Segmental,Domain‐Selective Perdeuteration and Small‐Angle Neutron Scattering for Structural Analysis of Multi‐Domain Proteins

Multi‐domain proteins play critical roles in fine‐tuning essential processes in cellular signaling and gene regulation. Typically, multiple globular domains that are connected by flexible linkers undergo dynamic rearrangements upon binding to protein, DNA or RNA ligands. RNA binding proteins (RBPs) represent an important class of multi‐domain proteins, which regulate gene expression by recognizing linear or structured RNA sequence motifs. Here, we employ segmental perdeuteration of the three RNA recognition motif (RRM) domains in the RBP TIA‐1 using Sortase A mediated protein ligation. We show that domain‐selective perdeuteration combined with contrast‐matched small‐angle neutron scattering (SANS), SAXS and computational modeling provides valuable information to precisely define relative domain arrangements. The approach is generally applicable to study conformational arrangements of individual domains in multi‐domain proteins and changes induced by ligand binding.     

Synthesis of an Aluminum Hydroxide Octamer through a Simple Dissolution Method

Multimeric oxo‐hydroxo Al clusters function as models for common mineral structures and reactions. Cluster research, however, is often slowed by a lack of methods to prepare clusters in pure form and in large amounts. Herein, we report a facile synthesis of the little known cluster Al₈(OH)₁₄(H₂O)₁₈(SO₄)₅ ( Al₈ ) through a simple dissolution method. We confirm its structure by single‐crystal X‐ray diffraction and show by ²⁷Al NMR spectroscopy, electrospray‐ionization mass spectrometry, and small‐ and wide‐angle X‐ray scattering that it also exists in solution. We speculate that Al₈ may form in natural water systems through the dissolution of aluminum‐containing minerals in acidic sulfate solutions, such as those that could result from acid rain or mine drainage. Additionally, the dissolution method produces a discrete Al cluster on a scale suitable for studies and applications in materials science.     

Evolution of Oxygen–Metal Electron Transfer and Metal Electronic States During Manganese Oxide Catalyzed Water Oxidation Revealed with In Situ Soft X‐Ray Spectroscopy

Manganese oxide (MnO_x) electrocatalysts are examined herein by in situ soft X‐ray absorption spectroscopy (XAS) and resonant inelastic X‐ray scattering (RIXS) during the oxidation of water buffered by borate (pH 9.2) at potentials from 0.75 to 2.25 V vs. the reversible hydrogen electrode. Correlation of L‐edge XAS data with previous mechanistic studies indicates Mn^IV is the highest oxidation state involved in the catalytic mechanism. MnO_x is transformed into birnessite at 1.45 V and does not undergo further structural phase changes. At potentials beyond this transformation, RIXS spectra show progressive enhancement of charge transfer transitions from oxygen to manganese. Theoretical analysis of these data indicates increased hybridization of the Mn?O orbitals and withdrawal of electron density from the O ligand shell. In situ XAS experiments at the O K‐edge provide complementary evidence for such a transition. This step is crucial for the formation of O₂ from water.     

Breslow Intermediates from a Thiazolin‐2‐ylidene and Fluorinated Aldehydes: XRD and Solution‐Phase NMR Spectroscopic Characterization

The first generation and X‐ray diffraction (XRD) analysis of a crystalline Breslow intermediate (BI) derived from a thiazolin‐2‐ylidene, that is, the aromatic heterocycle present in vitamin B₁, is reported. Key to success was the combined use of pentafluorobenzaldehyde and a thiazolin‐2‐ylidene carrying an enol‐stabilizing dispersion energy donor as N‐substituent. A so‐called primary intermediate (PI) could be isolated in protonated form (pPI) as well and analyzed by XRD. Furthermore, the first stable BI derived from an aromatic thiazolin‐2‐ylidene and an aliphatic aldehyde (trifluoroacetaldehyde) was prepared and characterized by NMR spectroscopy in solution. When switching to a saturated thiazolidin‐2‐ylidene, reaction with pentafluorobenzaldehyde afforded a new BI in solution (NMR spectroscopy). Attempts to crystallize the latter BI resulted in the isolation of a novel thiazolidin‐2‐ylidene dimer that had undergone rearrangement to a hexahydro[1,4]‐thiazino[3,2‐b]‐1,4‐thiazine.     

DNP‐Supported Solid‐State NMR Spectroscopy of Proteins Inside Mammalian Cells

Elucidating at atomic level how proteins interact and are chemically modified in cells represents a leading frontier in structural biology. We have developed a tailored solid‐state NMR spectroscopic approach that allows studying protein structure inside human cells at atomic level under high‐sensitivity dynamic nuclear polarization (DNP) conditions. We demonstrate the method using ubiquitin (Ub), which is critically involved in cellular functioning. Our results pave the way for structural studies of larger proteins or protein complexes inside human cells, which have remained elusive to in‐cell solution‐state NMR spectroscopy due to molecular size limitations.     

