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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

A conserved chaperone protein is required for the formation of a noncanonical type VI secretion system spike tip complex

Type VI secretion systems (T6SSs) are dynamic protein nanomachines found in Gram-negative bacteria that deliver toxic effector proteins into target cells in a contact-dependent manner. Prior to secretion, many T6SS effector proteins require chaperones and/or accessory proteins for proper loading onto the structural components of the T6SS apparatus. However, despite their established importance, the precise molecular function of several T6SS accessory protein families remains unclear. In this study, we set out to characterize the DUF2169 family of T6SS accessory proteins. Using gene co-occurrence analyses, we find that DUF2169-encoding genes strictly co-occur with genes encoding T6SS spike complexes formed by valine-glycine repeat protein G (VgrG) and DUF4150 domains. Although structurally similar to Pro-Ala-Ala-Arg (PAAR) domains, “PAAR-like” DUF4150 domains lack PAAR motifs and instead contain a conserved PIPY motif, leading us to designate them PIPY domains. Next, we present both genetic and biochemical evidence that PIPY domains require a cognate DUF2169 protein to form a functional T6SS spike complex with VgrG. This contrasts with canonical PAAR proteins, which bind VgrG on their own to form functional spike complexes. By solving the first crystal structure of a DUF2169 protein, we show that this T6SS accessory protein adopts a novel protein fold. Furthermore, biophysical and structural modeling data suggest that DUF2169 contains a dynamic loop that physically interacts with a hydrophobic patch on the surface of its cognate PIPY domain. Based on these findings, we propose a model whereby DUF2169 proteins function as molecular chaperones that maintain VgrG–PIPY spike complexes in a secretion-competent state prior to their export by the T6SS apparatus.

DUF2169↗
DOE OSTI2021

CO 2 -selective membranes containing amino acid salts for CO 2 /N 2 separation

In this paper, facilitated transport membranes comprising polyvinylamine (PVAm) as fixed carrier and different amino acid salts (AAS) as mobile carriers were synthesized for post-combustion capture. The AAS carriers were prepared by deprotonating alanine (Ala), lysine (Lys), and proline (Pro) with 2-(1-piperazinyl)ethylamine (PZEA). CO 2 separation performances of the membranes with these AAS carriers were compared, and the AAS effectiveness to facilitate transport of CO 2 was in the order of PZEA-Pro > PZEA-Lys > PZEA-Ala. Here, the membrane comprising 35 wt.% PVAm and 65 wt.% PZEA-Pro at 57 °C rendered a promising CO 2 permeance of 936 GPU and a CO 2 /N 2 mixed gas selectivity of 193. When the PVAm was reduced to 15 wt.%, i.e., its 20 wt.% was replaced by the mobile carrier of PZEA-Sar (sarcosinate), the permeance further improved to 947 GPU with a remarkable CO 2 /N 2 selectivity of 210. Moreover, thermal gravimetric analysis showed a good thermal stability of the membrane, and membrane stability testing also gave stable transport performance. Furthermore, spectroscopic ellipsometry analysis exhibited a uniform membrane selective layer and an excellent agreement on the membrane thickness of ca. 170 nm measured independently by SEM. In addition, the membranes presented in this paper surpassed both the Robeson upper bound and the modified upper bound, indicating a great potential for CO 2 capture.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Protein 4.1R affects photodynamic therapy for B16 melanoma by regulating the transport of 5-aminolevulinic acid

