RNA sculpting by the primordial Helix-clasp-Helix–Strand-Loop (HcH–SL) motif enforces chemical recognition enabling diverse KH domain functions
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60 APPLIED LIFE SCIENCES↗
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Deuteron off-resonance rotating frame relaxation for the characterization of slow motions in rotating and static solid-state proteins
Here, we demonstrate the feasibility of deuterium solid-state NMR off-resonance rotating frame relaxation measurements for studies of slow motions in biomolecular solids. The pulse sequence, which includes adiabatic pulses for magnetization alignment, is illustrated for static and magic-angle spinning conditions away from rotary resonances. We apply the measurements for three systems with selective deuterium labels at methyl groups: a) a model compound, Fluorenylmethyloxycarbonyl methionine-D 3 amino acid, for which the principles of the measurements and corresponding motional modeling based on rotameric interconversions are demonstrated; b) amyloid-β 1-40 fibrils labeled at a single alanine methyl group located in the disordered N-terminal domain. This system has been extensively studied in prior work and here serves as a test of the method for complex biological systems. The essential features of the dynamics consist of large-scale rearrangements of the disordered N-terminal domain and the conformational exchange between the free and bound forms of the domain, the latter one due to transient interactions with the structured core of the fibrils. and c) a 15-residue helical peptide which belongs to the predicted α-helical domain near the N-terminus of apolipoprotein B. The peptide is solvated with triolein and incorporates a selectively labeled leucine methyl groups. The method permits model refinement, indicating rotameric interconversions with a distribution of rate constants.
59 BASIC BIOLOGICAL SCIENCES↗
In situ observation of the magnetization configuration and reversal in cylindrical nanowires
Curvilinear magnetic structures often have unique magnetic behavior compared to their rectilinear counterparts. This is due to the unique curvilinear boundary conditions as well as the curvature induced Dzyaloshinskii–Moriya-like interaction and the curvature induced anisotropy. The effects of a curvilinear geometry are best studied in 3D structures, where the curvature can have a significant spatial extent. Of these 3D structures, the simplest structure to study is the cylindrical nanowire. Here, we have simulated the magnetization reversal in cylindrical NiFe nanowires and present in situ Lorentz TEM images to support the findings of the simulations. We studied the domain formation and reversal of nanowires with two distinct diameters that give rise to a different reversal behavior. We have, thus, found that the zero-field magnetization configuration in these wires can take on a double helix type of configuration. The reversal in these structures then proceeds through the winding and unwinding of these helical configurations rather than through domain wall propagation.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Large-eddy simulations of turbulent flows in arrays of helical- and straight-bladed vertical-axis wind turbines
Effects of helical-shaped blades on the flow characteristics and power production of finite-length wind farms composed of vertical-axis wind turbines (VAWTs) are studied numerically using large-eddy simulation (LES). Two helical-bladed VAWTs (with opposite blade twist angles) are studied against one straight-bladed VAWT in different array configurations with coarse, intermediate, and tight spacings. Statistical analysis of the LES data shows that the helical-bladed VAWTs can improve the mean power production in the fully developed region of the array by about 4.94%–7.33% compared with the corresponding straight-bladed VAWT cases. The helical-bladed VAWTs also cover the azimuth angle more smoothly during the rotation, resulting in about 47.6%–60.1% reduction in the temporal fluctuation of the VAWT power output. Using the helical-bladed VAWTs also reduces the fatigue load on the structure by significantly reducing the spanwise bending moment (relative to the bottom base), which may improve the longevity of the VAWT system to reduce the long-term maintenance cost.
17 WIND ENERGY↗
Rapidity-dependent spin decomposition of the nucleon
We revisit the two-dimensional Fourier transform of generalized parton distributions (GPDs) at nonzero skewness. At 𝜂 = 0 it reduces to the standard impact-parameter density, while at 𝜂 ≠ 0 it is an off-forward amplitude that we interpret as a genuine parton–nucleon correlation. Its overall strength (the transverse-plane integral of the density) is fixed by the GPD at the kinematic point 𝑡 =−𝑐 𝜂 =−4𝜂 2 𝑚$^{2}_{𝑁}$/(1 − 𝜂 2 ) and decreases monotonically with the rapidity gap Δ𝑦 = ln[(1+𝜂)/(1−𝜂)] = 2 artanh(𝜂). This rapidity dependence implies rapidity-modified Ji identities that connect helicity, orbital, and total angular momenta of the correlation in closed form. To quantify these effects, we construct leading-twist quark and gluon GPDs in a string-based conformal framework: conformal moments are parametrized by linear open- and closed-string Regge trajectories with slopes constrained by parton distribution functions (PDFs), hadron/glueball spectroscopy, and form-factor data, and GPDs are reconstructed over the full (𝑥,𝜂,𝑡) domain by Mellin-Barnes inversion with next-to-leading order evolution. We find qualitative agreement (and fair quantitative agreement within quoted uncertainties) for several moments and selected nonsinglet 𝑥-space channels at 𝜇 = 2 GeV when compared with lattice QCD, while we also identify channels with visible tension and discuss likely sources (PDF priors and 𝑡-slope systematics).
