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At least 595 records · Page 33
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Structural analysis and functional evaluation of the disordered ß–hexosyltransferase region from Hamamotoa (Sporobolomyces) singularis

Hamamotoa (Sporobolomyces) singularis codes for an industrially important membrane bound ß-hexosyltransferase (BHT), (BglA, UniprotKB: Q564N5) that has applications in the production of natural fibers such as galacto-oligosaccharides (GOS) and natural sugars found in human milk. When heterologously expressed by Komagataella phaffii GS115, BHT is found both membrane bound and soluble secreted into the culture medium. In silico structural predictions and crystal structures support a glycosylated homodimeric enzyme and the presence of an intrinsically disordered region (IDR) with membrane binding potential within its novel N-terminal region (1–110 amino acids). Additional in silico analysis showed that the IDR may not be essential for stable homodimerization. Thus, we performed progressive deletion analyses targeting segments within the suspected disordered region, to determine the N-terminal disorder region’s impact on the ratio of membrane-bound to secreted soluble enzyme and its contribution to enzyme activity. The ratio of the soluble secreted to membrane-bound enzyme shifted from 40% to 53% after the disordered N-terminal region was completely removed, while the specific activity was unaffected. Furthermore, functional analysis of each glycosylation site found within the C-terminal domain revealed reduced total secreted protein activity by 58%–97% in both the presence and absence of the IDR, indicating that glycosylation at all four locations is required by the host for the secretion of active enzyme and independent of the removed disordered N-terminal region. Overall, the data provides evidence that the disordered region only partially influences the secretion and membrane localization of BHT.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Mass spectrometry structural analysis of intrinsically disordered phosphoproteins

Phosphorylation is a ubiquitous protein modification that is known to play important roles in many biological phenomena including cell signaling, the opening and closing of membrane protein channels, and even triggering of amyloid protein aggregation. Despite the effects phosphorylation has on protein function, the impact phosphorylation has on the structure of proteins is not well understood. Here, to determine how phosphorylation affects the structure of proteins, top-down mass spectrometry (TD-MS) and ion mobility-mass spectrometry (IM-MS) were performed on various phosphorylated proteins and their dephosphorylated proteoforms. TD-MS with collision- and electron-based fragmentation techniques was utilized to locate phosphorylation sites on the intrinsically disordered amyloid proteins β-casein and α-synuclein. TD-MS also provided evidence that alkaline phosphatase dephosphorylates β-casein from the N-terminus to the C-terminus. Furthermore, IM-MS of common phosphorylated proteins such as β-casein, α-casein, ovalbumin, and phosvitin indicates that phosphorylation promotes compaction of protein structure in denaturing as well as native conditions. Increases in abundance of more compact conformers are also observed when the disease related amyloid protein α-synuclein is phosphorylated at serine 129. We interpret the increased abundance of more compact conformers when proteins are phosphorylated as evidence that salt bridges form between negatively charged phosphates and positively charged residues, which alters protein structure. Salt bridge formation due to phosphorylation could be a mechanism for regulating protein function and be responsible for many of the phenomena observed in nature.

Amyloid proteins↗
NASA NTRS2019

Structural Analysis Methods for the Roll-Out Solar Array Flight Experiment

The Roll-Out Solar Array (ROSA) flight experiment was launched to the International Space Station (ISS) on June 3rd, 2017. ROSA is an innovative, lightweight solar array with a flexible substrate that makes use of the stored strain energy in its composite structural members to provide deployment without the use of motors. This paper discusses the effort to model the structural dynamics of ROSA using finite element modeling. Two distinct and agnostic approaches were used by separate teams to assess the structural dynamics of the solar array prior to ground vibrational testing and flight testing. Results from each approach are compared to measured dynamics from accelerometers and photogrammetry data gathered on orbit. Advantages and disadvantages of each approach are discussed as are preliminary efforts to calibrate the models to the empirical data for the benefit of future modeling efforts on similar space structures.