Highlights: • Protein 4.1R knockout promoted the proliferation, migration, and invasion of B16 cells. • Protein 4.1R knockout induced a decrease expression of 5-ALA transporters GAT-1 and GAT-2. • Protein 4.1R knockout reduced the effect of PDT and downregulated the anti-tumor immune response induced by PDT. Melanoma is the most aggressive malignant tumor of skin cancer as it can grow rapidly and metastasize. Photodynamic therapy (PDT) is a promising cancer ablation method for skin tumors, although it lacks efficiency owing to factors such as tumor characteristics, delivery of photosensitizers, immune response in vivo etc. Extensive investigation of molecules that can potentially modulate treatment efficacy is required. Protein 4.1R is a cytoskeletal protein molecule. Previous studies have shown that protein 4.1R knockdown reduces PDT sensitivity in mouse embryonic fibroblast cells. However, the functional role of protein 4.1R in melanoma is unclear. In this study, we aimed to elucidate the effect of protein 4.1R on PDT for melanoma in mice and the mechanism of anti-tumor immunity. Our results indicated that CRISPR/Cas9-mediated protein 4.1R knockout promotes the proliferation, migration, and invasion of B16 cells. We further investigated the potential mechanism of protein 4.1R on tumor cell PDT sensitivity. Our results showed that protein 4.1R knockout reduced the expression of membrane transporters γ-aminobutyric acid transporter (GAT)-1 and (GAT)-2 in B16 cells, which affected 5-ALA transmembrane transport and reduced the efficiency of PDT on B16 cells. Protein 4.1R knockout downregulated the anti-tumor immune response triggered by PDT in vivo. In conclusion, our data suggest that protein 4.1R is an important regulator in PDT for tumors and may promote the progress and efficacy of melanoma treatment.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Two-Color IRMPD Applied to Conformationally Complex Ions: Probing Cold Ion Structure and Hot Ion Unfolding

Two-color infrared multiphoton dissociation (2C-IRMPD) spectroscopy is a technique that mitigates spectral distortions due to nonlinear absorption that is inherent to one-color IRMPD. We use a 2C-IRMPD scheme that incorporates two independently tunable IR sources, providing considerable control over the internal energy content and type of spectrum obtained by varying the trap temperature, the time delays and fluences of the two infrared lasers, and whether the first or second laser wavelength is scanned. In this work, we describe the application of this variant of 2C-IRMPD to conformationally complex peptide ions. The 2C-IRMPD technique is used to record near-linear action spectra of both cations and anions with temperatures ranging from 10 to 300 K. In this work, we also determine the conditions under which it is possible to record IR spectra of single conformers in a conformational mixture. Furthermore, we demonstrate the capability of the technique to explore conformational unfolding by recording IR spectra with widely varying internal energy in the ion. The protonated peptide ions YGGFL (NH 3 + -Tyr-Gly-Gly-Phe-Leu, Leu-enkephalin) and YGPAA (NH 3 + -Tyr-Gly-Pro-Ala-Ala) are used as model systems for exploring the advantages and disadvantages of the method when applied to conformationally complex ions.

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

Role of the Mobile Active Site Flap in IMP Dehydrogenase Inhibitor Binding

Inosine 5′-monophosphate dehydrogenase (IMPDH) is a promising antibiotic target. This enzyme catalyzes the NAD-dependent oxidation of inosine 5′-monophosphate (IMP) to xanthosine 5′-monophosphate (XMP), which is the rate-limiting step in guanine nucleotide biosynthesis. Bacterial IMPDH-specific inhibitors have been developed that bind to the NAD + site. These inhibitors display varied affinities to different bacterial IMPDHs that are not easily rationalized by X-ray crystal structures of enzyme–inhibitor complexes. Inspection of X-ray crystal structures of 25 enzyme–inhibitor complexes, including 10 newly described, suggested that a mobile active site flap may be a structural determinant of inhibitor potency. Saturation transfer difference NMR experiments also suggested that the flap may contact the inhibitors to varying extents in different IMPDHs. Flap residue Leu413 contacted some inhibitors but was not structured in the crystal structures of other inhibitor complexes. The substitution of Leu413 with Phe or Ala in Bacillus anthracis IMPDH had inhibitor-selective effects, suggesting residue 413 could be a structural determinant of affinity. Curiously, the Ala substitution increased the potency of most inhibitors, even those that contacted Leu413 in the crystal structures. Presteady-state and steady-state kinetics experiments showed that the Leu413Ala substitution had comparable effects on inhibitor binding to the noncovalent E·IMP complex and the covalent intermediate E-XMP*, suggesting that the flap had similar interactions in both complexes. These results demonstrate that contacts do not necessarily indicate favorable interactions, and poorly structured mobile regions should not be discounted when assessing binding determinants.

