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At least 73 records · Page 4

Enabling groundbreaking experiments that advance our understanding of the universe through accurate target specifications

The Target Fabrication (TFAB) team at the National Ignition Facility (NIF) is tasked with assembling and qualifying targets for physics experiments. These targets are critical components used in experiments that advance research in areas such as fusion energy, high-energy-density physics, and astrophysics. Target Fabrication Engineers (TFEs) are responsible for producing and validating target specifications, which are compiled into detailed specification packages. TFAB produces hundreds of targets annually, with each target requiring several specification datasheets that culminate in a comprehensive specification package. TFAB needs an efficient and accurate means to generate these specification datasheets to maintain the rigorous NIF shot schedule.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

On Transforming the Specific Force Vector for an ECEF Inertial Navigation System

An inertial measurement unit accumulates the instantaneous specific force applied to the sensor over a small window of time. Importantly, this accumulation occurs in the sensor’s frame, yet the specific force must be mathematically integrated in a different navigation frame, and these two frames may be rotating with respect to each other. Consequently, a correction is needed to not only account for the frame difference but also for the time variation in the frame difference. Many references provide derivations of this correction [1], but the derivation is often abbreviated, and important assumptions are sometimes left unstated. This memo addresses this gap and provides a clear derivation of the specific force transform with all assumptions specifically stated. This derivation is specific to the Earth-centered, Earth-fixed navigation frame, but, hopefully, the derivation is sufficiently clear that readers can apply it to other navigation frames. Generally, notation follows the same format as described in both [1, 2].

47 OTHER INSTRUMENTATION↗

Renewable Energy and Efficiency Technologies in Scenarios of U.S. Decarbonization in Two Types of Models: Comparison of GCAM Modeling and Sector-Specific Modeling

Energy system projections from analytic models inform actions ranging from short-term and local decisions, such as technology and infrastructure deployment, to global and long-term negotiations and targets. Computational limits require the designers of these models to trade off between coverage and resolution. Some models, such as the Global Change Analysis Model (GCAM), represent all energy sources and uses but at a relatively coarse level of resolution. GCAM balances global supply and demand of all energy carriers by endogenously projecting prices for energy sources and costs of greenhouse gas mitigation while capturing interlinkages between the energy system, water, agriculture and land use, the economy, and the climate. This global model was used to frame the Long-Term Strategy released by the White House in 2021 and has been used to inform national and global economy-wide decarbonization discussions and strategy development for decades. Other models instead focus on a portion of the energy sector with greater detail and resolution. The Regional Energy Deployment System (ReEDS) electricity-sector model, for example, projects capacity expansion with an emphasis on integration of variable renewable energy into the grid of the future. The Transportation Energy and Mobility Pathway Options (TEMPO) transportation-sector model enables analysis of household choices in adoption, charging, and use of electric vehicles. The Scout buildings-sector model supports detailed consideration of the policies and markets that can accelerate the adoption of energy conservation measures in buildings. Such sector-specific models are instrumental in informing technology research, sectoral planning strategies, and sector-specific aspects of greenhouse gas (GHG) mitigation strategies in the United States. These global and sector-specific modeling approaches can complement each other. The global approach ensures consistent, endogenous energy pricing and resource allocation, which can substantially diverge from current conditions in transformative scenarios, while the sector-specific approach facilitates representation of granular details across spatial, temporal, technological, and market dimensions that enable exploration of particular interactions and trade-offs. This report presents the results of recent work to explore the differences and tradeoffs between these approaches by comparing GCAM with the sector-specific ReEDS, TEMPO, and Scout models. The report compares both model structures and results, and discusses their potential relevance and applications.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

SPC-70486 Rev 0 Stirling Engine Prototype Performance Specification

Idaho National Laboratory (INL) is developing a small microreactor to produce electrical power utilizing a small nuclear core and Stirling engines under the Microreactor Application Research Validation and Evaluation (MARVEL) program. The purpose of this performance specification is to define requirements to build and test the Stirling Engine prototype, including interfacing with Kinnetech in the development/test of the engines. This specification includes prototyping components only and are not for use in the reactor. Prototype testing is a preliminary test to be conducted with conceptual equipment from which a final design will be developed. The results of the testing defined herein will not be used as a qualification test. The Stirling Engines have an engine controller module (QEC). Currently, the QEC doesn’t have a means to stop the engine. An analog controlled engine braking system must be developed and tested with the engine prototype. Any conflict between this specification and any supplementary specifications in the procurement documents requires written clarification from the Contractor prior to proceeding with any work. Any deviation from the procurement documents requires approval by the Contractor with the change request process.

