that reveal the differences between the Delta and/or Omicron mutations and its corresponding wild-type strain in terms of the role played by non-local amino acid interactions, their 3D shapes and sizes, as well as contribution to hydrogen bonding and partial charge distributions. Our results also show that the interaction of Omicron RBD with ACE2 significantly increased its bonding between amino acids at the interface providing information on the implications of penetration of S-protein into ACE2, and thus offering a possible explanation for its high infectivity. Our findings enable us to present, in more conspicuous atomic level detail, the effect of specific mutations that may help in predicting and/or mitigating the next variant of concern.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Synthetic antibodies against BRIL as universal fiducial marks for single-particle cryoEM structure determination of membrane proteins

We propose the concept of universal fiducials based on a set of pre-made semi-synthetic antibodies (sABs) generated by customized phage display selections against the fusion protein BRIL, an engineered variant of apocytochrome b562a. These sABs can bind to BRIL fused either into the loops or termini of different GPCRs, ion channels, receptors and transporters without disrupting their structure. A crystal structure of BRIL in complex with an affinity-matured sAB (BAG2) that bound to all systems tested delineates the footprint of interaction. Negative stain and cryoEM data of several examples of BRIL-membrane protein chimera highlight the effectiveness of the sABs as universal fiducial marks. Taken together with a cryoEM structure of sAB bound human nicotinic acetylcholine receptor, this work demonstrates that these anti-BRIL sABs can greatly enhance the particle properties leading to improved cryoEM outcomes, especially for challenging membrane proteins.

59 BASIC BIOLOGICAL SCIENCES↗

Beyond the Global Brain Differences: Intraindividual Variability Differences in 1q21.1 Distal and 15q11.2 BP1-BP2 Deletion Carriers

Carriers of the 1q21.1 distal and 15q11.2 BP1-BP2 copy number variants exhibit regional and global brain differences compared with noncarriers. However, interpreting regional differences is challenging if a global difference drives the regional brain differences. Intraindividual variability measures can be used to test for regional differences beyond global differences in brain structure. Magnetic resonance imaging data were used to obtain regional brain values for 1q21.1 distal deletion (n = 30) and duplication (n = 27) and 15q11.2 BP1-BP2 deletion (n = 170) and duplication (n = 243) carriers and matched noncarriers (n = 2350). Regional intra-deviation scores, i.e., the standardized difference between an individual’s regional difference and global difference, were used to test for regional differences that diverge from the global difference. For the 1q21.1 distal deletion carriers, cortical surface area for regions in the medial visual cortex, posterior cingulate, and temporal pole differed less and regions in the prefrontal and superior temporal cortex differed more than the global difference in cortical surface area. For the 15q11.2 BP1-BP2 deletion carriers, cortical thickness in regions in the medial visual cortex, auditory cortex, and temporal pole differed less and the prefrontal and somatosensory cortex differed more than the global difference in cortical thickness. We find evidence for regional effects beyond differences in global brain measures in 1q21.1 distal and 15q11.2 BP1-BP2 copy number variants. The results provide new insight into brain profiling of the 1q21.1 distal and 15q11.2 BP1-BP2 copy number variants, with the potential to increase understanding of the mechanisms involved in altered neurodevelopment.

15q11.2 BP1-BP2↗

Structures of HIV-1 Neutralizing Antibody 10E8 Delineate the Mechanistic Basis of Its Multi-Peak Behavior on Size-Exclusion Chromatography