Conformation↗
DOE OSTI2024

PpIX‐enabled fluorescence‐based detection and photodynamic priming of platinum‐resistant ovarian cancer cells under fluid shear stress

Over 75% percent of ovarian cancer patients are diagnosed with advanced-stage disease characterized by unresectable intraperitoneal dissemination and the presence of ascites, or excessive fluid build-up within the abdomen. Conventional treatments include cytoreductive surgery followed by multi-line platinum and taxane chemotherapy regimens. Despite an initial response to treatment, over 75% of patients with advanced-stage ovarian cancer will relapse and succumb to platinum-resistant disease. Recent evidence suggests that fluid shear stress (FSS), which results from the movement of fluid such as ascites, induces epithelial-to-mesenchymal transition and confers resistance to carboplatin in ovarian cancer cells. This study demonstrates, for the first time, that FSS-induced platinum resistance correlates with increased cellular protoporphyrin IX (PpIX), the penultimate downstream product of heme biosynthesis, the production of which can be enhanced using the clinically approved pro-drug aminolevulinic acid (ALA). These data suggest that, with further investigation, PpIX could serve as a fluorescence-based biomarker of FSS-induced platinum resistance. Additionally, this study investigates the efficacy of PpIX-enabled photodynamic therapy (PDT) and the secretion of extracellular vesicles under static and FSS conditions in Caov-3 and NIH:OVCAR-3 cells, two representative cell lines for high-grade serous ovarian carcinoma (HGSOC), the most lethal form of the disease. FSS induces resistance to ALA-PpIX-mediated PDT, along with a significant increase in the number of EVs. Finally, the ability of PpIX-mediated photodynamic priming (PDP) to enhance carboplatin efficacy under FSS conditions is quantified. These preliminary findings in monolayer cultures necessitate additional studies to determine the feasibility of PpIX as a fluorescence-based indicator, and mediator of PDP, to target chemoresistance in the context of FSS.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A mutagenic analysis of NahE, a hydratase-aldolase in the naphthalene degradative pathway

NahE is a hydratase-aldolase that converts o-substituted trans-benzylidenepyruvates (H, OH, or CO 2 - ) to benzaldehyde, salicylaldehyde, or 2-carboxybenzaldehyde, respectively, and pyruvate. The enzyme is in a bacterial degradative pathway for naphthalene, which is a toxic and persistent environmental contaminant. Sequence, crystallographic, and mutagenic analysis identified the enzyme as a member of the N-acetylneuraminate lyase (NAL) subgroup in the aldolase superfamily. As such, it has a conserved lysine (Lys183) and tyrosine (Tyr155), for Schiff base formation, as well as a GXXGE motif for binding of the pyruvoyl carboxylate group. A crystal structure of the selenomethionine derivative of NahE shows these active site elements along with nearby residues that might be involved in the mechanism and/or specificity. Mutations of five active site amino acids (Thr65, Trp128, Tyr155, Asn157, and Asn281) were constructed and kinetic parameters measured in order to assess the effect(s) on catalysis. Here, the results show that the two Trp128 mutants (Phe and Tyr) have the least effect on catalysis, whereas amino acids with bulky side chains at Thr65 (Val) and Asn281 (Leu) have the greatest effect. Changing Tyr155 to Phe and Asn157 to Ala also hinders catalysis, and the effects fall in between these extremes. These observations are put into a structural context using a crystal structure of the Schiff base of the reaction intermediate. Trapping experiments with substrate, Na(CN)BH 3 , and wild type enzyme and selected mutants mostly paralleled the kinetic analysis, and identified two salicylaldehyde-modified lysines: the active site lysine (Lys183) and one outside the active site (Lys279). The latter could be responsible for the observed inhibition of NahE by salicylaldehyde. Together, the results provide new insights into the NahE-catalyzed reaction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Thermal power plant upgrade via a rotating detonation combustor and retrofitted turbine with optimized endwalls

