Homoleptic Rare-Earth-Metal Sandwiches with Dibenzo[a,e]cyclooctatetraene Dianions.

A family of rare-earth complexes [RE(III) = Y, La, Gd, Tb, Dy, and Er] with doubly reduced dibenzo[a,e]cyclooctatetraene (DBCOT) has been synthesized and structurally characterized. X-ray diffraction analysis confirms that all products of the [RE(DBCOT)(THF)4][RE(DBCOT)2] composition consist of the anionic sandwich [RE(DBCOT)2]- and the cationic counterpart [RE(DBCOT)(THF)4]+. Within the sandwich, two elongated π decks are slightly bent toward the metal center (avg. 7.3°) with a rotation angle of 35.9-37.6°. The RE(III) ion is entrapped between the central eight-membered rings of DBCOT2- in a η8 fashion. The trends in the RE-COT bond lengths are consistent with the variations of the ionic radii of RE(III) centers. The 1H NMR spectra of the diamagnetic Y(III) and La(III) analogues illustrate the distinct solution behavior for the cationic and anionic parts in this series. Magnetic measurements for the Dy analogue reveal single-molecule magnetism, which was rationalized by considering the effect of crystal-field splitting for both building units analyzed by electronic structure calculations.

Structural aspects of RimP binding on small ribosomal subunit from Staphylococcus aureus.

Ribosome biogenesis is an energy-intense multistep process where even minimal defects can cause severe phenotypes up to cell death. Ribosome assembly is facilitated by biogenesis factors such as ribosome assembly factors. These proteins facilitate the interaction of ribosomal proteins with rRNA and correct rRNA folding. One of these maturation factors is RimP which is required for efficient 16S rRNA processing and 30S ribosomal subunit assembly. Here, we describe the binding mode of Staphylococcus aureus RimP to the small ribosomal subunit and present a 4.2 Å resolution cryo-EM reconstruction of the 30S-RimP complex. Together with the solution structure of RimP solved by NMR spectroscopy and RimP-uS12 complex analysis by EPR, DEER, and SAXS approaches, we show the specificity of RimP binding to the 30S subunit from S. aureus. We believe the results presented in this work will contribute to the understanding of the RimP role in the ribosome assembly mechanism.

Regression-Based Active Learning for Accessible Acceleration of Ultra-Large Library Docking.

Structure-based drug discovery is a process for both hit finding and optimization that relies on a validated three-dimensional model of a target biomolecule, used to rationalize the structure-function relationship for this particular target. An ultralarge virtual screening approach has emerged recently for rapid discovery of high-affinity hit compounds, but it requires substantial computational resources. This study shows that active learning with simple linear regression models can accelerate virtual screening, retrieving up to 90% of the top-1% of the docking hit list after docking just 10% of the ligands. The results demonstrate that it is unnecessary to use complex models, such as deep learning approaches, to predict the imprecise results of ligand docking with a low sampling depth. Furthermore, we explore active learning meta-parameters and find that constant batch size models with a simple ensembling method provide the best ligand retrieval rate. Finally, our approach is validated on the ultralarge size virtual screening data set, retrieving 70% of the top-0.05% of ligands after screening only 2% of the library. Altogether, this work provides a computationally accessible approach for accelerated virtual screening that can serve as a blueprint for the future design of low-compute agents for exploration of the chemical space via large-scale accelerated docking. With recent breakthroughs in protein structure prediction, this method can significantly increase accessibility for the academic community and aid in the rapid discovery of high-affinity hit compounds for various targets.

Mechanisms of inward transmembrane proton translocation.

