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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Mechanistic Studies of a Primitive Homolog of Nitrogenase Involved in Coenzyme F430 Biosynthesis

Methyl-coenzyme M reductase (MCR) is the key enzyme in the biological formation and anaerobic oxidation of methane (AOM). Methane is a potent greenhouse gas and the major component of natural gas. Given the abundance of natural gas reserves in remote areas, there is great current interest in a scalable bio-based process for the conversion of methane to liquid fuel or other high-value commodity chemicals. MCR holds much promise for use in such a methane bioconversion strategy. However, MCR cannot currently be produced in an active form in a heterologous host, due in large part to the lack of genetic and biochemical information about the production of holo MCR. In an effort to overcome this deficiency, our laboratory elucidated the biosynthetic pathway of the unique nickel-containing coenzyme of MCR, F430. The key step in coenzyme F430 biosynthesis (Cfb) was found to involve an unprecedented reductive cyclization reaction that converts Ni-sirohydrochlorin a , c -diamide to 15,17 3 -seco-F430-17 3 -acid. This remarkable transformation, which involves a 6-electron reduction of the isobacteriochlorin ring system, cyclization of the c -acetamide side chain to form a γ-lactam ring, and the formation of 7 stereocenters, is catalyzed by a primitive homolog of nitrogenase (CfbCD). Nitrogenase is a two-component metalloenzyme that catalyzes the ATP-dependent reduction of dinitrogen to ammonia (nitrogen fixation). Homologs of nitrogenase are also involved in the biosynthesis of the photosynthetic pigments chlorophyll and bacteriochlorophyll. Phylogenetic analysis of the CfbCD complex suggests that it is representative of a more ancient lineage of the nitrogenase superfamily, and a thorough investigation of its structure and function is likely to shed light on the mechanisms and evolution of these important metalloenzymes that catalyze multi-electron redox reactions. Moreover, a detailed understanding of the mechanism of the CfbCD complex may aid in the development of specific inhibitors to help reduce natural greenhouse gas emissions and can be exploited for the heterologous production of MCR for methane bioconversion. Towards these goals, the following Specific Aims will be pursued to determine the: 1) Identity of the CfbCD reaction product. The exact reaction catalyzed by CfbCD, including the number of electrons transferred and whether it involves enzymatic cyclization, is unclear. Several approaches, including reaction stoichiometry measurements, spectroelectrochemistry, and magnetic resonance spectroscopy will be applied to elucidate the structure of the reaction product and establish whether CfbCD is a reductase or reductive cyclase. 2) Structure, conformational dynamics, and oligomerization state changes of CfbCD. Significant insight into the mechanism and allosteric regulation of CfbCD can be obtained by assessing changes in the structure and dynamics of the complex during the catalytic cycle. To accomplish this, a combination of size-exclusion chromatography, hydrogen-deuterium exchange mass spectrometry, molecular dynamics simulations, and high-resolution structural methods will be employed. 3) Source, order, and stereochemistry of proton additions during CfbCD catalysis. Details regarding the order and stereochemistry of proton additions during the CfbCD reaction will be uncovered using a combined spectroscopic and computational approach. Complementary mechanistic studies employing site-directed mutagenesis and substrate analogs will establish the identity of active site acid residues and the possible involvement of substrate-assisted catalysis during the CfbCD reaction.

09 BIOMASS FUELS↗
NASA NTRS1993

Evolution of EF-hand calcium-modulated proteins. IV. Exon shuffling did not determine the domain compositions of EF-hand proteins

In the previous three reports in this series we demonstrated that the EF-hand family of proteins evolved by a complex pattern of gene duplication, transposition, and splicing. The dendrograms based on exon sequences are nearly identical to those based on protein sequences for troponin C, the essential light chain myosin, the regulatory light chain, and calpain. This validates both the computational methods and the dendrograms for these subfamilies. The proposal of congruence for calmodulin, troponin C, essential light chain, and regulatory light chain was confirmed. There are, however, significant differences in the calmodulin dendrograms computed from DNA and from protein sequences. In this study we find that introns are distributed throughout the EF-hand domain and the interdomain regions. Further, dendrograms based on intron type and distribution bear little resemblance to those based on protein or on DNA sequences. We conclude that introns are inserted, and probably deleted, with relatively high frequency. Further, in the EF-hand family exons do not correspond to structural domains and exon shuffling played little if any role in the evolution of this widely distributed homolog family. Calmodulin has had a turbulent evolution. Its dendrograms based on protein sequence, exon sequence, 3'-tail sequence, intron sequences, and intron positions all show significant differences.