21 - SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLAN↗

Spatial Study 2021: Sensor-Based Time Series of Surface Water Temperature, Specific Conductance, Total Dissolved Solids, pH, and Dissolved Oxygen from across Multiple Watersheds in the Yakima River Basin, Washington, USA (v3)

This dataset supports a broader study examining the drivers of spatial variability in sediment respiration rates in the Yakima River Basin. The dataset provides two-hour time series hydrological and water chemistry sensor data, manual chamber open channel respiration data, handheld sensor water chemistry data, river substrate grain size photos, general environmental context photos, and field metadata (including qualitative information on instream and river corridor characteristics) collected during the same two-week period at 47 sites within multiple rivers throughout the Yakima River Basin in Washington, USA. Grain size photos can be used to improve estimates of channel substrate D50 data. Related sample-based water chemistry data are published separately at https://data.ess-dive.lbl.gov/datasets/doi:10.15485/1898914.This dataset is comprised of four main folders, one containing three sensor-specific subfolders and the others containing photographs. The SFA_SpatialStudy_2021_SensorData main data folder includes file-level metadata (FLMD), data dictionary (dd), installation methods, field metadata, Ultrameter water chemistry data, field data collection protocols, international generic sample number (IGSN) mapping file, and a readme file. The “Sensor_Manual_Specifications” subfolder contains pdf files from the manufacturer of each sensor with details on the sensor specifications. Each sensor subfolder (BarotrollAtm, MantaRiver, and MinidotManualChamber) contains a sensor data subfolder for timeseries data and a subfolder for plots and summary statistics. The BarotrollAtm Data subfolder contains In Situ Rugged BaroTROLL pressure and temperature data. The MantaRiver Data subfolder contains Eureka Manta+ 35B multisonde temperature, specific conductance, and pH data. The MinidotManualChamber Data subfolder contains PME MiniDOT Logger dissolved oxygen (mg/L and percent saturation) and temperature data. The folder SFA_SpatialStudy_2021_EnvironmentalContextPhotos contains environmental context photographs and videos. The folders SFA_SpatialStudy_2021_SedimentQuadratPhotos_Part1 and SFA_SpatialStudy_2021_SedimentQuadratPhotos_Part2 contain sediment quadrat photographs. All files are .csv, .pdf, .R, .jpg, .jpeg, .mp4, or .mov. This data package was originally published September 2022. It was updated January 2023 (modified files) and June 2024 (new and modified files). See the change history in data package readme for more details.We acknowledge the Yakama Nation as owners and caretakers of the lands where we collected these data. We thank the Confederated Tribes and Bands of the Yakama Nation Tribal Council and Yakama Nation Fisheries for working with us to facilitate sample collection and optimization of data usage according to their values and worldview.

54 ENVIRONMENTAL SCIENCES↗

Structural and functional validation of a highly specific Smurf2 inhibitor

Smurf1 and Smurf2 are two closely related member of the HECT (homologous to E6AP carboxy terminus) E3 ubiquitin ligase family and play important roles in the regulation of various cellular processes. Both were initially identified to regulate transforming growth factor‐β and bone morphogenetic protein signaling pathways through regulating Smad protein stability and are now implicated in various pathological processes. Generally, E3 ligases, of which over 800 exist in humans, are ideal targets for inhibition as they determine substrate specificity; however, there are few inhibitors with the ability to precisely target a particular E3 ligase of interest. In this work, we explored a panel of ubiquitin variants (UbVs) that were previously identified to bind Smurf1 or Smurf2. In vitro binding and ubiquitination assays identified a highly specific Smurf2 inhibitor, UbV S2.4, which was able to inhibit ligase activity with high potency in the low nanomolar range. Orthologous cellular assays further demonstrated high specificity of UbV S2.4 toward Smurf2 and no cross‐reactivity toward Smurf1. Structural analysis of UbV S2.4 in complex with Smurf2 revealed its mechanism of inhibition was through targeting the E2 binding site. In summary, we investigated several protein‐based inhibitors of Smurf1 and Smurf2 and identified a highly specific Smurf2 inhibitor that disrupts the E2–E3 protein interaction interface.

