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At least 325 records · Page 18

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NASA NTRS1993

Encoding of head acceleration in vestibular neurons. I. Spatiotemporal response properties to linear acceleration

1. Extracellular recordings were made in and around the medial vestibular nuclei in decerebrated rats. Neurons were functionally identified according to their semicircular canal input on the basis of their responses to angular head rotations around the yaw, pitch, and roll head axes. Those cells responding to angular acceleration were classified as either horizontal semicircular canal-related (HC) or vertical semicircular canal-related (VC) neurons. The HC neurons were further characterized as either type I or type II, depending on the direction of rotation producing excitation. Cells that lacked a response to angular head acceleration, but exhibited sensitivity to a change in head position, were classified as purely otolith organ-related (OTO) neurons. All vestibular neurons were then tested for their response to sinusoidal linear translation in the horizontal head plane. 2. Convergence of macular and canal inputs onto central vestibular nuclei neurons occurred in 73% of the type I HC, 79% of the type II HC, and 86% of the VC neurons. Out of the 223 neurons identified as receiving macular input, 94 neurons were further studied, and their spatiotemporal response properties to sinusoidal stimulation with pure linear acceleration were quantified. Data were obtained from 33 type I HC, 22 type II HC, 22 VC, and 17 OTO neurons. 3. For each neuron the angle of the translational stimulus vector was varied by 15, 30, or 45 degrees increments in the horizontal head plane. In all tested neurons, a direction of maximum sensitivity was identified. An interesting difference among neurons was their response to translation along the direction perpendicular to that that produced the maximum response ("null" direction). For the majority of neurons tested, it was possible to evoke a nonzero response during stimulation along the null direction always had response phases that varied as a function of stimulus direction. 4. These spatiotemporal response properties were quantified in two independent ways. First, the data were evaluated on the basis of the traditional one-dimensional principle governed by the "cosine gain rule" and constant response phase at different stimulus orientations. Second, the response gain and phase values that were empirically determined for each orientation of the applied linear stimulus vector were fitted on the basis of a newly developed formalism that treats neuronal responses as exhibiting two-dimensional spatial sensitivity. Thus two response vectors were determined for each neuron on the basis of its response gain and phase at different stimulus directions in the horizontal head plane.(ABSTRACT TRUNCATED AT 400 WORDS).

NASA Discipline Neuroscience↗

DOE OSTI2023

Controlled catalyst-transfer polymerization in graphene nanoribbon synthesis

Exercising direct control over the unusual electronic structures arising from quantum confinement effects in graphene nanoribbons (GNRs) is intimately linked to geometric boundary conditions imposed by the structure of the ribbon. Besides composition and position of substitutional dopant atoms, the symmetry of the unit cell, width, length, and termination of a GNR govern its electronic structure. Here, we present a rational design that integrates each of these interdependent variables within a modular bottom-up synthesis. Our hybrid chemical approach relies on a catalyst-transfer polymerization that establishes excellent control over length, width, and end groups. Complemented by a surface-assisted cyclodehydrogenation step, uniquely enabled by matrix-assisted direct (MAD) transfer protocols, geometry and functional handles encoded in a polymer template are faithfully mapped onto the structure of the corresponding GNR. Bond-resolved scanning tunneling microscopy (BRSTM) and spectroscopy (STS) validate the robust correlation between polymer template design and GNR electronic structure.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Natural switches in behaviour rapidly modulate hippocampal coding

Throughout their daily lives, animals and humans often switch between different behaviours. However, neuroscience research typically studies the brain while the animal is performing one behavioural task at a time, and little is known about how brain circuits represent switches between different behaviours. Here we tested this question using an ethological setting: two bats flew together in a long 135 m tunnel, and switched between navigation when flying alone (solo) and collision avoidance as they flew past each other (cross-over). Bats increased their echolocation click rate before each cross-over, indicating attention to the other bat. Hippocampal CA1 neurons represented the bat’s own position when flying alone (place coding). Notably, during cross-overs, neurons switched rapidly to jointly represent the interbat distance by self-position. This neuronal switch was very fast—as fast as 100 ms—which could be revealed owing to the very rapid natural behavioural switch. The neuronal switch correlated with the attention signal, as indexed by echolocation. Interestingly, the different place fields of the same neuron often exhibited very different tuning to interbat distance, creating a complex non-separable coding of position by distance. Theoretical analysis showed that this complex representation yields more efficient coding. Overall, our results suggest that during dynamic natural behaviour, hippocampal neurons can rapidly switch their core computation to represent the relevant behavioural variables, supporting behavioural flexibility.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Database of Nonaqueous Proton-Conducting Materials