NASA Discipline Exobiology↗
NASA NTRS1992

Evolution of EF-hand calcium-modulated proteins. II. Domains of several subfamilies have diverse evolutionary histories

In the first report in this series we described the relationships and evolution of 152 individual proteins of the EF-hand subfamilies. Here we add 66 additional proteins and define eight (CDC, TPNV, CLNB, LPS, DGK, 1F8, VIS, TCBP) new subfamilies and seven (CAL, SQUD, CDPK, EFH5, TPP, LAV, CRGP) new unique proteins, which we assume represent new subfamilies. The main focus of this study is the classification of individual EF-hand domains. Five subfamilies--calmodulin, troponin C, essential light chain, regulatory light chain, CDC31/caltractin--and three uniques--call, squidulin, and calcium-dependent protein kinase--are congruent in that all evolved from a common four-domain precursor. In contrast calpain and sarcoplasmic calcium-binding protein (SARC) each evolved from its own one-domain precursor. The remaining 19 subfamilies and uniques appear to have evolved by translocation and splicing of genes encoding the EF-hand domains that were precursors to the congruent eight and to calpain and to SARC. The rates of evolution of the EF-hand domains are slower following formation of the subfamilies and establishment of their functions. Subfamilies are not readily classified by patterns of calcium coordination, interdomain linker stability, and glycine and proline distribution. There are many homoplasies indicating that similar variants of the EF-hand evolved by independent pathways.

Non-NASA Center↗
DOE OSTI2021

43-0434 Bridge Inspection Report 2021

The documentation includes the following: 1. 2021 NMDOT Bridge Inspection Report including Element Level Data Collection (in digital formats prepared by NMSU)--conforms to the National Bridge Inspection Standards and AASHTO Manual for Bridge Element Inspection; 2. 2021 Supplemental Report (in digital formats prepared by NMSU)--provides detailed information related to current condition of major bridge components; 3. 2021 Inspection Pictures (in digital format prepared by NMSU); 4. 2021 Delamination Map (in digital format prepared by LANL). During the 2021 inspection, three critical findings were reported to our LANL contact, Mr. Jonathan Stein, by text and/or email on June 26, 2021. 1. The south joint of the bridge had a modular section of the joint that could potentially come loose during the passing of vehicles. This was reported as a critical finding for safety. If the modular section becomes dislodged or deformed it could pose a serious hazard that could result in a punctured tire to vehicles, motorcyclists and/or bicyclist causing drivers/riders to lose control; 2. The bracket plate located at the north end of the bridge on the pedestrian walkway was corroded through and provides little protection to pedestrians and bicyclists. This was reported as a critical finding for safety to prevent injuries to people; 3. The north approach rail has three missing posts. These posts help ensure that traffic is redirected and the energy is absorbed by the rail. This was reported as a critical finding for safety. Additionally, the approach rail is on a curve with a nearby drop off. Immediate repair is recommended. Based on the 2021 inspection, the bridge deck is rated in "fair" condition. The chain drag performed on the deck identified several areas with delamination that are concentrated near the expansion joints, in the closure joint of the deck near the bridge centerline, and at the south end of the northbound lanes. The chain drag performed during the 2021 inspection revealed 215,333 sq. in. (1495 sq. ft) of delaminations and patched areas (not including the sidewalk). This is approximately a 600% increase from 2019. It is recommended that the delaminations and spalls with exposed rebar be repaired. The "delaminated area" map for the 2021 inspection is provided in the supplemental report.

