The structure of the Clostridium thermocellum RsgI9 ectodomain provides insight into the mechanism o
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Mahoney, Brendan J.↗
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Functional Relevance of CASP16 Nucleic Acid Predictions as Evaluated by Structure Providers
ABSTRACT Accurate biomolecular structure prediction enables the prediction of mutational effects, the speculation of function based on predicted structural homology, the analysis of ligand binding modes, experimental model building, and many other applications. Such algorithms to predict essential functional and structural features remain out of reach for biomolecular complexes containing nucleic acids. Here, we report a quantitative and qualitative evaluation of nucleic acid structures for the CASP16 blind prediction challenge by 12 of the experimental groups who provided nucleic acid targets. Blind predictions accurately model secondary structure and some aspects of tertiary structure, including reasonable global folds for some complex RNAs; however, predictions often lack accuracy in the regions of highest functional importance. All models have inaccuracies in non‐canonical regions where, for example, the nucleic‐acid backbone bends, deviating from an A‐form helix geometry, or a base forms a non‐standard hydrogen bond (not a Watson‐Crick base pair). These bends and non‐canonical interactions are integral to forming functionally important regions such as RNA enzymatic active sites. Additionally, the modeling of conserved and functional interfaces between nucleic acids and ligands, proteins, or other nucleic acids remains poor. For some targets, the experimental structures may not represent the only structure the biomolecular complex occupies in solution or in its functional life cycle, posing a future challenge for the community.
Biochemistry & Molecular Biology↗
Structural basis of template strand deoxyuridine promoter recognition by a viral RNA polymerase
Recognition of promoters in bacterial RNA polymerases (RNAPs) is controlled by sigma subunits. The key sequence motif recognized by the sigma, the -10 promoter element, is located in the non-template strand of the double-stranded DNA molecule ~10 nucleotides upstream of the transcription start site. Here, we explain the mechanism by which the phage AR9 non-virion RNAP (nvRNAP), a bacterial RNAP homolog, recognizes the -10 element of its deoxyuridine-containing promoter in the template strand. The AR9 sigma-like subunit, the nvRNAP enzyme core, and the template strand together form two nucleotide base-accepting pockets whose shapes dictate the requirement for the conserved deoxyuridines. A single amino acid substitution in the AR9 sigma-like subunit allows one of these pockets to accept a thymine thus expanding the promoter consensus. Our work demonstrates the extent to which viruses can evolve host-derived multisubunit enzymes to make transcription of their own genes independent of the host.
59 BASIC BIOLOGICAL SCIENCES↗
Structure-based design of a strain transcending AMA1-RON2L malaria vaccine
Apical membrane antigen 1 (AMA1) is a key malaria vaccine candidate and target of neutralizing antibodies. AMA1 binds to a loop in rhoptry neck protein 2 (RON2L) to form the moving junction during parasite invasion of host cells, and this complex is conserved among apicomplexan parasites. AMA1-RON2L complex immunization achieves higher growth inhibitory activity than AMA1 alone and protects mice against Plasmodium yoelii challenge. Here, three single-component AMA1-RON2L immunogens were designed that retain the structure of the two-component AMA1-RON2L complex: one structure-based design (SBD1) and two insertion fusions. All immunogens elicited high antibody titers with potent growth inhibitory activity, yet these antibodies did not block RON2L binding to AMA1. The SBD1 immunogen induced significantly more potent strain-transcending neutralizing antibody responses against diverse strains of Plasmodium falciparum than AMA1 or AMA1-RON2L complex vaccination. This indicates that SBD1 directs neutralizing antibody responses to strain-transcending epitopes in AMA1 that are independent of RON2L binding. This work underscores the importance of neutralization mechanisms that are distinct from RON2 blockade. The stable single-component SBD1 immunogen elicits potent strain-transcending protection that may drive the development of next-generation vaccines for improved malaria and apicomplexan parasite control.
60 APPLIED LIFE SCIENCES↗
Piezosuperconductivity: Novel effects in noncentrosymmetric superconductors
Here we study effects in noncentrosymmetric superconductors arising from their unique coupling of Cooper-pair condensate and elasticity. We show that although the much discussed Lifshitz coupling is not observable in a uniform bulk state, it strikingly endows dislocations with a fractional magnetic flux. We also predict a generation of voltage-free strain by a DC current in a P- and T-breaking Josephson junction. Viewing superconductors through the lens of higher-form symmetries we identify the Lifshitz coupling as a chemical potential for the approximately conserved winding number, drawing an analogy with pyroelectric insulators.
