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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 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Electrochemical cofactor recycling of bacterial microcompartments

Bacterial microcompartments (BMCs) are prokaryotic organelles that consist of a protein shell which sequesters metabolic reactions in its interior. While most of the substrates and products are relatively small and can permeate the shell, many of the encapsulated enzymes require cofactors that must be regenerated inside. We have analyzed the occurrence of an enzyme previously assigned as a cobalamin (vitamin B 12 ) reductase and, curiously, found it in many unrelated BMC types that do not employ B 12 cofactors. We propose Nicotinamide adenine dinucleotide (NAD+) regeneration as the function of this enzyme and name it Metabolosome Nicotinamide Adenine Dinucleotide Hydrogen (NADH) dehydrogenase (MNdh). Its partner shell protein BMC-T SE (tandem domain BMC shell protein of the single layer type for electron transfer) assists in passing the generated electrons to the outside. We support this hypothesis with bioinformatic analysis, functional assays, Electron Paramagnetic Resonance spectroscopy, protein voltammetry, and structural modeling verified with X-ray footprinting. This finding represents a paradigm for the BMC field, identifying a new, widely occurring route for cofactor recycling and a new function for the shell as separating redox environments.

bacterial microcompartment↗
DOE OSTI2022

The Function of Two Radical‐SAM Enzymes, HcgA and HcgG, in the Biosynthesis of the [Fe]‐Hydrogenase Cofactor

Abstract In the biosynthesis of the iron‐guanylylpyridinol (FeGP) cofactor, 6‐carboxymethyl‐5‐methyl‐4‐hydroxy‐2‐pyridinol ( 1 ) is 3‐methylated to form 2 , then 4‐guanylylated to form 3 , and converted into the full cofactor. HcgA‐G proteins catalyze the biosynthetic reactions. Herein, we report the function of two radical S ‐adenosyl methionine enzymes, HcgA and HcgG, as uncovered by in vitro complementation experiments and the use of purified enzymes. In vitro biosynthesis using the cell extract from the Methanococcus maripaludis Δ hcgA strain was complemented with HcgA or precursors 1 , 2 or 3 . The results suggested that HcgA catalyzes the biosynthetic reaction that forms 1 . We demonstrated the formation of 1 by HcgA using the 3 kDa cell extract filtrate as the substrate. Biosynthesis in the Δ hcgG system was recovered by HcgG but not by 3 , which indicated that HcgG catalyzes the reactions after the biosynthesis of 3 . The data indicated that HcgG contributes to the formation of CO and completes biosynthesis of the FeGP cofactor.

Arriaza‐Gallardo, Francisco J.↗
DOE OSTI2021

Efficient and reversible electron bifurcation with either normal or inverted potentials at the bifurcating cofactor

A longstanding mystery surrounding electron bifurcation is the significance of inverted (or “crossed”) reduction potentials of the two-electron bifurcating cofactor. Using a many-electron open-system kinetic model, we show that reversible and efficient electron bifurcation is possible without inverted reduction potentials at the bifurcating site if the absolute value of the difference between first and second reduction potentials of the bifurcating species is sufficiently large (on the scale of the redox-potential span of the high- and low-potential branches). Surprisingly, the case with strong, normally ordered potentials at the bifurcating cofactor can produce electron bifurcation that is just as effective as the case with strongly inverted potentials. Lastly, this finding amplifies the puzzle surrounding the recruitment of inverted potentials in the few well-characterized bifurcating systems of nature and suggests that electron bifurcating cofactors without strongly inverted potentials may yet be discovered.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Cofactor Complexes of DesD, a Model Enzyme in the Virulence-related NIS Synthetase Family

The understudied nonribosomal-peptide-synthetase-independent siderophore (NIS) synthetase family has been increasingly associated with virulence in bacterial species due to its key role in the synthesis of hydroxamate and carboxylate "stealth" siderophores. We have identified a model family member, DesD, from Streptomyces coelicolor , to structurally characterize using a combination of a wild-type and a Arg306Gln variant in apo , cofactor product AMP-bound, and cofactor reactant ATP-bound complexes. The kinetics in the family has been limited by solubility and reporter assays, so we have developed a label-free kinetics assay utilizing a single-injection isothermal-titration-calorimetry-based method. We report second-order rate constants that are 50 times higher than the previous estimations for DesD. Our Arg306Gln DesD variant was also tested under identical buffer and substrate conditions, and its undetectable activity was confirmed. These are the first reported structures for DesD, and they describe the critical cofactor coordination. This is also the first label-free assay to unambiguously determine the kinetics for an NIS synthetase.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Experimental and Computational Evaluation of Nicotinamide Cofactor Biomimetics