Chamberlain, Matthew K.↗
DOE OSTI2011

Optical and structural analysis of lead bismuth silicate glasses

Glasses having compositions 20PbO(79.5-x)Bi{sub 2}O{sub 3}xSiO{sub 2} (x = 10,30,50) doped with 0.5 mole% of Nd{sup 3+} ions were prepared by melt quench technique. The spectroscopic properties of the glasses were investigated using optical absorption and fluorescence spectra. The structural investigations of these glasses were carried out by recording the IR spectra. The variation of {Omega}{sub 2} with Bi{sub 2}O{sub 3} content has been attributed to changes in the asymmetry of the ligand field at the rare earth ion site and to the changes in the rare earth oxygen covalency. Heavy metal oxide glasses have been used as potential candidate in solid state laser, solar concentrators, optical detector, optical fiber and fluorescent display devices.

36 MATERIALS SCIENCE↗
DOE OSTI2012

Structural analysis and dimerization profile of the SCAN domain of the pluripotency factor Zfp206

Zfp206 (also named as Zscan10) belongs to the subfamily of C2H2 zinc finger transcription factors, which is characterized by the N-terminal SCAN domain. The SCAN domain mediates selfassociation and association between the members of SCAN family transcription factors, but the structural basis and selectivity determinants for complex formation is unknown. Zfp206 is important for maintaining the pluripotency of embryonic stem cells presumably by combinatorial assembly of itself or other SCAN family members on enhancer regions. To gain insights into the folding topology and selectivity determinants for SCAN dimerization, we solved the 1.85 A° crystal structure of the SCAN domain of Zfp206. In vitro binding studies using a panel of 20 SCAN proteins indicate that the SCAN domain Zfp206 can selectively associate with other members of SCAN family transcription factors. Deletion mutations showed that the N-terminal helix 1 is critical for heterodimerization. Double mutations and multiple mutations based on the Zfp206SCAN–Zfp110SCAN model suggested that domain swapped topology is a possible preference for Zfp206SCAN–Zfp110SCAN heterodimer. Together, we demonstrate that the Zfp206SCAN constitutes a protein module that enables C2H2 transcription factor dimerization in a highly selective manner using a domain-swapped interface architecture and identify novel partners for Zfp206 during embryonal development.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structural analysis of wild-type and Val120Thr mutant Candida boidinii formate dehydrogenase by X-ray crystallography

Candida boidinii NAD + -dependent formate dehydrogenase (CbFDH) has gained significant attention for its potential application in the production of biofuels and various industrial chemicals from inorganic carbon dioxide. The present study reports the atomic X-ray crystal structures of wild-type CbFDH at cryogenic and ambient temperatures, as well as that of the Val120Thr mutant at cryogenic temperature, determined at the Turkish Light Source ‘Turkish DeLight’. The structures reveal new hydrogen bonds between Thr120 and water molecules in the active site of the mutant CbFDH, suggesting increased stability of the active site and more efficient electron transfer during the reaction. Further experimental data is needed to test these hypotheses. Collectively, these findings provide invaluable insights into future protein-engineering efforts that could potentially enhance the efficiency and effectiveness of CbFDH.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2019

Structural Analysis and Performance-Based Validation of a Composite Wing Spar

Electric-motor powered aircraft possess the ability to operate with efficient energy delivery, but lack the operational range of internal combustion engine powered aircraft. This range limitation requires the use of high aspect ratio, thin-chord wings to minimize aerodynamic drag losses, which results in highly loaded composite spar structures. High aspect ratio wings are required to increase mission durations for a NASA-developed experimental multi-rotor electric powered aircraft denoted as the Scalable Convergent Electric Propulsion Technology and Operations Research (SCEPTOR) or “X-57”. This paper examines the structural performance of the composite main wing spars to validate spar strength using ply-based laminate finite element methods. Geometric scaling of a main spar test-section was initially proposed for proof-testing but sacrificed stability. Ply-based structures modeling with local structural features was implemented as a risk-reduction methodology. Ply-based modeling was selected to augment the conventional “building block” approach to reduce risk, and leverage a “performance-based” approval processes encouraged in Federal Aviation Administration (FAA) design guidance. Therefore, ply-based laminate modeling of the full-scale main spar and forward spar shear-web attachments were subsequently undertaken to determine load path complexity with predicted flight loads. Ply-based modeling included stress concentrations and interlaminate behavior at interface locations that can be obscured in traditional finite element sizing models. Analysis of the wing spar laminate ply-based models compared with bearing test coupon performance was used to reduce future wing assembly proof-testing burden and facilitate performance-based flight hardware safety for the X-57 experimental aircraft.

