Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Cell structure identification”

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 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Multiscale Cryo Electron Microscopy Reveals Interfacial Degradation and Stabilization in Battery Electrodes

Electrochemical interfaces are dynamic systems, evolving based on their local environment and reactant surface structures. The electrode-electrolyte interface in Li-ion batteries can be protective, limiting parasitic reactions with the electrolyte to passivate the surface [1]. Additionally, this interphase has an impact on the Li-ion transport through that layer based on its composition, bonding environment, and thickness. These parameters are challenging to collect and may vary depending on the electrode surface site investigated relative to its spatial position in a coin cell. This study will detail a multiscale cryogenic electron microscopy approach where millimeter-scale cross-sections through the coin cell batteries were made using a cryogenic stage within a fs-laser plasma focused ion beam (laser PFIB) with complementary energy dispersive X-ray spectroscopy able to detect variations in the composition at electrode interfaces [2]. Microscale cross-sectioning and lamella sample preparation of battery electrodes was conducted at the Center for Integrated Nanotechnologies using a Ga-ion focused ion beam (FIB) with air-free and cryo-transfer [3], followed by nanoscale mapping of composition and bonding within the CEI through cryo-scanning transmission electron microscopy (cryo-STEM) electron energy loss spectroscopy [4]. This multiscale approach enabled identification of millimeter-scale features of a battery stack with visualization of degradation in electrodes such as cracks in cathode particles, gas evolution, and SEI evolution; microscale interfacial characteristics, such as heterogeneity in the SEI or barrier layer and identification of electrolyte networks to the electrode surfaces; and nanoscale measurement of the CEI thickness, mapping of transition metal bonding within the cathode particles to identify loss of active materials, and identification of beneficial electrolyte additives incorporated into the CEI structure. This multiscale approach allows for a statistical understanding of the primary mechanisms and parasitic degradation pathways that impact performance by limiting the ion transport pathways within Li+ batteries.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Development of Selective Covalent Janus Kinase 3 Inhibitors

The Janus kinases (JAKs) and their downstream effectors, signal transducer and activator of transcription proteins (STATs), form a critical immune cell signaling circuit, which is of fundamental importance in innate immunity, inflammation, and hematopoiesis, and dysregulation is frequently observed in immune disease and cancer. The high degree of structural conservation of the JAK ATP binding pockets has posed a considerable challenge to medicinal chemists seeking to develop highly selective inhibitors as pharmacological probes and as clinical drugs. Here we report the discovery and optimization of 2,4-substituted pyrimidines as covalent JAK3 inhibitors that exploit a unique cysteine (Cys909) residue in JAK3. Investigation of structure–activity relationship (SAR) utilizing biochemical and transformed Ba/F3 cellular assays resulted in identification of potent and selective inhibitors such as compounds 9 and 45. A 2.9 Å cocrystal structure of JAK3 in complex with 9 confirms the covalent interaction. Compound 9 exhibited decent pharmacokinetic properties and is suitable for use in vivo. As a result, these inhibitors provide a set of useful tools to pharmacologically interrogate JAK3-dependent biology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

TIR-only protein RBA1 recognizes a pathogen effector to regulate cell death in Arabidopsis

Detection of pathogens by plants is mediated by intracellular nucleotide-binding site leucine-rich repeat (NLR) receptor proteins. NLR proteins are defined by their stereotypical multidomain structure: an N-terminal Toll–interleukin receptor (TIR) or coiled-coil (CC) domain, a central nucleotide-binding (NB) domain, and a C-terminal leucine-rich repeat (LRR). The plant innate immune system contains a limited NLR repertoire that functions to recognize all potential pathogens. We isolated Response to the bacterial type III effector protein HopBA1 (RBA1), a gene that encodes a TIR-only protein lacking all other canonical NLR domains. RBA1 is sufficient to trigger cell death in response to HopBA1. We generated a crystal structure for HopBA1 and found that it has similarity to a class of proteins that includes esterases, the heme-binding protein ChaN, and an uncharacterized domain of Pasteurella multocida toxin. Self-association, coimmunoprecipitation with HopBA1, and function of RBA1 require two previously identified TIR–TIR dimerization interfaces. Although previously described as distinct in other TIR proteins, in RBA1 neither of these interfaces is sufficient when the other is disrupted. These data suggest that oligomerization of RBA1 is required for function. As a result, our identification of RBA1 demonstrates that “truncated” NLRs can function as pathogen sensors, expanding our understanding of both receptor architecture and the mechanism of activation in the plant immune system.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Controllable topological insulator phases in litharge-phase InBi monolayer

