Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “structured”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,279 records · Page 71
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Revisiting the structures and phase transitions of Ba 2 NaNb 5 O 15

The room-temperature and low-temperature structure(s) of Ba 2 NaNb 5 O 15 (BNN) have been debated since the structure was proposed in the 1960s. This work revisits the structures and phase transitions of BNN, combining high-resolution X-ray and neutron powder diffraction with density functional theory calculations. Temperature-dependent high-resolution X-ray powder diffraction patterns are collected from 4 to 918 K, and sequential batch Rietveld refinement using a symmetry mode approach to describe the structure is used to extract the main structural changes as a function of temperature. The data show that the average structure of BNN is best described by the Ama2 space group, and no other structural phase transitions were observed below the ferroelastic transition. The symmetry mode analysis, combining results from diffraction and density functional theory, shows significant octahedral tilting and corrugations of both the A1 and A2 sites along the c direction. A strong correlation between the spontaneous strain and the octahedral tilting was observed, and a potential connection with emerging microstructure at low temperatures is proposed, all enabled by the symmetry mode approach used in this work.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Supply Chain Risk Management: Data Structuring

Supply chain risk management (SCRM) is an area of research that addresses both logistics concepts to maximize efficiency, reliability, and revenue as well as risk features, such as potential weak points, break points, and vulnerabilities within the supply chain. SCRM is used to find risks introduced at each node in a supply chain and how these risks can impact a company’s products, individuals, customers, and reputation. SCRM is a relatively new field, so standardized processes including data structuring are not fully documented. This paper explains the importance of a standard data structuring methodology and how it can enhance current SCRM efforts. Data ingest, structuring, and analysis are predominantly managed by humans. Automating some of the less complex steps can positively impact SCRM by allowing human analysts to focus on more strategic analyses. Types of data to be collected and structured are collected via publicly available information related to hardware, software, and corporate entities. After the data has been collected, the information is formatted in a specific manner, conforming to a schema, to allow for more effective and efficient ingest for further analysis. This paper outlines data structures used by Pacific Northwest National Laboratory for SCRM research and analysis purposes. These structures have been used for hundreds of analyses and have been successful in developing a common baseline. Data structuring is one of the first steps in data standardization, which will further mature and enhance the SCRM research area.

supply chain risk management, data structuring, re↗
DOE OSTI2024

Structure–property relations of sodium iron phosphate nuclear waste glasses: Effects of iron redox ratio and glass composition

Iron phosphate glasses, known for their exceptional chemical durability and potential applicability in nuclear waste management, have gained significant attention over the years. The structures of these glasses are complicated by the coexistence of Fe 3+ and Fe 2+ , which plays a crucial role in determining their structures and properties. Here, this work uses molecular dynamics simulations to study the structural changes in Na 2 O–Fe 2 O 3 –P 2 O 5 glasses with varying glass composition and Fe 2+ /Fe 3+ redox ratio. It was found that the redox ratio and modifier contents significantly affected the short-range and medium-range orders in the glasses. Significant changes in the local environments around P 5+ and Fe 3+ were observed, as reflected by the bond distances and coordination numbers. Na + cations are found to preferentially associate with Fe 3+ (rather than Fe 2+ ), whereas Fe 2+ has stronger association with P 5+ than Na + , confirming the structural role of Fe 2+ as a glass modifier. The disruptions in P–O–P linkages upon increasing FeO suggest that FeO causes glass depolymerization. These glasses achieved higher connectivity with increasing Fe 3+ / (Fe 3+ + Fe 2+ ) ratios, conerting phosphorous Q 2 to Q 3 units and iron Q 5 units to Q 4 units. The decrease of nonbridging oxygen fractions with increasing Fe 3+ / (Fe 3+ + Fe 2+ ) ratios, through creating P–O–Fe linkages, is the main reason of enhanced network connectivity. Quantitative structure–property relationship analyses with different structural descriptors were used to correlate with measured properties. The analyses provided valuable insights into structure–property relationships, emphasizing the importance of choosing relevant energy parameters and defining glass network connectivity, particularly in F net descriptors. It was found the Fe–O–P linkage density exhibits strong correlations to measured dissolution rates, supporting the importance of these linkages in improving the chemical durability in iron phosphate glasses.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2024

