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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 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Peripheral positions encode transport specificity in the small multidrug resistance exporters

In secondary active transporters, a relatively limited set of protein folds have evolved diverse solute transport functions. Because of the conformational changes inherent to transport, altering substrate specificity typically involves remodeling the entire structural landscape, limiting our understanding of how novel substrate specificities evolve. In the current work, we examine a structurally minimalist family of model transport proteins, the small multidrug resistance (SMR) transporters, to understand the molecular basis for the emergence of a novel substrate specificity. We engineer a selective SMR protein to promiscuously export quaternary ammonium antiseptics, similar to the activity of a clade of multidrug exporters in this family. Using combinatorial mutagenesis and deep sequencing, we identify the necessary and sufficient molecular determinants of this engineered activity. Using X-ray crystallography, solid-supported membrane electrophysiology, binding assays, and a proteoliposome-based quaternary ammonium antiseptic transport assay that we developed, we dissect the mechanistic contributions of these residues to substrate polyspecificity. We find that substrate preference changes not through modification of the residues that directly interact with the substrate but through mutations peripheral to the binding pocket. Our work provides molecular insight into substrate promiscuity among the SMRs and can be applied to understand multidrug export and the evolution of novel transport functions more generally.

Science & Technology - Other Topics↗
DOE OSTI2021

Parallel molecular mechanisms for enzyme temperature adaptation

The mechanisms that underly the adaptation of enzyme activities and stabilities to temperature are fundamental to our understanding of molecular evolution and how enzymes work. Here, we investigate the molecular and evolutionary mechanisms of enzyme temperature adaption, combining deep mechanistic studies with comprehensive sequence analyses of thousands of enzymes. We show that temperature adaptation in ketosteroid isomerase (KSI) arises primarily from one residue change with limited, local epistasis, and we establish the underlying physical mechanisms. This residue change occurs in diverse KSI backgrounds, suggesting parallel adaptation to temperature. Furthermore, we identify residues associated with organismal growth temperature across 1005 diverse bacterial enzyme families, suggesting widespread parallel adaptation to temperature. We assess the residue properties, molecular interactions, and interaction networks that appear to underly temperature adaptation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Single, Double and Quadruple Alanine Substitutions at Oligomeric Interfaces Identify Hydrophobicity as the Key Determinant of Human Neutrophil Alpha Defensin HNP1 Function

HNP1 is a human alpha defensin that forms dimers and multimers governed by hydrophobic residues, including Tyr 16 , Ile 20 , Leu 25 , and Phe 28 . Previously, alanine scanning mutagenesis identified each of these residues and other hydrophobic residues as important for function. Here we report further structural and functional studies of residues shown to interact with one another across oligomeric interfaces: I20A-HNP1 and L25A-HNP1, plus the double alanine mutants I20A/L25AHNP1 and Y16A/F28A-HNP1, and the quadruple alanine mutant Y16A/I20A/L25A/F28A-HNP1. We tested binding to HIV-1 gp120 and HNP1 by surface plasmon resonance, binding to HIV-1 gp41 and HNP1 by fluorescence polarization, inhibition of anthrax lethal factor, and antibacterial activity using the virtual colony count assay. Similar to the previously described single mutant W26A-HNP1, the quadruple mutant displayed the least activity in all functional assays, followed by the double mutant Y16A/F28A-HNP1. The effects of the L25A and I20A single mutations were milder than the double mutant I20A/ L25A-HNP1. Crystallographic studies confirmed the correct folding and disulfide pairing, and depicted an array of dimeric and tetrameric structures. These results indicate that side chain hydrophobicity is the critical factor that determines activity at these positions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

Special Analysis of the Area 3 Radioactive Waste Management Site at the Nevada National Security Site, Nye County, Nevada