Despite recent advances of layered square-net topological material models that possess ideal semimetallic electronic structures and promising potential in material applications, the identification of experimentally accessible two-dimensional square-net materials with related topological properties has proven challenging. Due to the highly tunable physical and topological properties of III-V semiconductors, we revisit the class of III-V materials and observe that the litharge-phase InBi is a layered square-net material and can be exfoliated into the InBi monolayer. We present a comprehensive first-principles study of the energy landscape of the InBi monolayer. We identify a paraelastic phase and three ferroelastic phases and study their topological properties. Specifically, we show that the paraelastic InBi monolayer is a trivial insulator due to the orbital-ordering-induced band inversion occurring between states with the same parity. Substituting one Bi atom per cell with another V-group element (N, P, As) or applying an electric field that breaks the inversion symmetry and changes the orbital onsite energy, the paraelastic InBi monolayer can be driven into the topological insulator phase. Furthermore, one of the ferroelastic phases of pure InBi, which can be obtained by gently straining the paraelastic phase, also possesses such topological insulating properties. Furthermore, these results provide several experimentally accessible routes to tune the nontrivial topology in the InBi monolayer, including creating heterostructures with piezoelectric or ferroelectric substrates and applying mechanical strain, making the InBi monolayer an ideal platform to study the interplay of reduced dimensionality, square-net chemical bonding networks, and band topology.

2-dimensional systems↗
DOE OSTI2024

A Semi‐Automated, High‐Throughput Approach for the Synthesis and Identification of Highly Photo‐Cytotoxic Iridium Complexes

Abstract The discovery of new compounds with pharmacological properties is usually a lengthy, laborious and expensive process. Thus, there is increasing interest in developing workflows that allow for the rapid synthesis and evaluation of libraries of compounds with the aim of identifying leads for further drug development. Herein, we apply combinatorial synthesis to build a library of 90 iridium(III) complexes (81 of which are new) over two synthesise‐and‐test cycles, with the aim of identifying potential agents for photodynamic therapy. We demonstrate the power of this approach by identifying highly active complexes that are well‐tolerated in the dark but display very low nM phototoxicity against cancer cells. To build a detailed structure–activity relationship for this class of compounds we have used density functional theory (DFT) calculations to determine some key electronic parameters and study correlations with the experimental data. Finally, we present an optimised semi‐automated synthesise‐and‐test protocol to obtain multiplex data within 72 hours.

Kench, Timothy↗
DOE OSTI2024

A Semi‐Automated, High‐Throughput Approach for the Synthesis and Identification of Highly Photo‐Cytotoxic Iridium Complexes

Abstract The discovery of new compounds with pharmacological properties is usually a lengthy, laborious and expensive process. Thus, there is increasing interest in developing workflows that allow for the rapid synthesis and evaluation of libraries of compounds with the aim of identifying leads for further drug development. Herein, we apply combinatorial synthesis to build a library of 90 iridium(III) complexes (81 of which are new) over two synthesise‐and‐test cycles, with the aim of identifying potential agents for photodynamic therapy. We demonstrate the power of this approach by identifying highly active complexes that are well‐tolerated in the dark but display very low nM phototoxicity against cancer cells. To build a detailed structure–activity relationship for this class of compounds we have used density functional theory (DFT) calculations to determine some key electronic parameters and study correlations with the experimental data. Finally, we present an optimised semi‐automated synthesise‐and‐test protocol to obtain multiplex data within 72 hours.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Synthetic data-driven deep learning for label-free autonomous atomic force microscopy

Atomic force microscopy (AFM) is a widely used tool for nanoscale characterization across materials science, energy research, and biology. However, its adoption in high-throughput materials discovery and statistically driven studies remains limited by a strong dependence on expert operator input and by the scarcity of annotated experimental AFM datasets needed to enable data-driven automation. Here, we introduce SimuScan, a synthetic-data–driven framework that enables reliable AFM feature identification, segmentation, and targeted imaging without requiring large manually labeled experimental datasets. SimuScan generates tunable, high-fidelity synthetic AFM images of defined morphologies while incorporating realistic experimental artifacts, including tip–sample convolution, noise, flattening distortions, and surface debris. These datasets are shown to support scalable, label-free training of modern deep learning models for AFM analysis. When integrated into data-driven AFM workflows, SimuScan-trained models can locate and analyze nanoscale structures across large datasets and guide targeted follow-up imaging. We validate this approach on nanostructured surfaces, DNA assemblies, and bacterial cells, demonstrating robust generalization across diverse sample types with minimal operator intervention. More broadly, this work establishes a general strategy for generating explicitly conditioned, task-relevant synthetic data to improve the reliability of downstream models in autonomous microscopy.

