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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 1,207 records · Page 67
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Structures of TOG1 and TOG2 from the human microtubule dynamics regulator CLASP1

Tubulin-binding TOG domains are found arrayed in a number of proteins that regulate microtubule dynamics. While much is known about the structure and function of TOG domains from the XMAP215 microtubule polymerase family, less in known about the TOG domain array found in animal CLASP family members. The animal CLASP TOG array promotes microtubule pause, potentiates rescue, and limits catastrophe. How structurally distinct the TOG domains of animal CLASP are from one another, from XMAP215 family TOG domains, and whether a specific order of structurally distinct TOG domains in the TOG array is conserved across animal CLASP family members is poorly understood. We present the x-ray crystal structures of Homo sapiens (H.s.) CLASP1 TOG1 and TOG2. The structures of H.s. CLASP1 TOG1 and TOG2 are distinct from each other and from the previously determined structure of Mus musculus (M.m.) CLASP2 TOG3. Comparative analyses of CLASP family TOG domain structures determined to date across species and paralogs supports a conserved CLASP TOG array paradigm in which structurally distinct TOG domains are arrayed in a specific order. H.s. CLASP1 TOG1 bears structural similarity to the free-tubulin binding TOG domains of the XMAP215 family but lacks many of the key tubulin-binding determinants found in XMAP215 family TOG domains. This aligns with studies that report that animal CLASP family TOG1 domains cannot bind free tubulin or microtubules. In contrast, animal CLASP family TOG2 and TOG3 domains have reported microtubule-binding activity but are structurally distinct from the free-tubulin binding TOG domains of the XMAP215 family. H.s. CLASP1 TOG2 has a convex architecture, predicted to engage a hyper-curved tubulin state that may underlie its ability to limit microtubule catastrophe and promote rescue. M.m. CLASP2 TOG3 has unique structural elements in the C-terminal half of its α-solenoid domain that our modeling studies implicate in binding to laterally-associated tubulin subunits in the microtubule lattice in a mode similar to, yet distinct from those predicted for the XMAP215 family TOG4 domain. The potential ability of the animal CLASP family TOG3 domain to engage lateral tubulin subunits may underlie the microtubule rescue activity ascribed to the domain. These findings highlight the structural diversity of TOG domains within the CLASP family TOG array and provide a molecular foundation for understanding CLASP-dependent effects on microtubule dynamics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Molecular basis of P[II] major human rotavirus VP8* domain recognition of histo-blood group antigens

Initial cell attachment of rotavirus (RV) to specific cell surface glycan receptors, which is the essential first step in RV infection, is mediated by the VP8* domain of the spike protein VP4. Recently, human histo-blood group antigens (HBGAs) have been identified as receptors or attachment factors for human RV strains. RV strains in the P[4] and P[8] genotypes of the P[II] genogroup share common recognition of the Lewis b (Le b ) and H type 1 antigens, however, the molecular basis of receptor recognition by the major human P[8] RVs remains unknown due to lack of experimental structural information. Here, we used nuclear magnetic resonance (NMR) spectroscopy-based titration experiments and NMR-derived high ambiguity driven docking (HADDOCK) methods to elucidate the molecular basis for P[8] VP8* recognition of the Leb (LNDFH I) and type 1 HBGAs. We also used X-ray crystallography to determine the molecular details underlying P[6] recognition of H type 1 HBGAs. Unlike P[6]/P[19] VP8*s that recognize H type 1 HBGAs in a binding surface composed of an α-helix and a β-sheet, referred as the “βα binding site”, the P[8] and P[4] VP8*s bind Le b HBGAs in a previously undescribed pocket formed by the edges of two β-sheets, referred to as the “ββ binding site”. Importantly, the P[8] and P[4] VP8*s retain binding capability to non-Le b type 1 HBGAs using the βα binding site. The presence of two distinct binding sites for Le b and non-Le b HBGA glycans in the P[8] and P[4] VP8* domains suggests host-pathogen co-evolution under structural and functional adaptation of RV pathogens to host glycan polymorphisms. Assessment and understanding of the precise impact of this co-evolutionary process in determining RV host ranges and cross-species RV transmission should facilitate improved RV vaccine development and prediction of future RV strain emergence and epidemics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Molecular To Mesoscale Targeting of Oxoanions with Multi-Tasking Hosts