Proton transport is indispensable for cell life. It is believed that molecular mechanisms of proton movement through different types of proton-conducting molecules have general universal features. However, elucidation of such mechanisms is a challenge. It requires true-atomic-resolution structures of all key proton-conducting states. Here we present a comprehensive function-structure study of a light-driven bacterial inward proton pump, xenorhodopsin, from Bacillus coahuilensis in all major proton-conducting states. The structures reveal that proton translocation is based on proton wires regulated by internal gates. The wires serve as both selectivity filters and translocation pathways for protons. The cumulative results suggest a general concept of proton translocation. We demonstrate the use of serial time-resolved crystallography at a synchrotron source with sub-millisecond resolution for rhodopsin studies, opening the door for principally new applications. The results might also be of interest for optogenetics since xenorhodopsins are the only alternative tools to fire neurons.

Influence of the Structure on Magnetic Properties of Calcium-Phosphate Systems Doped with Iron and Vanadium Ions.

The aim of this study was to prepare and characterize the glasses made of x(Fe2O3∙V2O5)∙(100 - x)[P2O5∙CaO] with x ranging of 0-50%. The contribution of Fe2O3 and V2O5 amount on the structure of P2O5·CaO matrix was investigated. The vitreous materials were characterized by XRD (X-ray diffraction analysis), EPR (Electron Paramagnetic Resonance) spectroscopy, and magnetic susceptibility measurements. A hyperfine structure typical for isolated V4+ ions was noticed to all spectra containing low amount of V2O5. The XRD spectra show the amorphous nature of samples, apart x = 50%. An overlap of the EPR spectrum of a broad line without the hyperfine structure characteristic of clustered ions was observed with increasing V2O5 content. The results of magnetic susceptibility measurements explain the antiferromagnetic or ferromagnetic interactions expressed between the iron and vanadium ions in the investigated glass.

Structural insights into the effects of glycerol on ligand binding to cytochrome P450.

New antitubercular drugs are vital due to the spread of resistant strains. Carbethoxyhexyl imidazole (CHImi) inhibits cytochrome P450 CYP124, which is a steroid-metabolizing enzyme that is important for the survival of Mycobacterium tuberculosis in macrophages. The available crystal structure of the CYP124-CHImi complex reveals two glycerol molecules in the active site. A 1.15 Šresolution crystal structure of the glycerol-free CYP124-CHimi complex reported here shows multiple conformations of CHImi and the CYP124 active site which were previously restricted by glycerol. Complementary molecular dynamics simulations show coherence of the ligand and enzyme conformations. Spectrophotometric titration confirmed the influence of glycerol on CHImi binding: the affinity decreases more than tenfold in glycerol-containing buffer. In addition, it also showed that glycerol has a similar effect on other azole and triazole CYP124 ligands. Together, these data show that glycerol may compromise structural-functional studies and impede rational drug-design campaigns.

Ferritin self-assembly, structure, function, and biotechnological applications.

Ferritin is a vital protein complex responsible for storing iron in almost all living organisms. It plays a crucial role in various metabolic pathways, inflammation processes, stress response, and pathogenesis of cancer and neurodegenerative diseases. In this review we discuss the role of ferritin in diseases, cellular iron regulation, its structural features, and its role in biotechnology. We also show that molecular mechanisms of ferritin self-assembly are key for a number of biotechnological and pharmaceutical applications. The assembly pathways strongly depend on the interface context of ferritin monomers and the stability of its different intermediate oligomers. To date, several schemes of self-assembly kinetics have been proposed. Here, we compare different self-assembly mechanisms and discuss the possibility of self-assembly control by switching between deadlock intermediate states.

Novel Chelating Agents for Zirconium-89-Positron Emission Tomography (PET) Imaging: Synthesis, DFT Calculation, Radiolabeling, and In Vitro and In Vivo Complex Stability.