Oxidoreductase enzymes are widely used biocatalysts due to their high enantioselectivity and broad substrate compatibility in useful transformations. Many oxidoreductases require nicotinamide cofactors (i.e., NAD(P)H). To replace this costly natural cofactor, synthetic nicotinamide cofactor biomimetics (NCBs) offer different shapes, binding affinities, and reducing potentials that exceed the capabilities of wild-type NAD(P)H. However, the ill-defined structure–activity relationships (SARs) of various NCBs slow rationally guided innovation, such as customized reducing potentials. Here, we dissect two essential elements of NCB design, holding the nicotinamide invariant. First, the linker length between the nicotinamide and an unconjugated aromatic ring uncovered unexpected benefits to redox activity for two or three carbon linkers. Second, substitution on this unconjugated aryl group (Ring 2) might not be expected to affect activity. However, SAR trends demonstrate substantial benefits to reductive potential conferred by electron-donating functionalities on Ring 2. Furthermore, catalysis by two enzymes demonstrates enzyme-dependent tolerance or sensitivity to the NCB structures. Density functional theory (DFT) and computational modeling provide a theoretical framework to understand and build upon these observations. Ring 2 reaches up to the nicotinamide to stabilize its positive charge after oxidation through π–π stacking and charge transfer. Thus, the systematic examination of NCB’s stability, electrochemical redox potentials, and kinetics uncovers trends for the improved design of NCBs.

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

Trafficking of a nitrogenase FeMo-cofactor assembly intermediate

The maturation of the unique FeMo-cofactor of molybdenum nitrogenase is a multistep process requiring the sequential action of a series of maturase complexes. As a final step, the NifEN complex forms FeMo-cofactor from the precursor NifB-co, also called L-cluster, through replacement of an apical iron ion by molybdenum and the attachment of an organic homocitrate ligand. NifB-co is delivered by a small cofactor chaperone, NifX, and initially bound near the surface of the maturase NifEN. Here, we report high-resolution cryo-electron microscopy structures of NifEN in complex with NifX, showing NifB-co binding to NifEN in full detail, capturing both interacting partners in the act of cluster transfer. In a dynamic transfer complex, the large metal cluster is coordinated by single residues from both NifEN and NifX. In silico studies concur with these structures but suggest a third, internal conversion site where cluster maturation likely takes place.

metalloproteins↗
DOE OSTI2025

Inter-cofactor protein remodeling rewires short-circuited transmembrane electron transfer

Intraprotein electron transfer (ET) requires explicit local control of the environment of cofactors to influence their intermolecular distances, relative orientations, and redox properties. Efficient, longer-range ET often utilizes molecular orbitals of aromatic residues present in the intervening space. Here, revitalization of a vestigial ET pathway in the bacterial photosynthetic reaction center is achieved by scanning with tryptophans to uncover markedly improved routes of electron conduction in a key stabilizing step spanning 15 Å between tetrapyrrole and quinone cofactors. This ET event is maximally enhanced by pairing one or more tryptophans with a threonine to influence quinone binding and/or redox potential. Synergistic effects of these substitutions increase the yield of that ET step to ~95%. Joining these substitutions with mutant residues that improve initial ET steps dramatically enhances transmembrane charge separation via this redesigned version of a pathway that is quantitatively inactive in the native protein-cofactor complex.

Biophysical chemistry↗
DOE OSTI2024

Long-Term Stability of Nicotinamide Cofactors in Common Aqueous Buffers: Implications for Cell-Free Biocatalysis

The use of nicotinamide cofactors in cell-free biocatalytic systems is necessitated by the high specificity that these enzymes show for their natural redox mediators. Unfortunately, isolation and use of natural cofactors is costly, which suggests that enhancing their stability is key to enabling their use in industrial processes. This study details NAD+ and NADH stability in three buffer systems (sodium phosphate, HEPES, and Tris) at 19 °C and 25 °C and for up to 43 d. In Tris, both NADH and NAD+ were found to be highly stable. NADH degradation rates of 4 μM/d (19 °C) and 11 μM/d (25 °C) were observed in Tris buffer, corresponding to >90% and 75% remaining after 43 d, respectively. Higher degradation rates (up to 34 μM/d) were observed when sodium phosphate or HEPES buffers were used. The effect of a mild increase in temperature was determined to be significant for long-term stability, and it was shown that degradation under these conditions can be easily monitored via UV–Vis, because the degradation proceeds via the oxidation/de-aromatization of the dihydropyridine ring. Overall, this work emphasizes that the choice of buffer system is consequential for bioreactor systems employing natural nicotinamide cofactors for extended periods of time.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2021