This work presents the assembly of 48 papers, representing 74 different compounds and blends, into a machine-readable database of nonaqueous proton-conducting materials. SMILES was used to encode the chemical structures of the molecules, and we tabulated the reported proton conductivity, proton diffusion coefficient, and material composition for a total of 3152 data points. The data spans a broad range of temperatures ranging from -70 to 260 °C. To explore this landscape of nonaqueous proton conductors, DFT was used to calculate the proton affinity of 18 unique proton carriers. The results were then compared to the activation energy derived from fitting experimental data to the Arrhenius equation. It was found that while the widely recognized positive correlation between the activation energy and proton affinity may hold among closely related molecules, this correlation does not necessarily apply across a broader range of molecules. This work serves as an example of the potential analyses that can be conducted using literature data combined with emerging research tools in computation and data science to address specific materials design problems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Building Neutron Scattering Infrastructure in Louisiana for Advanced Materials (Final Report)

The main objective of the Louisiana Consortium for Neutron Scattering (LaCNS) is to build a major neutron scattering infrastructure capable of treating both soft and hard materials. The goal is to create a sustainable effort having the quality, breadth, and depth necessary to produce competitive proposals including collaborative and center type proposals. Our scientific aim is to understand the role of coupling in emergent complex materials and its impact on the structure/property relationship and to explore how to tune the key couplings to guide the design of materials with the desired properties. This naturally includes building a base of users of the Spallation Neutron Source (SNS) and the High Flux Isotope Reactor (HFIR) in Louisiana; to train highly talented graduate and post-doctoral students in synthesis, neutron scattering, and simulation and modeling techniques, thereby helping to produce the next generation of scientist who use neutron scattering techniques as a crucial part of their research. The goal of our hard matter program is to understand the interplay between spin, charge, orbital, and lattice degrees of freedom in carefully selected complex materials. We have made considerable progress on number of complex systems including the oxide Sr3(Ru1-xMnx)2O7 where short-range magnetic ordering with anisotropic spin texture is initiated at the metal-insulator transition that clearly indicates a strong spin-charge coupling. Another critical area is in quantum materials. For example, in the topological semimetal BaMnSb2, we found a 3D canted antiferromagnetic Weyl semimetal with a 2D electronic structure and a nontrivial Berry phase. In addition, in the hexagonal chiral Mn1/3NbS2 system, we found soliton/soliton and soliton/antisoliton domain walls where the application of small fields or small currents can be used to control nanoscopic magnetic domains where the control of domain walls is crucially important for information storage. In addition, chemical transformation investigations were performed on the VISION instrument at Spallation Neutron Source (SNS). The soft matter effort was focused on understanding the role of non-covalent interactions on the structure and dynamics of fluid-based soft matter. One key focus was on sequence-defined (SD) amphiphilic peptoid polymers that allow encoding of molecular interactions and thereby systematic investigations of how charge directs the solution self-assembly of amphiphilic polymers in water. Another important area was on the dynamics of lipids self-assembled into membranes for exploring the permeability and mechanical using both neutron spin echo (NSE) spectroscopy and quasielastic neutron scattering (QENS) to distinguished between viscoelasticity and permeability at the molecular scale. Overall, the LaCNS project was quite successful, generating 145 publications and 245 presentations. Our graduate and post-doctoral students were well trained resulting in positions in national laboratories (Oak Ridge National Laboratory (ORNL), Argonne National Laboratory and Los Alamos National Laboratory), major research universities, and industry. We also developed a uniaxial pressure cell along with ORNL for SNS. A critical goal of this project was to establish a foundation for competing nationally in federally funded research programs. To this end, we were quite successful in generating over twenty-two federally and non-federally funded grants including awards from NSF, DOE, and DOD, and two early career awards. Equally important, we were able to secure a key major piece of instrumentation via a large ARO grant for a state-of-the-art electron microscope.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Signal Transduction Pathways of Chloroplast Quality Control (Final Report)