Forest structural complexity and ignition pattern influence simulated prescribed fire effects

Background: Forest structural characteristics, the burning environment, and the choice of ignition pattern each influence prescribed fire behaviors and resulting fire effects; however, few studies examine the influences and interactions of these factors. Understanding how interactions among these drivers can influence prescribed fire behavior and effects is crucial for executing prescribed fires that can safely and effectively meet management objectives. To analyze the interactions between the fuels complex and ignition patterns, we used FIRETEC, a three-dimensional computational fluid dynamics fire behavior model, to simulate fire behavior and effects across a range of horizontal and vertical forest structural complexities. For each forest structure, we then simulated three different prescribed fires each with a unique ignition pattern: strip-head, dot, and alternating dot. Results: Forest structural complexity and ignition pattern affected the proportions of simulated crown scorch, consumption, and damage for prescribed fires in a dry, fire-prone ecosystem. Prescribed fires in forests with complex canopy structures resulted in increased crown consumption, scorch, and damage compared to less spatially complex forests. The choice of using a strip-head ignition pattern over either a dot or alternating-dot pattern increased the degree of crown foliage scorched and damaged, though did not affect the proportion of crown consumed. We found no evidence of an interaction between forest structural complexity and ignition pattern on canopy fuel consumption, scorch, or damage. Conclusions: We found that forest structure and ignition pattern, two powerful drivers of fire behavior that forest managers can readily account for or even manipulate, can be leveraged to influence fire behavior and the resultant fire effects of prescribed fire. These simulation findings have critical implications for how managers can plan and perform forest thinning and prescribed burn treatments to meet risk management or ecological objectives.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Experimentally Validated Computational Modeling of Creep and Creep-Cracking for Nuclear Concrete Structures

In a Nuclear Power Plant, one of the most important components is the concrete nuclear reactor cavity, which serves both a structural and protective function as the biological radiation shield. Given that creep has been identified as a major knowledge gap in the assessment of nuclear structures (NUREG/CR-7153), this work helps to further the understanding of creep behavior of massive concrete containment structures for decades to enable safe and long-term operation of these facilities. This project has developed a robust, experimentally validated model to predict creep in nuclear concrete structures for up 60 years using short-term creep data thereby enabling a longer service life of critical facilities and early detection of structural failure. The work presented in this report is a pairing of computational and experimental methods. For the first time, the time temperature superposition (TTS) principle was successfully used to generate a uniaxial creep compliance master curve to predict mortar creep response for up to 22,500 days (nearly 60 years) at a reference temperature of 20°C. These data were used as input into finite element analysis (FEA) codes that use highly realistic random, 3D concrete microstructures from reconstructed coarse limestone aggregates. Finite element analysis performed provides the ability to quickly upscale mortar viscoelastic behavior to long-term concrete creep/relaxation data. A master creep compliance curve, constructed from the TTS principle, spanning 27 years, was used to validate two and a half decades of simulated concrete creep. Concurrently, three different simulated wall specimens were designed to mimic the behavior of post-tensioned concrete nuclear containment facility vessel walls over time as a result of concrete creep. The specimens were designed with different thicknesses, transverse and longitudinal reinforcement ratios, and level of post-tensioning stress. Each specimen contained various instrumentation to measure internal concrete temperature, concrete strain, and post-tensioning strain hourly for over 3 years. The concrete creep model developed in this project, based on the FEA concrete simulations, was applied to simulate the structural-scale experiments of prestressed concrete walls conducted in this project using the Grizzly code. These models can represent the effects of reinforcing and prestressing. Although there are some discrepancies with the experimental data, the model can predict the overall trends of the creep response in these experiments. One of these experimental models was also applied to an extended time to demonstrate how the findings from this study can be used to predict the behavior of actual structures of interest that have been in service for extended periods of time.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2021

AlphaFold Protein Structure Database for Sequence-Independent Molecular Replacement

