Parallel Conformation Research Articles

Isotope-edited vibrational circular dichroism study reveals a flexible N-terminal structure of islet amyloid peptide (NFGAIL) in amyloid fibril form: A site-specific local structural analysis

The short peptide fragment NFGAIL (IAPf) is a well-known amyloidogenic peptide (22–27), derived from human islet amyloid polypeptide(hIAPP), whose fibrillar structure is often used to better understand the wild-type hIAPP amyloid fibrils, associated with type II diabetes. Despite an extensive study, the fibrillar structure of IAPf at the amino acid residue level is still unclear. Herein, the vibrational circular dichroism(VCD) spectroscopic technique coupled with isotope labelling strategy has been used to study the site-specific local structure of IAPf amyloid fibrils. Two 13C labeled IAPfs were designed and used along with unlabelled IAPf to achieve this. The 13C labelled (on -C=O) glycine(IAPf-G) and phenylalanine (IAPf-F) residues were introduced into the IAPf sequence separately by replacing natural glycine (residue 24) and phenylalanine (residue 23), respectively. VCD spectral analysis on IAPf-G suggests that IAPf fibrils adopt parallel β-sheet conformation with glycine residues are part of β-sheet and in-register. Unlike IAPf-G, VCD analysis on IAPf-F reveals that phenylalanine residues exist in the turn/hairpin conformation rather than β-sheet region. Both VCD results thus suggest that IAPf amyloid fibril consists of a mixture of β-sheet as a major conformation involving GAIL and turn/hairpin as a minor conformation involving NF rather than an idealized β-sheet involving all the amino acids. While previous studies speculated that the full NFGAIL sequence could participate in the β-sheet formation, the present site-specific structural analysis of IAPf amyloid fibrils at residue level using isotope-edited VCD has gained significant attention. Such residue level information has important implications for understanding the role of NFGAIL sequence in the amyloid fibrillation of hIAPP.

Sterically Hindered Diarylethenes with a Benzobis(thiadiazole) Bridge: Enantiospecific Transformation and Reversible Photosuperstructures.

ConspectusPhotochromic diarylethenes featuring reversible regulation by external light irradiation have attracted increasing attention in versatile applications such as logic gates, supramolecular systems, liquid crystals, and super-resolution imaging because of their outstanding bistability and fatigue resistance. However, for typical diarylethene systems, there always exist three typical unsolved issues. The first is how to modulate the bistability between the open and closed forms from the viewpoint of ethene bridge aromaticity. The second is how to decrease and avoid the photoinactive parallel conformer in order to achieve a high quantum yield, since the open form possesses the photoactive antiparallel (ap) conformation and the photoinactive parallel (p) conformation. Because of the typical rapid rotation of the flexible side aryl groups, the two conformers cannot be separated efficiently, thereby resulting in a relatively low photocyclization quantum yield. The third is how to fulfill the enantiospecific transformation with reversibility to photomodulate the chirality. Stereochemically, the ap conformer with C2 symmetry can be further subdivided into a pair of enantiomers with P and M helicity originating from the central hexatriene moiety. Similarly, the rapid rotation can also lead to the loss of intrinsic chirality, restricting the development and application of light-driven chiroptical switches. Accordingly, it is desirable to construct a specific diarylethene system to break through these bottlenecks for real versatile applications.Our group has recently developed a unique sterically hindered diarylethene system based on benzobis(thiadiazole) as the ethene bridge for completely solving these issues. We introduce a low-aromaticity benzobis(thiadiazole) unit into the diarylethene as a central ethene bridge with incomparably high bistability. To block or freeze the rotation of flexible side aryls, we further incorporate a large bulky benzothiophene unit to induce a large steric hindrance, or rotation barrier, between the ethene bridge and side aryls, thereby successfully separating multiple conformers of the diarylethenes with high photocyclization quantum yields and enantiospecific photoreaction. Consequently, given such a fantastic building block, we enhance its performance by means of supramolecular self-assembly, thereby realizing unique conformer-dependent self-assembly as well as unprecedented concerted isomerization and enantiospecific photoreaction of photoresponsive metallacycles. In addition, decoration of the intrinsically chiral diarylethenes with mesogenic units can enable us to manipulate the helical superstructure of liquid crystals, thus achieving a multiple anticounterfeiting technique and a quadridimensional manipulable laser. We also unravel the dual aggregation-induced emission (AIE) behavior of the sterically hindered diarylethene, especially as applied in super-resolution imaging.