This report describes the methods and results of a special analysis (SA) of the Area 3 Radioactive Waste Management Site (RWMS) on the Nevada National Security Site (NNSS). The purpose of the SA is to determine if the approved performance assessment (PA) and composite analysis (CA) (Shott et al., 2001) remain valid. The Area 3 RWMS PA and CA were prepared as a single document and received conditional approval on October 6, 1999. A conditional Disposal Authorization Statement (DAS) for the Area 3 RWMS was issued on October 20, 1999. Since preparation of the approved PA and CA, new information and additional environmental monitoring data have been used to update the PA and CA. At the same time, continual advancements in computer processors and software have allowed improvement to the PA and CA models. Annual reviews of the PA and CA required by U.S. Department of Energy (DOE) Order DOE O 435.1 have documented multiple changes occurring since preparation of the PA and CA. Potentially important changes include: Development of a new and improved baseline PA and CA model implemented in the probabilistic GoldSim simulation platform. A significant increase in the waste inventory disposed at the site. Revision and updating of model parameters based on additional years of site monitoring data and new research and development results. Although changes have occurred, many important PA/CA issues remain unchanged, including the site conceptual model, important features, events, and processes, and the points of compliance. The SA is performed to document the current status of the PA/CA model and to quantitatively assess the impact of cumulative changes on the PA and CA results. The results of the SA are used to assess the validity of the approved PA/CA and make a determination if revision of the PA or CA is necessary. The SA was performed using the Area 3 RWMS, version 2.102, GoldSim model, the current baseline PA/CA model. Comparison of the maximum SA results with the PA performance objectives indicates that there continues to be a reasonable expectation of compliance. The resident exposure scenario was evaluated for compliance with the air pathway and all-pathways annual total effective dose (TED) performance objectives. The maximum mean air pathway TED, 7E-6 millisievert (mSv) at 1,000 years (y) has decreased relative to the approved PA and is significantly less than the 0.1 mSv limit. The maximum mean all-pathways annual TED, 7E-5 mSv at 1,000 y has increased but remains a small fraction of the 0.25 mSv limit. The SA maximum mean radon-222 (222Rn) flux density, 0.03 becquerel per square meter per second (Bq m-2 s-1), has increased relative to the PA results but is significantly less than the 0.74 Bq m-2 s-1 limit. The SA results continue to support a conclusion that the disposed waste inventory is protective of intruders and groundwater resources. The maximum mean intruder TED, 0.01 mSv for an acute construction scenario at the U-3ah/at disposal unit, was less than the 5 mSv performance measure. Site monitoring data and research results continue to support a conclusion that a groundwater pathway will not exist within the 1,000 y compliance period. Projected releases to the environment are a small fraction of the performance objectives. Cost-effective options for reducing releases further are unlikely to exist. Therefore, releases from the Area 3 RWMS are judged to be as low as reasonably achievable. Comparison of the maximum CA result with the 0.3 mSv CA dose constraint indicates that no action is required to reduce the dose from the Area 3 RWMS and all interacting sources of residual radioactive contamination. The SA maximum mean CA annual TED, 0.02 mSv at 1,000 y, has increased from the approved CA result but remains less than 10% of the dose constraint. The CA TED continues to be due predominantly to inhalation of plutonium-239 resuspended from soils contaminated by nuclear weapons tests conducted near the Area 3 RWMS. The SA results estimated with the Area 3 RWMS version 2.102 model indicate that changes to the PA and CA do not significantly alter the PA/CA results or conclusions. Although increases occur for the all-pathways annual TED, the 222Rn flux density, and the CA annual TED, all PA and CA results are a small fraction of the performance objectives or dose constraints. The same conclusion was reached for the approved PA and CA. The SA results continue to support a conclusion that there is a reasonable expectation of meeting all performance objectives and the CA dose constraint. There is no need to revise the DAS at this time. The SA results support a conclusion that the Area 3 RWMS PA and CA remain valid, and revision is not necessary at this time.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2017

