X-ray Crystallography Research Articles

Chaperone-mediated MHC-I peptide exchange in antigen presentation.

This work focuses on molecules that are encoded by the major histocompatibility complex (MHC) and that bind self-, foreign- or tumor-derived peptides and display these at the cell surface for recognition by receptors on T lymphocytes (T cell receptors, TCR) and natural killer (NK) cells. The past few decades have accumulated a vast knowledge base of the structures of MHC molecules and the complexes of MHC/TCR with specificity for many different peptides. In recent years, the structures of MHC-I molecules complexed with chaperones that assist in peptide loading have been revealed by X-ray crystallography and cryogenic electron microscopy. These structures have been further studied using mutagenesis, molecular dynamics and NMR approaches. This review summarizes the current structures and dynamic principles that govern peptide exchange as these relate to the process of antigen presentation.

Design of non-fused ring electron acceptors with “embracing-type” side chains for organic solar cells

Backbone planarity is an inherent structural feature for fused ring electron acceptors and one of important prerequisites for their high photovoltaic performance. However, for non-fused ring electron acceptors (NFREAs), it is a challenging task to achieve it. In this work, two NFREAs (Ph2TIC and BT2TIC) containing thiophene-benzene-thiophene or thiophene-benzothiadiazole-thiophene three non-fused aromatic rings in central scaffold were designed with an attempt to use a pair of 2,4,6-triisopropylphenyl substituents (referred as “embracing”-type side chains) at 3,3′-positions of the two thiophene units to lock the backbone in a planar conformation. X-ray crystallography revealed that Ph2TIC has a quasi-planar backbone, whereas BT2TIC shows a twisted one, but both tend to form two-dimensional layered arrays through intermolecular π-π stacking involving terminal acceptor moieties. UV–vis light-absorption spectroscopy showed that both compounds have similar optoelectronic properties either in dilute solutions or in solid film state, thus confirming the conformation-lock function of the “embracing”-type side chains. While for photophysical properties, BT2TIC displays a red-shifted broader light absorption spectrum as compared to Ph2TIC due to the introduction of an additional acceptor moiety in the structure. Ph2TIC and BT2TIC were evaluated as the acceptor materials in organic solar cells in combination with PM6, a typical donor polymer, and delivered the optimized power conversion efficiencies of 4.31 % and 3.78 %, respectively. Although the photovoltaic performances are modest, the work provides a new thought for maintaining the backbone planarity in NFREAs and would be useful in their future design.

Expression, purification and preliminary crystallographic analysis of bacterial transmembrane protein EfeU for iron import

The bacterial Efe system functions as an importer of free Fe2+ into cells independently of iron-chelating compounds such as siderophores and consisted of iron-binding protein EfeO, peroxidase EfeB, and transmembrane permease EfeU. While we and other researchers reported crystal structures of EfeO and EfeB, that of EfeU remains undetermined. In this study, we constructed expression system of EfeU derived from Escherichia coli, selected E. coli Rosetta-gami 2 (DE3) as an expression host, and succeeded in purification of the proteins which were indicated to form an oligomer by blue native PAGE. We obtained preliminary data of the X-ray crystallography, suggesting that expression and purification methods we established in this study enable structural analysis of the bacterial Efe system.

Unusual Stabilisation of Remarkably Bent Tetra-Cationic Tetra-radical Intermolecular Fe(III) μ-Oxo Tetranuclear Complexes.

A hitherto unknown series of air stable, π-conjugated, remarkably bent tetra-cation tetra-radical intermolecular Fe(III) μ-oxo tetranuclear complex, isolated from the dication diradical diiron(III) porphyrin dimers, has been synthesised and spectroscopically characterised along with single crystal X-ray structure determination of two such molecules. These species facilitate long-range charge/radical delocalisation through the bridge across the entire tetranuclear unit manifesting an unusually intense NIR band. Assorted spin states of Fe(III) centres are stabilised within these unique tetranuclear frameworks: terminal six-coordinate iron centres stabilise the admixed intermediate spin states while the central five-coordinate iron centres stabilise the high-spin states. Variable temperature magnetic susceptibility measurements indicated strong antiferromagnetic coupling for the Fe(III)-O-Fe(III) unit while the exchange interactions between the Fe centres and the porphyrin π-cation radicals are weaker as supported both by magnetic data and DFT calculations. The nature of orbital overlap between the SOMOs of Fe(III) and π* orbital of the porphyrin was found to rationalise the observed exchange coupling, establishing such a complex magnetic exchange in this tetranuclear model with a significant bioinorganic relevance.