We report the synthesis and evaluation of novel chelating agents for zirconium-89 (89Zr) with positron emission tomography (PET) imaging applications. New chelating agents NODHA, NOTHA, and NODHA-PY were constructed on 1,4,7-triazacyclononane (TACN) and possess hydroxamic acid or a pyridine ring as an acyclic binding moiety. The new chelating agents were theoretically studied for complexation with Zr(IV). Structures of Zr(IV)-NODHA, Zr(IV)-NOTHA, and Zr(IV)-NODHA-PY were predicted using density functional methods. NODHA was found to form stronger bonds with Zr(IV) when compared to NOTHA and NODHA-PY. The new chelating agents were evaluated for radiolabeling efficiency in binding 89Zr. The corresponding [89Zr]Zr-labeled chelators were evaluated for complex stability in human serum. All new chelating agents rapidly bound to 89Zr in excellent radiolabeling efficiency at room temperature. Among the new [89Zr]Zr-labeled chelators evaluated, [89Zr]Zr-NODHA showed the highest stability in human serum without losing 89Zr, and [89Zr]Zr-NODHA-PY released a considerable amount of 89Zr in human serum. [89Zr]Zr-NODHA, [89Zr]Zr-NODHA-PY, and [89Zr]Zr-DFO were comparatively evaluated for in vivo complex stability by performing biodistribution studies using normal mice. [89Zr]Zr-DFO had the lowest bone uptake at all time points, while [89Zr]Zr-NODHA-PY showed poor stability in mice as evidenced by high bone accumulation at the 24 h time point. [89Zr]Zr-NODHA exhibited better renal clearance but higher bone uptake than [89Zr]Zr-DFO.

Structural basis for receptor selectivity and inverse agonism in S1P5 receptors.

The bioactive lysophospholipid sphingosine-1-phosphate (S1P) acts via five different subtypes of S1P receptors (S1PRs) - S1P1-5. S1P5 is predominantly expressed in nervous and immune systems, regulating the egress of natural killer cells from lymph nodes and playing a role in immune and neurodegenerative disorders, as well as carcinogenesis. Several S1PR therapeutic drugs have been developed to treat these diseases; however, they lack receptor subtype selectivity, which leads to side effects. In this article, we describe a 2.2 Å resolution room temperature crystal structure of the human S1P5 receptor in complex with a selective inverse agonist determined by serial femtosecond crystallography (SFX) at the Pohang Accelerator Laboratory X-Ray Free Electron Laser (PAL-XFEL) and analyze its structure-activity relationship data. The structure demonstrates a unique ligand-binding mode, involving an allosteric sub-pocket, which clarifies the receptor subtype selectivity and provides a template for structure-based drug design. Together with previously published S1PR structures in complex with antagonists and agonists, our structure with S1P5-inverse agonist sheds light on the activation mechanism and reveals structural determinants of the inverse agonism in the S1PR family.

A feasible approach to tune the interaction of chitosan with sodium dodecyl sulfate.

Interaction of binary chitosan/nonionic surfactant (NIS) system with sodium dodecyl sulfate (SDS) in aqueous solution is described using turbodimetry, light scattering, electophoretic mobility and cryogenic electron microscopy. The formation of insoluble CHI/SDS complexes is weakened with a decrease in molecular weight of chitosan and critical micelle concentration of NIS as well as with an increase in NIS concentration. Soluble chitosan/NIS complexes absorb SDS molecules until the charge of mixed chitosan/NIS/SDS complexes reaches a critical value that depends on chitosan molecular weight followed by aggregation of primary electrostatic complexes via hydrogen bonding to complex nanoparticles. In contrast to formation of asymmetric swarm-like structures in the binary chitosan/SDS system, the aggregation of complex nanoparticles in the ternary chitosan/NIS/SDS system occurs by a head-to-tail binding mechanism with formation of elongated filamentous microstructures. The finding can be promising for preparation of microbiologically stable pharmaceutical and cosmetic compositions and drug delivery systems containing mixed surfactants.

Mechanisms of membrane protein crystallization in 'bicelles'.

