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At least 811 records · Page 45

Mapping structural and dynamic divergence across the MBOAT family

Membrane-bound O-acyltransferases (MBOATs) are membrane-embedded enzymes that catalyze acyl chain transfer to a diverse group of substrates, including lipids, small molecules, and proteins. MBOATs share a conserved structural core, despite wide-ranging functional specificity across both prokaryotes and eukaryotes. The structural basis of catalytic specificity, regulation and interactions with the surrounding environment remain uncertain. Here, we combine comparative molecular dynamics (MD) simulations with bioinformatics to assess molecular and interactional divergence across the family. In simulations, MBOATs differentially distort the bilayer depending on their substrate type. Additionally, we identify lipid binding sites surrounding reactant gates in the surrounding membrane. Complementary bioinformatic analyses reveal a conserved role for re-entrant loop-2 in MBOAT fold stabilization and a key hydrogen bond bridging DGAT1 dimerization. Finally, we predict differences in MBOAT solvation and water gating properties. These data are pertinent to the design of MBOAT-specific inhibitors that encompass dynamic information within cellular mimetic environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Complete inhibition of a polyol nucleation by a micromolar biopolymer additive

Preventing spontaneous crystallization of supersaturated solutions by additives is of critical interest to successful process design and implementation, with numerous applications in chemical, pharmaceutical, medical, pigment, and food industries, but challenges remain in laboratory and industry settings and fundamental understanding is lacking. When copresented with antifreeze proteins (AFPs), otherwise spontaneously crystallizing osmolytes are maintained at high supersaturations for months in over-wintering organisms. Thus, we here explore the inhibition phenomenon by AFPs, using persistent crystallization of a common sugar alcohol, D-mannitol, as a case study. We report experimentally that DAFP1, an insect AFP, completely inhibits D-mannitol nucleation. Computer simulations reveal a new mechanism for crystallization inhibition where the population of the crystal-forming conformers are selectively bound and randomized in solution by hydrogen bonding to the protein surface. These results highlight the advantages of using natural polymers to address crystallization inhibition challenges and suggest new strategies in controlling the nucleation processes.

59 BASIC BIOLOGICAL SCIENCES↗

Powder X-ray diffraction of altrenogest, C 21 H 26 O 2

The crystal structure of altrenogest has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Altrenogest crystallizes in space group P2 1 2 1 2 1 (#19) with a = 7.286 916(16), b = 10.580 333(19), c = 22.266 08(7) Å, V = 1716.671(6) Å 3 , and Z = 4 at 295 K. Thermal expansion between 113 and 295 K is anisotropic. An O–H···O hydrogen bond links the molecules into chains along the c-axis. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

36 MATERIALS SCIENCE↗

Crystal structure of nequinate, C 22 H 23 NO 4

The crystal structure of nequinate has been solved and refined using synchrotron X-ray powder diffraction data and optimized using density functional techniques. Nequinate crystallizes in the space group P2 1 /c (#14) with a = 18.35662(20), b = 11.68784(6), c = 9.06122(4) Å, β = 99.3314(5)°, V = 1918.352(13) Å 3 , and Z = 4. The crystal structure is dominated by the stacking of the approximately planar molecules. N–H∙∙∙O hydrogen bonds link adjacent molecules into chains parallel to the b-axis. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

36 MATERIALS SCIENCE↗

Crystal structure of ponazuril, C 18 H 14 F 3 N 3 O 6 S

The crystal structure of ponazuril has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional theory techniques. Ponazuril crystallizes in space group P2 1 /c (#14) with a = 8.49511(6), b = 12.38696(6), c = 18.84239(17) Å, β = 96.7166(4)°, V = 1969.152(12) Å 3 , and Z = 4. N–H∙∙∙O hydrogen bonds link the molecules into chains along the a-axis, with a graph set C1,1(6). The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