Diverse Reactivity of Amidinate-Supported Boron Centers with the Hypersilyl Anion and Access to a Monomeric Secondary Boron Hydride.

Diverse reactivity of the bulky tris(trimethylsilyl)silyl substituent [Si(SiMe3)3], also known as the hypersilyl group, was observed for amidinate-supported dichloro- and phenylchloroborane complexes. Treatment of the dichloroborane with potassium tris(trimethylsilyl)silyl led to the activation of the backbone β-carbon center and formation of saturated four-membered heterocyclic chloroboranes R'{Si(SiMe3)3}C(NR)2BCl [R' = Ph, R = Cy (3); R' = Ph, R = iPr (6); R' = tBu, R = Cy (8)], whereas the four-membered amidinate hypersilyl-substituted phenyl borane 4 {PhC(NCy)2B(Ph)[Si(SiMe3)3]} was observed for the case of an amidinate-supported phenylchloroborane. The highly deshielded 11B NMR spectroscopic resonance and the distinct difference in the 29Si NMR spectrum confirmed the presence of a σ-donating hypersilyl effect on compounds 3, 6, and 8. Reaction of 3 with the Lewis acid AlCl3 led to the formation of complex 11 in which an unusual cleavage of one of the C-N bonds of the amidinate backbone is observed. Nucleophilic substitution at the boron center of saturated chloroborane 3 with phenyllithium generated the phenylborane derivative 12, whereas the secondary monomeric boron hydride 13 was observed after treatment with alane (AlH3). All compounds (2-13) have been fully characterized by NMR spectroscopy and single-crystal X-ray structure determination studies.

The separability problem in molecular quantum systems: Information-Theoretic framework for Atoms in Molecules.

Even though molecules are fundamentally quantum entities, the concept of a molecule retains certain classical attributes concerning its constituents. This includes the empirical separability of a molecule into its three-dimensional, rigid structure in Euclidean space, a framework often obtained through experimental methods like X-Ray crystallography. In this work, we delve into the mathematical implications of partitioning a molecule into its constituent parts using the widely recognized Atoms-In-Molecules (AIM) schemes, aiming to establish their validity within the framework of Information Theory concepts. We have uncovered information-theoretical justifications for employing some of the most prevalent AIM schemes in the field of Chemistry, including Hirshfeld (stockholder partitioning), Bader's (topological dissection), and the quantum approach (Hilbert's space definition). In the first approach we have applied the generalized principle of minimum relative entropy derived from Sharma-Mittal relative entropy, avoiding the need for an arbitrary selection of reference promolecular atoms. Within the realm of topological-information partitioning, we have demonstrated that the Fisher information of Bader's atoms conform to a comprehensive theory based on the Principle of Extreme Physical Information. For the quantum approach we have presented information-theoretic justifications for conducting Löwdin symmetric transformations on the density matrix to form atomic Hilbert spaces.

Structure-Property Relationships for Potential Inversion From Electron Acceptors Based on Thiophene-Fused Triptycene Quinones, 1,4-Diketones and Their Malononitrile Adducts.

The synthesis and properties of a series of 11,11,12,12-tetracyano-9,10-anthraquinodimethane (TCAQ) inspired electron acceptors based on thiophene-fused quinone and triptycene motifs is presented. This has yielded insights into structure-property relationships for establishing and modulating simultaneous two-electron reduction processes in TCAQ analogues. These new compounds were synthesised using a Friedel-Crafts acylation between triptycene and thiophene-3,4-dicarbonyl chloride. Isomeric para-quinones featuring a [c]-fused thiophene on one side and a β,β- or α,β-fused triptycene on the other were isolated alongside a thiophene-3,4-diketone which bears two triptycene fragments. Knoevenagel condensation of these products with malononitrile produced a quinoidal bis(dicyanomethylene), an oxo-dicyanomethylene and an acyclic bis(dicyanomethylene). This series of new electron accepting molecules has been studied using X-ray crystallography and the implications of their 3D structures on NMR and UV/vis absorbance spectroscopy and cyclic voltammetry results have been ascertained with conclusions underpinned by computational methods.