04BM XFM Beamline Radiation Shielding Analysis

The radiation shielding of the 04-BM-XFM beam line is analyzed for the gas bremsstrahlung (GB) and synchrotron radiation (SR) sources. The GB as a source originates from the long straight section of the storage ring during normal operation when the primary electrons interact with the residual gas molecules in the beam transport pipe giving rise to bremsstrahlung radiation. When the safety shutters are open, this can stream through the beampipe into the first optical enclosure (FOE) and beyond and can result in a radiation environment that is present at a constant rate.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Structural Characterization of TRAF6 N-Terminal for Therapeutic Uses and Computational Studies on New Derivatives

Tumor necrosis factor receptor-associated factors (TRAFs) are a protein family with a wide variety of roles and binding partners. Among them, TRAF6, a ubiquitin ligase, possesses unique receptor binding specificity and shows diverse functions in immune system regulation, cellular signaling, central nervous system, and tumor formation. TRAF6 consists of an N-terminal Really Interesting New Gene (RING) domain, multiple zinc fingers, and a C-terminal TRAF domain. TRAF6 is an important therapeutic target for various disorders and structural studies of this protein are crucial for the development of next-generation therapeutics. Here, we presented a TRAF6 N-terminal structure determined at the Turkish light source “Turkish DeLight” to be 3.2 Å resolution at cryogenic temperature (PDB ID: 8HZ2). This structure offers insight into the domain organization and zinc-binding, which are critical for protein function. Since the RING domain and the zinc fingers are key targets for TRAF6 therapeutics, structural insights are crucial for future research. Separately, we rationally designed numerous new compounds and performed molecular docking studies using this template (PDB ID:8HZ2). According to the results, 10 new compounds formed key interactions with essential residues and zinc ion in the N-terminal region of TRAF6. Molecular dynamic (MD) simulations were performed for 300 ns to evaluate the stability of three docked complexes (compounds 256, 322, and 489). Compounds 256 and 489 was found to possess favorable bindings with TRAF6. These new compounds also showed moderate to good pharmacokinetic profiles, making them potential future drug candidates as TRAF6 inhibitors.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Binary architecture of the Na v 1.2-β2 signaling complex

To investigate the mechanisms by which β-subunits influence Na v channel function, we solved the crystal structure of the β2 extracellular domain at 1.35Å. We combined these data with known bacterial Na v channel structural insights and novel functional studies to determine the interactions of specific residues in β2 with Na v 1.2. We identified a flexible loop formed by 72 Cys and 75 Cys, a unique feature among the four β-subunit isoforms. Moreover, we found that 55 Cys helps to determine the influence of β2 on Na v 1.2 toxin susceptibility. Further mutagenesis combined with the use of spider toxins reveals that 55 Cys forms a disulfide bond with 910 Cys in the Na v 1.2 domain II pore loop, thereby suggesting a 1:1 stoichiometry. Our results also provide clues as to which disulfide bonds are formed between adjacent Na v 1.2 912/918 Cys residues. The concepts emerging from this work will help to form a model reflecting the β-subunit location in a Na v channel complex.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

The measles virus phosphoprotein interacts with the linker domain of STAT1

The measles virus (MV) phosphoprotein (P) and V proteins block the interferon (IFN) response by impeding phosphorylation of the signal transducer and activator of transcription 1 (STAT1) by the Janus kinase 1 (JAK1). We characterized how STAT1 mutants interact with P and JAK1 phosphorylation. Certain mutants of the linker, the Src-homology 2 domain (SH2), or the transactivation domain had reduced or abolished phosphorylation through JAK1 after IFN treatment. Other mutants, mainly localized in the linker, failed to interact with P as documented by the lack of interference with nuclear translocation. Thus the functional footprint of P on STAT1 localizes mainly to the linker domain; there is also some overlap with the STAT1 phosphorylation functional footprint on the SH2 domain. Based on these observations, we discuss how the MV-P might operate to inhibit the JAK/STAT pathway. - Highlights: • Residue in the linker and SH2 domains of STAT1 are important for MV-P interaction. • Residue in the linker and SH2 domains of STAT1 are important for STAT1 phosphorylation. • Residues interferring with both functions have similar location on STAT1. • The viral P and V proteins may operate in concert to inhibit the JAK/STAT pathway.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Network of epistatic interactions in an enzyme active site revealed by large-scale deep mutational scanning