Chloroplasts (photosynthetic plastids) of higher plants contain about 3000 proteins of which more than 95% are encoded by nuclear genes. To avoid the accumulation of reactive oxygen species that are the inherent by-product of photosynthesis, gene expression of these spatially separated genomes is regulated by two-way signaling. Thus, while plastid differentiation and development are largely under nuclear control, developmentally arrested or damaged plastids can regulate expression of nuclear genes via retrograde signaling pathways. In previous years of DOE-funded study, we performed a number of genetic screens that implicated the chloroplast-localized tetrapyrrole biosynthesis pathway as the source of both positive and stress-related retrograde signals. Using that work as a foundation, we have recently uncovered a new type of retrograde signal that leads to the selective removal of damaged chloroplasts from the cell. However, the mechanisms of such a chloroplast quality control pathway are not well characterized or understood.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Human sperm TMEM95 binds eggs and facilitates membrane fusion

Tmem95 encodes a sperm acrosomal membrane protein, whose knockout has a male-specific sterility phenotype in mice. Tmem95 knockout murine sperm can bind to, but do not fuse with, eggs. How TMEM95 plays a role in membrane fusion of sperm and eggs has remained elusive. Here, we utilize a sperm penetration assay as a model system to investigate the function of human TMEM95. We show that human TMEM95 binds to hamster egg membranes, providing evidence for a TMEM95 receptor on eggs. Using X-ray crystallography, we reveal an evolutionarily conserved, positively charged region of TMEM95 as a putative receptor-binding surface. Amino acid substitutions within this region of TMEM95 ablate egg-binding activity. We identify monoclonal antibodies against TMEM95 that reduce the number of human sperm fused with hamster eggs in sperm penetration assays. Strikingly, these antibodies do not block binding of sperm to eggs. Taken together, these results provide strong evidence for a specific, receptor-mediated interaction of sperm TMEM95 with eggs and suggest that this interaction may have a role in facilitating membrane fusion during fertilization.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Hyper Spectral Anomaly Detection

The HSA is a statistics based anomaly detection model. The model performs unsupervised anomaly detection, based on a datapoint's density and similarity within a dataset. Density and similarity data are encoded into an affinity matrix. The affinity matrix is evolved to summarize the data's structure on greater topographical scales within the data's function space. The set of evolved affinity matrices and an anomaly score vector are passed to a user defined penalized objective function. The penalized objective function of anomaly scores is then minimized. Data points where the absolute value of the z-scores of anomaly scores greater than a specified threshold are predicted as anomalies. A novel multi-filter feature has also been implemented. To reduce false positive rates, the multi-filter records the indexes of the HSA predictions. A new dataset and data loader are instantiated consisting of all the initial HSA predictions and non-anomalous data points in a 10% and 90% split respectively. The HSA is then run through this data set and a count of number of times a data point is predicted is kept. In this way the initial predictions may be compared with data spanning the entire dataset. After the multi-filter is complete, all datapoints will have an associated anomaly score, as well as a multi-filter prediction count to further filter the anomalous predictions.

Rogers, DempseyD [Idaho National Laboratory (INL),↗

NASA NTRS1999

Instrumentation and Methods to Measure Dynamic Forces During Exercise Using the Horizontal Exercise Machine

It is hypothesized that bone loss experienced by astronauts in zero gravity conditions may be curtailed by appropriate exercise. According to Wolf's law, bone regenerates when muscles produce stresses by pulling on the bone during daily activity and/or exercise on Earth. To use this theory to prevent or decrease bone loss, one needs to quantify musculoskeletal loads and relate them to bone density changes. In the context of the space program, it is desirable to determine musculoskeletal loads during exercise so that one may make similar measurements on Earth and in space. In this manner, load measurements on Earth may be used as reference to generate similar loads during exercise in space. A research project to investigate the effects of high-resistive exercise to decrease bone density loss underzero-gravity conditions is being carried out in Life Sciences Research Laboratories at NASA JSC. The project consists of a bed-rest study whereby subjects remain in horizontal position for seventeen weeks. During the study, a subset of those subjects executes a regime of resistive exercises in the horizontal exercise machine (HEM). The HEM was designed so that subjects remain horizontal while exercising to minimize gravity loading even during exercise. Bone density of each subject is measured throughout the duration of their participation. The objective of the study is to determine if the resistive exercises are effective in diminishing or eliminating bone loss. My participation in this project relates to instrumentation, measurement, and processing of signals from displacement sensors (optical encoders) and load-cells. Measurement of displacements will be used to determine the motion of the body during exercise, and load measurements will be used (along with displacement data) to determine forces and torques exerted on each section of the body during exercise. Further, I have assisted in specifying new sensors to be added to the HEM and to a new prototype resistive exercise machine called the Interim Resistive Exercise Device (IRED). New load cells and encoders should be mounted in these devices to obtain more complete kineto-dynamic information. This report includes a description of the instrumentation that was built to perform measurements in the HEM and the IRED, along with the software that was developed to collect the measurements. It also includes examples of measurements taken in the HEM. Finally, a plan is laid out that describes how these measurements may be used to determine forces exerted by muscles for each exercise.