42 ENGINEERING↗
DOE OSTI2024

Janus bottlebrush compatibilizers

Bottlebrush random copolymers (BRCPs), consisting of a random distribution of two homopolymer chains along a backbone, can segregate to the interface between two immiscible homopolymers. BRCPs undergo a reconfiguration, where each block segregates to one of the homopolymer phases, adopting a Janus-type structure, reducing the interfacial tension and promoting adhesion between the two homopolymers, thereby serving as a Janus bottlebrush copolymer (JBCP) compatibilizer. Here, we synthesized a series of JBCPs by copolymerizing deuterated or hydrogenated polystyrene (DPS/PS) and poly(tert-butyl acrylate) (PtBA) macromonomers using ruthenium benzylidene-initiated ring-opening metathesis polymerization (ROMP). Subsequent acid-catalyzed hydrolysis converted the PtBA brushes to poly(acrylic acid) (PAA). The JBCPs were then placed at the interface between DPS/PS homopolymers and poly(2-vinyl pyridine) (P2VP) homopolymers, where the degree of polymerization of the backbone (N BB ) and the grafting density (GD) of the JBCPs were varied. Neutron reflectivity (NR) was used to determine the interfacial width and segmental density distributions (including PS homopolymer, PS block, PAA block and P2VP homopolymer) across the polymer-polymer interface. Our findings indicate that the star-like JBCP with N BB = 6 produces the largest interfacial broadening. Increasing N BB to 100 (rod-like shape) and 250 (worm-like shape) reduced the interfacial broadening due to a decrease in the interactions between blocks and homopolymers by stretching of blocks. Decreasing the GD from 100% to 80% at N BB = 100 caused an increase the interfacial width, yet further decreasing the GD to 50% and 20% reduced the interfacial width, as 80% of GD may efficiently increase the flexibility of blocks and promote interactions between homopolymers, while maintaining relatively high number of blocks attached to one molecule. The interfacial conformation of JBCPs was further translated into compatibilization efficiency. Thin film morphology studies showed that only the lower N BB values (N BB = 6 and N BB = 24) and the 80% GD of N BB = 100 had bicontinuous morphologies, due to a sufficient binding energy that arrested phase separation, supported by mechanical testing using asymmetric double cantilever beam (ADCB) tests. These provide fundamental insights into the assembly behavior of JBCPs compatibilizers at homopolymer interfaces, opening strategies for the design of new BCP compatibilizers.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Closing the Loop on Automotive Carbon Fiber Prepreg Manufacturing Scrap

The project demonstrated how to “close the loop” on carbon fiber by integrating industrial carbon fiber scrap into new functional components in an automotive lightweighting application. The project serves as a validation of discontinuous recycled carbon fiber in a commercial context, while generating comprehensive material data throughout the production chain. To this end, the project exhibited increasing complexity as material evaluation progressed from benchtop to commercial scale through full-scale part production, with key material properties thoroughly characterized throughout the process. Of particular focus was the form of the fiber that was fed into compounding, as recycled fiber has historically been problematic to feed at commercial-scale. Carbon fiber is energy-intensive to manufacture, so reuse of existing fiber material can reduce costs and increase sustainability. Additionally, by integrating recovered short fiber into a thermoplastic, regrind processes can be used to provide feedstock for later generations of product. While regrind plastics are not “infinitely recyclable”, reusing the manufacturing scrap over several generations of products can greatly increase material sustainability and lower the fractional embodied energy of each successive product. As such, this project supports the IACMI technical goals of (1) 25% lower carbon fiber-reinforced polymer (CFRP) cost, (2) 50% reduction in CFRP embodied energy, and (3) 80% composite recyclability into useful products. The initial stage of the project involved down selecting surface treatment (sizing) chemistries. Sizing evaluations were performed on Vartega’s chemically recycled intermediate modulus fiber along with standard modulus dry scrap which was oversized with sizing provided by Michelman. More dramatic improvements from sizing were found on the standard rather than the intermediate modulus fibers. The strength of the chemically recycled individual fibers were evaluated by Michelman and ORNL through single fiber testing and found to be comparable to similarly evaluated virgin fibers. UDRI’s mechanical testing on injection molded test specimens identified similar mechanical properties and fiber distribution relative to benchmark specimens. Additional surface chemistry tests and visualizations were performed by the Colorado School of Mines to confirm close conformance between the benchmark and recycled-fiber specimens. As the mechanical test results exceeded the 80% threshold established as the go/no-go(GNG), the project scale was increased to use commercial-scale equipment that would both better characterize the manufacturing utility of the target product format and allow qualitative assessment of a complex commercial part. An upscaled compounding evaluation was performed with a 27 mm twin-screw compounding extruding using oversized standard modulus fibers that were formatted to improve bulk solids transfer. The project team anticipated that milestone mechanical benchmarks could be achieved given the favorable performance of the sized standard modulus material identified in the initial micro-compounding trials. While the mechanical performance did meet the milestone target for that phase of the project, mechanical properties for this standard modulus-based compound were still less than those of the Ford specification. To compare the performance, the project team oversized intermediate modulus dry fibers and compounded them with the project resin at BASF using a 40 mm compounder. Test specimen mechanical performance exceeded the targets laid out in both the project milestone and the Ford specification. A series of prototype parts were successfully molded, albeit with instances of short shot components due to the high thermal conductivity of the carbon fiber compared to glass fiber for which the prototype tool was designed for. The project demonstrated that recycled carbon fiber is a viable option in fiber reinforced compound, providing greatly increased strength and modulus for applications that require them. The “agglomerated” format that facilitated effective bulk solids transfer of recovered fiber showed promise for industrial application.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Aminobenzoic Acid Derivatives Obstruct Induced Fit in the Catalytic Center of the Ribosome

