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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.

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At least 631 records · Page 35
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

High-Resolution Structure of the Nuclease Domain of the Human Parvovirus B19 Main Replication Protein NS1

Two new structures of the N-terminal domain of the main replication protein, NS1, of human parvovirus B19 (B19V) are presented here. This domain (NS1-nuc) plays an important role in the “rolling hairpin” replication of the single-stranded B19V DNA genome, recognizing origin of replication sequences in double-stranded DNA, and cleaving (i.e., nicking) single-stranded DNA at a nearby site known as the terminal resolution site (trs). The three-dimensional structure of NS1-nuc is well conserved between the two forms, as well as with a previously solved structure of a sequence variant of the same domain; however, it is shown here at a significantly higher resolution (2.4 Å). Using structures of NS1-nuc homologues bound to single- and double-stranded DNA, models for DNA recognition and nicking by B19V NS1-nuc are presented that predict residues important for DNA cleavage and for sequence-specific recognition at the viral origin of replication.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Crystal structure of calpain-3 penta-EF-hand (PEF) domain - a homodimerized PEF family member with calcium bound at the fifth EF-hand

Calpains are Ca 2+ dependent intracellular cysteine proteases that cleave a wide range of protein substrates to help implement Ca 2+ signaling in the cell. The major isoforms of this enzyme family, calpain-1 and calpain-2, are heterodimers of a large and a small subunit, with the main dimer interface being formed through their C-terminal penta-EF hand (PEF) domains. Calpain-3, or p94, is a skeletal muscle-specific isoform that is genetically linked to limb-girdle muscular dystrophy. Biophysical and modeling studies with the PEF domain of calpain-3 support the suggestion that full-length calpain-3 exists as a homodimer. Here, we report the crystallization of calpain-3's PEF domain and its crystal structure in the presence of Ca 2+ , which provides evidence for the homodimer architecture of calpain-3 and supports the molecular model that places a protease core at either end of the elongated dimer. Unlike other calpain PEF domain structures, the calpain-3 PEF domain contains a Ca 2+ bound at the EF5-hand used for homodimer association. Three of the four Ca 2+ -binding EF-hands of the PEF domains are concentrated near the protease core, and have the potential to radically change the local charge within the dimer during Ca 2+ signaling. Examination of the homodimer interface shows that there would be steric clashes if the calpain-3 large subunit were to try to pair with a calpain small subunit.

Partha, Sarathy K.↗
DOE OSTI2016

Direct observation of the ferroelectric polarization in the layered perovskite Bi{sub 4}Ti{sub 3}O{sub 12}

We investigated the crystal structure and ferroelectric domains of Bi{sub 4}Ti{sub 3}O{sub 12} (BTO) by means of transmission electron microscopy (TEM) and single-crystal X-ray diffractometry. From the extinction rule, we determined that the space group in the ferroelectric phase of BTO is P1a1 rather than B2cb and B1a1 which have been proposed previously. We successfully refined the crystal structure based on the space group P1a1. The 180° and 90° ferroelectric domain structures were observed by the [001]-zone dark-field TEM imaging. In the 180° domain structure, we determined that one component of the polarization vector is parallel to the a-axis. An annular bright-field scanning transmission electron microscopy (ABF-STEM) was performed for the direct observation of the crystal structures. The ABF-STEM images displayed the contrasts with respect to every atomic position in spite of the highly distorted structure of BTO. We could evaluate the tilting and distortion of the [TiO{sub 6}] octahedra relatively. Therefore, we directly observed the ferroelectric displacements of Bi and Ti ions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2017

Crystal structure of the PDZ domain of mouse Dishevelled 1 and its interaction with CXXC5

Dishevelled (Dvl) plays a crucial role in Wnt signaling by interacting with membrane-bound receptors and downstream molecules through its PDZ domain. CXXC5 is one of the key molecules that interacts with Dvl and negatively regulates the Wnt/β-catenin pathway in osteoblast differentiation. Recently, the Dvl-CXXC5 interaction has been identified as an excellent target for osteoporosis treatment. Therefore, it is desirable to have detailed structural information for the Dvl-CXXC5 interaction. Although solution structures of the Dvl1 PDZ domain have been reported, a high-resolution crystal structure would provide detailed sidechain information that is essential for drug development. Here, we determined the first crystal structure of the Dvl-1 PDZ domain at a resolution of 1.76 Å, and compared it with its previously reported solution structure. The Dvl1 PDZ domain crystal belonged to the space group H32 with unit-cell parameters a = b = 72.837, c = 120.616, α = β = 90.00, γ = 120.00. The crystal structure of Dvl1 PDZ shared its topology with the previously reported structure determined by nuclear magnetic resonance (NMR); however, the crystal structure was quite different from the solution structure in both the secondary structural region and the ligand-binding pocket. Molecular modeling based on NMR and X-ray crystallographic data yielded detailed information about the Dvl1/CXXC5 interaction, which will be useful for designing inhibitors. - Highlights: • Crystal structure of PDZ domain of Dvl1 has been determined at 1.76 Å resolution. • NMR and X-ray crystal structure of PDZ domain is quite different in both the secondary structure and ligand binding pocket. • Molecular model of the Dvl1 PDZ and DBM peptide complex provides a detailed interaction between Dvl1 and CXXC5. • Dynamics data shows that the peptide binding pocket of the Dvl1 PDZ is stabilized upon CXXC5 binding.