Geological Factors Impacted Cadmium Availability and use as an Alternative Cofactor for Zinc in the Carbon Fixation Pathways of Marine Diatoms

Transition metal cofactors are crucial for many biological processes. Despite being primarily considered to be toxic, the transition metal cadmium (Cd) was discovered to be a substitute cofactor for zinc (Zn) in photosynthetic carbon fixation pathways of marine diatoms. However, it is not known how conditions in the geosphere impacted Cd availability and its incorporation as an alternative metal cofactor for phytoplankton. We employed mineral chemistry network analysis to investigate which geochemical factors may have influenced the availability of Cd and Zn during the putative time period that the alternative Cd-based pathway evolved. Our results show that Zn minerals are more chemically diverse than are Cd minerals, but Zn- and Cd-containing minerals have similar network centrality values when specifically considering sulfur (S)-containing species. Cadmium and Zn sulfides are the most common Cd- and Zn-containing mineral species over the past 500 million years. In particular, the Cd and Zn sulfides, respectively greenockite and sphalerite, were highly abundant during this time period. Furthermore, S-containing Cd and Zn minerals are commonly co-located in geologic time, allowing them to be weathered and transported to the ocean in tandem, rather than from separate sources. We suggest that the simultaneous weathering of Cd and Zn sulfides allowed for Cd to be a bioavailable direct substitute for Zn in protein complexes during periods of Zn depletion. The biogeochemical cycles of Zn and Cd exemplify the importance of the coevolution of the geosphere and biosphere in shaping primary production in the modern ocean.

Naman Srivastava↗
DOE OSTI2023

Structure of metallochaperone in complex with the cobalamin-binding domain of its target mutase provides insight into cofactor delivery

G-protein metallochaperone MeaB in bacteria [methylmalonic aciduria type A (MMAA) in humans] is responsible for facilitating the delivery of adenosylcobalamin (AdoCbl) to methylmalonyl-CoA mutase (MCM), the only AdoCbl-dependent enzyme in humans. Genetic defects in the switch III region of MMAA lead to the genetic disorder methylmalonic aciduria in which the body is unable to process certain lipids. Here, we present a crystal structure of Methylobacterium extorquens MeaB bound to a nonhydrolyzable guanosine triphosphate (GTP) analog guanosine-5'-[(β,γ)-methyleno]triphosphate (GMPPCP) with the Cbl-binding domain of its target mutase enzyme (MeMCM cbl ). This structure provides an explanation for the stimulation of the GTP hydrolyase activity of MeaB afforded by target protein binding. We find that upon MCM cbl association, one protomer of the MeaB dimer rotates ~180°, such that the inactive state of MeaB is converted to an active state in which the nucleotide substrate is now surrounded by catalytic residues. Importantly, it is the switch III region that undergoes the largest change, rearranging to make direct contacts with the terminal phosphate of GMPPCP. These structural data additionally provide insights into the molecular basis by which this metallochaperone contributes to AdoCbl delivery without directly binding the cofactor. Our data suggest a model in which GTP-bound MeaB stabilizes a conformation of MCM that is open for AdoCbl insertion, and GTP hydrolysis, as signaled by switch III residues, allows MCM to close and trap its cofactor. Substitutions of switch III residues destabilize the active state of MeaB through loss of protein:nucleotide and protein:protein interactions at the dimer interface, thus uncoupling GTP hydrolysis from AdoCbl delivery.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Orthogonal glycolytic pathway enables directed evolution of noncanonical cofactor oxidase