Achieving a better understanding of anion interactions both in solution and crystalline state was the overarching goal of this project. Anions are everywhere throughout Nature and play important roles in biological and environmental processes. They can be beneficial or deleterious or both in different situations and concentrations. For either reason it is important to have molecules that can bind anions for key needs that benefit society. However, recognition of specific anions is challenging due to the diffuse nature of their negative charge(s) as well as their various shapes and sizes. Understanding the basic properties of anions and how they interact with other molecules and ions in surrounding environments is key to selective recognition. In this project multi-tasking molecules for selective binding of targeted anions were designed to achieve cooperativity and synergism in one rather than multiple host molecules, including (1) cation:anion pair hosts for anions with charges of -2 or greater; (2) pH and redox activated hosts for on-off binding and release; and (3) multiple anion capture in extended host networks. Our design strategy was to combine the use of simple inexpensive building blocks and high yield synthetic pathways to provide economically feasible scale-up for applications. Oxoanions representing multiple shapes and charges were chosen based on having the potential for significant impact on DOE separations needs. Amide/amine-based macrocycles and urea/amine-based chelates and macrocycles with multiple hydrogen bonding sites provided the basic anion-binding frameworks. Successful multi-tasking outcomes were forthcoming in all three tasks. In Task 1, successful ion pair binding for anions with multiple charges was achieved. Furthermore, the ion pair molecules were capable of extended interactions through supramolecular intertwining, like fishing nets for capturing pools of fish (also fitting with Task 3). In Task 2, molecules were synthesized possessing on-off switches. These included a pH sensitive sensor for on-off binding of anions in general, as well as an electrochemical sensor selective for sulfate capture. Three new classes of extended anion host networks capable of binding multiple ions was a major outcome of Task 3. These systems included: anion sensitive, fluorescent organogels; channel-forming macrocycles for studying anion-water including larger macrocyclic cluster sandwiches; and, the offshoot of Task 1, fishing net ion-pair networks for higher valent anions. These strategies can be expanded in the future to other ions and molecules for a better understanding of intermolecular and interionic interactions.

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

Evolution of Thyroglobulin Loop Kinetics in EpCAM

Epithelial cell-activating molecule (EpCAM) is an important cancer biomarker and therapeutic target given its elevated expression in epithelial cancers. EpCAM is a type I transmembrane protein that forms cis-dimers along the thyroglobulin type-1A-like domain (TYD) in the extracellular region. The thyroglobulin loop (TY loop) within the TYD is structurally dynamic in the monomer state of human EpCAM, binding reversibly to a TYD site. However, it is not known if this flexibility is prevalent across different species. Here, we conduct over 17 μs of all-atom molecular dynamics simulations to study EpCAM TY loop kinetics of five different species, including human, mouse, chicken, frog, and fish. We find that the TY loop remains dynamic across evolution. In addition to the TYD binding site, we discover a second binding site for the TY loop in the C-terminal domain (CTD). Calculations of the dissociation rate constants from the simulation trajectories suggest a differential binding pattern of fish EpCAM and other organisms. Whereas fish TY loop has comparable binding for both TYD and CTD sites, the TY loops of other species preferably bind the TYD site. A hybrid construct of fish EpCAM with human TY loop restores the TYD binding preference, suggesting robust effects of the TY loop sequence on its dynamic behavior. Our findings provide insights into the structural dynamics of EpCAM and its implication in physiological functions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A dynamic charge-charge interaction modulates PP2A:B56 substrate recruitment

The recruitment of substrates by the ser/thr protein phosphatase 2A (PP2A) is poorly understood, limiting our understanding of PP2A-regulated signaling. Recently, the first PP2A:B56 consensus binding motif, LxxIxE, was identified. However, most validated LxxIxE motifs bind PP2A:B56 with micromolar affinities, suggesting that additional motifs exist to enhance PP2A:B56 binding. Here, we report the requirement of a positively charged motif in a subset of PP2A:B56 interactors, including KIF4A, to facilitate B56 binding via dynamic, electrostatic interactions. Using molecular and cellular experiments, we show that a conserved, negatively charged groove on B56 mediates dynamic binding. We also discovered that this positively charged motif, in addition to facilitating KIF4A dephosphorylation, is essential for condensin I binding, a function distinct and exclusive from PP2A-B56 binding. Together, these results reveal how dynamic, charge-charge interactions fine-tune the interactions mediated by specific motifs, providing a new framework for understanding how PP2A regulation drives cellular signaling.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structural insights into regulation of CNNM-TRPM7 divalent cation uptake by the small GTPase ARL15