Figueroa, Fernando↗

DOE OSTI2026

SEGUID v2: Extending SEGUID checksums for circular, linear, single- and double-stranded biological sequences

Background Synthetic biology involves combining different DNA fragments, each containing functional biological parts, to address specific problems. Fundamental gene-function research often requires cloning and propagating DNA fragments, such as those from the iGEM Parts Registry or Addgene, typically distributed as circular plasmids. Addgene’s repository alone offers around 150,000 plasmids. To ensure data integrity, cryptographic checksums can be calculated for the sequences. Each sequence has a unique checksum, making checksums useful for validation and quick lookups of associated annotations. For example, the SEGUID checksum uniquely identifies protein sequences with a 27-character string. Objectives The original SEGUID, while effective for protein sequences and single-stranded DNA (ssDNA), is not suitable for circular DNA since there is no natural starting position nor for double-stranded DNA (dsDNA) since two separate sequences are present. Challenges include how to uniquely represent linear dsDNA, circular ssDNA, and circular dsDNA. To meet these needs, we propose SEGUID v2, which extends the original SEGUID to handle additional types of sequences. Conclusions SEGUID v2 produces orientation and rotation invariant checksums for single-stranded, double-stranded, possibly staggered, linear, and circular DNA and RNA sequences. Customizable alphabets allow for other types of sequences. In contrast to the original SEGUID, which uses Base64, SEGUID v2 uses Base64url to encode the SHA-1 hash. This ensures SEGUID v2 checksums can be used as-is in filenames, regardless of platform, and in URLs, with minimal friction. Availability SEGUID v2 is readily available for major programming languages, distributed under the MIT license. JavaScript package seguid is available on npm, Python package seguid on PyPi, R package seguid on CRAN, and a Tcl script on GitHub. These tools, along with documentation, examples, and an online SEGUID Calculator , can be found at https://www.seguid.org .

Pereira, Humberto↗

DOE OSTI2025

Molecular and structural characterization of a Bacillus cereus strain producing an anthrax-like capsule

Bacillus cereus is a ubiquitous Gram-positive, spore-forming, rod-shaped saprophytic bacterium, occasionally reported to cause food-borne illnesses. However, instances of B. cereus strains harboring anthrax toxin and capsule genes have elevated certain strains as formidable pathogens and biothreats. This study focuses on the genomic analysis and the structural characterization of capsular material produced by the virulent B. cereus PATH2418 strain, isolated from the wound of a traumatic open fracture patient. The genome was sequenced using Nanopore MinION sequencing, revealing a chromosome of 5,270,283 bp and three plasmids. One plasmid, pATH1, was found to encode an operon for the biosynthesis of a bacterial capsule. This operon had sequence homology to the Bacillus anthracis capBCADE operon, which encodes the poly-γ-D-glutamate (PDGA) capsule. The capsule production in B. cereus PATH2418 was influenced by temperature and CO 2 levels. Structural analysis of the capsular material using a combined approach of nuclear magnetic resonance (NMR) and high-performance liquid chromatography (HPLC) techniques confirmed the presence of a high-molecular-weight poly-γ-glutamate capsule, with an enantiomeric composition of approximately 67% D-glutamic acid and 33% L-glutamic acid, matching that of B. anthracis.

Bacillus cereus↗

DOE OSTI2020

Surface plasmon polariton pulse shaping via two-dimensional Bragg grating pairs

Abstract We demonstrate control over the spatial and temporal properties of surface plasmon polaritons (SPPs) launched from nanohole arrays in silver. The arrays provide wave vector matching to allow the conversion of free-space photons into counter-propagating SPPs. SPPs launched from multiple arrays interfere at well-defined spatial positions, and the interference fringes form an all-SPP periodic nano-optical grating which evolves in space and time as the SPPs propagate. The spatio-temporal characteristics of the optical grating can be tuned through various nanohole array parameters such as tilt angle, separation, and array width. In addition, we examine multiperiodic arrays (MPAs) consisting of arrays with different pitches placed adjacent to one another. This platform allows the temporal interference of SPPs with different central wavelengths to be tailored through the MPA geometric and structural parameters. The temporal interference serves as an encoded signal, whereby the frequency components can be controlled by the array properties.