36 MATERIALS SCIENCE↗

Crystal structure of diclazuril, C 17 H 9 Cl 3 N 4 O 2

The crystal structure of diclazuril has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional theory techniques. Diclazuril crystallizes in space group P2 1 /a (#14) with a = 27.02080(18), b = 11.42308(8), c = 5.36978(5) Å, β = 91.7912(7)°, V = 1656.629(15) Å 3 , and Z = 4. The crystal structure consists of layers of molecules parallel to the ac-plane. A strong N–H∙∙∙O hydrogen bond links the molecules into dimers along the a-axis with a graph set R2,2(8). The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

36 MATERIALS SCIENCE↗

Crystal structure of halofuginone hydrobromide, C 16 H 18 BrClN 3 O 3 Br

The crystal structure of one form of halofuginone hydrobromide has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional theory techniques. Halofuginone hydrobromide crystallizes in space group P2 1 (#4) with a = 8.87398(13), b = 14.25711(20), c = 15.0153(3) Å, β = 91.6867(15)°, V = 1898.87(4) Å 3 , and Z = 4. The crystal structure consists of alternating layers (parallel to the ab-plane) of planar and nonplanar portions of the cations. N–H∙∙∙Br and O–H∙∙∙Br hydrogen bonds link the protonated piperidine rings and bromide anions into a two-dimensional network parallel to the ab-plane. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

36 MATERIALS SCIENCE↗

Crystal structure of toceranib, C 22 H 25 FN 4 O 2

The crystal structure of toceranib has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional theory techniques. Toceranib crystallizes in space group P2 1 /c (#14) with a = 10.6899(6), b = 24.5134(4), c = 7.8747(4) Å, β = 107.7737(13)°, V = 1965.04(3) Å 3 , and Z = 4. The crystal structure consists of stacks of approximately planar molecules, with N–H∙∙∙O hydrogen bonds between the layers. The commercial reagent sample was a mixture of two or more phases with toceranib being the dominant phase. The difference between the Rietveld-refined and DFT-optimized structures is larger than usual. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

36 MATERIALS SCIENCE↗

Crystal structure of oxfendazole, C 15 H 13 N 3 O 3 S

The crystal structure of oxfendazole has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional theory techniques. Oxfendazole crystallizes in space group P2 1 /c (#14) with a = 18.87326(26), b = 10.40333(5), c = 7.25089(5) Å, β = 91.4688(10)° V = 1423.206(10) Å 3 , and Z = 4. The crystal structure consists of stacks of the planar portions of the L-shaped molecules, resulting in layers parallel to the bc-plane. Only weak hydrogen bonds are present. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

36 MATERIALS SCIENCE↗

Crystal structure of anthraquinone-2-carboxylic acid, C 15 H 8 O 4

The crystal structure of anthraquinone-2-carboxylic acid has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional theory techniques. Anthraquinone-2-carboxylic acid crystallizes in space groupP-1 (#2) witha= 3.7942(2),b= 13.266(5),c= 22.835(15) Å,α= 73.355(30),β= 89.486(6),γ= 86.061(1)°,V= 1098.50(7) Å 3 , andZ= 4. The crystal structure contains two independent molecules of anthraquinone-2-carboxylic acid. Although the expected hydrogen-bonded dimers are present, the dimers are not centrosymmetric. The dimer contains one molecule of each planar low-energy conformation. The crystal structure consists of a herringbone array of centrosymmetric pairs of molecules parallel to thebc-plane. The molecules stack along the shorta-axis. The powder pattern has been submitted to ICDD® for inclusion in the Powder Diffraction File™ (PDF®).