Hydrophobic π-π stacking interactions and hydrogen bonds drive self-aggregation of luteolin in water

Luteolin is a flavonoid obtained from different plant species. It is known for its versatile biological activities. However, the beneficial effects of luteolin have been limited to small concentrations as a result of poor water solubility. This study aimed at investigating the hydrophobic interaction and hydration of luteolin towards the improvement of its solubility when used as a drug. We report the aggregation properties of luteolin in water by varying the number of monomers using atomistic molecular dynamics simulation. Results show that the equilibrium structure of luteolin occurs in an aggregated state with different structural arrangements. As the monomers size increase, the antiparallel flipped conformation dominates over T-shaped antiparallel, T-shaped parallel, and antiparallel conformations. The formation of intramolecular hydrogen bonding of 0.19 nm between the keto-enol groups results in hydrophobic characteristics. A larger cluster exhibits slow hydrogen bond dynamics for luteolin-luteolin than luteolin-water interaction. Water structure at large cluster size exhibited slow dynamics and low self-diffusion of luteolin. The existence of hydrophobic π-π and hydrogen bonds between luteolin molecules drives strong self-aggregation resulting in poor water solubility. Breakage of these established interactions would result in increased solubility of luteolin in water.

CO2 capture and a route to transform it in formic acid: a theoretical approach.

New organic frameworks (COFs) employing two coronene molecules forced to adopt a parallel conformation thus forming a molecular reactor are proposed. These COFs exhibit different distances between the coronene units, thus creating diverse electronic environments. The simulation of the trapping of CO2 and H2 molecules in the reactor hollow having distinct anchor fragments yields in the two cases formic acid. The analysis of the reaction profile allowed us to propose athermodynamically favored process. The nature of the frontier molecular orbitals in the involved processes is also discussed. Reaction profile of CO2 and H2 process to yield formic acid.

Probing Noncovalent Interactions in [3,3]Metaparacyclophanes.

Arene-arene interactions are fundamentally important in molecular recognition. To precisely probe arene-arene interactions in cyclophanes, we designed and synthesized (2,6-phenol)paracyclophanes and (2,6-aniline)paracyclophanes that possess two aromatic rings in close proximity. Fine-tuning the aromatic character of one aromatic ring by fluorine substituents enables investigations on the intramolecular interactions between the electron-rich phenol and aniline with tetra-H- and tetra-F-substituted benzene. pKa measurements revealed that the tetra-F-template increases the acidity of the phenol (ΔpKa = 0.55). X-ray crystallography and computational analyses demonstrated that all [3,3]metaparacyclophanes adopt cofacial parallel conformations, implying the presence of π-π stacking interactions. Advanced quantum chemical analyses furthermore revealed that both electrostatic interactions and orbital interactions provide the key contribution to the structure and stability of [3,3]metaparacyclophanes.

A transposon-introduced G-quadruplex motif is selectively retained and constrained to downregulate CYP321A1.