Over the past decade, pressure gain combustion research has promised over 10 percentage-points of increase in power plant thermal efficiency. Alas, to realize such potential gain, one must effectively couple the turbine with the detonation combustor, whose exhaust conditions differ substantially from current state of the art gas turbines. This paper presents a modeling approach that enables a superior thermodynamic cycle with a rotating detonation combustor and a retrofitted gas turbine by including a diffuser downstream of the combustor and by contouring the turbine endwall, while preserving the airfoil geometry. We propose a multi-step optimization strategy, parametrizing the endwall geometry with a few control points, without altering the airfoil geometry, and with the stage turbine efficiency as objective function. In a first step the turbine performance is assessed with steady inlet conditions by solving the steady three-dimensional Reynolds-Averaged Navier-Stokes equations. In a second step, the inlet conditions are unsteady, as predicted from a detonation combustor and a diffuser, and three-dimensional full unsteady simulations are performed with an unsteady Reynolds-Averaged Navier-Stokes solver. By altering the vane endwall, the steady optimization yielded an efficiency increase of 12% relative to the baseline, while the unsteady optimization resulted in 21% increase compared to the datum turbine. Finally, a full engine analysis demonstrated the superiority of pressure gain combustion which included a realistic thermodynamic cycle of the combustor, the diffuser and the optimized turbine components.

42 ENGINEERING↗
DOE OSTI2024

Comparison of methods for the NMR measurement of motionally averaged dipolar couplings

Motionally averaged dipolar couplings are an important tool for understanding the complex dynamics of catalysts, polymers, and biomolecules. While there is a plethora of solid-state NMR pulse sequences available for their measurement, in can be difficult to gauge the methods’ strengths and weaknesses. In particular, there has not been a comprehensive comparison of their performance in natural abundance samples, where 1H homonuclear dipolar couplings are important and the use of large MAS rotors may be required for sensitivity reasons. In this work, we directly compared some of the more common methods for measuring C–H dipolar couplings in natural abundance samples using L-alanine (L-Ala) and the N-formyl-L-methionyl-L-leucyl-L-phenylalanine (fMLF) tripeptide as model systems. Here, we evaluated their performance in terms of accuracy, resolution, sensitivity, and ease of implementation. We found that, despite the presence of 1H homonuclear dipolar interactions, all methods, with the exception of REDOR, were able to yield the reasonable dipolar coupling strengths for both mobile and static moieties. Of these methods, PDLF provides the most convenient workflow and precision at the expense of low sensitivity. In low-sensitivity cases, MAS-PISEMA and DIPSHIFT appear to be the better options.

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

Loss of biological control of enamel mineralization in amelogenin-phosphorylation-deficient mice

Amelogenin, the most abundant enamel matrix protein, plays several critical roles in enamel formation. Importantly, we previously found that the singular phosphorylation site at Ser16 in amelogenin plays an essential role in amelogenesis. Studies of genetically knock-in (KI) modified mice in which Ser16 in amelogenin is substituted with Ala that prevents amelogenin phosphorylation, and in vitro mineralization experiments, have shown that phosphorylated amelogenin transiently stabilizes amorphous calcium phosphate (ACP), the initial mineral phase in forming enamel. Furthermore, KI mice exhibit dramatic differences in the enamel structure compared with wild type (WT) mice, including thinner enamel lacking enamel rods and ectopic surface calcifications. Here, we now demonstrate that amelogenin phosphorylation also affects the organization and composition of mature enamel mineral. In this work, we compared WT, KI, and heterozygous (HET) enamel and found that in the WT elongated crystals are co-oriented within each rod, however, their c-axes are not aligned with the rods' axes. In contrast, in rod-less KI enamel, crystalline c-axes are less co-oriented, with misorientation progressively increasing toward the enamel surface, which contains spherulites, with a morphology consistent with abiotic formation. Furthermore, we found significant differences in enamel hardness and carbonate content between the genotypes. ACP was also observed in the interrod of WT and HET enamel, and throughout aprismatic KI enamel. In conclusion, amelogenin phosphorylation plays crucial roles in controlling structural, crystallographic, mechanical, and compositional characteristics of dental enamel. Thus, loss of amelogenin phosphorylation leads to a reduction in the biological control over the enamel mineralization process.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Development and biodistribution studies of 77 As-labeled trithiol RM2 bioconjugates for prostate cancer: Comparison of [ 77 As]As-trithiol-Ser-Ser-RM2 vs. [ 77 As]As-trithiol-Glu-Ser-RM2