Crystallographic phasing recovers the phase information that is lost during a diffraction experiment. Molecular replacement is a commonly used phasing method for crystal structures in the protein data bank. In one form it uses a protein sequence to search a structure database to find suitable templates for phasing. However, sequence information is not always available, such as when proteins are crystallized with unknown binding partner proteins or when the crystal is of a contaminant. The recent development of AlphaFold published the predicted protein structures for every protein from twenty distinct species. In this work, we tested whether AlphaFold-predicted E. coli protein structures were accurate enough to enable sequence-independent phasing of diffraction data from two crystallization contaminants of unknown sequence. Using each of more than 4000 predicted structures as a search model, robust molecular replacement solutions were obtained, which allowed the identification and structure determination of YncE and YadF. Our results demonstrate the general utility of the AlphaFold-predicted structure database with respect to sequence-independent crystallographic phasing.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Graph-Directed Approach for Downselecting Toxins for Experimental Structure Determination

Conotoxins are short, cysteine-rich peptides of great interest as novel therapeutic leads and of great concern as lethal biological agents due to their high affinity and specificity for various receptors involved in neuromuscular transmission. Currently, of the approximately 6000 known conotoxin sequences, only about 3% have associated structural characterization, which leads to a bottleneck in rapid high-throughput screening (HTS) for identification of potential leads or threats. In this work, we combine a graph-based approach with homology modeling to expand the library of conotoxin structures and to identify those conotoxin sequences that are of the greatest value for experimental structural characterization. The latter would allow for the rapid expansion of the known structural space for generating high quality template-based models. Our approach generalizes to other evolutionarily-related, short, cysteine-rich venoms of interest. Overall, we present and validate an approach for venom structure modeling and experimental guidance and employ it to produce a 290%-larger library of approximate conotoxin structures for HTS. We also provide a set of ranked conotoxin sequences for experimental structure determination to further expand this library.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Effect of Micro-Structural Dispersity of SiMo Ductile Iron on High Temperature Performance during Static Oxidation

High silicon and molybdenum (SiMo) ductile iron is commonly used for car exhaust systems, and its micro-structural dispersity depends on intrinsic parameters, which include alloy composition and inoculation efficiency, as well as extrinsic factors, such as casting wall thickness and molding material, which define cooling rate during solidification. Micro-structural dispersity is referred to as the degree of heterogeneity of sizes of structural constituencies within the microstructure. A variation in the micro-structural dispersity could impact the high temperature performance of SiMo ductile iron during static oxidation and transient thermo-mechanical loading conditions. In this study, static high temperature tests were performed on SiMo ductile iron solidified in a casting with varying wall thicknesses from 5 mm to 100 mm. The faster solidified specimens (taken from near chilled casting surfaces) had extremely high micro-structural dispersity as compared to the thicker section samples. After thermal exposure, each of the samples were characterized using 2D sections and 3D µCT images, and the results indicated an order of magnitude difference in graphite phase dispersity. The surface degradation was quantified after static oxidation experiments were implemented at temperature intervals between 650 °C and 800 °C. Non-destructive µCT 3D analysis and SEM/EDS were performed on cross sections and used to quantify the scale topology and structure. Carbon analysis was used to decouple the scale formation and decarburization phenomena that occurred within the samples. These methods enabled the quantification of the oxidation of the SiMo cast iron with different micro-structural dispersity levels after being exposed to high temperature static oxidation. Additionally, the complex material behavior during oxidation-assisted transient thermo-mechanical loading will be presented in a separate article.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Sparse and Random Sampling Techniques for High-Resolution, Full-Field, BSS-Based Structural Dynamics Identification from Video

Video-based techniques for identification of structural dynamics have the advantage that they are very inexpensive to deploy compared to conventional accelerometer or strain gauge techniques. When structural dynamics from video is accomplished using full-field, high-resolution analysis techniques utilizing algorithms on the pixel time series such as principal components analysis and solutions to blind source separation the added benefit of high-resolution, full-field modal identification is achieved. An important property of video of vibrating structures is that it is particularly sparse. Typically video of vibrating structures has a dimensionality consisting of many thousands or even millions of pixels and hundreds to thousands of frames. However the motion of the vibrating structure can be described using only a few mode shapes and their associated time series. As a result, emerging techniques for sparse and random sampling such as compressive sensing should be applicable to performing modal identification on video. This work presents how full-field, high-resolution, structural dynamics identification frameworks can be coupled with compressive sampling. The techniques described in this work are demonstrated to be able to recover mode shapes from experimental video of vibrating structures when 70% to 90% of the frames from a video captured in the conventional manner are removed.