59 BASIC BIOLOGICAL SCIENCES↗

Zika-specific neutralizing antibodies targeting inter-dimer envelope epitopes

Zika virus (ZIKV) is an emerging pathogen that causes devastating congenital defects. The overlapping epidemiology and immunologic cross-reactivity between ZIKV and dengue virus (DENV) pose complex challenges to vaccine design, given the potential for antibody-dependent enhancement of disease. Therefore, classification of ZIKV-specific antibody targets is of notable value. From a ZIKV-infected rhesus macaque, we identify ZIKV-reactive B cells and isolate potent neutralizing monoclonal antibodies (mAbs) with no cross-reactivity to DENV. We group these mAbs into four distinct antigenic groups targeting ZIKV-specific cross-protomer epitopes on the envelope glycoprotein. Co-crystal structures of representative mAbs in complex with ZIKV envelope glycoprotein reveal envelope-dimer epitope and unique dimer-dimer epitope targeting. All four specificities are serologically identified in convalescent humans following ZIKV infection, and representative mAbs from all four groups protect against ZIKV replication in mice. These results provide key insights into ZIKV-specific antigenicity and have implications for ZIKV vaccine, diagnostic, and therapeutic development.

59 BASIC BIOLOGICAL SCIENCES↗

Position-specific carbon isotopes of Murchison amino acids elucidate extraterrestrial abiotic organic synthesis networks

The Murchison meteorite is a well-studied carbonaceous chondrite with relatively high concentrations of amino acids thought to be endogenous to the meteorite, in part because they are characterized by carbon isotope (δ 13 C) values higher than those typical of terrestrial amino acids. Past studies have proposed that extraterrestrial amino acids in the Murchison meteorite could have formed by Strecker synthesis (for α-amino acids), Michael addition (for β-amino acids), or reductive amination, but a lack of constraints have prevented confident discrimination among these possibilities, or assignment of specific formation pathways to each of several specific amino acids. Position-specific carbon isotope analysis differentiates amongst these mechanisms by relating molecular sites to isotopically distinct carbon sources and by constraining isotope effects associated with elementary chemical reactions. Prior measurements of the position-specific carbon isotopic composition of α-alanine from the Murchison CM chondrite demonstrated that alanine’s high δ 13 C VPDB value is attributable to the amine carbon (δ 13 C VPDB = +142 ± 20‰), consistent with Strecker synthesis drawing on 13 C-rich carbonyl groups in precursors (Chimiak et al., 2021). Here, we measured the δ 13 C composition of fragment ions generated by electron impact ionization of derivatized α-alanine, β-alanine, and aspartic acid from Murchison via gas chromatography-Fourier transform mass spectrometry. α-Alanine’s amine carbon yielded δ 13 C VPDB = +109 ± 21‰, which is consistent with the previously measured value and with formation from 13 C-rich precursors. β-Alanine’s amine carbon presents a lower δ 13 C VPDB = +33 ± 24‰, which supports formation from 13 C-rich precursors but potentially via a Michael addition mechanism rather than Strecker synthesis. Aspartic acid’s amine carbon has δ 13 C VPDB = -14 ± 5‰, suggesting synthesis from precursors distinct from those that generated the alanine isomers. Further, these measurements indicate that Murchison amino acids are a mixture of compounds made from different synthesis mechanisms, though some subsets likely drew on the same substrates; this conclusion highlights the complexity of extraterrestrial organic synthesis networks and the potential of emerging methods of isotope ratio analysis to elucidate the details of those networks.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Direct Observations of Ion Densities at Functionalized Interfaces to Test Hypotheses Regarding the Origin of Specific Ion Effects

Interactions of anions with protonatable groups were investigated using X-ray fluorescence near total reflection (XFNTR) on floating monolayers at the surface of water. The number of ions attracted to the interfacial region, which XFNTR measures directly, is ion-specific as well as monolayer-specific. Our observation of the distinctly different behaviors of ClO 4 – and ReO 4 – , two ions with the same tetrahedral structure and almost the same sizes and hydration enthalpies, challenges current theories of ion specificity. Our observations are inconsistent with not only the Gouy–Chapman model (as expected) but also size-modified Poisson–Boltzmann theory and the “law of matching water affinity”. Furthermore, we suggest that factors other than ion size and ion–water interactions, including possibly ion–ion interactions and lateral ordering at the interface, must be considered to account for specific ion effects.