Insects utilize xenobiotic compounds to up- and downregulate cytochrome P450 monooxygenases (P450s) involved in detoxification of toxic xenobiotics including phytochemicals and pesticides. G-quadruplexes (G4)-forming DNA motifs are enriched in the promoter regions of transcription factors and function as cis-acting elements to regulate these genes. Whether and how P450s gain and keep G4 DNA motifs to regulate their expression still remain unexplored. Here, we show that CYP321A1, a xenobiotic-metabolizing P450 from Helicoverpa zea, a polyphagous insect of economic importance, has acquired and preserved a G4 DNA motif by selectively retaining a transposon known as HzIS1-3 that carries this G4 DNA motif in its promoter region. The HzIS1-3 G4 DNA motif acts as a silencer to suppress the constitutive and induced expression of CYP321A1 by plant allelochemicals flavone and xanthotoxin through folding into an intramolecular parallel or hybrid-1 conformation in the absence or presence of K+ . The G4 ligand N-methylmesoporphyrin IX (NMM) strengthens the silencing effect of HzIS1-3 G4 DNA motif by switching its structure from hybrid-1 to hybrid-2. The enrichment of transposons in P450s and other environment-adaptation genes implies that selective retention of G4 DNA motif-carrying transposons may be the main evolutionary route for these genes to obtain G4 DNA motifs.

RETRACTED: On the Possible Spatial Structures of the β-Amyloid

Spatial models of the β-structures of protein molecules, forming layers of amino acids, in principle, of unlimited length for both antiparallel and parallel conformation have been constructed. It is shown that the simplified flat Pauling models do not reflect the spatial structure of these layers. Using the recently developed theory of higher-dimensional polytopic prismahedrons, models of the volumetric filling of space with amino acid molecules are constructed. The constructed models for the first time mathematically describe the native structures of globular proteins.

Heterochirality-Mediated Cross-Strand Nested Hydrophobic Interaction Effects Manifested in Surface-Bound Peptide Assembly Structures.

Amino acid chirality has been envisioned as an important strategy to regulate structure and function of peptide self-assembled architectures. However, the molecular mechanism of chirality effects in peptide assemblies remains largely elusive. Here, the assembly structures of l-peptide polyphenylalanine F10 (FFFFFFFFFF) and block heterochiral peptide F5f5 (FFFFFfffff) composed of two FFFFF repeat blocks with opposite chirality were characterized at the single-molecule level by using scanning tunneling microscopy. Each peptide formed two distinctively different assembly structures on the HOPG surface, in which peptide chains took parallel and antiparallel β-sheet conformations, respectively. The molecular-level observations revealed that the staggered arrangement of cross-strand side chains achieved in the antiparallel β-sheet structure of the block heterochiral peptide facilitated intimate packing of side chains and maximized inter-residue van der Waals interactions, which led to more residues participating in assembly and greatly stabilized the β-sheet structure of the surface-bound peptide assembly, but such cross-strand nested interactions were not accessible in the heterochiral parallel β-sheet structure and the enantiomerically pure assembly structures. This work could contribute to the molecular insights of stereochemical interactions in peptide assemblies and feasibility of extending this block heterochirality pattern to other peptides with various lengths and amino acid compositions for structural regulations.

RHPS4 shifted the conformation ensemble equilibrium of Tel24 by preferentially stabilizing the (3 + 1) hybrid-2 conformation.

Telomeric G-quadruplexes have been a promising target for developing antitumor drugs with fewer side effects. The intracellular environment is usually in a state of molecular crowding. Studying the interaction mechanism among ligands and telomeric G-quadruplexes under crowded conditions is important for designing drugs that target telomeric G-quadruplexes. In the present study, the telomeric G-quadruplex Tel24 (TTAGGG)4 was found to fold into a conformational ensemble of parallel and (3 + 1) hybrid-2 conformations in solution with molecular crowding conditions created by PEG200. G-quadruplex-ligand 3,11-difluoro-6,8,13-trimethyl-8H-quino[4,3,2-kl] acridinium methosulfate (RHPS4) preferentially stabilized the (3 + 1) hybrid-2 conformation and shifted the conformational ensemble equilibrium of Tel24 towards the hybrid conformation. We also found that the (3 + 1) hybrid-2 conformation of Tel24 was more likely to form as compared to the parallel conformation in the conformational ensemble of Tel24. Overall, this study provides new insights into the conformation of telomere G-quadruplexes and their interactions with ligands in a physiological environment.