Despite remarkable progress, mainly due to the development of LCP and 'bicelle' crystallization, lack of structural information remains a bottleneck in membrane protein (MP) research. A major reason is the absence of complete understanding of the mechanism of crystallization. Here we present small-angle scattering studies of the evolution of the "bicelle" crystallization matrix in the course of MP crystal growth. Initially, the matrix corresponds to liquid-like bicelle state. However, after adding the precipitant, the crystallization matrix transforms to jelly-like state. The data suggest that this final phase is composed of interconnected ribbon-like bilayers, where crystals grow. A small amount of multilamellar phase appears, and its volume increases concomitantly with the volume of growing crystals. We suggest that the lamellar phase surrounds the crystals and is critical for crystal growth, which is also common for LCP crystallization. The study discloses mechanisms of "bicelle" MP crystallization and will support rational design of crystallization.

E-site drug specificity of the human pathogen Candida albicans ribosome.

Candida albicans is a widespread commensal fungus with substantial pathogenic potential and steadily increasing resistance to current antifungal drugs. It is known to be resistant to cycloheximide (CHX) that binds to the E-transfer RNA binding site of the ribosome. Because of lack of structural information, it is neither possible to understand the nature of the resistance nor to develop novel inhibitors. To overcome this issue, we determined the structure of the vacant C. albicans 80S ribosome at 2.3 angstroms and its complexes with bound inhibitors at resolutions better than 2.9 angstroms using cryo-electron microscopy. Our structures reveal how a change in a conserved amino acid in ribosomal protein eL42 explains CHX resistance in C. albicans and forms a basis for further antifungal drug development.

Lanthanide-mediated tuning of electronic and magnetic properties in heterotrimetallic cyclooctatetraenyl multidecker self-assemblies.

The synthesis of a novel family of homoleptic COT-based heterotrimetallic self-assemblies bearing the formula [LnKCa(COT)3(THF)3] (Ln(iii) = Gd, Tb, Dy, Ho, Er, Tm, and Yb) is reported followed by their X-ray crystallographic and magnetic characterization. All crystals conform to the monoclinic P21/c space group with a slight compression of the unit cell from 3396.4(2) Å3 to 3373.2(4) Å3 along the series. All complexes exhibit a triple-decker structure having the Ln(iii) and K(i) ions sandwiched by three COT2- ligands with an end-bound {Ca2+(THF)3} moiety to form a non-linear (153.5°) arrangement of three different metals. The COT2- ligands act in a η8-mode with respect to all metal centers. A detailed structural comparison of this unique set of heterotrimetallic complexes has revealed consistent trends along the series. From Gd to Yb, the Ln to ring-centroid distance decreases from 1.961(3) Å to 1.827(2) Å. In contrast, the separation of K(i) and Ca(ii) ions from the COT-centroid (2.443(3) and 1.914(3) Å, respectively) is not affected by the change of Ln(iii) ions. The magnetic property investigation of the [LnKCa(COT)3(THF)3] series (Ln(iii) = Gd, Tb, Dy, Ho, Er, and Tm) reveals that the Dy, Er, and Tm complexes display slow relaxation of their magnetization, in other words, single-molecule magnet (SMM) properties. This behaviour is dominated by thermally activated (Orbach-like) and quantum tunneling processes for [DyKCa(COT)3(THF)3] in contrast to [ErKCa(COT)3(THF)3], in which the thermally activated and Raman processes appear to be relevant. Details of the electronic structures and magnetic properties of these complexes are further clarified with the help of DFT and ab initio theoretical calculations.

True-atomic-resolution insights into the structure and functional role of linear chains and low-barrier hydrogen bonds in proteins.

Hydrogen bonds are fundamental to the structure and function of biological macromolecules and have been explored in detail. The chains of hydrogen bonds (CHBs) and low-barrier hydrogen bonds (LBHBs) were proposed to play essential roles in enzyme catalysis and proton transport. However, high-resolution structural data from CHBs and LBHBs is limited. The challenge is that their 'visualization' requires ultrahigh-resolution structures of the ground and functionally important intermediate states to identify proton translocation events and perform their structural assignment. Our true-atomic-resolution structures of the light-driven proton pump bacteriorhodopsin, a model in studies of proton transport, show that CHBs and LBHBs not only serve as proton pathways, but also are indispensable for long-range communications, signaling and proton storage in proteins. The complete picture of CHBs and LBHBs discloses their multifunctional roles in providing protein functions and presents a consistent picture of proton transport and storage resolving long-standing debates and controversies.