Small‐Angle Neutron Scattering Studies of Hemoglobin Confined Inside Silica Tubes of Varying Sizes

In addition to the chemical nature of the surface, the dimensions of the confining host exert a significant influence on confined protein structures; this results in immense biological implications, especially those concerning the enzymatic activities of the protein. This study probes the structure of hemoglobin (Hb), a model protein, confined inside silica tubes with pore diameters that vary by one order of magnitude (≈20–200 nm). The effect of confinement on the protein structure is probed by comparison with the structure of the protein in solution. Small‐angle neutron scattering (SANS), which provides information on protein tertiary and quaternary structures, is employed to study the influence of the tube pore diameter on the structure and configuration of the confined protein in detail. Confinement significantly influences the structural stability of Hb and the structure depends on the Si‐tube pore diameter. The high radius of gyration (R_g) and polydispersity of Hb in the 20 nm diameter Si‐tube indicates that Hb undergoes a significant amount of aggregation. However, for Si‐tube diameters greater or equal to 100 nm, the R_g of Hb is found to be in very close proximity to that obtained from the protein data bank (PDB) reported structure (R_g of native Hb=23.8 Å). This strongly indicates that the protein has a preference for the more native‐like non‐aggregated state if confined inside tubes of diameter greater or equal to 100 nm. Further insight into the Hb structure is obtained from the distance distribution function, p(r), and ab initio models calculated from the SANS patterns. These also suggest that the Si‐tube size is a key parameter for protein stability and structure.     

Charging OBO‐Fused Double [5]Helicene with Electrons

Chemical reduction of OBO‐fused double[5]helicene with Group 1 metals (Na and K) has been investigated for the first time. Two doubly‐reduced products have been isolated and structurally characterized by single‐crystal X‐ray diffraction, revealing a solvent‐separated ion triplet (SSIT) with Na⁺ ions and a contact‐ion pair (CIP) with K⁺ ion. As the key structural outcome, the X‐ray crystallographic analysis discloses the consequences of adding two electrons to the double helicene core in the SSIT without metal binding and reveals the preferential binding site in the CIP with K⁺ counterions. In both products, an increase in the twisting of the double helicene core upon charging was observed. The negative charge localization at the central core has been identified by theoretical calculations, which are in full agreement with X‐ray crystallographic and NMR spectroscopic results. Notably, it was confirmed that the two‐electron reduction of OBO‐fused double[5]helicene is reversible.     

Study of (Cyclic Peptide)–Polymer Conjugate Assemblies by Small‐Angle Neutron Scattering

We present a fundamental study into the self‐assembly of (cyclic peptide)–polymer conjugates as a versatile supramolecular motif to engineer nanotubes with defined structure and dimensions, as characterised in solution using small‐angle neutron scattering (SANS). This work demonstrates the ability of the grafted polymer to stabilise and/or promote the formation of unaggregated nanotubes by the direct comparison to the unconjugated cyclic peptide precursor. This ideal case permitted a further study into the growth mechanism of self‐assembling cyclic peptides, allowing an estimation of the cooperativity. Furthermore, we show the dependency of the nanostructure on the polymer and peptide chemical functionality in solvent mixtures that vary in the ability to compete with the intermolecular associations between cyclic peptides and ability to solvate the polymer shell.     

Simplicity Beneath Complexity: Counting Molecular Electrons Reveals Transients and Kinetics of Photodissociation Reactions

Time‐resolved pump–probe gas‐phase X‐ray scattering signals, extrapolated to zero momentum transfer, provide a measure of the number of electrons in a system, an effect that arises from the coherent addition of elastic scattering from the electrons. This allows to identify reactive transients and determine the chemical reaction kinetics without the need for extensive scattering simulations or complicated inversion of scattering data. We examine the photodissociation reaction of trimethylamine and identify two reaction paths upon excitation to the 3p state at 200 nm: a fast dissociation path out of the 3p state to the dimethyl amine radical (16.6±1.2 %) and a slower dissociation via internal conversion to the 3s state (83.4±1.2 %). The time constants for the two reactions are 640±130 fs and 74±6 ps, respectively. Additionally, it is found that the transient dimethyl amine radical has a N?C bond length of 1.45±0.02 Å and a C?N?C bond angle of 118°±4°.     

Small‐Angle Neutron Scattering from Elastomeric Networks in which the Junctions Alternate Regularly in their Functionality

We compute scattering form factors for SANS from labeled paths in Gaussian phantom networks in which junctions alternate regularly in their functionality (the number of chains emanating from a junction). Our calculations are based on the James‐Guth model of rubber‐like elasticity, which assumes that fluctuations are strain independent, while mean vectors transform affinely with the applied strain. Kratky plots for scattering from isotropic and uniaxially stretched bifunctional networks are computed and compared with corresponding plots for the simpler unifunctional networks. The results show the effects of the length of the labeled path, extent of deformation, direction of scattering with respect to the principal axis of the deformation and the functionalities of the network junctions.