Recent progress with the production of 72 As (2.49 Mev β + max (64%), 3.33 Mev β + max (16%), 834 keV (81%), t 1/2 : 26 h) and 77 As (0.683 Mev β- max (97%), 239 keV (1.59%), t 1/2 : 38.8 h) has facilitated their evaluation as a potential “theranostic pair” for PET imaging and radiotherapy. Our 3 rd generation trithiol chelate with two carboxylic acid groups was further developed as a bifunctional chelate for radioarsenic. The As complex with the trithiol chelate was synthesized and characterized. No carrier added (nca) [ 77 As][H 2 AsO 4 - ] was used for radiolabeling studies. Here, the trithiol chelate was conjugated to the RM2 peptide (DPhe-Gln-Trp-Ala-VaI-Gly-His-Sta-Leu-NH 2 ) via solid phase peptide synthesis with two different linkers, Ser-Ser and Glu-Ser. The trithiol chelate and its RM2 bioconjugates were radiolabeled with nca 77 As, and the RM2 bioconjugates were compared in initial biodistribution studies. The As diacid trithiol complex was characterized by 1 H NMR, 13 C NMR and HR-ESI-MS. The trithiol-RM2 precursor and As trithiol bioconjugates were characterized by HR-ESI-MS and/or LC-ESI-MS. Radiolabeling of the RM2 bioconjugates with 77 As resulted in over 85% radiochemical yield for [ 77 As]As-trithiol-Ser-Ser-RM2 ([ 77 As]8) and 90% for [ 77 As]As-trithiol-Glu-Ser-RM2 ([ 77 As]9). Both radiotracers demonstrated excellent in vitro stability (≥ 90% remaining intact through 24 h in PBS buffer) and were more hydrophilic than previous analogues based on log D 7.4 values. Biodistribution results of the two radiotracers in healthy CF-1 male mice demonstrated blockable pancreatic uptake at 1 h (82% for ([ 77 As]8 and 78% for [ 77 As]9) indicating specific gastrin-releasing peptide receptor (GRPR) uptake. The primary route of excretion was through the gastrointestinal system for both radiotracers. A new trithiol chelate with improved hydrophilicity was successfully conjugated to the RM2 peptide via two linkers, and high radiolabeling yield with nca 77 As was achieved. In vivo biodistribution studies with both radiotracers demonstrated blockable pancreatic uptake suggestive of specific receptor uptake.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2020

Observation of an Unexpected n -Type Semiconducting Behavior in the New Ternary Zintl Phase Eu 3 InAs 3

The ternary arsenides Eu 3 InAs 3 and Sr 3 InAs 3 have been obtained by reactions of the elements in In flux at 1373 K. Structure elucidation by single-crystal X-ray diffraction reveals that Eu 3 InAs 3 and Sr 3 InAs 3 adopt the same orthorhombic structure (space group Pnma, Z = 4, Ca 3 AlAs 3 structure type) with unit cell parameters a = 12.9179(9) Å, b = 4.3990(3) Å, c = 13.9337(10) Å and a = 13.0218(11) Å, b = 4.4364(4) Å, c = 14.1339(12) Å, respectively. The structure consists of linear chains of corner-sharing InAs4 tetrahedra, [InAs 2 As 2/2 ] 6– , and Eu 2+ /Sr 2+ cations. Therefore, both Eu 3 InAs 3 and Sr 3 InAs 3 are valence-precise Zintl phases. As expected from the closed-shell electronic configurations, semiconducting behavior is confirmed by resistivity measurements on single crystals for both and by electronic band structure calculations for Sr 3 InAs 3 . The temperature dependence of resistivity and the computational work are in agreement that Eu 3 InAs 3 and Sr 3 InAs 3 are intrinsic semiconductors with narrow band gaps. Thermopower measurement on single-crystalline samples of Eu 3 InAs 3 shows that in the whole measured temperature range, from 300 to 700 K, the values for the Seebeck coefficient are negative. The observation of a negative Seebeck coefficient with very large absolute value (>400–500 μV K –1 at 700 K) is unexpected among the Zintl phases and suggestive that electrons are the majority charge carriers. Such a rare, n-type charge transport in an undoped compound such as Eu 3 InAs 3 , a material that has not been purposely optimized, could indicate native “defect” chemistry, and not extrinsic doping, as a reason for the unusual behavior. Here, a possible explanation involves a mixed-valent Eu 2+ /Eu 3+ state, which might be inferred from the measured effective paramagnetic moment of 7.2 μB per Eu atom, which is lower than the theoretically predicted value for free-ion moment of 7.9 μ B /Eu.