Electronic properties and reactivity of oxidized graphene nanoribbons and their interaction with phenol.

The effect of the oxidized functional groups on the structural, electronic, and reactivity properties of armchair graphene nanoribbons has been investigated in the framework of the density functional theory. The presence of functional groups near the edges stabilizes the oxidized graphene nanoribbons (OGNRs) more than substituting near the center. Overall, we found slight differences in the electronic properties of OGNRs concerning the pristine ones. The oxygen contribution of functional groups to the DOS is found in the conducting energy bands far from the Fermi level. Consequently, the semiconducting behavior is maintained after doping. Based on the reactivity of OGNRs, the most promising nanostructures were proposed as adsorbents studying the interaction and complexation with phenol, a critical pollutant removed mainly by hydrotreating processes (HDO) to produce bio-oil. Parallel and perpendicular phenol conformations were found towards the OGNRs in the optimized complexes driven by a physisorption process. These results provide significant insights for catalytic processes that use biomass derivatives containing phenolic compounds. The physisorption of streams containing pollutants on OGNRs could be adapted to new technological applications for the remotion of aromatic compounds under environmentally friendly operational conditions.

Live-Cell Synchrotron-Based FTIR Evaluation of Metabolic Compounds in Brain Glioblastoma Cell Lines after Riluzole Treatment.

Glioblastoma multiforme (GBM) is the most aggressive brain tumor, characterized by short median survival and an almost 100% tumor-related mortality. The standard of care treatment for newly diagnosed GBM includes surgical resection followed by concomitant radiochemotherapy. The prevention of disease progression fails due to the poor therapeutic effect caused by the great molecular heterogeneity of this tumor. Previously, we exploited synchrotron radiation-based soft X-ray tomography and hard X-ray fluorescence for elemental microimaging of the shock-frozen GBM cells. The present study focuses instead on the biochemical profiling of live GBM cells and provides new insight into tumor heterogenicity. We studied bio-macromolecular changes by exploring the live-cell synchrotron-based Fourier transform infrared (SR-FTIR) microspectroscopy in a set of three GBM cell lines, including the patient-derived glioblastoma cell line, before and after riluzole treatment, a medicament with potential anticancer properties. SR-FTIR microspectroscopy shows that GBM live cells of different origins recruit different organic compounds. The riluzole treatment of all GBM cell lines mainly affected carbohydrate metabolism and the DNA structure. Lipid structures and protein secondary conformation are affected as well by the riluzole treatment: cellular proteins assumed cross β-sheet conformation while parallel β-sheet conformation was less represented for all GBM cells. Moreover, we hope that a new live-cell approach for GBM simultaneous treatment and examination can be devised to target cancer cells more specifically, i.e., future therapies can develop more specific treatments according to the specific bio-macromolecular signature of each tumor type.

Molecular insights into the selective binding mechanism targeting parallel human telomeric G-quadruplex

Stabilizing human telomere DNA G-quadruplex (G4) proves a promising anti-cancer strategy. Though plenty of G4 stabilizing molecules have been reported, little is known about their selective binding mechanism among various G4s. Recently, a designed monohydrazone derivative (compound 15) was reported to display specific preference in binding and stabilizing parallel human telomeric G4. To reveal the selective binding mechanism, a comparative theoretical investigation was performed on two monohydrazone derivatives (compounds 1 and 15) and three telomeric G4s showing parallel, hybrid-I, and hybrid-II conformations. Two probable binding modes, i.e. the end-stacking binding and the groove binding, were predicted by molecular dockings for each monohydrazone in its binding with the telomeric G4s. Further long-timescale molecular dynamics simulations reveal the conversion from the groove binding to the end-stacking binding for both compounds, indicating the preference of the end-stacking binding mode. Structural analysis together with binding free energy calculations show that the van der Waals interaction plays a leading role in ranking the binding affinity. By forming extensive van der Waals interactions, the parallel G4–15 binding complex shows the highest binding affinity, and the corresponding compound 15 exhibits the strongest stabilizing effect to the telomeric G4. These findings agree well with the experimental observations. Through characterizing the selective binding between monohydrazones and telomeric G4s at the atomic level, the current study provides support to the design of novel selective stabilizers targeting telomeric G4s.