The Escherichia coli (E. coli) ribosome can incorporate a variety of non-l-α-amino acid monomers into polypeptide chains in vitro but with poor efficiency. Although these monomers span a diverse set of compounds, there exists no high-resolution structural information regarding their positioning within the catalytic center of the ribosome, the peptidyl transferase center (PTC). Thus, details regarding the mechanism of amide bond formation and the structural basis for differences and defects in incorporation efficiency remain unknown. Within a set of three aminobenzoic acid derivatives–3-aminopyridine-4-carboxylic acid (Apy), ortho-aminobenzoic acid (oABZ), and meta-aminobenzoic acid (mABZ)–the ribosome incorporates Apy into polypeptide chains with the highest efficiency, followed by oABZ and then mABZ, a trend that does not track with the nucleophilicity of the reactive amines. Here, we report high-resolution cryo-EM structures of the ribosome with each of these three aminobenzoic acid derivatives charged on tRNA bound in the aminoacyl-tRNA site (A-site). The structures reveal how the aromatic ring of each monomer sterically blocks the positioning of nucleotide U2506, thereby preventing rearrangement of nucleotide U2585 and the resulting induced fit in the PTC required for efficient amide bond formation. They also reveal disruptions to the bound water network that is believed to facilitate formation and breakdown of the tetrahedral intermediate. Together, the cryo-EM structures reported here provide a mechanistic rationale for differences in reactivity of aminobenzoic acid derivatives relative to l-α-amino acids and each other and identify stereochemical constraints on the size and geometry of non-monomers that can be accepted efficiently by wild-type ribosomes.

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

SPARC: Structural properties associated with residue constraints

SPARC facilitates the generation of plausible hypotheses regarding underlying biochemical mechanisms by structurally characterizing protein sequence constraints. Such constraints appear as residues co-conserved in functionally related subgroups, as subtle pairwise correlations (i.e., direct couplings), and as correlations among these sequence features or with structural features. SPARC performs three types of analyses. First, based on pairwise sequence correlations, it estimates the biological relevance of alternative conformations and of homomeric contacts, as illustrated here for death domains. Second, it estimates the statistical significance of the correspondence between directly coupled residue pairs and interactions at heterodimeric interfaces. Third, given molecular dynamics simulated structures, it characterizes interactions among constrained residues or between such residues and ligands that: (a) are stably maintained during the simulation; (b) undergo correlated formation and/or disruption of interactions with other constrained residues; or (c) switch between alternative interactions. We illustrate this for two homohexameric complexes: the bacterial enhancer binding protein (bEBP) NtrC1, which activates transcription by remodeling RNA polymerase (RNAP) containing σ 54 , and for DnaB helicase, which opens DNA at the bacterial replication fork. Based on the NtrC1 analysis, we hypothesize possible mechanisms for inhibiting ATP hydrolysis until ADP is released from an adjacent subunit and for coupling ATP hydrolysis to restructuring of σ 54 binding loops. Based on the DnaB analysis, we hypothesize that DnaB ‘grabs’ ssDNA by flipping every fourth base and inserting it into cavities between subunits and that flipping of a DnaB-specific glutamine residue triggers ATP hydrolysis.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS1997