Antibody 10E8 is capable of effectively neutralizing HIV through its recognition of the membrane-proximal external region (MPER), and a suitably optimized version of 10E8 might have utility in HIV therapy and prophylaxis. However, 10E8 displays a three-peak profile on size-exclusion chromatography (SEC), complicating its manufacture. Here we show cis-trans conformational isomerization of the Tyr-Pro-Pro (YPP) motif in the heavy chain 3rd complementarity-determining region (CDR H3) of antibody 10E8 to be the mechanistic basis of its multipeak behavior. We observed 10E8 to undergo slow conformational isomerization and delineate a mechanistic explanation for effective comodifiers that were able to resolve its SEC heterogeneity and to allow an evaluation of the critical quality attribute of aggregation. We determined crystal structures of single and double alanine mutants of a key di-proline motif and of a light chain variant, revealing alternative conformations of the CDR H3. We also replicated both multi-peak and delayed SEC behavior with MPER-antibodies 4E10 and VRC42, by introducing a Tyr-Pro (YP) motif into their CDR H3s. Our results show how a conformationally dynamic CDR H3 can provide the requisite structural plasticity needed for a highly hydrophobic paratope to recognize its membrane-proximal epitope.

60 APPLIED LIFE SCIENCES↗

Optimized Substrate Positioning Enables Switches in the C–H Cleavage Site and Reaction Outcome in the Hydroxylation–Epoxidation Sequence Catalyzed by Hyoscyamine 6β-Hydroxylase

Hyoscyamine 6β-hydroxylase (H6H) is an Fe(II)- and 2-oxoglutarate-dependent (Fe/2OG) oxygenase that catalyzes the last two steps in the biosynthesis of scopolamine, a prolifically administered anti-nausea drug. After its namesake first reaction, H6H couples the newly installed C6-bonded oxygen to C7 to form the epoxide of scopolamine. Oxoiron(IV) (ferryl) intermediates initiate both reactions by cleaving C–H bonds, but it remains unclear how the enzyme switches target site and promotes (C6)O–C7 coupling in preference to C7 hydroxylation in the second step. In one possible epoxidation mechanism, the C6 oxygen would – analogously to mechanisms proposed for the Fe/2OG halogenases and, in the preceding paper, N-acetylnorloline synthase (LolO) – coordinate as alkoxide to the C7–H-cleaving ferryl intermediate to enable alkoxyl coupling to the ensuing C7 radical. Here we provide structural and kinetic evidence that H6H instead exploits the distinct spatial dependencies of competitive C–H-cleavage (C6 vs C7) and C–O-coupling (oxygen rebound vs cyclization) steps to promote the two-step sequence without substrate coordination or repositioning for the epoxidation step. Structural comparisons of ferryl-mimicking vanadyl complexes of wild-type H6H and a variant that preferentially hydroxylates C7 of 6-hydroxyhyoscyamine suggest that only a modest (~ 10°) shift in the Fe–O–H(C7) approach angle is sufficient to change the outcome. Finally, the observation that, in wild-type H6H, 2 H 2 O solvent also increases the C7-hydroxylation:epoxidation ratio by ~ 8-fold implies that the latter outcome requires cleavage of the alcohol O-H bond, which, unlike in the LolO oxacyclization, is not accomplished in advance of C–H cleavage.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structural basis for botulinum neurotoxin E recognition of synaptic vesicle protein 2

Botulinum neurotoxin E (BoNT/E) is one of the major causes of human botulism and paradoxically also a promising therapeutic agent. Here we determined the co-crystal structures of the receptor-binding domain of BoNT/E (H C E) in complex with its neuronal receptor synaptic vesicle glycoprotein 2A (SV2A) and a nanobody that serves as a ganglioside surrogate. These structures reveal that the protein-protein interactions between H C E and SV2 provide the crucial location and specificity information for H C E to recognize SV2A and SV2B, but not the closely related SV2C. At the same time, H C E exploits a separated sialic acid-binding pocket to mediate recognition of an N-glycan of SV2. Structure-based mutagenesis and functional studies demonstrate that both the protein-protein and protein-glycan associations are essential for SV2A-mediated cell entry of BoNT/E and for its potent neurotoxicity. Our studies establish the structural basis to understand the receptor-specificity of BoNT/E and to engineer BoNT/E variants for new clinical applications.

59 BASIC BIOLOGICAL SCIENCES↗