Materials Science↗

Crystal structure of alectinib hydrochloride Type I, C 30 H 35 N 4 O 2 Cl

The crystal structure of alectinib hydrochloride has been solved and refined using synchrotron X-ray powder diffraction data and optimized using density functional theory techniques. Alectinib hydrochloride crystallizes in space groupP2 1 /n(#14) with the following parameters:a= 12.67477(7),b= 10.44076(5),c= 20.38501(12) Å,β= 93.1438(7)°,V= 2693.574(18) Å 3 , andZ= 4 at 295 K. The crystal structure consists of stacks of molecules along theb-axis, and the stacks contain chains of strong N–H⋯Cl hydrogen bonds. One density functional theory calculation moved a proton from an N atom to the Cl, but another calculation yielded a more chemically reasonable result. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®)

Materials Science↗

Crystal structure of perfluorononanoic acid, C 9 HF 17 O 2

The crystal structure of perfluorononanoic acid (PFNA) was solved via parallel tempering using synchrotron powder diffraction data obtained from the Brockhouse X-ray Diffraction and Scattering (BXDS) Wiggler Lower Energy (WLE) beamline at the Canadian Light Source. PFNA crystallizes in monoclinic space group P2 1 /c (#14) with lattice parameters a = 26.172(1) Å, b = 5.6345(2) Å, c = 10.9501(4) Å, and β = 98.752(2)°. The crystal structure is composed of dimers, with pairs of PFNA molecules connected by hydrogen bonds via the carboxylic acid functional groups. The Rietveld-refined structure was compared to a density functional theory-optimized structure, and the root-mean-square Cartesian difference was larger than normally observed for correct powder structures. The powder data likely exhibited evidence of disorder which was not successfully modeled.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

Programming Amphiphilic Peptoid Oligomers for Hierarchical Assembly and Inorganic Crystallization

Natural organisms make a wide variety of exquisitely complex, nano-, micro-, and macroscale structured materials in an energy-efficient and highly reproducible manner. During these processes, the information-carrying biomolecules (e.g., proteins, peptides, and carbohydrates) enable (1) hierarchical organization to assemble scaffold materials and execute high-level functions and (2) exquisite control over inorganic materials synthesis, generating biominerals whose properties are optimized for their functions. Inspired by nature, significant efforts have been devoted to developing functional materials that can rival those natural molecules by mimicking in vivo functions using engineered proteins, peptides, DNAs, sequence-defined synthetic molecules (e.g., peptoids), and other biomimetic polymers. Among them, peptoids, a new type of synthetic mimetics of peptides and proteins, have received particular attention because they combine the merits of both synthetic polymers (e.g., high chemical stability and efficient synthesis) and biomolecules (e.g., sequence programmability and biocompatibility). The lack of both chirality and hydrogen bonds in their backbone results in a highly designable peptoid-based system with reduced structural complexity and side chain-chemistry-dominated properties. Here in this Account, we present our recent efforts in this field by programming amphiphilic peptoid sequences for (1) the controlled self-assembly into different hierarchically structured nanomaterials with favorable properties and (2) manipulating inorganic (nano)crystal nucleation, growth, and assembly into superstructures. First, we designed a series of amphiphilic peptoids with controlled side chain chemistries that self-assembled into 1D highly stiff and dynamic nanotubes, 2D membrane-mimetic nanosheets, hexagonally patterned nanoribbons, and 3D nanoflowers. These crystalline nanostructures exhibited sequence-dependent properties and showed promise for different applications. The corresponding peptoid self-assembly pathways and mechanisms were also investigated by leveraging in situ atomic force microscopy studies and molecular dynamics simulations, which showed precise sequence dependency. Second, inspired by peptide- and protein-controlled formation of hierarchical inorganic nanostructures in nature, we developed peptoid-based biomimetic approaches for controlled synthesis of inorganic materials (e.g., noble metals and calcite), in which we took advantage of the substantial side chain chemistry of peptoids and investigated the relationship between the peptoid sequences and the morphology and growth kinetics of inorganic materials. For example, to overcome the challenges (e.g., complexity of protein- and peptide-folding, poor thermal and chemical stabilities) facing the area of protein- and peptide-controlled synthesis of inorganic materials, we recently reported the design of sequence-defined peptoids for controlled synthesis of highly branched plasmonic gold particles. Moreover, we developed a rule of thumb for designing peptoids that predictively enabled the morphological evolution from spherical to coral-shaped gold nanoparticles (NPs). With this Account, we hope to stimulate the research interest of chemists and materials scientists and promote the predictive synthesis of functional and robust materials through the design of sequence-defined synthetic molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Ionic Liquids in Analytical Chemistry: Fundamentals, Technological Advances, and Future Outlook