Structures of outer-arm dynein array on microtubule doublet reveal a motor coordination mechanism

Thousands of outer-arm dyneins (OADs) are arrayed in the axoneme to drive a rhythmic ciliary beat. Coordination among multiple OADs is essential for generating mechanical forces to bend microtubule doublets (MTDs). Using electron microscopy, we determined high-resolution structures of Tetrahymena thermophila OAD arrays bound to MTDs in two different states. OAD preferentially binds to MTD protofilaments with a pattern resembling the native tracks for its distinct microtubule-binding domains. Upon MTD binding, free OADs are induced to adopt a stable parallel conformation, primed for array formation. Extensive tail-to-head (TTH) interactions between OADs are observed, which need to be broken for ATP turnover by the dynein motor. We propose that OADs in an array sequentially hydrolyze ATP to slide the MTDs. ATP hydrolysis in turn relaxes the TTH interfaces to effect free nucleotide cycles of downstream OADs. These findings lead to a model explaining how conformational changes in the axoneme produce coordinated action of dyneins.

Exploring Curious Covalent Bonding: Raman Identification and Thermodynamics of Perpendicular and Parallel Pancake Bonding (Pimers) of Ethyl Viologen Radical Cation Dimers.

Viologen radical cations can dimerize in solutions, and the resulting "pimers" were predicted to assemble into parallel and perpendicular conformers by density functional theory (DFT) calculations. Using resonance Raman, we could identify both perpendicular and parallel forms of ethyl viologen dimers. The distinction between the two forms was accomplished by studying the formation of a host-guest complex with γ-cyclodextrin. The dimer's perpendicular form was excluded due to the host cavity size, and γ-cyclodextrin addition caused a decrease in peak intensities at 1171, 1511, and 1602 cm-1 that could be assigned to the perpendicular form. DFT modeling of the vibrational spectra under preresonance conditions allowed us to assign the remaining vibrational modes for the parallel and perpendicular forms. Using variable-temperature UV-vis, the bond dissociation energy (ΔH) for this pancake-bonded dimer was measured as 13.1 ± 0.2 kcal/mol. This type of covalent pancake bonding is a challenge to properly describe using DFT methods. Previously, B97D was found to best describe the ΔG of this dimerization (Angew. Chem. 2017, 129, 9563-9567), but this method underestimates the ΔH by 6 kcal/mol. Of the 11 functionals tested, we found that B3LYP with Grimme's D3 dispersion effect can best reproduce the ΔH. Energy decomposition analysis of the bonding energy showed that solvation effects were the most important contributor-polar solvents are needed to overcome the Coulomb repulsion between the two positively charged monomers. Dispersion effects are second in importance and appear larger than the favorable orbital interaction obtained by singly occupied molecular orbital (SOMO)-SOMO orbital overlap. This study brings forth important insights into the curious cases of covalent bonding between two π-delocalized radicals.