60 APPLIED LIFE SCIENCES↗
NASA NTRSDate not supplied

Advances in Automation of Overset Structured Volume Mesh Generation and Domain Connectivity

Automation of overset structured surface mesh generation has recently been accomplished by the creation of face, edge, and node meshes based on Boundary Representation solids as the geometry input. The current work continues the automation effort in overset volume mesh generation and domain connectivity based on the auto-generated surface meshes. All near-body curvilinear volume meshes are automatically generated using hyperbolic methods. Automation of this step is enabled by appropriate surface grid point distribution, and selection of boundary-splay and smoothing parameters based on concave and convex surface features. The off-body domain is covered by two automatically generated grid systems. The first contains a single Cartesian mesh with a uniform core enclosing all near-body volume meshes and stretched layers that extend to the far field, while the second consists of a set of small stretched Cartesian grids covering pockets of off-body orphan points. With high quality mesh overlap mostly guaranteed by the surface meshing scheme, orphan points that need to be covered by the second Cartesian mesh system are located away from the fine grid spacing region near the wall. Using line-segment and ray-pierce tests against the surface grids, hole-cutting is accomplished on both near and off-body volume grids resulting in appropriate clearances from the wall. The complete mesh generation automation process is demonstrated on five test cases where flow solutions are also computed and compared with solutions obtained using other methods.

TTT↗
DOE OSTI2020

Understanding the structural basis of HIV-1 restriction by the full length double-domain APOBEC3G

APOBEC3G, a member of the double-domain cytidine deaminase (CD) APOBEC, binds RNA to package into virions and restrict HIV-1 through deamination-dependent or deamination-independent inhibition. Mainly due to lack of a full-length double-domain APOBEC structure, it is unknown how CD1/CD2 domains connect and how dimerization/multimerization is linked to RNA binding and virion packaging for HIV-1 restriction. We report rhesus macaque A3G structures that show different inter-domain packing through a short linker and refolding of CD2. The A3G dimer structure has a hydrophobic dimer-interface matching with that of the previously reported CD1 structure. A3G dimerization generates a surface with intensified positive electrostatic potentials (PEP) for RNA binding and dimer stabilization. Unexpectedly, mutating the PEP surface and the hydrophobic interface of A3G does not abolish virion packaging and HIV-1 restriction. The data support a model in which only one RNA-binding mode is critical for virion packaging and restriction of HIV-1 by A3G.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Structural and Biochemical Basis for Ubiquitin Ligase Recruitment by Arrestin-related Domain-containing Protein-3 (ARRDC3)

After protracted stimulation, the β2-adrenergic receptor and many other G-protein-coupled receptors are ubiquitinated and down-regulated. Arrestin-related domain-containing protein-3 (ARRDC3) has been proposed to recruit the ubiquitin ligase Nedd4 to the β2-adrenergic receptor. ARRDC3 contains two PPXY motifs that could potentially interact with any of the four WW domains of Nedd4. Here we dissect the interaction determinants. ARRDC3 PPXY-Nedd4 WW dissociation constants vary from unmeasurable to K d = 3 μM for the third WW domain of Nedd4 binding to the first PPXY motif of ARRDC3. Structures of the uncomplexed and PPXY 1 -bound WW3 domain were determined at 1.1 and 1.7 Å resolution. The structures revealed conformational changes upon binding and the hydrogen bonding network in exquisite detail. Tight packing of ARRDC3 Val-352', part of a 3 10 helix at the C terminus of PPXY 1 , is important for high affinity binding to WW3. Although no single WW domain is strictly essential for the binding of Nedd4 and ARRDC3 expressed in HEK293 cells, high affinity binding of full-length ARRDC3 and Nedd4 is driven by the avid interaction of both PPXY motifs with either the WW2-WW3 or WW3-WW4 combinations, with K d values as low as 300 nM.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Atomic Resolution Probing of Phase Transformations and Domain Evolution During Large Superelastic Deformation in Ferroelectrics with in situ TEM