Cystathionine-β-synthase (CBS)-pair domain divalent metal cation transport mediators (CNNMs) are an evolutionarily conserved family of magnesium transporters. They promote efflux of Mg 2+ ions on their own and influx of divalent cations when expressed with the transient receptor potential ion channel subfamily M member 7 (TRPM7). Recently, ADP-ribosylation factor-like GTPase 15 (ARL15) has been identified as CNNM-binding partner and an inhibitor of divalent cation influx by TRPM7. Here, we characterize ARL15 as a GTP and CNNM-binding protein and demonstrate that ARL15 also inhibits CNNM2 Mg 2+ efflux. The crystal structure of a complex between ARL15 and CNNM2 CBS-pair domain reveals the molecular basis for binding and allowed the identification of mutations that specifically block binding. A binding deficient ARL15 mutant, R95A, failed to inhibit CNNM and TRPM7 transport of Mg 2+ and Zn 2+ ions. Structural analysis and binding experiments with phosphatase of regenerating liver 2 (PRL2 or PTP4A2) showed that ARL15 and PRLs compete for binding CNNM to coordinate regulation of ion transport by CNNM and TRPM7.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

An expanded role for the transcription factor WRINKLED1 in the biosynthesis of triacylglycerols during seed development

The transcription factor WRINKLED1 ( WRI1 ) is known as a master regulator of fatty acid synthesis in developing oilseeds of Arabidopsis thaliana and other species. WRI1 is known to directly stimulate the expression of many fatty acid biosynthetic enzymes and a few targets in the lower part of the glycolytic pathway. However, it remains unclear to what extent and how the conversion of sugars into fatty acid biosynthetic precursors is controlled by WRI 1. To shortlist possible gene targets for future in-planta experimental validation, here we present a strategy that combines phylogenetic foot printing of cis-regulatory elements with additional layers of evidence. Upstream regions of protein-encoding genes in A. thaliana were searched for the previously described DNA-binding consensus for WRI1, the ASML1/WRI1 (AW)-box. For about 900 genes, AW-box sites were found to be conserved across orthologous upstream regions in 11 related species of the crucifer family. For 145 select potential target genes identified this way, affinity of upstream AW-box sequences to WRI1 was assayed by Microscale Thermophoresis. This allowed definition of a refined WRI1 DNA-binding consensus. We find that known WRI1 gene targets are predictable with good confidence when upstream AW-sites are phylogenetically conserved, specifically binding WRI1 in the in vitro assay, positioned in proximity to the transcriptional start site, and if the gene is co-expressed with WRI1 during seed development. When targets predicted in this way are mapped to central metabolism, a conserved regulatory blueprint emerges that infers concerted control of contiguous pathway sections in glycolysis and fatty acid biosynthesis by WRI1. Several of the newly predicted targets are in the upper glycolysis pathway and the pentose phosphate pathway. Of these, plastidic isoforms of fructokinase ( FRK 3) and of phosphoglucose isomerase ( PGI 1) are particularly corroborated by previously reported seed phenotypes of respective null mutations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Revisiting Competitive Adsorption of Small Molecules in the Metal–Organic Framework Ni-MOF-74

To precisely evaluate the potential of metal-organic frameworks (MOFs) for gas separation and purification applications, it is crucial to understand how various molecules competitively adsorb inside MOFs. In this paper, we combine in situ infrared spectroscopy with ab initio calculations to investigate the mechanisms associated with co-adsorption of a number of small molecules including CO, NO, and CO 2 inside the prototypical framework Ni-MOF-74. Surprisingly, we find that the displacement of CO bound inside Ni-MOF-74 (binding energy of 53 kJ/mol) is readily driven by CO 2 exposure, even though CO 2 has a noticeably weaker binding energy of only 41 kJ/mol; meanwhile, the significantly more strongly binding NO molecule (90 kJ/mol) is not able to easily displace bound CO inside Ni-MOF74. These results show that single-phase binding energies of a molecule inside the MOF cannot completely describe their interaction with the MOF in the presence of other guest molecules. Here, we unveil a number of crucial factors such as the kinetic barrier, partial pressure, secondary binding sites, and guest-host/lateral interactions that control the co-adsorption process and combined with the binding energy are better descriptors of the behavior and adsorption of gas mixtures inside MOFs.