Millan-Solsona, Ruben [Oak Ridge National Laborato↗
DOE OSTI2024

Image registration for in situ X-ray nano-imaging of a composite battery cathode with deformation

The structural and chemical evolution of battery electrodes at the nanoscale plays an important role in affecting the cell performance. Nano-resolution X-ray microscopy has been demonstrated as a powerful technique for characterizing the evolution of battery electrodes under operating conditions with sensitivity to their morphology, compositional distribution and redox heterogeneity. In real-world batteries, the electrode could deform upon battery operation, causing challenges for the image registration which is necessary for several experimental modalities, e.g. XANES imaging. To address this challenge, this work develops a deep-learning-based method for automatic particle identification and tracking. This approach was not only able to facilitate image registration with good robustness but also allowed quantification of the degree of sample deformation. The effectiveness of the method was first demonstrated using synthetic datasets with known ground truth. The method was then applied to an experimental dataset collected on an operating lithium battery cell, revealing a high degree of intra- and interparticle chemical complexity in operating batteries.

25 ENERGY STORAGE↗
NASA NTRS2008

High- and low-LET Radiation-induced Chromosome Aberrations in Human Epithelial Cells Cultured in 3-dimensional Matrices

Energetic heavy ions pose a great health risk to astronauts who participate in extended ISS missions and will be an even greater concern for future manned lunar and Mars missions. High-LET heavy ions are particularly effective in causing various biological effects, including cell inactivation, genetic mutations, cataracts and cancer induction. Most of these biological endpoints are closely related to chromosomal damage, which can be utilized as a biomarker for radiation insults. Previously, we had studied low- and high-LET radiation-induced chromosome aberrations in human epithelial cells cultured in 2-dimension (2D) using the multicolor banding fluorescence in situ hybridization (mBAND) technique. However, it has been realized that the biological response to radiation insult in a 2D in vitro cellular environment can differ significantly from the response in 3-dimension (3D) or at the actual tissue level. In this study, we cultured human epithelial cells in 3D to provide a more suitable model for human tissue. Human mammary epithelial cells (CH184B5F5/M10) were grown in Matrigel to form 3D structures, and exposed to Fe-ions at NASA Space Radiation Laboratory (NSRL) at the Brookhaven National Laboratory or 137Cs-gamma radiation source at the University of Texas MD Anderson Cancer Center. After exposure, cells were allowed to repair for 16hr before dissociation and subcultured at low density in 2D. G2 and metaphase chromosomes in the first cell cycle were collected in the first cell cycle after irradiation using a chemical-induced premature chromosome condensation (PCC) technique, and chromosome aberrations were analyzed using mBAND technique. With this technique, individually painted chromosomal bands on one chromosome allowed the identification of interchromosomal aberrations (translocation to unpainted chromosomes) and intrachromosomal aberrations (inversions and deletions within a single painted chromosome). Our data indicate a significant difference in the chromosome aberration yield between 2D and 3D cell cultures after gamma exposures, but not after Fe ion exposures. Therefore, the Relative Biological Effect (RBE) for induction of chromosome aberrations obtained in a 2D model may not accurately represent RBE values obtained for tissue exposure.

Hada, M.↗
DOE OSTI2016

The Mycobacterium tuberculosis desaturase DesA1 (Rv0824c) is a Ca{sup 2+} binding protein