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

Yb Substitution and Ultralow Thermal Conductivity of the Ca 3– x Yb x AlSb 3 (0 ≤ x ≤ 0.81(1)) System

Here, a series of Yb-substituted Zintl phases in the Ca 3–x Yb x AlSb 3 (0 ≤ x ≤ 0.81(1)) system has been synthesized by initial arc melting and post-heat treatment, and their isotypic crystal structures were characterized by both powder and single crystal X-ray diffraction analysis. All four title compounds adopted the Ca 3 AlAs 3 -type structure (space group Pnma, Pearson code oP28, Z = 4). The overall structure can be described as a combination of the 1-dimensional (1D) infinite chain of ∞ 1 [Al(Sb 2 Sb 2/2 )] formed by two vertices sharing [AlSb 4 ] tetrahedral moieties and three Ca 2+ /Yb 2+ mixed sites located in between these 1D chains. The charge balance and the resultant independency of the 1D chains in the title system were explained by the Zintl-Klemm formalism [Ca 2+ /Yb 2+ ] 3 [(4b-Al 1– )(1b-Sb 2– ) 2 (2b-Sb 1– ) 2/2 ]. A series of DFT calculations proved that (1) the band overlap between the d-orbital states from two types of cations and the p-orbital states from Sb at the high symmetry Γ point implied a heavily doped degenerate semiconducting behavior of the quaternary Ca 2 YbAlSb 3 model and (2) the site preference of Yb for the M1 site was due to the electronic-factor criterion based on the Q values of each atomic site. The electron localization function calculations also proved that the two different shapes of lone pairs of the Sb atoms—the “umbrella-shape” and the “C-shape”—are determined by local geometry and the coordination environment on the anionic frameworks. Thermoelectric measurements of the quaternary title compound Ca 2.19(1) Yb 0.81 AlSb 3 showed an approximately two times larger ZT value than that of ternary Ca 3 AlSb 3 at 623 K due to increased electrical conductivity and ultralow thermal conductivity originated from Yb substitution for Ca.

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

An In Situ , Automated High-Explosives Aging Method Utilizing Two-Dimensional Gas Chromatography–Mass Spectrometry

Understanding chemical changes that occur in high explosives as they age is of great importance to the safe employment and storage of these compounds. Traditional methods of aging high explosives even under accelerated aging conditions are time intensive with durations on the order of months to years. The nature of traditional aging analyses reduces each sample to a snapshot data point often separated widely in time, requiring many assumptions as to how the degradation products develop. Further complicating matters, several analytical techniques are typically employed for each sample analysis in order to ascertain an entire picture of the decomposition pathways. To address these shortcomings with existing methods, a new method of accelerated aging of high explosives utilizing comprehensive two-dimensional gas chromatography coupled to high-resolution mass spectrometry (GC × GC-HRMS) was developed using 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (CL-20) as a model compound for method development. This in situ automated method reduces the time scale of aging to a matter of hours using the inlet of the GC × GC as the aging vessel. GC × GC in combination with HRMS allowed for the collection of both evolved gases and other decomposition products produced during the entire aging process in real time with HRMS providing far greater certainty in identification of explosives aging products. Additionally, this method allowed for a higher throughput of samples with greatly simplified sample preparation. Chemometric analysis of the GC × GC-HRMS data set via the alteration analysis (ALA) enabled discovery of statistically significant chemical changes providing insight into the variation of decomposition pathways with varying aging temperatures.