High pressure promotes binding of the allosteric inhibitor Zn2+-cyclen in crystals of activated H-Ras.

In this work, we experimentally investigate the potency of high pressure to drive a protein toward an excited state where an inhibitor targeted for this state can bind. Ras proteins are small GTPases cycling between active GTP-bound and inactive GDP-bound states. Various states of GTP-bound Ras in active conformation coexist in solution, amongst them, state 2 which binds to effectors, and state 1, weakly populated at ambient conditions, which has a low affinity for effectors. Zn2+-cyclen is an allosteric inhibitor of Ras protein, designed to bind specifically to the state 1. In H-Ras(wt).Mg2+.GppNHp crystals soaked with Zn2+-cyclen, no binding could be observed, as expected in the state 2 conformation which is the dominant state at ambient pressure. Interestingly, Zn2+-cyclen binding is observed at 500 MPa pressure, close to the nucleotide, in Ras protein that is driven by pressure to a state 1 conformer. The unknown binding mode of Zn2+-cyclen to H-Ras can thus be fully characterized in atomic details. As a more general conjunction from our study, high pressure x-ray crystallography turns out to be a powerful method to induce transitions allowing drug binding in proteins that are in low-populated conformations at ambient conditions, enabling the design of specific inhibitors.

Supramolecular clumps of μ2-1,3-acetate bridges of Cd(II)-Salen complex: Synthesis, spectroscopic characterization, crystal structure, DFT quantization's, and antifungal photodynamic therapy

The article divulges the crystal growth, synthesis, and X-ray structure characterization of one centrosymmetric cadmium complex, [Cd{CdL(μ2-1,3-acetate)}2] using Salen ligand (SL). The complex is further characterized using spectroscopic and analytical techniques, including DRS, SEM-EDX, PXRD, and ICP-MS. The crystallographic study showed that the complex has a monoclinic space P21/c. Addison parameters (Ʈ) show the hexagonal geometry of the central Cd(II) metal ion. Hirshfeld surface and 2-D fingerprint confirm supramolecular contacts despite weak C–H⋯O and C–H···π interactions. Energy frameworks, FMOs, global reactivity parameters, MEP, and energy bandgap explain the complex reactivity outlook. The complex inter- and intramolecular bonding interactions were explored through natural bond orbital (NBO), QTAIM, NCI-RDG, Electron Location Function (ELF), and Localized Orbital Locator (LOL) quantization methods. In addition, the complex and its synthetic components in vitro antibacterial efficacy were investigated using Gram-positive and Gram-negative microbial strains. SAR (structure-activity relationship) correlates with biological potency. Molecular docking assessed antimicrobial potency with proteins S. aureus (PDB ID: 1JIJ), C. albicans (PDB ID: 1M7A), E. coli (PDB ID: 1T9U), P. aeruginosa (PDB ID: 2UV0), and A. Niger (PDB ID: 3K4P). The findings are backed by the Protein-Ligand Interaction Profiler (PLIP). The antifungal potency and cell viability test of C. albicans were conducted using photodynamic therapy (APDT).

New eremophilane-type sesquiterpenes from Synotis solidaginea

Eleven new highly oxygenated eremophilane-type sesquiterpenoids were isolated from the whole plant of Synotis solidaginea, including two pairs of C-8 S/R epimers. The structures of the new compounds were elucidated on the basis of detailed spectroscopic analysis and the absolute configurations of 1 and 9 were confirmed by single-crystal X-ray crystallography using Cu Kα radiation. All the isolates were tested for the inhibition of LPS-stimulated NO production in macrophage-like mouse monocytic leukemia RAW264.7 cells. Compound 1 exhibited weak inhibitory effects with an IC50 of 71.2 μM.