Cooperative interactions between amino acids are critical for protein function. A genetic reflection of cooperativity is epistasis, which is when a change in the amino acid at one position changes the sequence requirements at another position. To assess epistasis within an enzyme active site, we utilized CTX-M β-lactamase as a model system. CTX-M hydrolyzes β-lactam antibiotics to provide antibiotic resistance, allowing a simple functional selection for rapid sorting of modified enzymes. We created all pairwise mutations across 17 active site positions in the β-lactamase enzyme and quantitated the function of variants against two β-lactam antibiotics using next-generation sequencing. Context-dependent sequence requirements were determined by comparing the antibiotic resistance function of double mutations across the CTX-M active site to their predicted function based on the constituent single mutations, revealing both positive epistasis (synergistic interactions) and negative epistasis (antagonistic interactions) between amino acid substitutions. The resulting trends demonstrate that positive epistasis is present throughout the active site, that epistasis between residues is mediated through substrate interactions, and that residues more tolerant to substitutions serve as generic compensators which are responsible for many cases of positive epistasis. Additionally, we show that a key catalytic residue (Glu166) is amenable to compensatory mutations, and we characterize one such double mutant (E166Y/N170G) that acts by an altered catalytic mechanism. These findings shed light on the unique biochemical factors that drive epistasis within an enzyme active site and will inform enzyme engineering efforts by bridging the gap between amino acid sequence and catalytic function.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Co-assembly of Peptide Amphiphiles and Lipids into Supramolecular Nanostructures Driven by Anion–π Interactions

Co-assembly of binary systems driven by specific non-covalent interactions can greatly expand the structural and functional space of supramolecular nanostructures. We report here on the self-assembly of peptide amphiphiles and fatty acids driven primarily by anion–π interactions. The peptide sequences investigated were functionalized with a perfluorinated phenylalanine residue to promote anion–π interactions with carboxylate headgroups in fatty acids. These interactions were verified here by NMR and circular dichroism experiments as well as investigated using atomistic simulations. Positioning the aromatic units close to the N-terminus of the peptide backbone near the hydrophobic core of cylindrical nanofibers leads to strong anion–π interactions between both components. With a low content of dodecanoic acid in this position, the cylindrical morphology is preserved. However, as the aromatic units are moved along the peptide backbone away from the hydrophobic core, the interactions with dodecanoic acid transform the cylindrical supramolecular morphology into ribbon-like structures. Increasing the ratio of dodecanoic acid to PA leads to either the formation of large vesicles in the binary systems where the anion–π interactions are strong, or a heterogeneous mixture of assemblies when the peptide amphiphiles associate weakly with dodecanoic acid. Furthermore, our findings reveal how co-assembly involving designed specific interactions can drastically change supramolecular morphology and even cross from nano to micro scales.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Structures of Adnectin/Protein Complexes Reveal an Expanded Binding Footprint

Adnectins are targeted biologics derived from the tenth type III domain of human fibronectin ({sup 10}Fn3), a member of the immunoglobulin superfamily. Target-specific binders are selected from libraries generated by diversifying the three {sup 10}Fn3 loops that are analogous to the complementarity determining regions of antibodies. The crystal structures of two Adnectins were determined, each in complex with its therapeutic target, EGFR or IL-23. Both Adnectins bind different epitopes than those bound by known monoclonal antibodies. Molecular modeling suggests that some of these epitopes might not be accessible to antibodies because of the size and concave shape of the antibody combining site. In addition to interactions from the Adnectin diversified loops, residues from the N terminus and/or the {beta} strands interact with the target proteins in both complexes. Alanine-scanning mutagenesis confirmed the calculated binding energies of these {beta} strand interactions, indicating that these nonloop residues can expand the available binding footprint.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Ascorbic acid as DNase I inhibitor in prevention of male infertility