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

13 C ENDOR Characterization of the Central Carbon within the Nitrogenase Catalytic Cofactor Indicates That the CFe 6 Core Is a Stabilizing “Heart of Steel”

Substrates and inhibitors of Mo-dependent nitrogenase bind and react at Fe ions of the active-site FeMo-cofactor [7Fe–9S–C–Mo–homocitrate] contained within the MoFe protein α-subunit. The cofactor contains a CFe 6 core, a carbon centered within a trigonal prism of six Fe, whose role in catalysis is unknown. Targeted 13 C labeling of the carbon enables electron-nuclear double resonance (ENDOR) spectroscopy to sensitively monitor the electronic properties of the Fe–C bonds and the spin-coupling scheme adopted by the FeMo-cofactor metal ions. Here this report compares 13 CFe 6 ENDOR measurements for (i) the wild-type protein resting state (E 0 ; α-Val 70 ) to those of (ii) α-Ile 70 , (iii) α-Ala 70 -substituted proteins; (iv) crystallographically characterized CO-inhibited “hi-CO” state; (v) E 4 (4H) Janus intermediate, activated for N 2 binding/reduction by accumulation of 4[ e– /H + ]; (vi) E 4 (2H)* state containing a doubly reduced FeMo-cofactor without Fe-bound substrates; and (vii) propargyl alcohol reduction intermediate having allyl alcohol bound as a ferracycle to FeMo-cofactor Fe6. All states examined, both S = 1/2 and 3/2 exhibited near-zero 13 C isotropic hyperfine coupling constants, $^Ca$ = [-1.3 ↔ +2.7] MHz. Density functional theory computations and natural bond orbital analysis of the Fe-C bonds show that this occurs because a (3 spin-up/3 spin-down) spin-exchange configuration of CFe 6 Fe-ion spins produces cancellation of large spin-transfers to carbon in each Fe–C bond. Previous X-ray diffraction and DFT both indicate that trigonal-prismatic geometry around carbon is maintained with high precision in all these states. The persistent structure and Fe–C bonding of the CFe 6 core indicate that it does not provide a functionally dynamic (hemilabile) “beating heart”-instead it acts as “a heart of steel”, stabilizing the structure of the FeMo-cofactor-active site during nitrogenase catalysis.

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

Affinity-matured homotypic interactions induce spectrum of PfCSP structures that influence protection from malaria infection

The generation of high-quality antibody responses to Plasmodium falciparum (Pf) circumsporozoite protein (PfCSP), the primary surface antigen of Pf sporozoites, is paramount to the development of an effective malaria vaccine. Here we present an in-depth structural and functional analysis of a panel of potent antibodies encoded by the immunoglobulin heavy chain variable (IGHV) gene IGHV3-33, which is among the most prevalent and potent antibody families induced in the anti-PfCSP immune response and targets the Asn-Ala-Asn-Pro (NANP) repeat region. Cryo-electron microscopy (cryo-EM) reveals a remarkable spectrum of helical antibody-PfCSP structures stabilized by homotypic interactions between tightly packed fragments antigen binding (Fabs), many of which correlate with somatic hypermutation. We demonstrate a key role of these mutated homotypic contacts for high avidity binding to PfCSP and in protection from Pf malaria infection. Together, these data emphasize the importance of anti-homotypic affinity maturation in the frequent selection of IGHV3–33 antibodies and highlight key features underlying the potent protection of this antibody family.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Two DOT1 enzymes cooperatively mediate efficient ubiquitin-independent histone H3 lysine 76 tri-methylation in kinetoplastids

In higher eukaryotes, a single DOT1 histone H3 lysine 79 (H3K79) methyltransferase processively produces H3K79me2/me3 through histone H2B mono-ubiquitin interaction, while the kinetoplastid Trypanosoma brucei di-methyltransferase DOT1A and tri-methyltransferase DOT1B efficiently methylate the homologous H3K76 without H2B mono-ubiquitination. Based on structural and biochemical analyses of DOT1A, we identify key residues in the methyltransferase motifs VI and X for efficient ubiquitin-independent H3K76 methylation in kinetoplastids. Substitution of a basic to an acidic residue within motif VI (Gx 6 K ) is essential to stabilize the DOT1A enzyme-substrate complex, while substitution of the motif X sequence VYGE by CAKS renders a rigid active-site loop flexible, implying a distinct mechanism of substrate recognition. We further reveal distinct methylation kinetics and substrate preferences of DOT1A (H3K76me0) and DOT1B (DOT1A products H3K76me1/me2) in vitro, determined by a Ser and Ala residue within motif IV, respectively, enabling DOT1A and DOT1B to mediate efficient H3K76 tri-methylation non-processively but cooperatively, and suggesting why kinetoplastids have evolved two DOT1 enzymes.

59 BASIC BIOLOGICAL SCIENCES↗