Schiff baseAlkyne precursor for1,2,3-Triazole functionalized organosiliconas a PotentialSensor for Zn(II)andAntioxidantActivity

Schiff base linked1,2,3-triazole silane5has been synthesized through the Schiff base terminated alkyne with azido via click chemistry,the compound4 structure elucidated through X-ray crystallography, and the compound5 is well characterized through different techniques such asFT-IR, 1H and 13C NMR and Mass spectrometry. UV–visible sensing studies of synthesized compounds4 and5 have been performed, and both are efficient in detectingZn(II) ion, but compound 5 has imparted a higher mode of attraction to Zn(II) with limit of detection (LOD) value (1.4 x 10-6M) wherethe compound 4 is calculated to be (1.25 x 10-5M). By Job's method, the stoichiometric ratio of compound5 and Zn(II) iscalculated to bea 1:1 ratio. The complex of compound 5 with Zn(II) was prepared. A radical and oxidative species are responsible for the deteriorating of stabilized molecules. The synthesized compound 5hasantioxidant propertiesthat can potentially scavenge 2,2-diphenyl-1-picrylhydrazyl (DPPH) radicals. Further to verify the mode of binding interaction between compound 5andZn(II), computational Density functional theory (DFT) study was evaluated.

Cytotoxic and Antibacterial Meroterpenoids Isolated from the Marine-Derived Fungus Talaromyces sp. M27416.

Three novel meroterpenoids, taladrimanins B-D (1-3), were isolated from the marine-derived fungus Talaromyces sp. M27416, alongside three biogenetically related compounds (4-6). We delineated taladrimanin B's (1) structure using HRESIMS and NMR, confirmed its configuration via quantum chemical NMR analysis and DP4+ methodology, and verified it through X-ray crystallography. ECD calculations determined the absolute configuration of compound 1, while comparative NMR and ECD analyses elucidated the absolute configurations of 2 and 3. These compounds are drimane-type meroterpenoids with a C10 polyketide unit (8R-configuration). We proposed a biosynthetic pathway and noted that compound 1 showed cytotoxic activity against MKN-45 and 5637 cell lines and selective antibacterial effects against Staphylococcus aureus CICC 10384.

1H, 13C, and 15N backbone and methyl group resonance assignments of ricin toxin A subunit

Ricin is a potent plant toxin that targets the eukaryotic ribosome by depurinating an adenine from the sarcin-ricin loop (SRL), a highly conserved stem-loop of the rRNA. As a category-B agent for bioterrorism it is a prime target for therapeutic intervention with antibodies and enzyme blocking inhibitors since no effective therapy exists for ricin. Ricin toxin A subunit (RTA) depurinates the SRL by binding to the P-stalk proteins at a remote site. Stimulation of the N-glycosidase activity of RTA by the P-stalk proteins has been studied extensively by biochemical methods and by X-ray crystallography. The current understanding of RTA’s depurination mechanism relies exclusively on X-ray structures of the enzyme in the free state and complexed with transition state analogues. To date we have sparse evidence of conformational dynamics and allosteric regulation of RTA activity that can be exploited in the rational design of inhibitors. Thus, our primary goal here is to apply solution NMR techniques to probe the residue specific structural and dynamic coupling active in RTA as a prerequisite to understand the functional implications of an allosteric network. In this report we present de novo sequence specific amide and sidechain methyl chemical shift assignments of the 267 residue RTA in the free state and in complex with an 11-residue peptide (P11) representing the identical C-terminal sequence of the ribosomal P-stalk proteins. These assignments will facilitate future studies detailing the propagation of binding induced conformational changes in RTA complexed with inhibitors, antibodies, and biologically relevant targets.

Effect of hydroxy groups on structural, electronic, and biological properties of methyl carbazate containing hydroxy benzaldehyde-based imines. A combined experimental and theoretical investigation