The hallmark feature of Mycobacterium tuberculosis (M.tb) the causative agent of human tuberculosis, is its complex lipid rich cell wall comprised primarily of mycolic acids, long chain fatty acids that play a key role in structural stability and permeability of the cell wall. In addition, they are involved in inhibiting phagosome-lysosome fusion and aid in granuloma formation during the pathogenic process. M.tb DesA1 is an essential acyl-acyl carrier protein desaturase predicted to catalyze the introduction of position specific double bonds during the biosynthesis of mycolic acids. This protein is one among three annotated desaturases (DesA1-3) in the M.tb genome but is unique in containing a βγ-crystallin Greek key signature motif, a well-characterized fold known to mediate Ca{sup 2+} binding in both prokaryotic and eukaryotic organisms. Using Isothermal Titration Calorimetry and {sup 45}CaCl{sub 2} overlay, we demonstrate that Ca{sup 2+} binds to DesA1. Spectroscopic measurements suggested that this binding induces changes in protein conformation but does not lead to significant alterations in the secondary structure of the protein, a feature common to several βγ-crystallins. An M. smegmatis strain over-expressing M.tb desA1 showed a Ca{sup 2+} dependent variation in surface phenotype, revealing a functional role for Ca{sup 2+}in DesA1 activity. This study represents the first identification of a Ca{sup 2+} binding βγ-crystallin in M.tb, emphasizing the implicit role of Ca{sup 2+} in the pathogenesis of M.tb. - Highlights: • Mycobacterium tuberculosis DesA1 is an essential acyl-ACP desaturase. • DesA1 was identified to contain a βγ-crystallin Greek key signature motif. • Ca{sup 2+} binds to DesA1 with an affinity of 53 μM and induces changes in its conformation. • M. smegmatis overexpressing M.tb DesA1 shows a Ca{sup 2+} dependent phenotype. • Targetting the Ca{sup 2+} dependent function of DesA1 could be of therapeutic value.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

Defect Engineering in Multinary Earth‐Abundant Chalcogenide Photovoltaic Materials

Application of zinc‐blende‐related chalcogenide absorbers such as CdTe and Cu(In,Ga)Se 2 (CIGSe) has enabled remarkable advancement in laboratory‐ and commercial‐scale thin‐film photovoltaic performance; however concerns remain regarding the toxicity (CdTe) and scarcity (CIGSe/CdTe) of the constituent elements. Recently, kesterite‐based Cu 2 ZnSn(S,Se) 4 (CZTSSe) materials have emerged as attractive non‐toxic and earth‐abundant absorber candidates. Despite the similarities between CZTSSe and CIGSe/CdTe, the record power conversion efficiency of CZTSSe solar cells (12.6%) remains significantly lower than that of CIGSe (22.6%) and CdTe (22.1%) devices, with the performance gap primarily being attributed to cationic disordering and associated band tailing. To capture the promise of kesterite‐like materials as prospective “drop‐in” earth‐abundant replacements for closely‐related CIGSe, current research has focused on several key directions to control disorder, including: (i) examination of the interaction between processing conditions and atomic site disorder, (ii) isoelectronic cation substitution to introduce ionic size mismatch, and (iii) structural diversification beyond the zinc‐blende‐type coordination environment. In this review, recent efforts targeting accurate identification and engineering of anti‐site disorder in kesterite‐based CZTSSe are considered. Lessons learned from CZTSSe are applied to other complex chalcogenide semiconductors, in an effort to develop promising pathways to avoid anti‐site disordering and associated band tailing in future high‐performance earth‐abundant photovoltaic technologies.

Shin, Donghyeop↗
DOE OSTI2022

EstG is a novel esterase required for cell envelope integrity in Caulobacter

Proper regulation of the bacterial cell envelope is critical for cell survival. Identification and characterization of enzymes that maintain cell envelope homeostasis is crucial, as they can be targets for effective antibiotics. In this study, we have identified a novel enzyme, called EstG, whose activity protects cells from a variety of lethal assaults in the α-proteobacterium Caulobacter crescentus. Despite homology to transpeptidase family cell wall enzymes and an ability to protect against cell-wall-targeting antibiotics, EstG does not demonstrate biochemical activity toward cell wall substrates. Instead, EstG is genetically connected to the periplasmic enzymes OpgH and BglX, responsible for synthesis and hydrolysis of osmoregulated periplasmic glucans (OPGs), respectively. The crystal structure of EstG revealed similarities to esterases and transesterases, and we demonstrated esterase activity of EstG in vitro. Using biochemical fractionation, we identified a cyclic hexamer of glucose as a likely substrate of EstG. Further, this molecule is the first OPG described in Caulobacter and establishes a novel class of OPGs, the regulation and modification of which are important for stress survival and adaptation to fluctuating environments. Our data indicate that EstG, BglX, and OpgH comprise a previously unknown OPG pathway in Caulobacter. Ultimately, we propose that EstG is a novel enzyme that instead of acting on the cell wall, acts on cyclic OPGs to provide resistance to a variety of cellular stresses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Establishment and Characterization of Two Novel Cholangiocarcinoma Cell Lines