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

Structure–Function Relationships in Sequence-Controlled Copolymers for Rare Earth Element Chelation

The ability to tune material function through primary sequence is a defining feature of biological macromolecules, allowing precise control over structure and target interactions in complex aqueous environments. However, translating sequence–structure–function relationships to synthetic macromolecules is challenging due to their dispersity in sequence, conformation, and composition. Here, we report systematic studies of amphiphilic polymer chelators designed to probe how composition and patterning influence binding affinity and selectivity for rare earth elements (REEs), a series of technologically relevant metals with challenging separation profiles. A library of copolymers varying hydrophobic monomer composition and patterning was synthesized via reversible addition–fragmentation chain transfer (RAFT) polymerization, spanning statistical, gradient, and block architectures. REE binding was quantified using a high-throughput colorimetric assay, and reconstruction of polymer ensembles using kinetic stochastic simulations enabled quantitative comparisons of sequence heterogeneity, linking local monomer colocalization to emergent REE binding. Further, we investigated the role of different hydrophobic comonomers in tuning metal coordination, with binding trends linked to structural features that influence binding site desolvation. Complementary dynamic light scattering (DLS) and small-angle X-ray scattering (SAXS) measurements showed that both polymer and monomer architecture modulate metal-induced conformational changes, and that multichain assembly behavior emerges beyond critical hydrophobic thresholds. Sequence control also altered REE selectivity, with nonmonotonic differences observed across compositionally identical polymers with different sequence architectures. Together, these findings establish design principles that connect polymer sequence and structure to binding performance, guiding the design of macromolecular chelators with enhanced affinity and selectivity for applications in separations, sensing, and catalysis.

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

The structure of importin α and the nuclear localization peptide of ChREBP, and small compound inhibitors of ChREBP–importin α interactions

The carbohydrate response element binding protein (ChREBP) is a glucose-responsive transcription factor that plays a critical role in glucose-mediated induction of genes involved in hepatic glycolysis and lipogenesis. In response to fluctuating blood glucose levels ChREBP activity is regulated mainly by nucleocytoplasmic shuttling of ChREBP. Under high glucose ChREBP binds to importin α and importin β and translocates into the nucleus to initiate transcription. We have previously shown that the nuclear localization signal site (NLS) for ChREBP is bipartite with the NLS extending from Arg158 to Lys190. Here, we report the 2.5 Å crystal structure of the ChREBP-NLS peptide bound to importin α. The structure revealed that the NLS binding is monopartite, with the amino acid residues K171RRI174 from the ChREBP-NLS interacting with ARM2–ARM5 on importin α. We discovered that importin α also binds to the primary binding site of the 14-3-3 proteins with high affinity, which suggests that both importin α and 14-3-3 are each competing with the other for this broad-binding region (residues 117–196) on ChREBP. We screened a small compound library and identified two novel compounds that inhibit the ChREBP-NLS/importin α interaction, nuclear localization, and transcription activities of ChREBP. These candidate molecules support developing inhibitors of ChREBP that may be useful in treatment of obesity and the associated diseases.

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

Hydrogenation and C-S bond activation pathways in thiophene and tetrahydrothiophene reactions on sulfur-passivated surfaces of Ru, Pt, and Re nanoparticles