Interactions present in differently substituted hydroxy based imine derivatives were characterised and identified by the utilisation of spectroscopic techniques in conjunction with X-ray crystallography and theoretical computations. All the target compounds ‘a-c’ crystallises in monoclinic crystal system with P21/c and C2/c space groups. CH…Pi and Pi…Pi interaction are the characteristic interactions present in the target compounds ‘a-c’ The most significant contributions to the crystal packing were found using Hirshfeld surface analysis, and potential contact points were identified. H…H, O…H and C…H contacts and π stacking interactions are the dominant contacts observed in all the crystals these results showed that hydrogen bonding and hydrophobic interactions were significantly present. Furthermore, investigations related to calculations of the molecular electrostatic potential and frontier molecular orbital (highest occupied–lowest unoccupied) were carried out for the optimised structure. The HOMO-LUMO energy gap made it possible to determine the molecule's chemical hardness, chemical inertness, electronegativity, and electrophilicity index, which showed its possible kinetic stability and reactivity. The target compounds' predicted activity spectra (PASS) showed that these compounds exhibit significant Testosterone 17beta-dehydrogenase (NADP+) inhibition activity, with Pa 7.18–7.95. Finally, Testosterone 17beta-dehydrogenase (NADP+) (PDB-ID 3KLP) was used to conduct molecular docking investigations of compounds ‘a-c’. Due to their tiny size and lack of rigidity, which enable them to bind well at any position, a and b exhibit higher binding free energies of -7.08 and -7.00 kcal/mol and inhibition constants of 0.1 and 1.2 µM than compound c.

Interactions of phenylalanine derivatives with human tyrosinase: lessons from experimental and theoretical studies.

The pigmentation of the skin, modulated by different actors in melanogenesis, is mainly due to the melanins (protective pigments). In humans, these pigments' precursors are synthetized by an enzyme known as tyrosinase (TyH). The regulation of the enzyme activity by specific modulators (inhibitors or activators) can offer a means to fight hypo- and hyper-pigmentations responsible for medical, psychological and societal handicaps. Herein, we report the investigation of phenylalanine derivatives as TyH modulators. Interacting with the binuclear copper active site of the enzyme, phenylalanine derivatives combine effects induced by combination with known resorcinol inhibitors and natural substrate/intermediate (amino acid part). Computational studies including docking, molecular dynamics and free energy calculations combined with biological activity assays on isolated TyH and in human melanoma MNT-1 cells, and X-ray crystallography analyses with the TyH analogue Tyrp1, provide conclusive evidence of the interactions of phenylalanine derivatives with human tyrosinase. In particular, our findings indicate that an analogue of L-DOPA, namely (S)-3-amino-tyrosine, stands out as an amino phenol derivative with inhibitory properties against TyH.

Growth and superconductivity of the Kagome metal CsV3(Sb1-xSex)5 single crystals

In this Letter, CsV3(Sb1-xSex)5 (0 ≤ x ≤ 0.1) crystals were grown using a Sb-rich self-flux method, and studied by XRD, Laue Diffraction, SEM, EDS, and magnetization measurements. It was found that at low doping concentration (x≤ 0.08), the crystal has good quality, and the nominal and actual components are basically consistent. At x = 0.1, the crystal quality decreases, and the actual doping amount starts to be slightly lower than the nominal value. Se doping suppresses superconducting transition due to its band filling effect and negative chemical pressure effect on CsV3Sb5. In addition, Se doping also has an inhibitory effect on the CDW transition in CsV3Sb5. Compared with hole type dopants, this electronic type dopant has a weaker inhibitory effect on TCDW, indicating an asymmetric response of electronic characteristics to carrier charge symbols in the system.

X-ray structure and enzymatic study of a bacterial NADPH oxidase highlight the activation mechanism of eukaryotic NOX.

NADPH oxidases (NOX) are transmembrane proteins, widely spread in eukaryotes and prokaryotes, that produce reactive oxygen species (ROS). Eukaryotes use the ROS products for innate immune defense and signaling in critical (patho)physiological processes. Despite the recent structures of human NOX isoforms, the activation of electron transfer remains incompletely understood. SpNOX, a homolog from Streptococcus pneumoniae, can serves as a robust model for exploring electron transfers in the NOX family thanks to its constitutive activity. Crystal structures of SpNOX full-length and dehydrogenase (DH) domain constructs are revealed here. The isolated DH domain acts as a flavin reductase, and both constructs use either NADPH or NADH as substrate. Our findings suggest that hydride transfer from NAD(P)H to FAD is the rate-limiting step in electron transfer. We identify significance of F397 in nicotinamide access to flavin isoalloxazine and confirm flavin binding contributions from both DH and Transmembrane (TM) domains. Comparison with related enzymes suggests that distal access to heme may influence the final electron acceptor, while the relative position of DH and TM does not necessarily correlate with activity, contrary to previous suggestions. It rather suggests requirement of an internal rearrangement, within the DH domain, to switch from a resting to an active state. Thus, SpNOX appears to be a good model of active NOX2, which allows us to propose an explanation for NOX2's requirement for activation.