79 ASTRONOMY AND ASTROPHYSICS↗

NASA NTRS1993

Recent experiences with implementing a video based six degree of freedom measurement system for airplane models in a 20 foot diameter vertical spin tunnel

A model space positioning system (MSPS), a state-of-the-art, real-time tracking system to provide the test engineer with on line model pitch and spin rate information, is described. It is noted that the six-degree-of-freedom post processor program will require additional programming effort both in the automated tracking mode for high spin rates and in accuracy to meet the measurement objectives. An independent multicamera system intended to augment the MSPS is studied using laboratory calibration methods based on photogrammetry to characterize the losses in various recording options. Data acquired to Super VHS tape encoded with Vertical Interval Time Code and transcribed to video disk are considered to be a reasonable priced choice for post editing and processing video data.

Snow, Walter L.↗

NASA NTRS2009

Hardware Implementation of Serially Concatenated PPM Decoder

A prototype decoder for a serially concatenated pulse position modulation (SCPPM) code has been implemented in a field-programmable gate array (FPGA). At the time of this reporting, this is the first known hardware SCPPM decoder. The SCPPM coding scheme, conceived for free-space optical communications with both deep-space and terrestrial applications in mind, is an improvement of several dB over the conventional Reed-Solomon PPM scheme. The design of the FPGA SCPPM decoder is based on a turbo decoding algorithm that requires relatively low computational complexity while delivering error-rate performance within approximately 1 dB of channel capacity. The SCPPM encoder consists of an outer convolutional encoder, an interleaver, an accumulator, and an inner modulation encoder (more precisely, a mapping of bits to PPM symbols). Each code is describable by a trellis (a finite directed graph). The SCPPM decoder consists of an inner soft-in-soft-out (SISO) module, a de-interleaver, an outer SISO module, and an interleaver connected in a loop (see figure). Each SISO module applies the Bahl-Cocke-Jelinek-Raviv (BCJR) algorithm to compute a-posteriori bit log-likelihood ratios (LLRs) from apriori LLRs by traversing the code trellis in forward and backward directions. The SISO modules iteratively refine the LLRs by passing the estimates between one another much like the working of a turbine engine. Extrinsic information (the difference between the a-posteriori and a-priori LLRs) is exchanged rather than the a-posteriori LLRs to minimize undesired feedback. All computations are performed in the logarithmic domain, wherein multiplications are translated into additions, thereby reducing complexity and sensitivity to fixed-point implementation roundoff errors. To lower the required memory for storing channel likelihood data and the amounts of data transfer between the decoder and the receiver, one can discard the majority of channel likelihoods, using only the remainder in operation of the decoder. This is accomplished in the receiver by transmitting only a subset consisting of the likelihoods that correspond to time slots containing the largest numbers of observed photons during each PPM symbol period. The assumed number of observed photons in the remaining time slots is set to the mean of a noise slot. In low background noise, the selection of a small subset in this manner results in only negligible loss. Other features of the decoder design to reduce complexity and increase speed include (1) quantization of metrics in an efficient procedure chosen to incur no more than a small performance loss and (2) the use of the max-star function that allows sum of exponentials to be computed by simple operations that involve only an addition, a subtraction, and a table lookup. Another prominent feature of the design is a provision for access to interleaver and de-interleaver memory in a single clock cycle, eliminating the multiple clock-cycle latency characteristic of prior interleaver and de-interleaver designs.