36 MATERIALS SCIENCE↗

Role of Intradomain Heterogeneity on Ion and Polymer Dynamics in Block Polymer Electrolytes: Investigating Interfacial Mobility and Ion-Specific Dynamics and Transport

Block polymers show promise as solid-state battery electrolytes due to the optimization of conductive and mechanical properties enabled via tuning of block chemistry and length. We investigate a polystyrene-block-poly(oligo-oxyethylene methacrylate) (PS-b-POEM) electrolyte doped with various lithium salts to investigate the role of molecular structure on ion transport properties and on local ion dynamics and associations. Anion charge becomes more delocalized with increasing size, reducing the coupling between salt ions while increasing coupling between ion and polymer chain motions and creating a more mobile overall environment. We observe support for this ion-polymer coupling via 1 H, 7 Li and 19 F NMR spectroscopy, from which we obtain ion-specific mobility transition temperatures that differ from the polymer glass transition temperature. We also note faster transport and weaker local energetic interactions with anion size using temperature-dependent NMR diffusometry. 1 H NMR spectroscopy further elucidates polymer chain dynamics and enables quantification of the temperature-dependent fraction of the conducting block that is immobile near the PS-POEM domain interface. As a result, NMR thus represents a species-specific and timescale-specific platform to quantify phase and interface behavior, and to correlate ion-specific transport with polymer chain dynamics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Isoform- and ligand-specific modulation of the adhesion GPCR ADGRL3/Latrophilin3 by a synthetic binder

Adhesion G protein-coupled receptors (aGPCRs) are cell-surface proteins with large extracellular regions that bind to multiple ligands to regulate key biological functions including neurodevelopment and organogenesis. Modulating a single function of a specific aGPCR isoform while affecting no other function and no other receptor is not trivial. Here, we engineered an antibody, termed LK30, that binds to the extracellular region of the aGPCR ADGRL3, and specifically acts as an agonist for ADGRL3 but not for its isoform, ADGRL1. The LK30/ADGRL3 complex structure revealed that the LK30 binding site on ADGRL3 overlaps with the binding site for an ADGRL3 ligand – teneurin. In cellular-adhesion assays, LK30 specifically broke the trans-cellular interaction of ADGRL3 with teneurin, but not with another ADGRL3 ligand – FLRT3. Our work provides proof of concept for the modulation of isoform- and ligand-specific aGPCR functions using unique tools, and thus establishes a foundation for the development of fine-tuned aGPCR-targeted therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗

Structural basis of agonist specificity of α 1A -adrenergic receptor

α 1 -adrenergic receptors (α 1 -ARs) play critical roles in the cardiovascular and nervous systems where they regulate blood pressure, cognition, and metabolism. However, the lack of specific agonists for all α 1 subtypes has limited our understanding of the physiological roles of different α 1 -AR subtypes, and led to the stagnancy in agonist-based drug development for these receptors. Here we report cryo-EM structures of α 1A -AR in complex with heterotrimeric G-proteins and either the endogenous common agonist epinephrine or the α 1A -AR-specific synthetic agonist A61603. These structures provide molecular insights into the mechanisms underlying the discrimination between α 1A -AR and α 1B -AR by A61603. Guided by the structures and corresponding molecular dynamics simulations, we engineer α 1A -AR mutants that are not responsive to A61603, and α 1B -AR mutants that can be potently activated by A61603. Together, these findings advance our understanding of the agonist specificity for α 1 -ARs at the molecular level, opening the possibility of rational design of subtype-specific agonists.