X-ray structure and enzymatic study of a bacterial NADPH oxidase highlight the activation mechanism of eukaryotic NOX

NADPH oxidases (NOX) are transmembrane proteins, widely spread in eukaryotes and prokaryotes, that produce reactive oxygen species (ROS). Eukaryotes use the ROS products for innate immune defense and signaling in critical (patho)physiological processes. Despite the recent structures of human NOX isoforms, the activation of electron transfer remains incompletely understood. SpNOX, a homolog from Streptococcus pneumoniae, can serves as a robust model for exploring electron transfers in the NOX family thanks to its constitutive activity. Crystal structures of SpNOX full-length and dehydrogenase (DH) domain constructs are revealed here. The isolated DH domain acts as a flavin reductase, and both constructs use either NADPH or NADH as substrate. Our findings suggest that hydride transfer from NAD(P)H to FAD is the rate-limiting step in electron transfer. We identify significance of F397 in nicotinamide access to flavin isoalloxazine and confirm flavin binding contributions from both DH and Transmembrane (TM) domains. Comparison with related enzymes suggests that distal access to heme may influence the final electron acceptor, while the relative position of DH and TM does not necessarily correlate with activity, contrary to previous suggestions. It rather suggests requirement of an internal rearrangement, within the DH domain, to switch from a resting to an active state. Thus, SpNOX appears to be a good model of active NOX2, which allows us to propose an explanation for NOX2’s requirement for activation.

Pyramidalization of the Carboxamide sp2-Center in Peptide Structures.

A CSD search in the Cambridge Crystallographic Database for the substructure N-CαH-C'(═O)-N gave 24,180 peptide structures for analysis of the pyramidalization of the sp2-hybridized carboxamide group C'(═O)NCα, which had not been investigated before. The dependence of the pyramidalization θ = O-N-C'-Cα on the rotation angle ψ = O═C'-Cα-N about bond C'-Cα resulted in a curve with three maxima, three minima, and six zero-crossings. Surprisingly, the ψ/θ analysis of the individual amino acid building blocks showed that all of them exhibited similar curves, irrespective of their different R substituents. This unusual behavior is explained by a 3-fold short-range potential set up by the three covalent bonds, emanating from Cα. The tie-up of the rotation angle ψ and the pyramidalization θ in a rigid coupling is remarkable. In the 24,180 peptide structures, subjected to X-ray crystallography, there is no dynamics. For peptides in solution, the rotation/pyramidalization curve ψ/θav determines the degree of pyramidalization θ, when the rotation angle ψ runs through a full 360° circle. Density functional theory (DFT) calculations of alaninamide supported the analysis.

Na3Ge2P3: A Zintl Phase Featuring [P3Ge-GeP3] Dimers as Building Blocks.

Recently, ternary lithium phosphidotetrelates have attracted interest particularly due to their high ionic conductivities, while corresponding sodium and heavier alkali metal compounds have been less investigated. Hence, we report the synthesis and characterization of the novel ternary sodium phosphidogermanate Na3Ge2P3, which is readily accessible via ball milling of the elements and subsequent annealing. According to single crystal X-ray structure determination, Na3Ge2P3 crystallizes in the monoclinic space group P21/c (no. 14.) with unit cell parameters of a = 7.2894(6) Å, b = 14.7725(8) Å, c = 7.0528(6) Å, β = 106.331(6)° and forms an unprecedented two-dimensional polyanionic network in the b/c plane of interconnected [P3Ge-GeP3] building units. The system can also be interpreted as differently sized ring structures that interconnect and form a two-dimensional network. A comparison with related ternary compounds from the corresponding phase system as well as with the binary compound GeP shows that the polyanionic network of Na3Ge2P3 resembles an intermediate step between highly condensed cages and discrete polyanions, which highlights the structural variety of phosphidogermanates. The structure is confirmed by 23Na- and 31P-MAS NMR measurements and Raman spectroscopy. Computational investigation of the electronic structure reveals that Na3Ge2P3 is an indirect band gap semiconductor with a band gap of 2.9 eV.