Isolation of novel ribozymes that ligate AMP-activated RNA substrates

BACKGROUND: The protein enzymes RNA ligase and DNA ligase catalyze the ligation of nucleic acids via an adenosine-5'-5'-pyrophosphate 'capped' RNA or DNA intermediate. The activation of nucleic acid substrates by adenosine 5'-monophosphate (AMP) may be a vestige of 'RNA world' catalysis. AMP-activated ligation seems ideally suited for catalysis by ribozymes (RNA enzymes), because an RNA motif capable of tightly and specifically binding AMP has previously been isolated. RESULTS: We used in vitro selection and directed evolution to explore the ability of ribozymes to catalyze the template-directed ligation of AMP-activated RNAs. We subjected a pool of 10(15) RNA molecules, each consisting of long random sequences flanking a mutagenized adenosine triphosphate (ATP) aptamer, to ten rounds of in vitro selection, including three rounds involving mutagenic polymerase chain reaction. Selection was for the ligation of an oligonucleotide to the 5'-capped active pool RNA species. Many different ligase ribozymes were isolated; these ribozymes had rates of reaction up to 0.4 ligations per hour, corresponding to rate accelerations of approximately 5 x10(5) over the templated, but otherwise uncatalyzed, background reaction rate. Three characterized ribozymes catalyzed the formation of 3'-5'-phosphodiester bonds and were highly specific for activation by AMP at the ligation site. CONCLUSIONS: The existence of a new class of ligase ribozymes is consistent with the hypothesis that the unusual mechanism of the biological ligases resulted from a conservation of mechanism during an evolutionary replacement of a primordial ribozyme ligase by a more modern protein enzyme. The newly isolated ligase ribozymes may also provide a starting point for the isolation of ribozymes that catalyze the polymerization of AMP-activated oligonucleotides or mononucleotides, which might have been the prebiotic analogs of nucleoside triphosphates.