Gauge-gravity dualities↗
X-ray pulse generation with ultra-fast flipping of its orbital angular momentum
A method to temporally tailor the properties of X-ray radiation carrying Orbital Angular Momentum (OAM) is presented. In simulations, an electron beam is prepared with a temporally modulated micro-bunching structure which, when radiating at the second harmonic in a helical undulator, generates OAM light with a corresponding temporally modulated intensity. This method is shown to generate attosecond pulse trains of OAM light without the need for any additional external optics, making the wavelength range tunable. In addition to the OAM pulse train, the method can be adapted to generate radiation where the handedness of the OAM mode may also be temporally modulated (flipped).
43 PARTICLE ACCELERATORS↗
Proceedings of RIKEN BNL Research Center Workshop: Small-x Physics in the EIC Era [Slides]
Understanding the high energy limit of hadronic and nuclear collisions is at the forefront of nuclear and particle physics. When boosted to ultrahigh energies, all hadrons and nuclei eventually transform into a universal form of matter called the Color Glass Condensate (CGC). The CGC is characterized by the high density (saturation) of small-x gluons which leads to distinct experimental signatures. Tantalizing hints of the CGC have been observed at HERA, RHIC and the LHC, but the prospects for the discovery of the CGC are more promising at future experiments such as the Electron-Ion Collider (EIC) at BNL Indeed, according to the National Science Academy report published in 2019, one of the three major goals of the EIC is to address the nature of the gluon saturation. (The other two are the mass and spin structure of the nucleons.) With this in mind, the small-x community is gearing up to meet the challenges of the EIC era. Over the past several years, there has been impressive progress in the next-to-leading order (NLO) calculations in the CGC framework of various observables such as single hadron production in proton-nucleus collisions, inclusive and exclusive dijet and trijet production in Deep Inelastic Scattering (DIS), jet-plus-photon production in DIS, etc. We expect that NLO calculations will be the standard tool to confront future experimental data at the EIC. Another emerging trend of the community is the interplay between small-x physics and spin physics. The RHIC result for the gluon helicity ΔG has underscored the necessity to understand the longitudinal spin structure of the proton at small-x. There have been theoretical indications that a significant fraction of spin and orbital angular momentum is stored in the small-x region. As for the transversely polarized proton, a surprising new connection between the gluon Sivers function at small-x and the QCD Odderon has been pointed out and its implications at the EIC has been discussed. In view of these developments, we think it is timely to organize a dedicated workshop on small-x physics to summarize the present status of the field and to discuss future directions. A major focus of this workshop will be to identify outstanding problems that could significantly benefit from collaborative efforts amongst scientists working on formal, phenomenological, and computational aspects of small-x physics.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
Determinants of Stereoselectivity in Monoterpene Synthases
Monoterpene synthases (MTSs) catalyze the conversion of an achiral prenyl diphosphate precursor, most commonly geranyl diphosphate (GPP), into structurally and stereochemically diverse products. However, remains poorly understood. Here, we combine enzymatic assays with six MTSs and selected variants, along with extensive molecular dynamics simulations to the mechanistic basis of stereoselectivity. We demonstrate that the preferred helical binding conformation of GPP, determined from free-energy calculations and selected crystal structures of MTSs, correlates well with the experimentally determined stereoselectivity of MTSs, whereas only a poor correlation is observed between the binding of enantiomers of linalyl diphosphate (LPP), a chiral intermediate of MTS catalysis, and the stereochemical reaction outcomes. Free energy maps indicate that enzyme-bound GPP conformers preferentially occupy regions that enable a direct and stereochemically faithful transition from GPP to subsequent carbocations. In contrast, LPP frequently populates regions of the energy surface where conformational scrambling can occur, thus leading to a lack of correlation between LPP enantiomer binding and product stereochemistry. Overall, these findings establish that the configuration of GPP is the primary determining factor for stereochemical outcomes in MTSs, offering a new framework for designing stereoselective terpene synthases.