Background: Cholangiocarcinoma (CCA) is a rare, aggressive and highly lethal tumor. The disease is very difficult to diagnose and multi-modality treatments are ineffective. To improve our understanding of the biological characteristics of CCA, and facilitate the identification of valid treatments, an in-depth characterization of two novel Chinese patient-derived primary CCA cell lines was performed. Methods: Two CCA cell lines were developed and labelled ZJU-0826 and -1125. The two cell lines were characterized with respect to phenotypic, molecular, biomarker, functional and histological properties. Results: Two novel cell lines were cultured for 2 years, and maintained for more than 100 passages. They retained their typical biliary epithelial morphology and ultrastructure. The population doubling times of ZJU-0826, and -1125 were 63.84 h and 44.73 h, respectively. The cells exhibited near-triploid karyotypes with complex structural aberrations. ZJU-1125 cells had mutations in TP53 exons. Short tandem repeats genotyping confirmed the human origin and difference between lines. An immunophenotype analysis showed that ZJU-0826 is positive for CD44, CD29, Pdx1, CD236, FoxA1, FoxA2, and Nanog, and ZJU-1125 positive for CD44, CD29, CD133, Pdx1, FoxA1, FoxA2, and Nanog. ZJU-1125 had greater invasion ability in vitro and tumorigenicity than those of ZJU-0826. Conclusions: Our results confirm the validity of the ZJU-0826 and -1125 as representative models for the elucidation of the molecular pathogenesis of perihilar CCA, and intrahepatic CCA in both in vitro and in vivo studies, respectively.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
NASA NTRS1991

Processes of deep terrestrial mantles and cores

Ultrahigh pressure experiments are currently focused on revealing processes occurring deep inside planets. This is in addition to the traditional emphasis on the constitution of planetary interiors, such as the identification of the high pressure perovskite phase of (Mg,Fe)SiO3 as the predominant mineral inside the Earth, and probably Venus. For example, experiments show that the mechanism of geochemical differentiation, separation of partial melts, differs fundamentally in the lower mantles of Earth and Venus than at near surface conditions. In addition to structural transformations, changes in chemical bonding caused by pressure can also be significant for planetary interiors. Measurements of AC and DC electrical conductivity can be obtained at ultrahigh pressures and temperatures, to greater than 80 GPa and 3000 K simultaneously, using the laser heated diamond cell. Anhydrous lower mantle assemblages (perovskite + or - oxide phases) exhibit an electrical conductivity that depends strongly on Fe content. Contrary to traditional assumptions, temperature affects the conductivity of lower mantle assemblages relatively little. The Earth's deep focus seismicity can be explained by the recycling of water into the mantle.

Jeanloz, Raymond↗
DOE OSTI2019

Arabinose Conjugates Diagnostic of Ferulate-Ferulate and Ferulate-Monolignol Cross-Coupling Are Released by Mild Acidolysis of Grass Cell Walls

Ferulate (FA) units esterified to grass arabinoxylans are involved in cross-linking cell wall polymers. Here, this contention is strengthened by the identification of FA homo- and heterodimers esterified to methyl arabinofuranoside (MeAra) units after their release from the xylan by mild acidolysis in dioxane/methanol/HCl. Acidolysis of poorly lignified maize bran cell walls provided diferulate (DFA) isomers, including those from 8–5, 8–O–4, and 5–5 interunit bonding, esterified to one or two MeAra units. Acidolysis of lignified grass samples released crossed dimers esterified to one MeAra unit and derived from the β–O–4 coupling of coniferyl alcohol to FA esters. The evaluation of these heterodimeric esters by LC-UV of their aglycones revealed that the parent structures occur in significant amounts in lignified cell walls (0.5–1 mg/g expressed as FA equivalents). The current results position mild acidolysis as an efficient strategy to obtain improved details regarding the FA-mediated cross-linking of grass cell walls.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Listeria monocytogenes wall teichoic acid decoration in virulence and cell‐to‐cell spread