Moore, James B.↗
DOE OSTI2021

Characterization and structural analysis of a thermophilic GH11 xylanase from compost metatranscriptome

Xylanase is efficient for xylan degradation and widely applied in industries. We found a GH11 family xylanase (Xyn11A) with high thermostability and catalytic activity from compost metatranscriptome. This xylanase has the optimal reaction temperature at 80 °C with the activity of 2907.3 U/mg. The X-ray crystallographic structure shows a typical “right hand” architecture, which is the characteristics of the GH11 family enzymes. Comparing it with the mesophilic XYN II, a well-studied GH11 xylanase from Trichoderma reesei, Xyn11A is more compact with more H-bonds. Our mutagenic results show that the electrostatic interactions in the thumb and palm region of Xyn11A could result in its high thermostability and activity. Introducing a disulfide bond at the N-terminus further increased its optimal reaction temperature to 90 °C with augmented activity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Structural analysis of extracellular ATP-independent chaperones of streptococcal species and protein substrate interactions

ABSTRACT During infection, bacterial pathogens rely on secreted virulence factors to manipulate the host cell. However, in gram-positive bacteria, the molecular mechanisms underlying the folding and activity of these virulence factors after membrane translocation are not clear. Here, we solved the protein structures of two secreted parvulin and two secreted cyclophilin-like peptidyl-prolyl isomerase (PPIase) ATP-independent chaperones found in gram-positive streptococcal species. The extracellular parvulin-type PPIase, PrsA inStreptococcus pneumoniaeandStreptococcus mutansmaintain dimeric crystal structures reminiscent of folding catalysts that consist of two domains, a PPIase and foldase domain. Structural comparison of the two cyclophilin-like extracellular chaperones fromS. pneumoniaeandStreptococcus pyogeneswith other cyclophilins demonstrates that this group of cyclophilin-like chaperones has novel structural appendages formed by 9- and 24-residue insertions. Furthermore, we demonstrate that deletion ofprsAandslrAgenes impairs the secretion of the cholesterol-dependent pore-forming toxin, pneumolysin inS. pneumoniae. Using protein pull-down and biophysical assays, we demonstrate a direct interaction between PrsA and SlrA with Ply. Then, we developed chaperone-assisted folding assays that show that theS. pneumoniaePrsA and SlrA extracellular chaperones accelerate pneumolysin folding. In addition, we demonstrate that SlrA and, for the first time,S. pyogenes PpiA exhibit PPIase activity and can bind the immunosuppressive drug, cyclosporine A. Altogether, these findings suggest a mechanistic role for streptococcal PPIase chaperones in the activity and folding of secreted virulence factors such as pneumolysin. IMPORTANCE Streptococcal species are a leading cause of lower respiratory infections that annually affect millions of people worldwide. During infection, streptococcal species secrete a medley of virulence factors that allow the bacteria to colonize and translocate to deeper tissues. In many gram-positive bacteria, virulence factors are secreted from the cytosol across the bacterial membrane in an unfolded state. The bacterial membrane-cell wall interface is exposed to the potentially harsh extracellular environment, making it difficult for native virulence factors to fold before being released into the host. ATP-independent PPIase-type chaperones, PrsA and SlrA, are thought to facilitate folding and stabilization of several unfolded proteins to promote the colonization and spread of streptococci. Here, we present crystal structures of the molecular chaperones of PrsA and SlrA homologs from streptococcal species. We provide evidence that theStreptococcus pyogenesSlrA homolog, PpiA, has PPIase activity and binds to cyclosporine A. In addition, we show thatStreptococcus pneumoniaePrsA and SlrA directly interact and fold the cholesterol-dependent pore-forming toxin and critical virulence determinant, pneumolysin.