36 MATERIALS SCIENCE↗
Substrate Channeling via a Transient Protein-Protein Complex: The case of D-Glyceraldehyde-3-Phosphate Dehydrogenase and L-Lactate Dehydrogenase
Molecular dynamics studies showed that LDH and GAPDH tetramers can form a complex which can breakdown when the enzymes are saturated with NADH molecules. The interaction sites are conserved between LDH isozymes from heart and muscle cells, and between GAPDH molecules from rabbit and yeast cells. Positive electric fields between the NAD(H) binding sites showed that NAD(H) channeling within LDH-GAPDH complex can be an extension of NAD(H) channeling between the adjacent subunits within LDH and GAPDH tetramers. Analytical ultracentrifugation and enzyme kinetics studies indicated that LDH and GAPDH molecules can form a transient channeling complex. The transient complex can support the channeled and the diffusive paths in parallel, the relative contribution from each path depends on the off-rates for (GAPDH-NADH)-LDH complex and GAPDH-NADH complex. Negative cooperativity in NADH binding to different subunits in GAPDH tetramers can provide allosteric regulation of NADH channeling from GAPDH to LDH.
INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMI↗
Insight into the autoproteolysis mechanism of the RsgI9 anti‐σ factor from Clostridium thermocellum
Abstract Clostridium thermocellum is a potential microbial platform to convert abundant plant biomass to biofuels and other renewable chemicals. It efficiently degrades lignocellulosic biomass using a surface displayed cellulosome, a megadalton sized multienzyme containing complex. The enzymatic composition and architecture of the cellulosome is controlled by several transmembrane biomass‐sensing RsgI‐type anti‐σ factors. Recent studies suggest that these factors transduce signals from the cell surface via a conserved RsgI extracellular (CRE) domain (also called a periplasmic domain) that undergoes autoproteolysis through an incompletely understood mechanism. Here we report the structure of the autoproteolyzed CRE domain from the C. thermocellum RsgI9 anti‐σ factor, revealing that the cleaved fragments forming this domain associate to form a stable α/β/α sandwich fold. Based on AlphaFold2 modeling, molecular dynamics simulations, and tandem mass spectrometry, we propose that a conserved Asn‐Pro bond in RsgI9 autoproteolyzes via a succinimide intermediate whose formation is promoted by a conserved hydrogen bond network holding the scissile peptide bond in a strained conformation. As other RsgI anti‐σ factors share sequence homology to RsgI9, they likely autoproteolyze through a similar mechanism.
Takayesu, Allen↗
Structure of an open K ATP channel reveals tandem PIP 2 binding sites mediating the Kir6.2 and SUR1 regulatory interface
ATP-sensitive potassium (K ATP ) channels, composed of four pore-lining Kir6.2 subunits and four regulatory sulfonylurea receptor 1 (SUR1) subunits, control insulin secretion in pancreatic β-cells. K ATP channel opening is stimulated by PIP 2 and inhibited by ATP. Mutations that increase channel opening by PIP 2 reduce ATP inhibition and cause neonatal diabetes. Although considerable evidence has implicated a role for PIP 2 in K ATP channel function, previously solved open-channel structures have lacked bound PIP 2 , and mechanisms by which PIP 2 regulates K ATP channels remain unresolved. Here, we report the cryoEM structure of a K ATP channel harboring the neonatal diabetes mutation Kir6.2-Q52R, in the open conformation, bound to amphipathic molecules consistent with natural C18:0/C20:4 long-chain PI(4,5)P 2 at two adjacent binding sites between SUR1 and Kir6.2. The canonical PIP 2 binding site is conserved among PIP 2 -gated Kir channels. The non-canonical PIP 2 binding site forms at the interface of Kir6.2 and SUR1. Functional studies demonstrate both binding sites determine channel activity. Kir6.2 pore opening is associated with a twist of the Kir6.2 cytoplasmic domain and a rotation of the N-terminal transmembrane domain of SUR1, which widens the inhibitory ATP binding pocket to disfavor ATP binding. The open conformation is particularly stabilized by the Kir6.2-Q52R residue through cation-π bonding with SUR1-W51. Together, these results uncover the cooperation between SUR1 and Kir6.2 in PIP 2 binding and gating, explain the antagonistic regulation of K ATP channels by PIP 2 and ATP, and provide a putative mechanism by which Kir6.2-Q52R stabilizes an open channel to cause neonatal diabetes.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Structural characterization of a GNAT family acetyltransferase from Elizabethkingia anophelis bound to acetyl-CoA reveals a new dimeric interface