Highlights: • As a known dietary antioxidant ascorbic acid protects sperm DNA. • Another possible mechanism of sperm DNA protection by ascorbic acid was evaluated. • Ascorbic acid was investigated on DNase I inhibiton in vitro. • Molecular docking study was performed. • By inhibiting DNase I ascorbic acid could prevent sperm DNA fragmentation. Apoptotic and/or ROS-induced DNA fragmentation in sperm cells may contribute to the development of male infertility. As the known dietary antioxidant, ascorbic acid prevents ROS production and protects sperm cells from DNA damage. Here, we found that ascorbic acid has the ability to inhibit DNase I, one of the main endonucleases involved in DNA fragmentation during apoptosis. Site Finder and Molecular docking defined the ascorbic acid interactions with the most important residues of DNase I, including H-donor interactions with Asp 168 and Asn 170, and H-acceptor interaction with Asn 170. As a furan derivative, ascorbic acid could be considered a pioneer of substrate-based DNase I inhibitors. The results indicate to another possible mechanism for prevention of male infertility by ascorbic acid.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

TCR crosslinking promotes Crk adaptor protein binding to tyrosine-phosphorylated CD3ζ chain

T cell antigen receptor (TCR) binding of a peptide antigen presented by antigen-presenting cells (APCs) in the context of surface MHC molecules initiates signaling events that regulate T cell activation, proliferation and differentiation. A key event in the activation process is the phosphorylation of the conserved tyrosine residues within the CD3 chain immunoreceptor tyrosine-based activation motifs (ITAMs), which operate as docking sites for SH2 domain-containing effector proteins. Phosphorylation of the CD3ζ ITAMs renders the CD3 chain capable of binding the ζ-chain associated protein 70 kDa (ZAP70), a protein tyrosine kinase that is essential for T cell activation. We found that TCR/CD3 crosslinking in Jurkat T cells promotes the association of Crk adaptor proteins with the transiently phosphorylated CD3ζ chain. Pull down assays using bead-immobilized GST fusion proteins revealed that the Crk-SH2 domain mediates binding of phospho-CD3ζ. Phospho-CD3ζ binding is selective and is mediated by the three types of Crk, including CrkI, CrkII, and CrkL, but not by other SH2 domain-containing adaptor proteins, such as Grb2, GRAP and Nck. Crk interaction with phospho-CD3ζ is rapid and transient, peaking 1 min post TCR/CD3 crosslinking. The results suggest the involvement of Crk adaptor proteins in the early stages of T cell activation in which Crk might help recruiting effector proteins to the vicinity of the phospho-CD3ζ and contribute to the fine-tuning of the TCR/CD3-coupled signal transduction pathways. - Highlights: • TCR/CD3 crosslinking promotes Crk adaptor protein binding to tyrosine phosphorylated CD3ζ. • Crk interaction with phospho-CD3ζ is mediated by Crk-SH2 binding to CD3ζ phosphotyrosyl residues. • Interaction with phospho-CD3ζ is selective for Crk adaptor proteins. • Crk binding to tyrosine phosphorylated CD3ζ is independent of ZAP70.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Interactions involved in pH protection of the alphavirus fusion protein

The alphavirus membrane protein E1 mediates low pH-triggered fusion of the viral and endosome membranes during virus entry. During virus biogenesis E1 associates as a heterodimer with the transmembrane protein p62. Late in the secretory pathway, cellular furin cleaves p62 to the mature E2 protein and a peripheral protein E3. E3 remains bound to E2 at low pH, stabilizing the heterodimer and thus protecting E1 from the acidic pH of the secretory pathway. Release of E3 at neutral pH then primes the virus for fusion during entry. Here we used site-directed mutagenesis and revertant analysis to define residues important for the interactions at the E3–E2 interface. Our data identified a key residue, E2 W235, which was required for E1 pH protection and alphavirus production. Our data also suggest additional residues on E3 and E2 that affect their interacting surfaces and thus influence the pH protection of E1 during alphavirus exit.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Stigmatellin Probes the Electrostatic Potential in the QB Site of the Photosynthetic Reaction Center