Thiophene-H2 reactions proceed via sulfur removal and hydrogenation routes on dispersed metal nanoparticles that become decorated by refractory S-adlayers during catalysis. The identity and kinetic relevance of the required elementary steps are described here based on rates measured at S-chemical potentials set by H2S/H2 ratios similar to those prevalent during practical catalysis on Re, ReSx, Ru, and Pt catalysts. Free energies for S adatom formation (from H2S decomposition and H2 evolution) are strongly exothermic (< -50 kJ mol-1 on Pt(111) and < -150 kJ mol-1 on Re and Ru(0001)), but strong repulsions between S adatoms cause adsorption free energies to increase significantly with coverage on all three surfaces, preventing complete monolayer formation. These adlayers, composed of unreactive S-atoms (S') that cover 1/3–2/3 ML leave residual interstitial spaces (*) that bind S-atoms (S*), intermediates, and transition states reversibly, as required for catalytic turnovers. The number and binding properties of these interstices depend on the identity and chemical state of the nanoparticle bulk phase, which influences S'-binding and coverages and cause large differences in direct desulfurization and hydrogenation turnover rates (per exposed metal atom) on dispersed Re, ReSx, Ru, and Pt. The identity and kinetic relevance of elementary steps for desulfurization (to C4¬ hydrocarbons) and hydrogenation (to tetrahydrothiophene; THT) are similar among these catalysts; they involve the kinetically-relevant formation of a thiophene-derived intermediate (monohydrothiophene on Re and ReSx; dihydrothiophene on Ru and Pt) that either cleaves its C-S bond or “over-hydrogenates” to THT in one surface sojourn. THT then undergoes C-S bond cleavage in secondary reactions that correct such over-hydrogenation to form the more unsaturated species that cleave C-S bonds. THT/C4 product ratios are insensitive to H2S/H2 ratios and thiophene pressure, even though active interstitial spaces are covered by kinetically-detectable coverages of S* and thiophene; therefore, primary and secondary reactions must involve the same active surfaces. The observed increase in THT/C4 ratios with H2 pressure shows that THT formation transition states involve a larger number of H-atoms than for C-S cleavage. The requirement for bound species with intermediate unsaturation (between THT and thiophene) for C-S bond cleavage is reminiscent of the H-shuttling required in C-C and C-O hydrogenolysis, reactions that involve the partial dehydrogenation of alkanes and alkanols, respectively, to weaken such bonds and to increase the formation entropy of the relevant transition states via the evolution of H2(g). These mechanistic details challenge prevalent paradigms about different site requirements for hydrogenation and desulfurization pathways and about how metal-sulfur bond energies act as descriptors of reactivity; in fact, such binding energies merely act to define the refractory S-adlayers that enable the formation of weakly-binding interstices that reversibly bind intermediates and transition states, thus allowing catalytic turnovers.

Yik, Edwin↗
DOE OSTI2022

Crystal structures and functional analysis of the ZnF5-WWE1-WWE2 region of PARP13/ZAP define a distinctive mode of engaging poly(ADP-ribose)

PARP13/ZAP (zinc-finger antiviral protein) acts against multiple viruses by promoting degradation of viral mRNA. PARP13 has four N-terminal zinc (Zn) fingers that bind CG-rich nucleotide sequences, a C-terminal ADP ribosyltransferase fold, and a central region with a fifth Zn finger and tandem WWE domains. The central PARP13 region, ZnF5-WWE1-WWE2, is implicated in binding poly(ADP-ribose); however, there are limited insights into its structure and function. We present crystal structures of ZnF5-WWE1-WWE2 from mouse PARP13 in complex with ADP-ribose and in complex with ATP. The crystal structures and binding studies demonstrate that WWE2 interacts with ADP-ribose and ATP, whereas WWE1 does not have a functional binding site. Binding studies with poly(ADP-ribose) ligands indicate that WWE2 serves as an anchor for preferential binding to the terminal end of poly(ADP-ribose) chains. The composite ZnF5-WWE1-WWE2 structure forms an extended surface to engage ADP-ribose chains, representing a distinctive mode of recognition that provides a framework for investigating the impact of poly(ADP-ribose) on PARP13 function.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Designer molecules of the synaptic organizer MDGA1 reveal 3D conformational control of biological function