General control non-repressible 5 (GCN5)-related N-acetyltransferases (GNATs) catalyse the acetylation of a diverse range of substrates, thereby orchestrating a variety of biological processes within prokaryotes and eukaryotes. GNAT enzymes can catalyze the transfer of an acetyl group from acetyl coenzyme A to substrates such as aminoglycoside antibiotics, amino acids, polyamines, peptides, vitamins, catecholamines, and large macromolecules including proteins. Although GNATs generally exhibit low to moderate sequence identity, they share a conserved catalytic fold and conserved structural motifs. In this current study we characterize the high-resolution X-ray crystallographic structure of a GNAT enzyme bound with acetyl-CoA from Elizabethkingia anophelis , an important multi-drug resistant bacterium. The tertiary structure is comprised of six α-helices and nine β-strands, and is similar with other GNATs. We identify a new and uncharacterized GNAT dimer interface, which is conserved in at least two other unpublished GNAT structures. This suggests that GNAT enzymes can form at least five different types of dimers, in addition to a range of other oligomers including trimer, tetramer, hexamer, and dodecamer assemblies. The high-resolution structure presented in this study is suitable for future in-silico docking and structure–activity relationship studies.
59 BASIC BIOLOGICAL SCIENCES↗
Parity- and Time-Reversal-Violating Nuclear Forces
Parity-violating and time-reversal conserving (PVTC) and parity-violating and time-reversal-violating (PVTV) forces in nuclei form only a tiny component of the total interaction between nucleons. The study of these tiny forces can nevertheless be of extreme interest because they allow one to obtain information on fundamental symmetries using nuclear systems. The PVTC interaction derives from the weak interaction between the quarks inside nucleons and nuclei, therefore the study of PVTC effects opens a window on the quark-quark weak interaction. The PVTV interaction is sensitive to more exotic interactions at the fundamental level, in particular to strong CP violation in the Standard Model Lagrangian, or even to exotic phenomena predicted in various beyond-the-Standard-Model scenarios. The presence of these interactions can be revealed either by studying various asymmetries in polarized scattering of nuclear systems, or by measuring the presence of non-vanishing permanent electric dipole moments of nucleons, nuclei and diamagnetic atoms and molecules. In this contribution, we review the derivation of the nuclear PVTC and PVTV interactions within various frameworks. We focus in particular on the application of chiral effective field theory, which allows for a more strict connection with the fundamental interactions at the quark level. We investigate PVTC and PVTV effects induced by these potentials on several few-nucleon observables, such as the longitudinal asymmetries in proton-proton scattering and the 3 He($\vec{n}$,p) 3 H reaction, the radiative neutron-proton capture, and the electric dipole moments of the deuteron and the trinucleon system.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
The N-terminus of varicella-zoster virus glycoprotein B has a functional role in fusion
Varicella-zoster virus (VZV) is a medically important alphaherpesvirus that induces fusion of the virion envelope and the cell membrane during entry, and between cells to form polykaryocytes within infected tissues during pathogenesis. All members of the Herpesviridae , including VZV, have a conserved core fusion complex composed of glycoproteins, gB, gH and gL. The ectodomain of the primary fusogen, gB, has five domains, DI-V, of which DI contains the fusion loops needed for fusion function. We recently demonstrated that DIV is critical for fusion initiation, which was revealed by a 2.8Å structure of a VZV neutralizing mAb, 93k, bound to gB and mutagenesis of the gB-93k interface. To further assess the mechanism of mAb 93k neutralization, the binding site of a non-neutralizing mAb to gB, SG2, was compared to mAb 93k using single particle cryogenic electron microscopy (cryo-EM). The gB-SG2 interface partially overlapped with that of gB-93k but, unlike mAb 93k, mAb SG2 did not interact with the gB N-terminus, suggesting a potential role for the gB N-terminus in membrane fusion. The gB ectodomain structure in the absence of antibody was defined at near atomic resolution by single particle cryo-EM (3.9Å) of native, full-length gB purified from infected cells and by X-ray crystallography (2.4Å) of the transiently expressed ectodomain. Both structures revealed that the VZV gB N-terminus (aa72-114) was flexible based on the absence of visible structures in the cryo-EM or X-ray crystallography data but the presence of gB N-terminal peptides were confirmed by mass spectrometry. Notably, N-terminal residues 109 KSQD 112 were predicted to form a small α-helix and alanine substitution of these residues abolished cell-cell fusion in a virus-free assay. Importantly, transferring the 109 AAAA 112 mutation into the VZV genome significantly impaired viral propagation. These data establish a functional role for the gB N-terminus in membrane fusion broadly relevant to the Herpesviridae .