Abstract Noncanonical cofactor biomimetics (NCBs) such as nicotinamide mononucleotide (NMN + ) provide enhanced scalability for biomanufacturing. However, engineering enzymes to accept NCBs is difficult. Here, we establish a growth selection platform to evolve enzymes to utilize NMN + -based reducing power. This is based on an orthogonal, NMN + -dependent glycolytic pathway in Escherichia coli which can be coupled to any reciprocal enzyme to recycle the ensuing reduced NMN + . With a throughput of >10 6 variants per iteration, the growth selection discovers a Lactobacillus pentosus NADH oxidase variant with ~10-fold increase in NMNH catalytic efficiency and enhanced activity for other NCBs. Molecular modeling and experimental validation suggest that instead of directly contacting NCBs, the mutations optimize the enzyme’s global conformational dynamics to resemble the WT with the native cofactor bound. Restoring the enzyme’s access to catalytically competent conformation states via deep navigation of protein sequence space with high-throughput evolution provides a universal route to engineer NCB-dependent enzymes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Tracing the incorporation of the “ninth sulfur” into the nitrogenase cofactor precursor with selenite and tellurite

We report Molybdenum nitrogenase catalyses the reduction of N 2 to NH 3 at its cofactor, an [(R-homocitrate)MoFe 7 S 9 C] cluster synthesized via the formation of a [Fe 8 S 9 C] L-cluster prior to the insertion of molybdenum and homocitrate. We have previously identified a [Fe 8 S 8 C] L*-cluster, which is homologous to the core structure of the L-cluster but lacks the ‘ninth sulfur’ in the belt region. However, direct evidence and mechanistic details of the L*- to L-cluster conversion upon ‘ninth sulfur’ insertion remain elusive. Here we trace the ‘ninth sulfur’ insertion using SeO 3 2- and TeO 3 2- as ‘labelled’ SO 3 2- . Biochemical, electron paramagnetic resonance and X-ray absorption spectroscopy/extended X-ray absorption fine structure studies suggest a role of the ‘ninth sulfur’ in cluster transfer during cofactor biosynthesis while revealing the incorporation of Se 2- - and Te 2- -like species into the L-cluster. Density functional theory calculations further point to a plausible mechanism involving in situ reduction of SO 3 2- to S 2- , thereby suggesting the utility of this reaction to label the catalytically important belt region for mechanistic investigations of nitrogenase.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Proton transfer during reduction of the catalytic metallo-cofactors of the three nitrogenase isozymes

Nitrogenase catalyzes biological nitrogen fixation, the conversion of atmospheric N 2 into bioavailable ammonia. The three nitrogenase isozymes—Mo-nitrogenase, V-nitrogenase, and Fe-nitrogenase—utilize catalytic cofactors distinguished by their metal composition (Fe 7 M, M = Mo, V, or Fe; denoted FeM-co). Their catalytic cycles involve stepwise addition of 8[e−/H+] to FeM-co, generating intermediates designated E n , where n is the number of [e − /H + ] delivered. The electron-transfer has been extensively characterized, but the proton delivery has not. Here, we investigate [e − /H + ] delivery during early-stage conversions, primarily E 0 → E 1 (H), for each of the three nitrogenases, using as reductants γ-ray-generated thermolyzed, mobile electrons at 77 K, and radiation-generated solvent radicals during subsequent annealing to higher temperatures. Our results show E 0 → E 1 (H) conversion differs among the three MFe-proteins. The FeMo-co of MoFe-protein accepts an electron (ET) during 77 K γ-irradiation, but proton transfer (PT) to generate E 1 (H) is only enabled by conformational or thermodynamic activation upon cryoannealing to ∼200 K(ET/PT). For VFe-protein, E 1 (H) forms during annealing at-and-above 210 K by electron-transfer to FeV-co from radicals through proton-coupled electron transfer (PCET), which too is enabled by activated proton transfer. FeFe-protein differs in directly exhibiting delivery of protons at 77 K, which together with the mobile electrons react to form E 1 (H). This could well occur by PCET at 77 K, but does not preclude the possibility of sequential 77 K electron/proton transfer (ET/PT). In addition, 450 nm photolysis reveals the E 1 (H) state of FeV-co, like that of FeFe-co, contains a hydride bound to a formally oxidized cofactor. The mechanistic differences observed here provide a contribution towards understanding the sources of catalytic differences among the three nitrogenase isozymes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Cofactor maturase NifEN: A prototype ancient nitrogenase?