The development of new analytical methods most often focus on novel materials used to impart selectivity or sensitivity to the protocol. Ionic liquids (ILs) are a class of solvents that have been extensively explored as promising materials for various applications and continue to be explored due to their tunable physicochemical properties. These materials possess melting temperatures below 100 °C and can interact with analytes through a multitude of interactions afforded by their readily tunable chemical structure. These interactions include electrostatic, dispersive, hydrogen bonding, π–π, and dipolar interactions and can be modulated or strengthened based on the functional groups present within the chemical structure. ILs consist predominately of organic cations and either inorganic or organic anions, both of which can be functionalized with desired moieties. Common cation and anions found in IL chemical structures are presented in Figure 1. The unique polarity afforded by the ionic structure has also led to their increasing use in areas including sample preparation, chemical separations, electrochemistry, mass spectrometry, and spectroscopy.

Zeger, Victoria R. [Iowa State Univ., Ames, IA (Un↗

Scanning Electrochemical Microscopy for Kinetic Investigations in Viscous Deep Eutectic Solvents: Identifying Practical Approach Curves and Deviations from Electron Transfer Models

Determining heterogeneous electrochemical electron transfer (ET) kinetics in electrolytes with a wide range of physical properties is of great interest for achieving high-performance redox flow batteries. Among such electrolytes, concentrated hydrogen-bonded electrolytes (CoHBEs), including deep eutectic solvents (DESs), have recently garnered significant attention. Unfortunately, traditional Tafel analysis using macroelectrodes often encounters issues with mass transfer limitations in CoHBEs with high viscosities, thereby restricting kinetic analysis to a narrow potential window. Here, in this work, we introduce a methodology for evaluating ET kinetics in viscous DES using the scanning electrochemical microscopy (SECM). We first determined practical solutions to SECM tip positioning in ethaline DES, which yield pseudopositive feedback responses. Lattice Boltzmann method (LBM) simulations helped us rationalize the impact of the fluid and concentration fields, as well as tip geometry, tip approach velocity v, and the solvent viscosity ηs, on the shape of the approach curves. In addition to successfully recreating approach curves over a variety of conditions, we found that approaching a conductor ensured a practical point where the normalized tip response (Ni T = 2) converged at L = 0.7 within ∼10% error regardless of tip velocity. With positioning capabilities at hand, we investigated the kinetics of Fe 3+ /Fe 2+ redox couple in aqueous and the ethaline media. The experimental kinetic results were interpreted using the Butler–Volmer (BV) and Marcus–Hush–Chidsey (MHC) models. For ethaline, a nonideal kinetic behavior was observed, potentially attributed to solvent dynamics within DESs or to the interplay of chloride anions in the charge transfer process.

electrodes↗

Hyperfusogenic Mutations Destabilize the Postfusion Six-Helix Bundle of the Measles Virus Fusion Glycoprotein