59 BASIC BIOLOGICAL SCIENCES↗
Virtual Time III, Part 1: Unified Virtual Time Synchronization for Parallel Discrete Event Simulation
Algorithms for synchronization of parallel discrete event simulation have historically been divided between conservative methods that require lookahead but not rollback, and optimistic methods that require rollback but not lookahead. In this paper we present a new approach in the form of a framework called Unified Virtual Time (UVT) that unifies the two approaches, combining the advantages of both within a single synchronization theory. Whenever timely lookahead information is available, a logical process (LP) executes conservatively using an irreversible event handler. When lookahead information is not available the LP does not block, as it would in a classical conservative execution, but instead executes optimistically using a reversible event handler. The switch from conservative to optimistic synchronization and back is decided on an event-by-event basis by the simulator, transparently to the model code. UVT treats conservative synchronization algorithms as optional accelerators for an underlying optimistic synchronization algorithm, enabling the speed of conservative execution whenever it is applicable, but otherwise falling back on the generality of optimistic execution. We describe UVT in a novel way, based on fundamental invariants, monotonicity requirements, and synchronization rules. UVT permits zero-delay messages and pays careful attention to tie-handling using superposition. We prove that under fairly general conditions a UVT simulation always makes progress in virtual time. This is Part 1 of a trio of papers describing the UVT framework for PDES, mixing conservative and optimistic synchronization and integrating throttling control.
97 MATHEMATICS AND COMPUTING↗
Reassessing Hybrid Vigor or Hybrid Dysfunction Using Physiological Trade-Offs in an Endangered Salamander System
Fitness of interspecific hybrids can be higher or lower than that of their parental genotypes, with major ramifications for evolution and conservation. A recent study found that hybrid tiger salamanders had higher metabolic rates than their parental forms. Specifically, the ratio of resting metabolic rate to water loss, which was used as a measure of performance, was greater in hybrids. Recent genetic research showed that over half of the experimental subjects in that study were genetically pure California tiger salamanders (Ambystoma californiense) misclassified as hybrids. We reanalyzed the data using the corrected identification of hybrids and parentals. As expected, updating the classification revealed even stronger evidence for differences between hybrids and parentals. Hybrids had higher resting metabolic rates and greater water loss than parentals. The ratio of resting metabolic rate to water loss was also higher in hybrids. However, we suggest that this ratio might not be a positive measure of salamander performance. Higher metabolic rate means higher energy expenditure, and higher water loss suggests increased risk of desiccation. Both are major challenges for terrestrial amphibians, especially salamanders, which are hypothesized to be low-energy, low-water-loss specialists. Under this hypothesis, the ratio of energy expenditure to water loss is a ratio of two costs rather than a ratio of benefit to cost. While our analyses corroborate and strengthen the previous statistical results, we suggest that high resting metabolic rate is better interpreted as hybrid dysfunction, not vigor. Here, both hypotheses are speculative, and specific research on the fitness effects of these physiological differences is needed to resolve this important ecological question.
Ambystoma californiense↗
Deep learning symmetries and their Lie groups, algebras, and subalgebras from first principles
Abstract We design a deep-learning algorithm for the discovery and identification of the continuous group of symmetries present in a labeled dataset. We use fully connected neural networks to model the symmetry transformations and the corresponding generators. The constructed loss functions ensure that the applied transformations are symmetries and the corresponding set of generators forms a closed (sub)algebra. Our procedure is validated with several examples illustrating different types of conserved quantities preserved by symmetry. In the process of deriving the full set of symmetries, we analyze the complete subgroup structure of the rotation groups SO (2), SO (3), and SO (4), and of the Lorentz group S O ( 1 , 3 ) . Other examples include squeeze mapping, piecewise discontinuous labels, and SO (10), demonstrating that our method is completely general, with many possible applications in physics and data science. Our study also opens the door for using a machine learning approach in the mathematical study of Lie groups and their properties.