Intrinsically brittle Ferroelectrics have attractive applications such as flexible/wearable electronic devices and mechanically-written high-density memory that depend on both functional and mechanical performance. One potential way to mitigate their brittle behavior is through large superelastic deformation stemming from strain-driven phase transformations and domain evolution. Therefore, in this work, we investigated free-standing single-crystal BaTiO 3 and Pb(Mg 1/3 Nb 2/3 )O 3 -PbTiO 3 sub-micrometer pillars during large superelastic deformation, directly observing the stress-induced phase transformations and domain evolution by using in situ Scanning Transmission Electron Microscope (STEM). We found ultra-small and multiple-phase coexistence with sizes down to a few unit cells, and we were able to study them at atomic resolution while under load. Notably, extremely small phase transformation structures and domain structures are often introduced during the large superelastic deformations since the stress field is not screened in ferroelectrics, as compared to the situation with electrical field or thermal cycling.

36 MATERIALS SCIENCE↗
DOE OSTI2013

Transition micromagnetic structures in asymmetric vortexlike domain walls (Static solutions and dynamic reconstructions)

The possible types of transition structures with a three-dimensional magnetization distribution over regions in the vortex asymmetric domain walls that exist in magnetically uniaxial soft magnetic films with in-plane anisotropy are studied by computer simulation in terms of a micromagnetic approach. It is shown that the possible structure types include both the type of vertical Bloch lines that was discussed earlier in other works and new types, namely, singular (Bloch) points and clusters consisting of vertical Bloch lines and Bloch points. The spatial configurations of the transition structures are calculated and their topological properties are found. The numerical simulation of the dynamics of closely spaced substructure regions reveals various scenarios of their interaction, including annihilation accompanied by energy release and the excitation of nonlinear waves.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2018

High-resolution crystal structures of the D1 and D2 domains of protein tyrosine phosphatase epsilon for structure-based drug design

Here, new crystal structures are presented of the isolated membrane-proximal D1 and distal D2 domains of protein tyrosine phosphatase epsilon (PTPε), a protein tyrosine phosphatase that has been shown to play a positive role in the survival of human breast cancer cells. A triple mutant of the PTPε D2 domain (A455N/V457Y/E597D) was also constructed to reconstitute the residues of the PTPε D1 catalytic domain that are important for phosphatase activity, resulting in only a slight increase in the phosphatase activity compared with the native D2 protein. The structures reported here are of sufficient resolution for structure-based drug design, and a microarray-based assay for high-throughput screening to identify small-molecule inhibitors of the PTPε D1 domain is also described.

Lountos, George T.↗
DOE OSTI2019

Dynamic structure of the full-length scaffolding protein NHERF1 influences signaling complex assembly

The Na+/H+ exchange regulatory cofactor 1 (NHERF1) protein modulates the assembly and intracellular trafficking of several transmembrane G protein–coupled receptors (GPCRs) and ion transport proteins with the membrane–cytoskeleton adapter protein ezrin. We applied in this report solution NMR and small-angle neutron scattering (SANS) to structurally characterize full-length NHERF1 and disease-associated variants that are implicated in impaired phosphate homeostasis. Using NMR, we mapped the modular architecture of NHERF1, which is composed of two structurally-independent PDZ domains that are connected by a flexible, disordered linker. We observed that the ultra-long and disordered C-terminal tail of NHERF1 has a type 1 PDZ-binding motif that interacts weakly with the proximal, second PDZ domain to form a dynamically autoinhibited structure. Using ensemble-optimized analysis of SANS data, we extracted the molecular size distribution of structures from the extensive conformational space sampled by the flexible chain. Our results revealed that NHERF1 is a diffuse ensemble of variable PDZ domain configurations and a disordered C-terminal tail. The joint NMR/SANS data analyses of three disease variants (L110V, R153Q, and E225K) revealed significant differences in the local PDZ domain structures and in the global conformations compared with the WT protein. Furthermore, we show that the substitutions affect the affinity and kinetics of NHERF1 binding to ezrin and to a C-terminal peptide from G protein–coupled receptor kinase 6A (GRK6A). Significant insight into the modulation of the intrinsic flexibility of NHERF1 by disease-associated point mutations that alter the dynamic assembly of signaling complexes are provided in this work.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Crystal structures of wild‐type Trichoderma reesei Cel7A catalytic domain in open and closed states

Trichoderma reesei Cel7A efficiently hydrolyses cellulose. We report here the crystallographic structures of the wild‐type Tr Cel7A catalytic domain (CD) in an open state and, for the first time, in a closed state. Molecular dynamics (MD) simulations indicate that the loops along the CD tunnel move in concerted motions. Together, the crystallographic and MD data suggest that the CD cycles between the tense and relaxed forms that are characteristic of work producing enzymes. Analysis of the interactions formed by R251 provides a structural rationale for the concurrent decrease in product inhibition and catalytic efficiency measured for product‐binding site mutants.