Fusion of the host membrane and viral envelope by class I viral fusion proteins is driven by the assembly of a postfusion six-helix bundle formed through antiparallel interactions between N-terminal (HR1) and C-terminal (HR2) heptad-repeat regions. Although mutations in these regions of the measles virus (MeV) fusion (F) glycoprotein are known to promote neuropathogenic and hyperfusogenic phenotypes, their effects on postfusion core stability have not been systematically examined. Here, we combine peptide biophysics and X-ray crystallography to interrogate how mutations within the HR2 domain, present in native neuropathogenic MeV isolates (e.g., L454W and N462K) and laboratory-generated hyperfusogenic variants (e.g., L454M and T461A), influence postfusion 6HB assembly. Circular dichroism (CD) spectroscopy reveals that, with few exceptions, these mutations decrease postfusion core stability, despite their association with enhanced fusion activity. We also report the first crystal structure of the wild-type MeV postfusion core as well as structures of six hyperfusogenic variants, enabling high-resolution comparison of the molecular basis of destabilization. Structural analysis shows that these effects arise from localized perturbations to steric packing, hydrogen bonding networks, and helix-stabilizing interactions within HR2, while the overall 6HB architecture remains conserved. Together, these results indicate that hyperfusogenic mutations are not associated with stabilization of the postfusion state and are instead consistent with models in which hyperfusogenicity arises from a reduction in the energetic barrier to fusion, potentially through effects on prefusion stability or triggering efficiency. These findings establish key sequence-structure–stability relationships governing coiled-coil assembly and provide a framework for the design of HR1- and HR2-based fusion inhibitors.

Genetics↗

Improved Protein Semi-Synthesis Enables Biophysical Studies of Thioamide Destabilization of β-Sheet Interactions

Abstract Thioamides are natural post-translational modifications of the peptide backbone and can be introduced synthetically to probe protein folding or functionalize peptides for translational applications. In this work, we demonstrate that thioamide-containing peptides with C-terminal thioesters can be efficiently generated using Knorr pyrazole activation and used in subsequent native chemical ligation reactions to generate thioamide-containing proteins. We compare this method to acyl azide activation and find that both routes provide similar yields. We also investigate ultrasound-mediated desulfurization of the ligation site cysteine for potential advantages over chemical radical initiators. Scaling up our syntheses allows us to study thioamide perturbations to the β-sheet region of the B1 domain of protein G (GB1) as well as β-strand interactions in amyloid fibrils of the Parkinson’s disease protein α-synuclein. In both contexts, we observe dramatic destabilization of the β-sheet networks, manifested in decreased GB1 thermal stability and altered folding and slowed aggregation of α-synuclein. These findings illustrate the impact that a single atom substitution can have on cooperative hydrogen-bonding networks and prompt future study of both systems.

Yanagawa, Evan S. K. [University of Pennsylvania ,↗

Interconnection of the Antenna Pigment 8-HDF and Flavin Facilitates Red-Light Reception in a Bifunctional Animal-like Cryptochrome

Cryptochromes are ubiquitous flavin-binding light sensors closely related to DNA-repairing photolyases. The animal-like cryptochrome CraCRY from the green alga Chlamydomonas reinhardtii challenges the paradigm of cryptochromes as pure blue-light receptors by acting as a (6-4) photolyase, using 8-hydroxy-5-deazaflavin (8-HDF) as a light-harvesting antenna with a 17.4 Å distance to flavin and showing spectral sensitivity up to 680 nm. The expanded action spectrum is attributed to the presence of the flavin neutral radical (FADH•) in the dark, despite a rapid FADH• decay observed in vitro in samples exclusively carrying flavin. Herein, the red-light response of CraCRY carrying flavin and 8-HDF was studied, revealing a 3-fold prolongation of the FADH• lifetime in the presence of 8-HDF. Millisecond time-resolved ultraviolet-visible spectroscopy showed the red-light-induced formation and decay of an absorbance band at 458 nm concomitant with flavin reduction. Time-resolved Fourier transform infrared (FTIR) spectroscopy and density functional theory attributed these changes to the deprotonation of 8-HDF, challenging the paradigm of 8-HDF being permanently deprotonated in photolyases. FTIR spectra showed changes in the hydrogen bonding network of asparagine 395, a residue suggested to indirectly control flavin protonation, indicating the involvement of N395 in the stabilization of FADH•. Fluorescence spectroscopy revealed a decrease in the energy transfer efficiency of 8-HDF upon flavin reduction, possibly linked to 8-HDF deprotonation. Finally, the discovery of the interdependence of flavin and 8-HDF beyond energy transfer processes highlights the essential role of the antenna, introducing a new concept enabling CraCRY and possibly other bifunctional cryptochromes to fulfill their dual function.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