47 OTHER INSTRUMENTATION↗
NASA NTRS1994

Control-nonlinear-nonstationary structural response and radiation near a supersonic jet

This paper is on the control of nonlinear-nonstationary vibration of a frame-stringer structure resulting from high levels of excitation from a nearby supersonic jet exhaust. The structure exhibits periodic, chaotic, or random behaviors when forced by high-intensity sound from a supersonic jet exhaust with 'shock' loading superimposed on a broadband response. The time history of the pressure, showing the rotation and flapping of the shock structure in the jet column due to large-scale instabilities, indicates that the response is not only nonlinear but also nonstationary. The acoustic pressure radiated by the structure also contains shocks and the formation of harmonics with distance. Control of the structural response is achieved by actively forcing the structure with an actuator at the shock oscillation frequency whose amplitude is locked into a self-control cycle. Results show that the peak power level is reduced by a factor of 63, or 18 dB. As a result, new broadband components emerge with at least four harmonics. At accelerating and decelerating supersonic speeds, the exhaust from the jet induces higher transient loading on the nearby flexible structure due to the occurrence of multiple shock from the jet.

TRT-EXPERIMENTAL↗
NASA NTRS2014

Proteins with Novel Structure, Function and Dynamics

Recently, a small enzyme that ligates two RNA fragments with the rate of 10(exp 6) above background was evolved in vitro (Seelig and Szostak, Nature 448:828‐831, 2007). This enzyme does not resemble any contemporary protein (Chao et al., Nature Chem. Biol. 9:81‐83, 2013). It consists of a dynamic, catalytic loop, a small, rigid core containing two zinc ions coordinated by neighboring amino acids, and two highly flexible tails that might be unimportant for protein function. In contrast to other proteins, this enzyme does not contain ordered secondary structure elements, such as alpha‐helix or beta‐sheet. The loop is kept together by just two interactions of a charged residue and a histidine with a zinc ion, which they coordinate on the opposite side of the loop. Such structure appears to be very fragile. Surprisingly, computer simulations indicate otherwise. As the coordinating, charged residue is mutated to alanine, another, nearby charged residue takes its place, thus keeping the structure nearly intact. If this residue is also substituted by alanine a salt bridge involving two other, charged residues on the opposite sides of the loop keeps the loop in place. These adjustments are facilitated by high flexibility of the protein. Computational predictions have been confirmed experimentally, as both mutants retain full activity and overall structure. These results challenge our notions about what is required for protein activity and about the relationship between protein dynamics, stability and robustness. We hypothesize that small, highly dynamic proteins could be both active and fault tolerant in ways that many other proteins are not, i.e. they can adjust to retain their structure and activity even if subjected to mutations in structurally critical regions. This opens the doors for designing proteins with novel functions, structures and dynamics that have not been yet considered.

Proteins↗
NASA NTRS2021

Damage Tolerance of Candidate Sandwich Structure for the Space Launch System (SLS) Payload Adapter Fitting (PAF)

This Technical Memorandum presents results from a damage tolerance study undertaken in support of the payload adapter fitting (PAF) for the Space Launch System (SLS) program at NASA’s Marshall Space Flight Center (MSFC). The study consisted of determining the compression-after-impact (CAI) strength of candidate carbon/epoxy face sheet sandwich structure that has been identified for potential use to manufacture the PAF hardware. Two types of core material that have been considered for use on the PAF structure were used in this study. One was an aluminum honeycomb and the other was a Rohacell foam. Levels of barely visible impact damage (BVID) were determined for the types of sandwich structure tested in this study and this level of damage was used for CAI strength testing. It was found that the honeycomb core sandwich structure failed by face sheet failure and the foam core sandwich structure failed by core shear failure. CAI strength values were normalized by weight of the sandwich structure since lower mass is desirable for this structure.