Srividya, Narayanan (ORCID:0000000179347987)↗
Crystal structure of an RNA/DNA strand exchange junction
Short segments of RNA displace one strand of a DNA duplex during diverse processes including transcription and CRISPR-mediated immunity and genome editing. These strand exchange events involve the intersection of two geometrically distinct helix types—an RNA:DNA hybrid (A-form) and a DNA:DNA homoduplex (B-form). Although previous evidence suggests that these two helices can stack on each other, it is unknown what local geometric adjustments could enable A-on-B stacking. Here we report the X-ray crystal structure of an RNA-5′/DNA-3′ strand exchange junction at an anisotropic resolution of 1.6 to 2.2 Å. The structure reveals that the A-to-B helical transition involves a combination of helical axis misalignment, helical axis tilting and compression of the DNA strand within the RNA:DNA helix, where nucleotides exhibit a mixture of A- and B-form geometry. These structural principles explain previous observations of conformational stability in RNA/DNA exchange junctions, enabling a nucleic acid architecture that is repeatedly populated during biological strand exchange events.
59 BASIC BIOLOGICAL SCIENCES↗
Coupling of Ca 2+ and voltage activation in BK channels through the αB helix/voltage sensor interface
Large-conductance Ca 2+ and voltage-activated K + (BK) channels control membrane excitability in many cell types. BK channels are tetrameric. Each subunit is composed of a voltage sensor domain (VSD), a central pore-gate domain, and a large cytoplasmic domain (CTD) that contains the Ca 2+ sensors. While it is known that BK channels are activated by voltage and Ca 2+ , and that voltage and Ca 2+ activations interact, less is known about the mechanisms involved. In this work we explore these mechanisms by examining the gating contribution of an interface formed between the VSDs and the αB helices located at the top of the CTDs. Proline mutations in the αB helix greatly decreased voltage activation while having negligible effects on gating currents. Analysis with the Horrigan, Cui, and Aldrich model indicated a decreased coupling between voltage sensors and pore gate. Proline mutations decreased Ca 2+ activation for both Ca 2+ bowl and RCK1 Ca 2+ sites, suggesting that both high-affinity Ca 2+ sites transduce their effect, at least in part, through the αB helix. Mg 2+ activation also decreased. The crystal structure of the CTD with proline mutation L390P showed a flattening of the first helical turn in the αB helix compared to wild type, without other notable differences in the CTD, indicating that structural changes from the mutation were confined to the αB helix. These findings indicate that an intact αB helix/VSD interface is required for effective coupling of Ca 2+ binding and voltage depolarization to pore opening and that shared Ca 2+ and voltage transduction pathways involving the αB helix may be involved.
59 BASIC BIOLOGICAL SCIENCES↗
Structure of pre-miR-31 reveals an active role in Dicer–TRBP complex processing
As an essential posttranscriptional regulator of gene expression, microRNA (miRNA) levels must be strictly maintained. The biogenesis of many miRNAs is mediated by trans-acting protein partners through a variety of mechanisms, including remodeling of the RNA structure. miR-31 functions as an oncogene in numerous cancers, and interestingly, its biogenesis is not known to be regulated by protein-binding partners. Therefore, the intrinsic structural properties of the precursor element of miR-31 (pre-miR-31) can provide a mechanism by which its biogenesis is regulated. We determined the solution structure of pre-miR-31 to investigate the role of distinct structural elements in regulating processing by the Dicer–TRBP complex. We found that the presence or absence of mismatches within the helical stem does not strongly influence Dicer–TRBP processing of the pre-miRNAs. However, both the apical loop size and structure at the Dicing site are key elements for discrimination by the Dicer–TRBP complex. Interestingly, our NMR-derived structure reveals the presence of a triplet of base pairs that link the Dicer cleavage site and the apical loop. Mutational analysis in this region suggests that the stability of the junction region strongly influences processing by the Dicer–TRBP complex. Our results enrich our understanding of the active role that RNA structure plays in regulating miRNA biogenesis, which has direct implications for the control of gene expression.
59 BASIC BIOLOGICAL SCIENCES↗
The intrinsically disordered protein TgIST from Toxoplasma gondii inhibits STAT1 signaling by blocking cofactor recruitment
Signal transducer and activator of transcription (STAT) proteins communicate from cell-surface receptors to drive transcription of immune response genes. The parasite Toxoplasma gondii blocks STAT1-mediated gene expression by secreting the intrinsically disordered protein TgIST that traffics to the host nucleus, binds phosphorylated STAT1 dimers, and occupies nascent transcription sites that unexpectedly remain silenced. Here we define a core region within internal repeats of TgIST that is necessary and sufficient to block STAT1-mediated gene expression. Cellular, biochemical, mutational, and structural data demonstrate that the repeat region of TgIST adopts a helical conformation upon binding to STAT1 dimers. The binding interface is defined by a groove formed from two loops in the STAT1 SH2 domains that reorient during dimerization. TgIST binding to this newly exposed site at the STAT1 dimer interface alters its conformation and prevents the recruitment of co-transcriptional activators, thus defining the mechanism of blocked transcription.