Summary Wall teichoic acid (WTA) comprises a class of glycopolymers covalently attached to the peptidoglycan of gram positive bacteria. In Listeria monocytogenes , mutations that prevent addition of certain WTA decorating sugars are attenuating. However, the steps required for decoration and the pathogenic process interrupted are not well described. We systematically examined the requirement for WTA galactosylation in a mouse oral‐virulent strain by first creating mutations in four genes whose products conferred resistance to a WTA‐binding bacteriophage. WTA biochemical and structural studies indicated that galactosylated WTA was directly required for bacteriophage adsorption and that mutant WTA lacked appreciable galactose in all except one mutant – which retained a level ca. 7% of the parent. All mutants were profoundly attenuated in orally infected mice and were impaired in cell‐to‐cell spread in vitro. Confocal microscopy of cytosolic mutants revealed that all expressed ActA on their cell surface and formed actin tails with a frequency similar to the parent. However, the mutant tails were significantly shorter – suggesting a defect in actin based motility. Roles for the gene products in WTA galactosylation are proposed. Identification and interruption of WTA decoration pathways may provide a general strategy to discover non‐antibiotic therapeutics for gram positive infections. © 2016 John Wiley & Sons Ltd

Spears, Patricia A.↗
DOE OSTI2018

Loss of PiT-2 results in abnormal bone development and decreased bone mineral density and length in mice

Highlights: • PiT-2 deficiency decreased mineral density in craniofacial and long bones in mice. • Bone length was reduced in long bones in PiT-2 deficient mice. • Trabecular and cortical bone mineral density were decreased in PiT-2 deficient mice. • Static bone morphometric parameters were altered in PiT-2 deficient mice. • PiT-2 deficiency altered craniofacial bone morphology. Normal bone mineralization requires phosphate oversaturation in bone matrix vesicles, as well as normal regulation of phosphate metabolism via the interplay among bone, intestine, and kidney. In turn, derangement of phosphate metabolism greatly affects bone function and structure. The type III sodium-dependent phosphate transporters, PiT-1 and PiT-2, are believed to be important in tissue phosphate metabolism and physiological bone formation, but their requirement and molecular roles in bone remain poorly investigated. In order to decipher the role of PiT-2 in bone, we examined normal bone development, growth, and mineralization in global PiT-2 homozygous knockout mice. PiT-2 deficiency resulted in reduced vertebral column, femur, and tibia length as well as mandibular dimensions. Micro-computed tomography analysis revealed that bone mineral density in the mandible, femur, and tibia were decreased, indicating that maintenance of bone function and structure is impaired in both craniofacial and long bones of PiT-2 deficient mice. Both cortical and trabecular thickness and mineral density were reduced in PiT-2 homozygous knockout mice compared with wild-type mice. These results suggest that PiT-2 is involved in normal bone development and growth and plays roles in cortical and trabecular bone metabolism feasibly by regulating local phosphate transport and mineralization processes in the bone. Further studies that evaluate bone cell-specific loss of PiT-2 are now warranted and may yield insight into complex mechanisms of bone development and growth, leading to identification of new therapeutic options for patients with bone diseases.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

SIMBAD : a sequence-independent molecular-replacement pipeline

The conventional approach to finding structurally similar search models for use in molecular replacement (MR) is to use the sequence of the target to search against those of a set of known structures. Sequence similarity often correlates with structure similarity. Given sufficient similarity, a known structure correctly positioned in the target cell by the MR process can provide an approximation to the unknown phases of the target. An alternative approach to identifying homologous structures suitable for MR is to exploit the measured data directly, comparing the lattice parameters or the experimentally derived structure-factor amplitudes with those of known structures. Here, SIMBAD , a new sequence-independent MR pipeline which implements these approaches, is presented. SIMBAD can identify cases of contaminant crystallization and other mishaps such as mistaken identity (swapped crystallization trays), as well as solving unsequenced targets and providing a brute-force approach where sequence-dependent search-model identification may be nontrivial, for example because of conformational diversity among identifiable homologues. The program implements a three-step pipeline to efficiently identify a suitable search model in a database of known structures. The first step performs a lattice-parameter search against the entire Protein Data Bank (PDB), rapidly determining whether or not a homologue exists in the same crystal form. The second step is designed to screen the target data for the presence of a crystallized contaminant, a not uncommon occurrence in macromolecular crystallography. Solving structures with MR in such cases can remain problematic for many years, since the search models, which are assumed to be similar to the structure of interest, are not necessarily related to the structures that have actually crystallized. To cater for this eventuality, SIMBAD rapidly screens the data against a database of known contaminant structures. Where the first two steps fail to yield a solution, a final step in SIMBAD can be invoked to perform a brute-force search of a nonredundant PDB database provided by the MoRDa MR software. Through early-access usage of SIMBAD , this approach has solved novel cases that have otherwise proved difficult to solve.

59 BASIC BIOLOGICAL SCIENCES↗