sandwich structure↗
NASA NTRSDate not supplied

Hot Structure Concepts and Materials for Space Exploration Project

Hot structures are multifunctional material systems that integrate the functions of thermal protection systems (TPS) and primary structure to increase mass efficiency in aerospace vehicles. The goal of this project was to improve our capabilities for developing lightweight, reusable, and reliable hot structures concepts to enable advanced space exploration missions. Specifically, current hot structure carbon/carbon (C/C) composite material systems have low interlaminar strength, which can lead to material failures at low load levels, and large material property variability in as-fabricated parts. Two parallel paths were followed to address these shortcomings. First, analysis models were developed to identify the conditions under which excessive interlaminar stresses occur and to evaluate the potential of stitching the C/C laminae to improve the interlaminar thermal-structural response. This effort included the development of high-fidelity, fracture-based thermal-structural finite element analysis models to evaluate critical features needed to produce efficient hot structure concepts. The second path focused on developing atomistic and mesoscale simulation tools to model the fabrication process in an effort to reduce the time and cost of production while improving the quality of the resulting parts. Aspects of the process currently being investigated include the infusion of the matrix precursor into the fiber preform, the cure of the precursor molecules into their polymeric form, and the carbonization and graphitization of the polymer to form the carbon matrix material. Results of the 6-month study are presented herein.

thermal↗
NASA NTRSDate not supplied

Structures and Materials Research at NASA Langley Research Center

NASA explores the unknown in air and space, innovates for the benefit of humanity, and inspires the world through discovery. The Structures and Materials discipline at NASA Langley Research Center supports this mission through advanced materials and manufacturing approaches applied to innovative structural concepts. We start with synthesizing novel material systems and applying tools and methods to predict and validate their static, dynamic, durability and damage tolerance behavior. We mature materials from test tube to test flight by developing manufacturing techniques that enable the advancement of aerospace structures from concept to reality. We develop advanced measurement techniques for health management and nondestructive evaluation. We draw on our structures and materials core capabilities to enable safe, reliable lightweight aerospace structures for application in all environments. You will find the results of our work in the assembly of large structures in space and on other planets, vehicles that carry crew into space, vehicles that operate at high speeds and in extreme environments, and technology for passenger and crew safety in commercial aviation. This presentation will provide an overview of Langley Research Center’s role within the agency, then focus on how current Structures and Materials research areas support a variety of NASA missions in space operations, exploration, and aeronautics.

Structures↗
NASA NTRS2022

Structural and chemical complexity of minerals: An update

The complexities of chemical composition and crystal structure are fundamental characteristics of minerals that have high relevance to the understanding of their stability, occurrence and evolution. This review summarises recent developments in the field of mineral complexity and outlines possible directions for its future elaboration. The database of structural and chemical complexity parameters of minerals is updated by H-correction of structures with unknown H positions and the inclusion of new data. The revised average complexity values (arithmetic means) for all minerals are 3.54(2) bits/atom and 345(10) bits/cell (based upon 4443 structure reports). The distributions of atomic information amounts, chemIG and strIG, versus the number of mineral species fit the normal modes, whereas the distributions of total complexities, chemIG,total and strIG,total, along with numbers of atoms per formula and per unit cell are log normal. The three most complex mineral species known today are ewingite, morrisonite and ilmajokite, all either discovered or structurally characterised within the last five years. The most important complexity-generating mechanisms in minerals are: (1) the presence of isolated large clusters; (2) the presence of large clusters linked together to form three-dimensional frameworks; (3) formation of complex three-dimensional modular frameworks; (4) formation of complex modular layers; (5) high hydration state in salts with complex heteropolyhedral units; and (6) formation of ordered superstructures of relatively simple structure types. The relations between symmetry and complexity are considered. The analysis of temporal dynamics of mineralogical discoveries since 1875 with the step of 25 years show the increasing chemical and structural complexities of human knowledge of the mineral kingdom in the history of mineralogy. In the Earth’s history, both diversity and complexity of minerals experience dramatic increases associated with the formation of Earth’s continental crust, initiation of plate tectonics and the Great Oxidation event.

complexity↗
DOE OSTI2021

Ab Initio Study of Atomic and Electronic Structure of Promising Ba4XMn3O12 (X = Nb, Ce, Pr) Oxides for Solar Thermochemical Hydrogen Production