59 BASIC BIOLOGICAL SCIENCES↗
Transition between protein-like and polymer-like dynamic behavior: Internal friction in unfolded apomyoglobin depends on denaturing conditions
Equilibrium dynamics of different folding intermediates and denatured states is strongly connected to the exploration of the conformational space on the nanosecond time scale and might have implications in understanding protein folding. For the first time, the same protein system apomyoglobin has been investigated using neutron spin-echo spectroscopy in different states: native-like, partially folded (molten globule) and completely unfolded, following two different unfolding paths: using acid or guanidinium chloride (GdmCl). While the internal dynamics of the native-like state can be understood using normal mode analysis based on high resolution structural information of myoglobin, for the unfolded and even for the molten globule states, models from polymer science are employed. The Zimm model accurately describes the slowly-relaxing, expanded GdmCl-denaturated state, ignoring the individuality of the different aminoacid side chain. The dynamics of the acid unfolded and molten globule state are similar in the framework of the Zimm model with internal friction, where the chains still interact and hinder each other: the first Zimm relaxation time is as large as the internal friction time. Transient formation of secondary structure elements in the acid unfolded and presence of α-helices in the molten globule state lead to internal friction to a similar extent.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Harnessing peptide–cellulose interactions to tailor the performance of self-assembled, injectable hydrogels
Taking inspiration from natural systems, such as spider silk and mollusk nacre, that employ hierarchical assembly to attain robust material performance, we leveraged matrix–filler interactions within reinforced polymer–peptide hybrids to create self-assembled hydrogels with enhanced properties. Specifically, cellulose nanocrystals (CNCs) were incorporated into peptide–polyurea (PPU) hybrid matrices to tailor key hydrogel features through matrix–filler interactions. Herein, we examined the impact of peptide repeat length and CNC loading on hydrogelation, morphology, mechanics, and thermal behavior of PPU/CNC composite hydrogels. The addition of CNCs into PPU hydrogels resulted in increased gel stiffness; however, the extent of reinforcement of the nanocomposite gels upon nanofiller inclusion also was driven by PPU architecture. Temperature-promoted stiffening transitions observed in nanocomposite PPU hydrogels were dictated by peptide segment length. Analysis of the peptide secondary structure confirmed shifts in the conformation of peptidic domains (α-helices or β-sheets) upon CNC loading. Finally, PPU/CNC hydrogels were probed for their injectability characteristics, demonstrating that nanofiller–matrix interactions were shown to aid rapid network reformation (∼10 s) upon cessation of high shear forces. Overall, this research showcases the potential of modulating matrix–filler interactions within PPU/CNC hydrogels through strategic system design, enabling the tuning of functional hydrogel characteristics for diverse applications.
42 ENGINEERING↗
Crystallography Reveals Metal‐Triggered Restructuring of β‐Hairpins
Abstract Metal binding to β‐sheets occurs in many metalloproteins and is also implicated in the pathology of Alzheimer's disease. De novo designed metallo‐β‐sheets have been pursued as models and mimics of these proteins. However, no crystal structures of canonical β‐sheet metallopeptides have yet been obtained, in stark contrast to many examples for ɑ‐helical metallopeptides, leading to a poor understanding for their chemistry. To address this, we have engineered tryptophan zippers, stable 12‐residue β‐sheet peptides, to bind Cu(II) ions and obtained crystal structures through single crystal X‐ray diffraction (SC‐XRD). We find that metal binding triggers several unexpected supramolecular assemblies that demonstrate the range of higher‐order structures available to metallo‐β‐sheets. Overall, these findings underscore the importance of crystallography in elucidating the rich structural landscape of metallo‐β‐sheet peptides.
Thuc Dang, Viet↗
Structure of orthoreovirus RNA chaperone σNS, a component of viral replication factories
Abstract The mammalian orthoreovirus (reovirus) σNS protein is required for formation of replication compartments that support viral genome replication and capsid assembly. Despite its functional importance, a mechanistic understanding of σNS is lacking. We conducted structural and biochemical analyses of a σNS mutant that forms dimers instead of the higher-order oligomers formed by wildtype (WT) σNS. The crystal structure shows that dimers interact with each other using N-terminal arms to form a helical assembly resembling WT σNS filaments in complex with RNA observed using cryo-EM. The interior of the helical assembly is of appropriate diameter to bind RNA. The helical assembly is disrupted by bile acids, which bind to the same site as the N-terminal arm. This finding suggests that the N-terminal arm functions in conferring context-dependent oligomeric states of σNS, which is supported by the structure of σNS lacking an N-terminal arm. We further observed that σNS has RNA chaperone activity likely essential for presenting mRNA to the viral polymerase for genome replication. This activity is reduced by bile acids and abolished by N-terminal arm deletion, suggesting that the activity requires formation of σNS oligomers. Our studies provide structural and mechanistic insights into the function of σNS in reovirus replication.