Moision, Bruce↗

DOE OSTI2023

Encoding multistate charge order and chirality in endotaxial heterostructures

Abstract High-density phase change memory (PCM) storage is proposed for materials with multiple intermediate resistance states, which have been observed in 1 T -TaS 2 due to charge density wave (CDW) phase transitions. However, the metastability responsible for this behavior makes the presence of multistate switching unpredictable in TaS 2 devices. Here, we demonstrate the fabrication of nanothick verti-lateral H -TaS 2 /1 T -TaS 2 heterostructures in which the number of endotaxial metallic H -TaS 2 monolayers dictates the number of resistance transitions in 1 T -TaS 2 lamellae near room temperature. Further, we also observe optically active heterochirality in the CDW superlattice structure, which is modulated in concert with the resistivity steps, and we show how strain engineering can be used to nucleate these polytype conversions. This work positions the principle of endotaxial heterostructures as a promising conceptual framework for reliable, non-volatile, and multi-level switching of structure, chirality, and resistance.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

High-Accuracy Angle Generator for Angular Calibrations to Support Optical Metrology Laboratories and Light Source Facilities

The overarching vision for this project was to build the most accurate full-rotation angular positioning system in the Americas, and that goal remains. In labs performing similar work, the environment is typically closer to a clean room than an office space, like we had before the upgrades. We are now positioned to achieve our intended result with our upgraded infrastructure, system hardware, calibration techniques, and software. As detailed below, the combination of the pandemic schedule and technical challenges have set us back, but we will continue on the path toward our vision beyond the end of this Phase 2. It’s too important for us, for industry, and for the nation not to do so.

47 OTHER INSTRUMENTATION↗

DOE OSTI2024

Identification and characterization of the low molecular mass ferredoxins involved in central metabolism in Heliomicrobium modesticaldum

The homodimeric Type I reaction center (RC) from Heliomicrobium modesticaldum lacks the PsaC subunit found in Photosystem I and instead uses the interpolypeptide [4Fe–4S] cluster F X as the terminal electron acceptor. Our goal was to identify which of the small mobile dicluster ferredoxins encoded by the H. modesticaldum genome are capable of accepting electrons from the heliobacterial RC (HbRC) and pyruvate:ferredoxin oxidoreductase (PFOR), a key metabolic enzyme. Analysis of the genome revealed seven candidates: HM1_1462 (PshB1), HM1_1461 (PshB2), HM1_2505 (Fdx3), HM1_0869 (FdxB), HM1_1043, HM1_0357, and HM1_2767. Heterologous expression in Escherichia coli and studies using time-resolved optical spectroscopy revealed that only PshB1, PshB2, and Fdx3 are capable of accepting electrons from the HbRC and PFOR. Modeling studies using AlphaFold show that only PshB1, PshB2, and Fdx3 should be capable of docking on PFOR at a positively charged patch that overlays a surface-proximal [4Fe–4S] cluster. Proteomic analysis of wild-type and gene deletion strains ΔpshB1, ΔpshB2, ΔpshB1pshB2, and Δfdx3 grown under nitrogen-replete conditions revealed that Fdx3 is undetectable in the wild-type, ΔpshB1, and Δfdx3 strains, but it is present in the ΔpshB2 and ΔpshB1pshB2 strains, implying that Fdx3 may substitute for PshB2. When grown under nitrogen-deplete conditions, Fdx3 is present in the wild-type and all deletion strains except for Δfdx3. None of the knockout strains demonstrated significant impairment during chemotrophic dark growth on pyruvate, photoheterotrophic light growth on pyruvate, or phototrophic growth on acetate+CO 2 , indicating a high degree of redundancy among these three electron transfer proteins. As a result, loss of both PshB1 and PshB2, but not FdxB, resulted in poor growth under N 2 -fixing conditions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Structure of the poxvirus decapping enzyme D9 reveals its mechanism of cap recognition and catalysis

Poxviruses encode decapping enzymes that remove the protective 5' cap from both host and viral mRNAs to commit transcripts for decay by the cellular exonuclease Xrn1. Decapping by these enzymes is critical for poxvirus pathogenicity by means of simultaneously suppressing host protein synthesis and limiting the accumulation of viral double-stranded RNA (dsRNA), a trigger for antiviral responses. Here we present a high-resolution structural view of the vaccinia virus decapping enzyme D9. This Nudix enzyme contains a domain organization different from other decapping enzymes in which a three-helix bundle is inserted into the catalytic Nudix domain. The 5' mRNA cap is positioned in a bipartite active site at the interface of the two domains. Specificity for the methylated guanosine cap is achieved by stacking between conserved aromatic residues in a manner similar to that observed in canonical cap-binding proteins VP39, eIF4E, and CBP20, and distinct from eukaryotic decapping enzyme Dcp2.

59 BASIC BIOLOGICAL SCIENCES↗