Nitrogenase plays a key role in the global nitrogen cycle; yet, the evolutionary history of nitrogenase and, particularly, the sequence of appearance between the homologous, yet distinct NifDK (the catalytic component) and NifEN (the cofactor maturase) of the extant molybdenum nitrogenase, remains elusive. Here, we report the ability of NifEN to reduce N 2 at its surface-exposed L-cluster ([Fe 8 S 9 C]), a structural/functional homolog of the M-cluster (or cofactor; [(R-homocitrate)MoFe 7 S 9 C]) of NifDK. Furthermore, we demonstrate the ability of the L-cluster–bound NifDK to mimic its NifEN counterpart and enable N 2 reduction. These observations, coupled with phylogenetic, ecological, and mechanistic considerations, lead to the proposal of a NifEN-like, L-cluster–carrying protein as an ancient nitrogenase, the exploration of which could shed crucial light on the evolutionary origin of nitrogenase and related enzymes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Comprehensive analysis of the human ESCRT-III-MIT domain interactome reveals new cofactors for cytokinetic abscission

The 12 related human ESCRT-III proteins form filaments that constrict membranes and mediate fission, including during cytokinetic abscission. The C-terminal tails of polymerized ESCRT-III subunits also bind proteins that contain Microtubule-Interacting and Trafficking (MIT) domains. MIT domains can interact with ESCRT-III tails in many different ways to create a complex binding code that is used to recruit essential cofactors to sites of ESCRT activity. Here, we have comprehensively and quantitatively mapped the interactions between all known ESCRT-III tails and 19 recombinant human MIT domains. We measured 228 pairwise interactions, quantified 60 positive interactions, and discovered 18 previously unreported interactions. We also report the crystal structure of the SPASTIN MIT domain in complex with the IST1 C-terminal tail. Three MIT enzymes were studied in detail and shown to: (1) localize to cytokinetic midbody membrane bridges through interactions with their specific ESCRT-III binding partners (SPASTIN-IST1, KATNA1-CHMP3, and CAPN7-IST1), (2) function in abscission (SPASTIN, KATNA1, and CAPN7), and (3) function in the ‘NoCut’ abscission checkpoint (SPASTIN and CAPN7). Our studies define the human MIT-ESCRT-III interactome, identify new factors and activities required for cytokinetic abscission and its regulation, and provide a platform for analyzing ESCRT-III and MIT cofactor interactions in all ESCRT-mediated processes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Hydroxy-substituted electron deficient Pd porphyrin cofactors illuminate ultrafast proton transfer reactions

Coordinated electron and proton movement drive bioenergetic functions. Relative to electron transfer reactions, tracking proton transport over fast-to-ultrafast time scales is challenging. Optical resolution of proton transfer dynamics can take advantage of chromophoric photoacids that not only trigger proton migration upon photoexcitation, but produce distinct spectroscopic changes associated with protonation/deprotonation. Here, in this work, we report the design of a hydroxy-substituted electron deficient Pd porphyrin, PPd(C 6 F 5 ) 3 OH; upon photoexcitation, the acidity constant of this weak acid (pKa = 6.49) dramatically drops (pKa* = 0.97). Electronic excitation of PPd(C 6 F 5 ) 3 OH triggers an ultrafast proton transfer reaction (PPd(C 6 F 5 ) 3 OH +:B + hυ → 1[PPd(C 6 F 5 ) 3 OH]* +:B → 1 [PPd(C 6 F 5 ) 3 O]−* + HB + ; τ PT = 342 fs) to a H-bonded base (B) in solution. Both PPd(C 6 F 5 ) 3 OH and its conjugate anion PPd(C 6 F 5 ) 3 O − exhibit distinct vis-NIR spectral features for their respective ground and excited states. Because the electroni-cally excited triplet lifetimes of these species exceed tens of microseconds, the PPd(C 6 F 5 ) 3 OH photoacid defines an ideal cofactor to probe light-triggered proton release and track long-range proton migration in protein environments.

Palladium↗
DOE OSTI2023

How thermal fluctuations influence the function of the FeMo cofactor in nitrogenase enzymes

The catalytic mechanism of N 2 fixation by nitrogenase remains unresolved in how the strong N≡N bond is activated and why the reductive elimination of H 2 is required. Here, we use density functional theory and physiologically relevant thermal simulations to elucidate the mechanism of the complete nitrogenase catalytic cycle. Over the accumulation of four reducing equivalents, we find that protons and electrons transfer to the FeMo cofactor to weaken and break its bridge Fe–S bond, leading to temporary H 2 S formation that exposes the Fe sites to weakly bind N 2 . Remarkably, we find that subsequent H 2 formation is responsible for chemical activation to an N=N double bond accompanied by a low barrier for H 2 release. We emphasize that finite temperature effects smooth out mechanistic differences between DFT functionals observed at 0 K, thus leading to a consistent understanding as to why H formation is an obligatory step in N 2 adsorption and activation.

DFT↗