MDGAs (MAM domain-containing glycosylphosphatidylinositol anchors) are synaptic cell surface molecules that regulate the formation of trans-synaptic bridges between neurexins (NRXNs) and neuroligins (NLGNs), which promote synaptic development. Mutations in MDGAs are implicated in various neuropsychiatric diseases. MDGAs bind NLGNs in cis on the postsynaptic membrane and physically block NLGNs from binding to NRXNs. In crystal structures, the six immunoglobulin (Ig) and single fibronectin III domains of MDGA1 reveal a striking compact, triangular shape, both alone and in complex with NLGNs. Whether this unusual domain arrangement is required for biological function or other arrangements occur with different functional outcomes is unknown. Here, we show that WT MDGA1 can adopt both compact and extended 3D conformations that bind NLGN2. Designer mutants targeting strategic molecular elbows in MDGA1 alter the distribution of 3D conformations while leaving the binding affinity between soluble ectodomains of MDGA1 and NLGN2 intact. In contrast, in a cellular context, these mutants result in unique combinations of functional consequences, including altered binding to NLGN2, decreased capacity to conceal NLGN2 from NRXN1β, and/or suppressed NLGN2-mediated inhibitory presynaptic differentiation, despite the mutations being located far from the MDGA1-NLGN2 interaction site. Thus, the 3D conformation of the entire MDGA1 ectodomain appears critical for its function, and its NLGN-binding site on Ig1-Ig2 is not independent of the rest of the molecule. As a result, global 3D conformational changes to the MDGA1 ectodomain via strategic elbows may form a molecular mechanism to regulate MDGA1 action within the synaptic cleft.

MDGAs↗
DOE OSTI2020

Cobalt-Group 13 Complexes Catalyze CO 2 Hydrogenation via a Co(-I)/Co(I) Redox Cycle

The Co(-I) dihydrogen complexes, [(η 2 -H 2 )CoML]-, where ML is the group 13 metalloligand, N(o-(NCH 2 PiPr 2 )C 6 H 4 ) 3 M, and M is Al, Ga, or In, were previously reported ( J. Am. Chem. Soc. 2017, 139, 6570-6573). In this work, the related Co(-I) end-on dinitrogen adducts, [(N 2 )CoML]-, were isolated and investigated as precatalysts for CO 2 hydrogenation. The Co–Ga catalyst was highly active, achieving 19,200 formate turnovers with an initial turnover frequency of 27,000 h –1 under 34 atm of 1:1 CO 2 /H 2 and using Verkade’s proazaphosphatrane as a base at ambient temperature. The Co–Al catalyst was moderately active, while the Co–In complex was inactive. Hence, tuning the group 13 ion greatly influences the catalytic activity at the Co site. To elucidate the role of the group 13 support, experimental and theoretical mechanistic studies of the Co–Ga and Co–Al catalysts were conducted. The Co(-I) H 2 species are potent hydride donors with estimated thermodynamic hydricities (ΔG° H– ) of 32.0(1) and 37.4(1) kcal/mol in CH 3 CN for M = Al and Ga, respectively. By acting as masked Co(I) dihydrides, the Co(-I) H 2 species operate via an unusual Co(-I)/Co(I) redox cycle. After hydride transfer to CO 2 , the resulting intermediate is the Co(I) hydride complex, HCoML, which was independently synthesized and structurally characterized for M = Al and Ga. The Gibbs free energy for H 2 binding, ΔG° bind (1 atm), to generate (η 2 -H 2 )HCoML was slightly more favorable for HCoGaL (-4.2(1) kcal/mol) than for HCoAlL (-2.7(1) kcal/mol). In the subsequent step, the deprotonation reaction to regenerate the initial catalyst was much more favorable for (η 2 -H 2 )HCoGaL (pK a of 31.4, CH 3 CN) than for (η 2 -H 2 )HCoAlL (pK a of 34.3). Finally, the straightforward substitution of Al with Ga perturbs the energy profile of the catalytic reaction (|ΔΔG° H– | = 5.4 kcal/mol, |ΔΔG° bind | = 1.5 kcal/mol, and |ΔΔG° K a | = 4.0 kcal/mol) and thus provides a thermodynamic rationale for the higher catalytic efficiency of Co–Ga over Co–Al.