ATP synthase FOF1 structure, function, and structure-based drug design.

ATP synthases are unique rotatory molecular machines that supply biochemical reactions with adenosine triphosphate (ATP)-the universal "currency", which cells use for synthesis of vital molecules and sustaining life. ATP synthases of F-type (FOF1) are found embedded in bacterial cellular membrane, in thylakoid membranes of chloroplasts, and in mitochondrial inner membranes in eukaryotes. The main functions of ATP synthases are control of the ATP synthesis and transmembrane potential. Although the key subunits of the enzyme remain highly conserved, subunit composition and structural organization of ATP synthases and their assemblies are significantly different. In addition, there are hypotheses that the enzyme might be involved in the formation of the mitochondrial permeability transition pore and play a role in regulation of the cell death processes. Dysfunctions of this enzyme lead to numerous severe disorders with high fatality levels. In our review, we focus on FOF1-structure-based approach towards development of new therapies by using FOF1 structural features inherited by the representatives of this enzyme family from different taxonomy groups. We analyzed and systematized the most relevant information about the structural organization of FOF1 to discuss how this approach might help in the development of new therapies targeting ATP synthases and design tools for cellular bioenergetics control.

Biogenic Ferrihydrite Nanoparticles Produced by Klebsiella oxytoca: Characterization, Physicochemical Properties and Bovine Serum Albumin Interactions.

The synthesis of nanoparticles inside microorganisms is an economical alternative to chemical and physical methods of nanoparticle synthesis. In this study, ferrihydrite nanoparticles synthesized by Klebsiella oxytoca bacterium in special conditions were characterized by scanning electron microscopy (SEM), energy-dispersive X-ray analysis (EDS), small-angle X-ray (SAXS), UV-Vis spectroscopy, fluorescence, fluorescence resonance energy transfer (FRET), and molecular docking. The morphology and the structure of the particles were characterized by means of SEM and SAXS. The elemental content was determined by means of the EDS method. The absorption properties of the ferrihydrite nanoparticles were investigated by UV-Vis spectroscopy. The binding mechanism of the biogenic ferrihydrite nanoparticles to Bovine Serum Albumin (BSA) protein, studied by fluorescence, showed a static and weak process, combined with FRET. Protein denaturation by temperature and urea in the presence of the ferrihydrite nanoparticles demonstrated their influence on the unfolding process. The AutoDock Vina and UCSF Chimera programs were used to predict the optimal binding site of the ferrihydrite to BSA and to find the location of the hydrophobic cavities in the sub-domain IIA of the BSA structure.

Doubly-Reduced Pentacene in Different Coordination Environments: X-ray Crystallographic and Theoretical Insights into Structural and Electronic Changes.

Chemical reduction of pentacene (C22 H14 , 1) with Group 1 metals ranging from Li to Cs revealed that 1 readily undergoes a two-fold reduction to afford a doubly-reduced 12- anion in THF. With the help of 18-crown-6 ether used as a secondary coordinating agent, five π-complexes of 12- with different alkali metal counterions have been isolated and fully characterized. This series of complexes enables the first evaluation of alkali-metal ion binding patterns and structural changes of the 12- dianion based on the crystallographically confirmed examples. The difference in coordination of the smallest Li+ ion vs. heavier Group 1 congeners has been demonstrated. In addition, the use of benzo-15-crown-5 in the reaction of 1 with Na metal allowed the isolation of the unique solvent-separated ion product with a "naked" dianion, 12- . The detailed structural analyses of the series revealed the C-C bond alteration and core deformation of pentacene upon two-fold reduction and complexation. The negative charge localization at the central six-membered ring of 12- identified by theoretical calculations corroborates with the X-ray crystallographic results. Subsequent in-depth theoretical analysis provided a detailed description of changes in the electronic structure and aromaticity of pentacene upon reduction.