A new inhibition mechanism in the multifunctional catalytic hemoglobin dehaloperoxidase as revealed by the DHP A(V59W) mutant: A spectroscopic and crystallographic study

As multifunctional catalytic hemoglobins, dehaloperoxidase isoenzymes A and B (DHP A and B) are among the most versatile hemoproteins in terms of activities displayed. The ability of DHP to bind over twenty different substrates in the distal pocket might appear to resemble the promiscuousness of monooxygenase enzymes, yet there are identifiable substrate-specific interactions that can steer the type of oxidation (O-atom vs. electron transfer) that occurs inside the DHP distal pocket. Here, we have investigated the DHP A(V59W) mutant in order to probe the limits of conformational flexibility in the distal pocket as it relates to the genesis of this substrate-dependent activity differentiation. The X-ray crystal structure of the metaquo DHP A(V59W) mutant (PDB 3K3U) and the V59W mutant in complex with fluoride [denoted as DHP A(V59W-F)] (PDB 7MNH) show significant mobility of the tryptophan in the distal pocket, with two parallel conformations having W59-N[Formula: see text] H-bonded to a heme-bound ligand (H2O or F[Formula: see text], and another conformation [observed only in DHP A(V59W-F)] that brings W59 sufficiently close to the heme as to preclude axial ligand binding. UV-vis and resonance Raman spectroscopic studies show that DHP A(V59W) is 5-coordinate high spin (5cHS) at pH 5 and 6-coordinate high spin (6cHS) at pH 7, whereas DHP A(V59W-F) is 6cHS from pH 5 to 7. Enzyme assays confirm robust peroxidase activity at pH 5, but complete loss of activity at pH 7. We find no evidence that tryptophan plays a role in the oxidation mechanism ([Formula: see text]. radical formation). Instead, the data reveal a new mechanism of DHP inhibition, namely a shift towards a non-reactive form by OH[Formula: see text] ligation to the heme-Fe that is strongly stabilized (presumably through H-bonding interactions) by the presence of W59 in the distal cavity.

Investigation By NMR Spectroscopy of the Structural Characteristics of Modified Oligo-Nucleotides with Pendant Porphyrins

Exerting control over the position and distance of the porphyrins along a specifically designed oligonucleotidic scaffold was our main goal over the past years. Indeed, in naturally occurring light-harvesting complexes, biopolymer scaffolds hold pigments at intermolecular distances that optimize photon capture, electronic coupling, and energy transfer. We thus focused on the synthesis of four uridine-porphyrin conjugates (a monomer, dimer, tetramer and octamer) dedicated to adopt a pre-organized conformation with face-to-face porphyrins, and capable to self-organize in a stable sandwich type complexe with bidentate base such as DABCO. Using a similar strategy as the one used in antisense research, an artificial nucleotidic backbone was built from modified deoxy-uridine units linked with a more rigid linker than the phosphodiester moieties found in natural oligonucleotides. Antisense research uses modified oligonucleotides, less flexible than natural strands, to pre-organize the system toward the obtaining of stable double helices between synthesized and natural oligonucleotides. A modified oligonucleotidic backbone was here used to target a parallel conformation of the porphyrins appended to each deoxy-uridine moiety. To provide a rigid environment for the porphyrins, the uridine units were coupled in 3’-5’ stepwise fashion using ether-ester type of spacer of suitable length, and porphyrins were anchored to the uridine by means of robust carbon-carbon bonds. To investigate the conformation of our four uridine-porphyrin conjugates, they were subjected to a comprehensive conformational analysis by using NMR spectroscopy. The collected NOE NMR data highlighted characteristic and strong interactions indicating that the glycosidic angle between the ribose and uracil base is anti. In order to further invastigate the conformation of this family of molecules, NMR experiments were carried out at variable temperature. At low temperature, the signals of the porphyrinic protons decoalesce showing two sets of b-pyrrolic protons. Similar observations are made for the signals corresponding to the sugar moieties and especially the H1’ protons, indicating molecular motions within our porphyrin-uridin arrays. These results testify in favor of the existence of a dynamic process between C3’-endo and C2’-endo conformations.We thus document the fact that the choice of rigid spacers is not the only way to pre-organize bis-porphyrins, and that some well-chosen nucleosidic linkers offer an interesting option for the synthesis of such devices. Furthermore, the chirality and enantio-purity of the nucleosidic linkers paves the way toward the selective complexation of enantio-pure bidentate guests and the resolution of racemates. Acknowledgements This work was supported by the CNRS and the French Ministry of Research. References Merkas, M. Zinic, R. Rein, N. Solladié, J. Porphyrins Phthalocyanines 2019, 23, 797-812. Figure 1