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

A monomeric mycobacteriophage immunity repressor utilizes two domains to recognize an asymmetric DNA sequence

Regulation of bacteriophage gene expression involves repressor proteins that bind and downregulate early lytic promoters. A large group of mycobacteriophages code for repressors that are unusual in also terminating transcription elongation at numerous binding sites (stoperators) distributed across the phage genome. Here we provide the X-ray crystal structure of a mycobacteriophage immunity repressor bound to DNA, which reveals the binding of a monomer to an asymmetric DNA sequence using two independent DNA binding domains. The structure is supported by small-angle X-ray scattering, DNA binding, molecular dynamics, and in vivo immunity assays. We propose a model for how dual DNA binding domains facilitate regulation of both transcription initiation and elongation, while enabling evolution of other superinfection immune specificities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Discovery of dual-activity small-molecule ligands of Pseudomonas aeruginosa LpxA and LpxD using SPR and X-ray crystallography

The lipid A biosynthesis pathway is essential in Pseudomonas aeruginosa. LpxA and LpxD are the first and third enzymes in this pathway respectively, and are regarded as promising antibiotic targets. The unique structural similarities between these two enzymes make them suitable targets for dual-binding inhibitors, a characteristic that would decrease the likelihood of mutational resistance and increase cell-based activity. We report the discovery of multiple small molecule ligands that bind to P. aeruginosa LpxA and LpxD, including dual-binding ligands. Binding poses were determined for select compounds by X-ray crystallography. The new structures reveal a previously uncharacterized magnesium ion residing at the core of the LpxD trimer. In addition, ligand binding in the LpxD active site resulted in conformational changes in the distal C-terminal helix-bundle, which forms extensive contacts with acyl carrier protein (ACP) during catalysis. These ligand-dependent conformational changes suggest a potential allosteric influence of reaction intermediates on ACP binding, and vice versa. Taken together, the novel small molecule ligands and their crystal structures provide new chemical scaffolds for ligand discovery targeting lipid A biosynthesis, while revealing structural features of interest for future investigation of LpxD function.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Gaseous cyclodextrin- closo -dodecaborate complexes χCD·B 12 X 12 2– (χ = α, β, and γ; X = F, Cl, Br, and I): electronic structures and intramolecular interactions

A fundamental understanding of cyclodextrin- closo -dodecaborate inclusion complexes is of great interest in supramolecular chemistry. Herein, we report a systematic investigation on the electronic structures and intramolecular interactions of perhalogenated closo -dodecaborate dianions B 12 X 12 2– (X = F, Cl, Br and I) binding to α-, β-, and γ-cyclodextrins (CDs) in the gas phase using combined negative ion photoelectron spectroscopy (NIPES) and density functional theory (DFT) calculations. The vertical detachment energy (VDE) of each complex and electronic stabilization of each dianion due to the CD binding (ΔVDE, relative to the corresponding isolated B 12 X 12 2– ) are determined from the experiments along α-, β- and γ-CD in the form of VDE (ΔVDE): 4.00 (2.10), 4.33 (2.43), and 4.30 (2.40) eV in X = F; 4.09 (1.14), 4.64 (1.69), and 4.69 (1.74) eV in X = Cl; 4.11 (0.91), 4.58 (1.38), and 4.70 (1.50) eV in X = Br; and 3.54 (0.74), 3.88 (1.08), and 4.05 (1.25) eV in X = I, respectively. All complexes have significantly higher VDEs than the corresponding isolated dodecaborate dianions with ΔVDE spanning from 0.74 eV at (α, I) to 2.43 eV at (β, F), sensitive to both host CD size and guest substituent X. DFT-optimized complex structures indicate that all B 12 X 12 2– prefer binding to the wide openings of CDs with the insertion depth and binding motif strongly dependent on the CD size and halogen X. Dodecaborate anions with heavy halogens, i.e. , X = Cl, Br, and I, are found outside of α-CD, while B 12 F 12 2– is completely wrapped by γ-CD. Partial embedment of B 12 X 12 2– into CDs is observed for the other complexes via multipronged B–X … H–O/C interlocking patterns. The simulated spectra based on the density of states agree well with those of the experiments and the calculated VDEs well reproduce the experimental trends. Molecular orbital analyses suggest that the spectral features at low binding energies originated from electrons detached from the dodecaborate dianion, while those at higher binding energies are derived from electron detachment from CDs. Energy decomposition analyses reveal that the electrostatic interaction plays a dominating role in contributing to the host–guest interactions for the X = F series partially due to the formation of a O/C–H … X–B hydrogen bonding network, and the dispersion forces gradually become important with the increase of halogen size.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