Bodenheimer, Annette M.↗
DOE OSTI2017

Structure of an unconventional SH3 domain from the postsynaptic density protein Shank3 at ultrahigh resolution

The Shank family comprises three large multi-domain proteins playing central roles as protein scaffolds in the neuronal postsynaptic density. The Shank proteins are closely linked to neuropsychiatric diseases, such as autism spectrum disorders. One characteristic domain in the Shank family is the SH3 domain, assumed to play a role in protein-protein interactions; however, no specific ligand binding to any Shank SH3 domain has been described. We solved the crystal structure of the SH3 domain from Shank3 at sub-atomic resolution. While the structure presents the canonical SH3 domain fold, the binding site for proline-rich peptides is not conserved. In line with this, no binding of Pro-rich sequences by the Shank3 SH3 domain was observed. Sequence comparisons indicate that all Shank isoforms have similarly lost the classical Pro-rich peptide binding site from the SH3 domain. Whether the corresponding site in the Shank SH3 domains has evolved to bind a non-poly-Pro target sequence is currently not known. Our work provides an intriguing example of the evolution of a well-characterized protein-protein interaction domain within the context of multi-domain protein scaffolds, allowing the conservation of structural features, but losing canonical functional sites. The data are further discussed in light of known mutations in the SH3 domain or its vicinity in the different Shank isoforms. - Highlights: • The SH3 domain from Shank3 was studied at sub-atomic resolution. • The Shank family has lost the canonical peptide-binding site of the SH3 domain. • The Shank SH3 domain may have lost or altered canonical SH3 domain functions.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Structure of the lutein-binding domain of human StARD3 at 1.74 Å resolution and model of a complex with lutein

A crystal structure of the lutein-binding domain of human StARD3 (StAR-related lipid-transfer protein 3; also known as MLN64) has been refined to 1.74 Å resolution. A previous structure of the same protein determined to 2.2 Å resolution highlighted homology with StARD1 and shared cholesterol-binding character. StARD3 has since been recognized as a carotenoid-binding protein in the primate retina, where its biochemical function of binding lutein with specificity appears to be well suited to recruit this photoprotective molecule. The current and previous structures correspond closely to each other (r.m.s.d. of 0.25 Å), especially in terms of the helix-grip fold constructed around a solvent-filled cavity. Regions of interest were defined with alternate conformations in the current higher-resolution structure, including Arg351 found within the cavity and Ω1, a loop of four residues found just outside the cavity entrance. Models of the complex with lutein generated by rigid-body docking indicate that one of the ionone rings must protrude outside the cavity, and this insight has implications for molecular interactions with transport proteins and enzymes that act on lutein. Interestingly, models with the ϵ-ionone ring characteristic of lutein pointing towards the bottom of the cavity were associated with fewer steric clashes, suggesting that steric complementarity and ligand asymmetry may play a role in discriminating lutein from the other ocular carotenoids zeaxanthin and meso -zeaxanthin, which only have β-ionone rings.

Biochemistry & Molecular Biology↗
DOE OSTI2014

Process Controlled Multiscale Morphologies in Metal-containing Block Copolymer Thin Films

Poly(styrene-block-ferrocenyldimethylsilane) (PS-b-PFS) is a metal-containing block copolymer that exhibits certain advantages as a mask for lithographic applications. These advantages include compatibility with a wide range of substrates, ease of control over domain morphologies and robust stability to etch plasma, which aid in the development of high-aspect-ratio patterns. An asymmetric cylinder-forming PS-b-PFS copolymer is subjected to different processing to manipulate the morphology of the phase-separated domains. Control of film structure and domain morphology is achieved by adjusting the film thickness, mode of annealing, and/or annealing time. Changing the process from thermal or solvent annealing to hybrid annealing (thermal and then solvent annealing in sequence) leads to the formation of mesoscale spherulitic and dendritic morphologies. In this communication, we show that reversing the order of the hybrid annealing (solvent annealing first and then thermal annealing) of relatively thick films (>100 nm) on homogeneously thick substrates develops disordered lamellar structure. Furthermore, the same processing applied on a substrate with a thin, mechanically flexible window in the center leads to the formation of sub-micron scale concentric ring patterns. Enhanced material mobility in the thick film during hybrid annealing along with dynamic rippling effects that may arise from the vibration of the thin window during spin casting are likely causes for these morphologies.

Block copolymer↗