59 BASIC BIOLOGICAL SCIENCES↗
Structural Asymmetry and Chiral-Induced Spin Selectivity in Chiral Palladium-Halide Semiconductors
Chiral Pb-free metal-halide semiconductors (MHSs) have attracted considerable attention in the field of spintronics due to various interesting spin-related properties and chiral-induced spin selectivity (CISS) effect. Despite their excellent chemical and structural tunability, the material scope and crystal structure of Pb-free chiral MHSs exhibiting the CISS effect are still limited; chiral MHSs that have metal-halide structures of octahedra and tetrahedra are only reported. Here, we report a new class of chiral MHSs, of which palladium (Pd)-halides are formed in 1D square-pyramidal structures or 0D square-planar structures, with a general formula of ((R/S-MBA) 2 PdBr 4 ) 1-x ((R/S-MBA) 2 PdCl 4 ) x (MBA = methylbenzylammonium; x = 0, 0.25, 0.5, 0.75, and 1) for the first time. The crystals adopt the 1D helical chain of Pd-halide square-pyramid (for x = 0, 0.25, 0.5, and 0.75) and 0D structure of Pd-halide square-plane (for x = 1). All the Pd-halides are distorted by the interaction between the halide and the chiral organic ammonium and arranged in a noncentrosymmetric position. Circular dichroism (CD) for ((R/S-MBA) 2 PdBr 4 ) 1-x ((R/S-MBA) 2 PdCl 4 ) x indicates that chirality was transferred from chiral organic ammonium to Pd-halide inorganics. ((R-MBA) 2 PdBr 4 ) 1-x ((R-MBA) 2 PdCl 4 ) x (x = 0, 0.25, 0.5, and 0.75) shows a distortion index of 0.127-0.128, which is the highest value among the previously reported chiral MHSs to the best of our knowledge. We also find that (R/S-MBA) 2 Pd(Br 1-x Cl x ) 4 crystals grow along the out-of-plane direction during spin coating and have high c-axis orientation and crystallinity, and (R/S-MBA) 2 Pd(Br 1-x Cl x ) 4 (x = 0 and 0.5) crystals exhibit a CISS effect in polycrystalline bulk films. In conclusion, these results demonstrate the possibility of a new metal-halide series with square-planar structures or square-pyramidal structures for future spintronic applications.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Mechanism of filament formation in UPA-promoted CARD8 and NLRP1 inflammasomes
NLRP1 and CARD8 are related cytosolic sensors that upon activation form supramolecular signalling complexes known as canonical inflammasomes, resulting in caspase-1 activation, cytokine maturation and/or pyroptotic cell death. NLRP1 and CARD8 use their C-terminal (CT) fragments containing a caspase recruitment domain (CARD) and the UPA (conserved in UNC5, PIDD, and ankyrins) subdomain for self-oligomerization, which in turn form the platform to recruit the inflammasome adaptor ASC (apoptosis-associated speck-like protein containing a CARD) or caspase-1, respectively. Here, we report cryo-EM structures of NLRP1-CT and CARD8-CT assemblies, in which the respective CARDs form central helical filaments that are promoted by oligomerized, but flexibly linked, UPAs surrounding the filaments. Through biochemical and cellular approaches, we demonstrate that the UPA itself reduces the threshold needed for NLRP1-CT and CARD8-CT filament formation and signalling. Structural analyses provide insights on the mode of ASC recruitment by NLRP1-CT and the contrasting direct recruitment of caspase-1 by CARD8-CT. We also discover that subunits in the central NLRP1 CARD filament dimerize with additional exterior CARDs, which roughly doubles its thickness and is unique among all known CARD filaments. Finally, we engineer and determine the structure of an ASC CARD –caspase-1 CARD octamer, which suggests that ASC uses opposing surfaces for NLRP1, versus caspase-1, recruitment. Together these structures capture the architecture and specificity of the active NLRP1 and CARD8 inflammasomes in addition to key heteromeric CARD-CARD interactions governing inflammasome signalling.
59 BASIC BIOLOGICAL SCIENCES↗