59 BASIC BIOLOGICAL SCIENCES↗

Using phage display for rational engineering of a higher-affinity humanized 3’ phosphohistidine-specific antibody

Abstract Histidine phosphorylation is a non-canonical post-translational modification (PTM), with 1-phosphohistidine (1-pHis) and 3-phosphohistidine (3-pHis) isoforms, that is understudied due to a lack of robust reagents, including high-affinity pHis-specific antibodies. Engineering pHis antibodies is challenging due to the labile nature of its phosphoramidate (P-N) bond. We developed a strategy for in vitro engineering of antibodies for the detection of native 3-pHis targets, in which the rabbit SC44-8 anti-3-pTza mAb is humanized into a scaffold (hSC44) that is suitable for phage display. Six unique Fab phage-displayed hSC44 scaffold libraries were screened for antibodies that bound 3-pHis with higher affinity and had specificity for 3-pHis versus 3-pTza. hSC44.20N32F L , the best engineered antibody, has ~10-fold higher affinity for 3-pHis than parental hSC44. Eleven new Fab structures, including the first antibody-pHis peptide structures, together with structural and quantum mechanical calculations, provided molecular insights into 3-pHis and 3-pTza discrimination by hSC44.20N32F L and the increased affinity obtained through engineering. We demonstrated the utility of these high-affinity 3-pHis-specific antibodies for the recognition of pHis proteins in mammalian cells by immunoblotting and immunofluorescence staining. Our work describes a general method for engineering labile PTM-specific antibodies and provides novel antibodies for investigating the role of 3-pHis in cell biology.

Martyn, Gregory D.↗

Integrating N -glycan and CODEX imaging reveal cell-specific protein glycosylation in healthy human lung

Identifying cell-specific glycan structures in human lungs is critical for understanding the chemistry and mechanisms that guide cell–cell and cell–matrix interactions and determining nuanced functions of specific glycosylation. Our dual-modality omics platform, which uses matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) to profile glycan chemistry at 50 μm × 50 μm scale, combined with co-detection by indexing (CODEX) to provide cell identification from the exact same tissue section, is a significant step in this direction. It enabled us to detect, differentiate, and reveal chemical properties of N-glycans in the various cell types of a human lung, suggesting the cell-specific function of distinct carbohydrate moieties. This innovative technological combination bridges the gap between the specific protein glycosylation and their cellular origin, paving the way for targeted studies in the lungs and many other human tissues where glycans mediate cell–cell recognition events.

Veličković, Dušan [Pacific Northwest National Labo↗

Multisubstrate specificity shaped the complex evolution of the aminotransferase family across the tree of life

Aminotransferases (ATs) are an ancient enzyme family that play central roles in core nitrogen metabolism, essential to all organisms. However, many of the AT enzyme functions remain poorly defined, limiting our fundamental understanding of the nitrogen metabolic networks that exist in different organisms. Here, we traced the deep evolutionary history of the AT family by analyzing AT enzymes from 90 species spanning the tree of life (ToL). We found that each organism has maintained a relatively small and constant number of ATs. Mapping the distribution of ATs across the ToL uncovered that many essential AT reactions are carried out by taxon-specific AT enzymes due to wide-spread nonorthologous gene displacements. This complex evolutionary history explains the difficulty of homology-based AT functional prediction. Biochemical characterization of diverse aromatic ATs further revealed their broad substrate specificity, unlike other core metabolic enzymes that evolved to catalyze specific reactions today. Interestingly, however, we found that these AT enzymes that diverged over billion years share common signatures of multisubstrate specificity by employing different nonconserved active site residues. These findings illustrate that AT family enzymes had leveraged their inherent substrate promiscuity to maintain a small yet distinct set of multifunctional AT enzymes in different taxa. This evolutionary history of versatile ATs likely contributed to the establishment of robust and diverse nitrogen metabolic networks that exist throughout the ToL. The study provides a critical foundation to systematically determine diverse AT functions and underlying nitrogen metabolic networks across the ToL.