The two-step metal oxide water-splitting cycle is one of the most viable approach for Solar Thermochemical Hydrogen (STCH) production. Challenges exist in finding suitable oxides that can satisfy thermodynamics of the STCH redox cycle under viable range of temperatures and partial pressures. Recently, BXM family members, i.e., Ba4NbMn3O12 (BNM), Ba4CeMn3O12 (BCM), Ba4PrMn3O12 (BPM) are discovered to exhibit promising STCH performance. However, the magnetic degrees of freedom of their experimental crystal structures is not characterized, and only hypothetical models exist for their electronic structure. We performed Monte-Carlo sampling for the magnetic spin arrangement of Mn atoms to provide explicit atomic structure models for their ground state 12R polytype and determined the most stable spin configuration for each member after structure relaxation using density functional theory (DFT) calculations. We also elucidate the most stable charge configuration (Mn3+/Mn4+ arrangement) for BNM among the existing hypothesis in literature. We investigate these strongly correlated oxides using different levels of theory (DFT+U, Hybrid-DFT) to develop better understanding of their electronic structure. These calculations allowed us to develop a model based on molecular orbital interactions that help explain the observed changes in their experimental x-ray spectroscopy measurements. Thereby, help link differences in electronic structure of BXM family members to their varying water-splitting behavior. These structure models will further facilitate future in-depth defect studies to model STCH redox cycle of these oxides.

atomic and magnetic structure↗
DOE OSTI2022

Subcomponent Validation of Composite Joints for Marine Energy Structures

The Marine Energy Advanced Materials project addresses the barriers and uncertainties facing marine renewable energy developers in using composite materials for load-bearing structures. Sponsored by the U.S. Department of Energy's Water Power Technologies Office, the multiyear project comprises of collaborators from the National Renewable Energy Laboratory (NREL), Sandia National Laboratories, Pacific Northwest National Laboratory (PNNL), Montana State University (MSU), Florida Atlantic University (FAU), and industry stakeholders. As part of the Marine Energy Advanced Materials project, marine renewable energy industry surveys and assessments were conducted to identify key materials and knowledge gaps that hinder the adoption of composite materials in marine renewable energy structures. Specific knowledge gaps highlighted for composite materials were environmental effects, fatigue strengths, and bonded and bolted interconnects (composite/composite and composite/metal). It was concluded that many of these gaps could be addressed through subcomponent validation; consequently, a program was developed at NREL with the goals of developing subcomponent validation methods for appropriate marine energy materials, which would improve the understanding of design allowables for full-scale structural components and joints. Ultimately, the aim is to reduce timelines and costs associated with full-scale structural validation efforts while also providing near-net-scale static and fatigue data of composite/metal subcomponents for marine renewable energy systems. To approach these goals, a testing program was developed at NREL to investigate a variety of materials and structural design details at the subcomponent scale to understand (a) the effects of harsh and corrosive marine energy environments and (b) the static and fatigue strengths of the complex geometries. The recent study from this testing program is perhaps the largest that has ever been conducted with respect to specimen scale and geographic diversity of underwater environmental conditions that the specimens were subjected to. A variety of specimen geometries were designed by NREL to highlight key features of multimaterial (composite/composite or metal/composite) interconnects that may be used in marine renewable energy structural designs. The designs used several different composite matrices, adhesives, and marine-grade steels, which were highlighted in the surveys as being the most appropriate for harsh marine environments. Composite panels were then manufactured at MSU, and were subsequently manufactured into test specimens by NREL. The specimens were shipped to FAU and PNNL for conditioning in ocean water tanks at various temperatures for an extended period. The specimens were then returned to NREL for structural validation. This presentation will provide an overview of recent advances within the testing program in terms of specimen design and test methods, and will discuss results and key findings of the subcomponent testing program to date at NREL.

adhesives↗
DOE OSTI2025

Standardized Residue Numbering and Secondary Structure Nomenclature in the Class D β-Lactamases

Over 1370 class D β-lactamases are currently known, and they pose a serious threat to the effective treatment of many infectious diseases, particularly in some pathogenic bacteria where evolving carbapenemase activity has been reported. Detailed understanding of their molecular biology, enzymology, and structural biology are critically important, but the lack of a standardized residue numbering scheme and inconsistent secondary structure annotation has made comparative analyses sometimes difficult and cumbersome. Compounding this, in the post-AlphaFold world where we currently find ourselves, an extraordinary wealth of detailed structural information on these enzymes is literally at our fingertips; therefore it is vitally important that a standard numbering system is in place to facilitate the accurate and straightforward analysis of their structures. In conclusion, here we present a residue numbering and secondary structure scheme for the class D enzymes based on the sequence and structure of OXA-48 and apply it to test targets to demonstrate the ease with which it can be used.

59 BASIC BIOLOGICAL SCIENCES↗