Cryo‐EM Structures of Outer‐arm Dynein Array Bound to Microtubule Doublet Reveal a Mechanism for Motor Coordination

Eukaryotic cilia are evolutionarily conserved organelles that are responsible for cellular motility, sensory reception, embryonic development and intercellular communication. A typical motile cilium is characterized by its ʹ9 + 2ʹ scaffold, composed of nine microtubule doublets (MTDs), and a central pair complex (CPC). Two rows of axonemal dyneins, the outer-arm dynein (OAD) and inner-arm dynein (IAD), power the ciliary beating by sliding two adjacent MTDs. OAD is the key motor protein that generates the majority of mechanical forces required for this fundamental cellular process. A complete OAD is ~1.5-2 megadalton in size and contains two (mammals) or three (in ciliates and algae) heavy chains (HCs), two intermediate chains (ICs) and a variety of light chains (LCs). Each OAD is divided into a head region that contains AAA+ rings for ATP hydrolysis and a tail that holds together the whole complex. The tail is permanently attached to MTD A-tubule, while the head region of each HC contains a microtubule-binding domain (MTBD) which binds and releases MTD B-tubule depending on the nucleotide-binding states. Thousands of OADs are arrayed in the axoneme to drive a rhythmic ciliary beat, which is required to OADs locally synchronize their conformations and coordinate with each other. Current understanding is mainly based on cryo-electron tomography (cryo-ET) which suggests that adjacent OADs are indirectly connected via a series of linker structures. Nevertheless, it is largely unclear how the OAD arrays are formed and why the array is important for ciliary beat. Furthermore, the mechanism underlying the motor coordination remains elusive. We set out to reveal the mechanism of motor coordination to shed lights on how the conformational changes of arrayed OAD are linked to force generation and beating propagation. We use the model system T. thermophila for biochemical and cryo-EM analysis. T. thermophila OAD is the first discovered dynein, which contains three HCs (α-, β- and γ-HC), two ICs (IC2 and IC3) and a set of indefinite LCs. We reconstitute the purified OADs onto MTD to mimic the native OAD arrays and determined the structures of free OAD and OAD arrays bound to MTDs (OAD-MTD) in two different microtubule-binding states (MTBS) by cryo-electron microscopy (cryo-EM). We show that microtubule binding induces free OADs to spontaneously adopt a parallel conformation, which is primed for array formation in a tail-to-head (TTH) manner. The conformations of arrayed OADs are synchronized in either microtubule-binding state. The array involves extensive network interactions and is coordinately remodeled when OADs take one step forward from MTBS-1 to MTBS-2. The TTH interactions remain nearly unchanged in both states but need to be broken to allow MTBS alteration during mechanochemical cycle. Nucleotide treatment on the OAD-MTD array reveals that it is the ATP hydrolysis that temporarily relaxes the TTH interfaces to allow free nucleotide cycle of downstream OADs. In combination with previously reported cryo-ET structures, we propose a most detailed mechanism of how OADs coordinate with each other to move one step on MTD and a possible model for ciliary beat propagation.

Triggering G‐Quadruplex Conformation Switching with [7]Helicenes

The dynamic interplay between two types of chiral structures; fully conjugated racemic hetero[7]helicenes and DNA strands prone to fold into G-quadruplex structures is described. Both the [7]helicenes and the G-quadruplex DNA structures exist in more than one conformation in solution. We show that the structures interact with and stabilise each other, mutually amplifying and stabilising certain conformations at increased temperatures. The [7]helicene ligands L1 and L2 stabilise the parallel conformation of k-ras significantly, whereas hybrid (K+ ) and antiparallel (Na+ ) h-telo G-quadruplexes are stabilised upon conformational switching into altered G-quadruplex conformations. Both L1 and L2 induce parallel G-quadruplexes from hybrid structures (K+ ) and L1 induces hybrid G-quadruplexes from antiparallel conformations (Na+ ). Enantioselective binding of one helicene enantiomer is observed for helicene ligand L2, and VTCD melting experiments are used to estimate the racemisation barrier of the helicene.