59 BASIC BIOLOGICAL SCIENCES↗

An expectation–maximization framework for comprehensive prediction of isoform-specific functions

Advances in RNA sequencing technologies have achieved an unprecedented accuracy in the quantification of mRNA isoforms, but our knowledge of isoform-specific functions has lagged behind. There is a need to understand the functional consequences of differential splicing, which could be supported by the generation of accurate and comprehensive isoform-specific gene ontology annotations. We present isoform interpretation, a method that uses expectation–maximization to infer isoform-specific functions based on the relationship between sequence and functional isoform similarity. We predicted isoform-specific functional annotations for 85 617 isoforms of 17 900 protein-coding human genes spanning a range of 17 430 distinct gene ontology terms. Comparison with a gold-standard corpus of manually annotated human isoform functions showed that isoform interpretation significantly outperforms state-of-the-art competing methods. We provide experimental evidence that functionally related isoforms predicted by isoform interpretation show a higher degree of domain sharing and expression correlation than functionally related genes. We also show that isoform sequence similarity correlates better with inferred isoform function than with gene-level function.

59 BASIC BIOLOGICAL SCIENCES↗

Environment-specific virocell metabolic reprogramming

Abstract Viruses impact microbial systems through killing hosts, horizontal gene transfer, and altering cellular metabolism, consequently impacting nutrient cycles. A virus-infected cell, a “virocell,” is distinct from its uninfected sister cell as the virus commandeers cellular machinery to produce viruses rather than replicate cells. Problematically, virocell responses to the nutrient-limited conditions that abound in nature are poorly understood. Here we used a systems biology approach to investigate virocell metabolic reprogramming under nutrient limitation. Using transcriptomics, proteomics, lipidomics, and endo- and exo-metabolomics, we assessed how low phosphate (low-P) conditions impacted virocells of a marine Pseudoalteromonas host when independently infected by two unrelated phages (HP1 and HS2). With the combined stresses of infection and nutrient limitation, a set of nested responses were observed. First, low-P imposed common cellular responses on all cells (virocells and uninfected cells), including activating the canonical P-stress response, and decreasing transcription, translation, and extracellular organic matter consumption. Second, low-P imposed infection-specific responses (for both virocells), including enhancing nitrogen assimilation and fatty acid degradation, and decreasing extracellular lipid relative abundance. Third, low-P suggested virocell-specific strategies. Specifically, HS2-virocells regulated gene expression by increasing transcription and ribosomal protein production, whereas HP1-virocells accumulated host proteins, decreased extracellular peptide relative abundance, and invested in broader energy and resource acquisition. These results suggest that although environmental conditions shape metabolism in common ways regardless of infection, virocell-specific strategies exist to support viral replication during nutrient limitation, and a framework now exists for identifying metabolic strategies of nutrient-limited virocells in nature.

59 BASIC BIOLOGICAL SCIENCES↗

Essential amino acids in the Plant-Conserved and Class-Specific Regions of cellulose synthases

The Plant-Conserved Region (P-CR) and the Class-Specific Region (CSR) are two plant-unique sequences in the catalytic core of cellulose synthases (CESAs) for which specific functions have not been established. Here, we used site-directed mutagenesis to replace amino acids and motifs within these sequences predicted to be essential for assembly and function of CESAs. We developed an in vivo method to determine the ability of mutated CesA1 transgenes to complement an Arabidopsis (Arabidopsis thaliana) temperature-sensitive root-swelling1 (rsw1) mutant. Replacement of a Cys residue in the CSR, which blocks dimerization in vitro, rendered the AtCesA1 transgene unable to complement the rsw1 mutation. Examination of the CSR sequences from 33 diverse angiosperm species showed domains of high-sequence conservation in a class-specific manner but with variation in the degrees of disorder, indicating a nonredundant role of the CSR structures in different CESA isoform classes. The Cys residue essential for dimerization was not always located in domains of intrinsic disorder. Expression of AtCesA1 transgene constructs, in which Pro417 and Arg453 were substituted for Ala or Lys in the coiled-coil of the P-CR, were also unable to complement the rsw1 mutation. Despite an expected role for Arg457 in trimerization of CESA proteins, AtCesA1 transgenes with Arg457Ala mutations were able to fully restore the wild-type phenotype in rsw1. Our data support that Cys662 within the CSR and Pro417 and Arg453 within the P-CR of Arabidopsis CESA1 are essential residues for functional synthase complex formation, but our data do not support a specific role for Arg457 in trimerization in native CESA complexes.

59 BASIC BIOLOGICAL SCIENCES↗