Microbiology↗
NASA NTRS1989

Development of higher-order modal methods for transient thermal and structural analysis

A force-derivative method which produces higher-order modal solutions to transient problems is evaluated. These higher-order solutions converge to an accurate response using fewer degrees-of-freedom (eigenmodes) than lower-order methods such as the mode-displacement or mode-acceleration methods. Results are presented for non-proportionally damped structural problems as well as thermal problems modeled by finite elements.

Camarda, Charles J.↗
NASA NTRS1992

Structural analysis of low-speed composite propfan blades for the LRCSW wind tunnel model

The Naval Weapons Center at China Lake, CA, is currently in the process of evaluating propulsion systems for the Long Range Conventional Standoff Weapons (LRCSW). At present, the Advanced Counter-Rotating Propfan system is being considered. The methodologies are documented which were used to structurally analyze the 0.55 scale CM1 composite propfan blades for the LRCSW with COBSTRAN and MSC/NASTRAN. Significant results are also reported.

Ernst, Michael A.↗
DOE OSTI2011

Structural Analysis of the Receptor Binding Domain of Botulinum Neurotoxin Serotype D

Botulinum neurotoxins (BoNTs) are the most toxic proteins known. The mechanism for entry into neuronal cells for serotypes A, B, E, F, and G involves a well understood dual receptor (protein and ganglioside) process, however, the mechanism of entry for serotypes C and D remains unclear. To provide structural insights into how BoNT/D enters neuronal cells, the crystal structure of the receptor binding domain (S863-E1276) for this serotype (BoNT/D-HCR) was determined at 1.65{angstrom} resolution. While BoNT/D-HCR adopts an overall fold similar to that observed in other known BoNT HCRs, several major structural differences are present. These structural differences are located at, or near, putative receptor binding sites and may be responsible for BoNT/D host preferences. Two loops, S1195-I1204 and K1236-N1244, located on both sides of the putative protein receptor binding pocket, are displaced >10{angstrom} relative to the corresponding residues in the crystal structures of BoNT/B and G. Obvious clashes were observed in the putative protein receptor binding site when the BoNT/B protein receptor synaptotagmin II was modeled into the BoNT/D-HCR structure. Although a ganglioside binding site has never been unambiguously identified in BoNT/D-HCR, a shallow cavity in an analogous location to the other BoNT serotypes HCR domains is observed in BoNT/D-HCR that has features compatible with membrane binding. A portion of a loop near the putative receptor binding site, K1236-N1244, is hydrophobic and solvent-exposed and may directly bind membrane lipids. Liposome-binding experiments with BoNT/D-HCR demonstrate that this membrane lipid may be phosphatidylethanolamine.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Structural Analysis and Electrochemical Properties of Bimetallic Palladium-Platinum Aerogels Prepared by a Two-Step Gelation Process

Multimetallic aerogels have emerged as promising unsupported and high-surface-area metal materials for different applications in heterogeneous catalysis and electrochemistry, which are fabricated using a gelation process characterized by the controlled aggregation of metallic nanoparticles to form a macroscopic network structure in aqueous solution. However, the achievement of the structural homogeneity of the multimetallic aerogels in terms of the diameter of the nanochains and the chemical composition at the nano- and the macro-scale is still a great challenge. In this paper, we investigated two Pd-Pt aerogels prepared by the two-step gelation method. The structural homogeneity and chemical distribution of both metals inside the aerogels were analyzed by using high-resolution (scanning) transmission microscopy, energy-dispersive X-ray spectroscopy, extended X-ray absorption fine structure spectroscopy and cyclic voltammetry. The Pd-Pt aerogels show the presence of Pd/Pt-rich domains inside the long-range framework. It is evident that the initial monometallic features dominate over alloying during the gelation process. Although the same synthetic approach for Pd-Pt aerogels with different atomic ratios was used, we observed that the sizes of these monometallic domains varied strongly between the Pd-rich and Pt-rich aerogels. The presence of such metal clusters influenced the electrochemical robustness of the Pd-Pt aerogels dramatically. Further, electrochemical durability investigations revealed that the aerogels with a high content of Pd are less stable because of the gradual dissolution of the less noble metal particularly inside the Pd-rich domains. A chemical and structural homogeneity might improve the lifetime of the Pd-Pt aerogels under electrochemical conditions. In this work, we provide a better understanding of the structure and chemical distribution of the bimetallic aerogel framework prepared by the two-step gelation process.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Enhancing Plastic Recycling Through Nano-Scale Structure Analysis in Custom Block Copolymer Filaments (Rev.1)