NASA Discipline Exobiology↗
NASA NTRSDate not supplied

Rational Design of Nanoplasmonic Array Geometries for Biosensing

Background: Molecular diagnostics provide early and accurate diagnosis, which is essential for the prevention and treatment of infectious as well as chronic diseases. These tests are designed to detect disease-specific bioanalytes such as nucleic acid (DNA or RNA) or protein (antigens, antibodies) biomarkers. In the context of infectious disease diagnosis, nucleic acid-based detection methods are known to provide more specific and sensitive results. Here, the presence of a unique sequence belonging to the pathogenic genomic material is targeted to identify species, organism, genera and/or antimicrobial resistant gene markers. The majority of the common nucleic acid based diagnostic techniques require amplification (polymerase chain reaction, isothermal amplification etc.) of the pathogenic genetic material prior to detection impacting diagnostic speed, complexity, and cost thereby limiting ease of use. Thus, the development of simplified nucleic acid-based diagnostics that can be even used in resource-poor settings may hugely benefit patients across the globe. Nanopath is a molecular diagnostics company utilizing a solid-state nanosensor to enable sequence-specific detection of target nucleic acids without the need of amplification. These nanostructures enable ultra-sensitive biomarker detection using geometric, feature-dependent properties highly dependent on the local dielectric environment, allowing them to be sensitive to low concentration binding events. This paper describes an application of this approach to provide highly relevant clinical information within a single doctor’s office visit. Intro: The Nanopath team is in collaboration with NASA (National Aeronautics and Space Administration) and NIST (National Institute of Standards and Technology) to push the bounds of the fundamental physics associated with their biosensing platform. The ability of metals to support electromagnetic surface waves gives rise to surface plasmons when optically illuminated. This property, and its strong sensitivity to changes in the local refractive index, allows for the use of metal nanoparticles as ultra-sensitive transducers. In prior work by members of this team, ensembles of randomly oriented nanoparticles (i.e., colloidal nanorods dispersed on chip) were employed for sequence-specific nucleic acid sensing (1-3). While these particle sensors have the advantage of rapid fabrication, they suffer from low sensitivity and quality factor due to the random particle dispersity. In contrast, in this study we employ ordered array nanoparticle ensembles which can be used to improve sensor sensitivity and figure-of-merit. Study Methods Overview: In this talk, we detail the results of sensing experiments and computational simulations to outline a rational design of the structure of these plasmonic nanoparticle arrays for biomolecular sensing. Through simulation and experiment, we iteratively tailor nanostructure dimension to provide high quality signal and large resonance shifts upon modeled nucleic acid binding. In particular, full-wave electromagnetic simulations were conducted using Lumerical photonic simulation software in which periodic boundary conditions were applied in the x- and y- dimensions for each of the nanoplasmonic sensor geometries. To simulate the resonance response to changes in the bulk solution in contact with the sensor surface, the refractive index of the surrounding media was changed appropriately. Nucleic acid hybridization events were modeled using either using spherical structures approximating the relevant radius of genomic material as estimated by polymer models, or as conformal layers with the known refractive indices for nucleic acids. On the basis of initial simulations, nanosensors were fabricated using traditional electron-beam lithography protocols at NIST. To evaluate consensus between simulations and experiments, bulk sensing experiments were carried out in which the resonance peaks were obtained by submerging the sensors in refractive index standards. Key nanosensor characteristics including resonance peak locations, resonance peak shifts as a function of refractive index, and figure of merit (FOM) of extinction curves were examined between the experimental and simulation results prior to proceeding with simulations on additional geometries and more complex solution conditions, and further device fabrication. This iterative process is repeated toward a rational design of nanoplasmonic array geometries for biosensing optimizing response for targeted disease detection. In summary, this study puts forth a methodology for rational design and characterization of regularly spaced nanoparticle arrays for optics-based biosensing. The results of this study will allow for more informed design of nanostructure geometries towards sequence-specific nucleic acid detection. These improved designs have the potential to improve clinical sensitivity and limit-of-detection across disease indication.

sensor↗
DOE OSTI2021

Implication of rare genetic variants of NODAL and ACVR1B in congenital heart disease patients from Indian population

Highlights: • Screening of 300 CHD patients revealed two rare missense variants (p.P51L & p.D327E) in NODAL. • A novel missense variation p.M345I was identified in ACVR1B. • Bioinformatic analyses suggested that these variants could have deleterious role. • Three-dimensional modelling suggested conformation changes in the mutated proteins compared to wild-type. • In vitro studies demonstrated that missense variants affect the function of NODAL and ACVR1B. NODAL signaling plays an essential role in vertebrate embryonic patterning and heart development. Accumulating evidences suggest that genetic mutations in TGF-β/NODAL signaling pathway can cause congenital heart disease in humans. To investigate the implication of NODAL signaling in isolated cardiovascular malformation, we have screened 300 non-syndromic CHD cases and 200 controls for NODAL and ACVR1B by Sanger sequencing and identified two rare missense (c.152C > T; p.P51L and c.981 T > A; p.D327E) variants in NODAL and a novel missense variant c.1035G > A; p.M345I in ACVR1B. All these variants are absent in 200 controls. Three-dimensional protein-modelling demonstrates that both p.P51L and p.D327E variations of NODAL and p.M345I mutation of ACVR1B, affect the tertiary structure of respective proteins. Variants of NODAL (p.P51L and p.D327E) and ACVR1B (p.M345I), significantly reduce the transactivation of AR3-Luc, (CAGA){sub 12}-Luc and (SBE){sub 4}-Luc promoters. Moreover, qRT-PCR results have also deciphered a reduction in the expression of cardiac-enriched transcription factors namely Gata4, Nkx2-5, and Tbx5 in both the mutants of NODAL. Decreased expression of, Gata4, Nkx2-5, Tbx5, and lefty is observed in p.M345I mutant of ACVR1B as well. Additionally, reduced phosphorylation of SMAD2/3 in response to these variants, suggests impaired NODAL signaling and possibly responsible for defective cell fate decision and differentiation of cardiomyocytes leading to CHD phenotype.

60 APPLIED LIFE SCIENCES↗