97 MATHEMATICS AND COMPUTING↗
Neutral-current neutrino scattering from the deuteron
Neutral-current neutrino scattering from the deuteron leading to proton-neutron final states is considered using an approach that incorporates relativistic dynamics and consequently provides robust modeling at relatively high energies and momenta. In this work the focus is placed on the fully exclusive reaction where both the proton and neutron in the final state are assumed to be detected. Accordingly, the incident neutrino energy, the neutrino scattering angle and the scattered neutrino's energy can all be reconstructed. It is shown that for specific choices of kinematics the reaction proceeds mainly via scattering from the proton, while for other choices of kinematics it proceeds mainly from the neutron. Specific asymmetries are introduced to focus on these attributes. Measurements in both regions have the potential to yield valuable information on the nucleon's electroweak form factors at momentum transfers up to a (GeV/c)$^2$. In particular, the cross sections are shown to be very sensitive to the isoscalar axial-vector form factor, and sensitive but less so to the magnetic strangeness form factor. Comparisons with other reactions, specifically charge-changing neutrino reactions and both parity-conserving and -violating electron scattering, have the potential to provide new ways to test the Standard Model.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
The REDTOP experiment: Rare $\eta/\eta^{\prime}$ Decays To Probe New Physics
The $\eta$ and $\eta^{\prime}$ mesons are nearly unique in the particle universe since they are almost Goldstone bosons and the dynamics of their decays are strongly constrained. The integrated $\eta$-meson samples collected in earlier experiments amount to $\sim10^{9}$ events. A new experiment, REDTOP (Rare Eta Decays To Probe New Physics), is being proposed, with the intent of collecting a data sample of order 10$^{14}$ $\eta$ (10$^{12}$ $\eta^{\prime}$) for studying very rare decays. Such statistics are sufficient for investigating several symmetry violations, and for searching for particles and fields beyond the Standard Model. In this work we present several studies evaluating REDTOP sensitivity to processes that couple the Standard Model to New Physics through all four of the so-called \emph{portals}: the Vector, the Scalar, the Axion and the Heavy Lepton portal. The sensitivity of the experiment is also adequate for probing several conservation laws, in particular $CP$, $T$ and Lepton Universality, and for the determination of the $\eta$ form factors, which is crucial for the interpretation of the recent measurement of muon $g-2$.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Energy-momentum-conserving stochastic differential equations and algorithms for the nonlinear Landau-Fokker-Planck equation
Coulomb collision is a fundamental diffusion process in plasmas that can be described by the Landau-Fokker-Planck (LFP) equation or the stochastic differential equation (SDE). While energy and momentum are conserved exactly in the LFP equation, they are conserved only on average by the conventional corresponding SDEs, suggesting that the underlying stochastic process may not be well defined by such SDEs. Here, in this study, we derive new SDEs with exact energy-momentum conservation for the Coulomb collision by factorizing the collective effect of field particles into individual particles and enforcing Newton's third law. These SDEs, when interpreted in the Stratonovich sense, have a particularly simple form that represents pure diffusion between particles without drag. To demonstrate that the new SDEs correspond to the LFP equation, we develop numerical algorithms that converge to the SDEs and preserve discrete conservation laws. Simulation results are presented in a benchmark of various relaxation processes.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Efficient Reformulation of Linear and Nonlinear Solid-Phase Diffusion in Lithium-ion Battery Models using Symmetric Polynomials: Mass Conservation and Computational Efficiency
Lithium-ion batteries are typically modeled using porous electrode theory coupled with various transport and reaction mechanisms, along with suitable discretization or approximations for the solid-phase diffusion equation. The solid-phase diffusion equation represents the main computational burden for typical pseudo-2-dimensional (p2D) models since these equations in the pseudo r -dimension must be solved at each point in the computational grid. This substantially increases the complexity of the model as well as the computational time. Traditional approaches towards simplifying solid-phase diffusion possess certain significant limitations, especially in modeling emerging electrode materials which involve phase changes and variable diffusivities. A computationally efficient representation for solid-phase diffusion is discussed in this paper based on symmetric polynomials using Orthogonal Collocation and Galerkin formulation (weak form). A systematic approach is provided to increase the accuracy of the approximation (p form in finite element methods) to enable efficient simulation with a minimal number of semi-discretized equations, ensuring mass conservation even for non-linear diffusion problems involving variable diffusivities. These methods are then demonstrated by incorporation into the full p2D model, illustrating their advantages in simulating high C-rates and short-time dynamic operation of Lithium-ion batteries.
25 ENERGY STORAGE↗