Ambiguities in and completeness of SAS data analysis of membrane proteins: the case of the sensory rhodopsin II-transducer complex.

Membrane proteins (MPs) play vital roles in the function of cells and are also major drug targets. Structural information on proteins is vital for understanding their mechanism of function and is critical for the development of drugs. However, obtaining high-resolution structures of membrane proteins, in particular, under native conditions is still a great challenge. In such cases, the low-resolution methods small-angle X-ray and neutron scattering (SAXS and SANS) might provide valuable structural information. However, in some cases small-angle scattering (SAS) provides ambiguous ab initio structural information if complementary measurements are not performed and/or a priori information on the protein is not taken into account. Understanding the nature of the limitations may help to overcome these problems. One of the main problems of SAS data analysis of solubilized membrane proteins is the contribution of the detergent belt surrounding the MP. Here, a comprehensive analysis of how the detergent belt contributes to the SAS data of a membrane-protein complex of sensory rhodopsin II with its cognate transducer from Natronomonas pharaonis (NpSRII-NpHtrII) was performed. The influence of the polydispersity of NpSRII-NpHtrII oligomerization is the second problem that is addressed here. It is shown that inhomogeneity in the scattering length density of the detergent belt surrounding a membrane part of the complex and oligomerization polydispersity significantly impacts on SAXS and SANS profiles, and therefore on 3D ab initio structures. It is described how both problems can be taken into account to improve the quality of SAS data treatment. Since SAS data for MPs are usually obtained from solubilized proteins, and their detergent belt and, to a certain extent, oligomerization polydispersity are sufficiently common phenomena, the approaches proposed in this work might be used in SAS studies of different MPs.

Amyloid-beta peptide (25-35) triggers a reorganization of lipid membranes driven by temperature changes.

The amyloid-beta peptide (Aß) is considered a key factor in Alzheimer's disease (AD) ever since the discovery of the disease. The understanding of its damaging influence has however shifted recently from large fibrils observed in the inter-cellular environment to the small oligomers interacting with a cell membrane. We studied the effect of temperature on the latter interactions by evaluating the structural characteristics of zwitterionic phosphatidylcholine (PC) membranes with incorporated Aß25-35 peptide. By means of small angle neutron scattering (SANS), we have observed for the first time a spontaneous reformation of extruded unilamellar vesicles (EULVs) to discoidal bicelle-like structures (BLSs) and small unilamellar vesicles (SULVs). These changes in the membrane self-organization happen during the thermodynamic phase transitions of lipids and only in the presence of the peptide. We interpret the dramatic changes in the membrane's overall shape with parallel changes in its thickness as the Aß25-35 triggered membrane damage and a consequent reorganization of its structure. The suggested process is consistent with an action of separate peptides or small size peptide oligomers rather than the result of large Aß fibrils.

Stepwise Generation of Mono-, Di-, and Triply-Reduced Warped Nanographenes: Charge-Dependent Aromaticity, Surface Nonequivalence, Swing Distortion, and Metal Binding Sites.

The stepwise chemical reduction of a molecular warped nanographene (WNG) having a negatively curved π-surface and defined C80 H30 composition with Cs metal used as the reducing and complexing agent allowed the isolation of three different reduced states with one, two, and three electrons added to its π-conjugated system. This provided a unique series of nanosized carbanions with increasing negative charge for in-depth structural analysis of consequences of controlled electron charging of non-planar nanographenes, using X-ray crystallographic and computational tools. The 3D molecular electrostatic potential (MEP) maps identified the negative charge localization at the central part of the WNG surface where selective coordination of Cs+ ions is confirmed crystallographically. In-depth theoretical investigation revealed a complex response of the WNG to the stepwise electron acquisition. The extended and contorted π-surface of the WNG undergoes subtle swinging distortions that are accompanied by notable changes in the electronic structure and site-dependent aromaticity of the resulting carbanions.