Trizbenzim, Cu-Trizbenzim and Zn-Trizbenzim as G-Quadruplex Inducing and Stabilizing Compounds on Human Telomeric Sequence and their Anticancer Properties.

The benzimidazole and their derivatives have rich biological relevance with respect to available natural amino acids and their role in protein folding and quaternary conformations. Thus the ligand trizbenzim and their Cu(II) and Zn(II) metal complexes were prepared to induce G-quadruplex conformation even under no-salt conditions with remarkable anticancer activities. The ligand N,N',N''-Tris-(1H-benzoimidazol-2-ylmethyl)-[1,3,5]triazine-2,4,6-triamine ( trizbenzim) and its Cu and Zn complexes (Cu-trizbenzim, Zn-trizbenzim) were synthesized and characterized by IR, NMR, and MALDI-TOF techniques. The pure ligand and its complexes interacted with human telomere DNA sequence d(TTAGGG), HTelo8and HTelo20and the interactions were followed by circular dichroism spectroscopy, FID assay, and molecular docking techniques. The compounds were tested for anticancer activity towards selected cell lines. All the three compounds stabilized the HTelo8 and HTelo20 in parallel and antiparallel G-quadruplex conformations with salt conditions. Under no-salt conditions, the compounds induce and stabilize the G-quadruplex conformation in antiparallel topology selectively. The pure ligand, Cu-trizbenzim, and Zn-trizbenzim were involved in partial or classical intercalation and some backbone interactions on the strand. The FID assay using thiazole orange intercalator supports the proposed intercalation mode of binding for the three compounds, especially for the pure ligand and the Cu-complex. The MOE docking experiments using X-ray and NMR derived G-quadruplex models with the title compounds extensively support the G-quadruplex induction and stabilization of the telomere sequence by these compounds. The guanines bases involved in the G-tetrad formation interact well with the triazine and the benzimidazole part of the ligand through strong π-π interactions. The primary mode of binding is described as end stacking and intercalation of the compounds to the G-quadruplex structures. The Cu-trizbenzim exhibited more anticancer property in comparison to the pure ligand and the Zntrizbenzim complex. The IC50 values were in the nanomolar range from 50 to 150nM in concentration. This novel self-induction of G-quadruplex is novel without the presence of alkali metal ions.

Structure analysis of the proteins associated with polyA repeat expansion disorders

Repeat regions are low-complexity regions in the human genome that largely code for intrinsic disorder in proteins. Expansions outside the normal thresholds in repeat regions are likely to be pathogenic, leading to the so-called repeat expansion diseases. There have been numerous studies on the most common group of repeat expansion diseases, which are the polyglutamine (polyQ) repeat expansion diseases, but there has been much less work done on the second-largest group of expansion repeats disorders, which involves the expansion of polyalanine (polyA) repeat tracts. In this article, we present a comprehensive study of the structural changes predicted using I-TASSER when comparing the wild type and enlarged structures of all known polyA expansion disorders. The results show that there is a reduction in α helices, an increase in extended strands in parallel and/or anti-parallel β-sheet conformation, an increase in random coils/loops and irregular elements, and a large increase in solvent-accessible surface area. When compared to the findings in polyQ expansions disorders we see similar trends, suggesting that the polyQ and polyA repeat expansion causes similar effects on the respective proteins, which lead to higher misfolding and aggregation propensities. Communicated by Ramaswamy H. Sarma