As plastic production continues to increase, new methods to combat plastic waste are needed. This paper explores upcycling, a way to increase the utility or value of waste plastic. This can be done using block copolymers as compatibilizers. Block copolymers are made of two immiscible polymer blocks that phase separate on the nanoscale, forming small structures. The orientation of these nano-scale structures influences mechanical properties, and we show that orientation can be controlled by directional 3D (three dimensional) printing. Using small-angle X-ray scattering (SAXS), we analyze block copolymer filaments extruded at varying speeds. The SAXS data provide a baseline understanding of nano-scale structure in these unique filaments for future use in 3D printing experiments.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Structure analysis of a Mn-doped willemite-type compound, H{sub 0.12}(Zn{sub 1.89(3)}Mn{sub 0.05(1)}□{sub 0.06})Si{sub 1.00(1)}O{sub 4}

Large single crystals of a well-known green phosphor, Mn-doped willemite (α-Zn{sub 2}SiO{sub 4})-type compound were grown from molten MnF{sub 2}/Li{sub 2}MoO{sub 4}. In this structure Mn{sup 2+} and defects partially replace Zn{sup 2+} at two independent sites, and there are no cation species in the middle of six-membered ring channels. As a consequence of 3% defective sites (□), this structure may have protons for ensuring its electrostatic neutrality. Although the position of H{sup +} could not be clearly found the present study indicates the presence of protons in the vicinity of oxygens to make relative short H⋯O bonds below 1.6 Å. Two unusual, broad IR bands about 1780 and 2360 cm{sup −1} can be explained by disordering of strongly bonded O···H groups. This compound represents a structural unit, H{sub 0.12}(Zn{sub 1.89(3)}Mn{sub 0.05(1)}□{sub 0.06})Si{sub 1.00(1)}O{sub 4}, based on X-ray single crystal diffraction, electron microprobe, and FT-IR spectroscopy. - Graphical abstract: A willemite-type compound, H{sub 0.12}(Zn{sub 1.89(3)}Mn{sub 0.05(1)}□{sub 0.06})Si{sub 1.00(1)}O{sub 4} exhibits protons near to oxygens in the skirt of four- and six-membered ring channels, as a result of defects at two crystallographically different Zn sites. Display Omitted - Highlights: • Structure properties of a 0.05 Mn-doped α-Zn{sub 2}SiO{sub 4} compound using X-ray single crystal diffraction. • Static disorder of Zn, Mn, and defects in the framework of α-Zn{sub 2}SiO{sub 4}. • Sign of strong H⋯O bonds, observed in FT-IR spectroscopy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1975

Water vapor weathering of Taurus-Littrow orange soil - A pore-structure analysis

A pore-volume analysis was performed on water vapor adsorption data previously obtained on a fresh sample of Taurus-Littrow orange soil, and the analysis was repeated on the same sample after its exposure to moist air for a period of approximately six months. The results indicate that exposure of an outgassed sample to high relative pressures of water vapor can result in the formation of substantial micropore structure, the precise amount being dependent on the sample pretreatment, particularly the outgassing temperature. Micropore formation is explained in terms of water penetration into surface defects. In contrast, long-term exposure to moist air at low relative pressures appears to reverse the process with the elimination of micropores and enlargement of mesopores possibly through surface diffusion of metastable adsorbent material. The results are considered with reference to the storage of lunar samples.

Cadenhead, D. A.↗