The electrostatic potential in the secondary quinone (QB) binding site of the reaction center (RC) of the photosynthetic bacterium Rhodobacter sphaeroides determines the rate and free energy change (driving force) of electron transfer to QB. It is controlled by the ionization states of residues in a strongly interacting cluster around the QB site. Reduction of the QB induces change of the ionization states of residues and binding of protons from the bulk. Stigmatellin, an inhibitor of the mitochondrial and photosynthetic respiratory chain, has been proven to be a unique voltage probe of the QB binding pocket. It binds to the QB site with high affinity, and the pK value of its phenolic group monitors the local electrostatic potential with high sensitivity. Investigations with different types of detergent as a model system of isolated RC revealed that the pK of stigmatellin was controlled overwhelmingly by electrostatic and slightly by hydrophobic interactions. Measurements showed a high pK value (>11) of stigmatellin in the QB pocket of the dark-state wild-type RC, indicating substantial negative potential. When the local electrostatics of the QB site was modulated by a single mutation, L213Asp/Ala, or double mutations, L213Asp-L212Glu/Ala-Ala (AA), the pK of stigmatellin dropped to 7.5 and 7.4, respectively, which corresponds to a >210 mV increase in the electrostatic potential relative to the wild-type RC. This significant pK drop (DpK > 3.5) decreased dramatically to (DpK > 0.75) in the RC of the compensatory mutant (AAþM44Asn/AAþM44Asp). Our results indicate that the L213Asp is the most important actor in the control of the electrostatic potential in the QB site of the dark-state wild-type RC, in good accordance with conclusions of former studies using theoretical calculations or light-induced charge recombination assay.

Gerencsér, László↗
DOE OSTI2012

Unique Structural and Nucleotide Exchange Features of the Rho1 GTPase of Entamoeba histolytica

The single-celled human parasite Entamoeba histolytica possesses a dynamic actin cytoskeleton vital for its intestinal and systemic pathogenicity. The E. histolytica genome encodes several Rho family GTPases known to regulate cytoskeletal dynamics. EhRho1, the first family member identified, was reported to be insensitive to the Rho GTPase-specific Clostridium botulinum C3 exoenzyme, raising the possibility that it may be a misclassified Ras family member. Here, we report the crystal structures of EhRho1 in both active and inactive states. EhRho1 is activated by a conserved switch mechanism, but diverges from mammalian Rho GTPases in lacking a signature Rho insert helix. EhRho1 engages a homolog of mDia, EhFormin1, suggesting a role in mediating serum-stimulated actin reorganization and microtubule formation during mitosis. EhRho1, but not a constitutively active mutant, interacts with a newly identified EhRhoGDI in a prenylation-dependent manner. Furthermore, constitutively active EhRho1 induces actin stress fiber formation in mammalian fibroblasts, thereby identifying it as a functional Rho family GTPase. EhRho1 exhibits a fast rate of nucleotide exchange relative to mammalian Rho GTPases due to a distinctive switch one isoleucine residue reminiscent of the constitutively active F28L mutation in human Cdc42, which for the latter protein, is sufficient for cellular transformation. Nonconserved, nucleotide-interacting residues within EhRho1, revealed by the crystal structure models, were observed to contribute a moderating influence on fast spontaneous nucleotide exchange. Collectively, these observations indicate that EhRho1 is a bona fide member of the Rho GTPase family, albeit with unique structural and functional aspects compared with mammalian Rho GTPases.

59 BASIC BIOLOGICAL SCIENCES↗