Search

The Kv family of voltage-gated potassium channels regulate neuronal excitability. The biophysical characteristic of Kv channels can be matched to the needs of different neurons by forming homotetrameric or heterotetrameric channels within one of four subfamilies. The cytoplasmic tetramerization (T1) domain plays a major role in dictating the compatibility of different Kv subunits. The only Kv subfamily missing a representative structure of the T1 domain is the Kv2 family. We used X-ray crystallography to solve the structure of the human Kv2.1 T1 domain. The structure is similar to other T1 domains but surprisingly formed a pentamer instead of a tetramer. In solution the Kv2.1 T1 domain also formed a pentamer as determined with in-line SEC-MALS-SAXS and negative stain EM. The Kv2.1 T1-T1 interface involves electrostatic interactions including a salt bridge formed by the negative charges in a previously described CDD motif, and inter-subunit coordination of zinc. We show that zinc binding is important for stability. In conclusion, the Kv2.1 T1 domain behaves differently from the other Kv T1 domains which may reflect the versatility of Kv2.1, the only Kv subfamily that can assemble with the regulatory KvS subunits and scaffold ER-plasma membrane contacts.

SARS-CoV-2 and other coronaviruses pose major threats to global health, yet computational efforts to understand them have largely overlooked the process of budding, a key part of the coronavirus life cycle. When expressed together, coronavirus M and E proteins are sufficient to facilitate budding into the ER-Golgi intermediate compartment (ERGIC). To help elucidate budding, we ran atomistic molecular dynamics (MD) simulations using the Feig laboratory’s refined structural models of the SARS-CoV-2 M protein dimer and E protein pentamer. Our MD simulations consisted of M protein dimers and E protein pentamers in patches of membrane. By examining where these proteins induced membrane curvature in silico, we obtained insights around how the budding process may occur. Multiple M protein dimers acted together to induce global membrane curvature through protein-lipid interactions while E protein pentamers kept the membrane planar. These results could eventually help guide development of antiviral therapeutics which inhibit coronavirus budding.

The lipid-anchored small G protein Ras is a central regulator of cellular signal transduction processes, thereby functioning as a molecular switch. Ras forms a nanocluster on the plasma membrane by modifying lipids in the hypervariable region (HVR) at the C-terminus to exhibit physiological functions. In this study, we demonstrated that chemical modification of cysteine residues in HVR with caged compounds (instead of lipidation) induces multimerization of H-Ras. The sulfhydryl-reactive caged compound, 2-nitrobenzyl bromide, was stoichiometrically incorporated into the cysteine residue of HVR and induced the formation of the Ras multimer. Light irradiation induced the elimination of the 2-nitrobenzyl group, resulting in the conversion of the multimer to a monomer. Size-exclusion chromatography coupled with high-performance liquid chromatography and small-angle x-ray scattering analysis revealed that H-Ras forms a pentamer. Electron microscopic observation of the multimer showed a circular ring shape, which is consistent with the structure estimated from x-ray scattering. The shape of the multimer may reflect the physiological state of Ras. It was suggested that the multimerization and monomerization of H-Ras were controlled by modification with a caged compound in HVR under light irradiation.

Aronia melanocarpa (MICHX.) ELLIOTT, which belongs to the Rosaceae family, has increasingly come into focus of research due to the high content of polyphenols. In addition to antioxidative properties, further health-promoting effects of these polyphenols are still of interest. Especially, the proanthocyanidins offer thereby huge opportunities due to their high structural heterogeneity. Therefore, the present study focuses on the topoisomerase inhibiting effects of oligomeric proanthocyanidins (PACs), which are potentially depended on their degree of polymerization. The investigated PACs isolated from Aronia berries were characterized by chromatographic techniques and liquid chromatography-high-resolution mass spectrometry. Four PAC enriched fractions were obtained from Aronia pomace containing 47 PACs with a degree of polymerization from three to six. Due to the low yield of hexamers, the potential inhibiting effects against human topoisomerase were investigated for the trimer to pentamer fractions. The relaxation and decatenation assays were performed to examine the inhibiting effect on topoisomerases under cell-free conditions. Moreover, rapid isolation of topoisomerase cleavage complexes in human colon carcinoma HT29 cells was performed to evaluate the effect on topoisomerases in a cell-based system. The fractions demonstrated inhibitory potential on topoisomerases I and II. In sum, an increasing effect strength depending on the degree of polymerization was shown.

The electronic structures of the lowest energy spin-states of the cationic, neutral and anionic bare boron pentamer clusters have been investigated by means of high level multiconfigurational type calculations, in view of the large static and dynamical electron correlation effects for these species. We found that B5+ resembles a singlet spin-state perfect pentagon, which bears no intra-annular chemical bonding interactions, as shown by our analysis of the electron delocalization carried out in terms of the normalized Giambiagi ring-current index, and the total and adjacent atom-pair delocalization indices. However, its lowest-energy triplet and quintet spin-state isomers have C2v symmetry, with large intra-annular chemical bonding interactions. This geometrical feature extends to both the neutral and the anionic species. Namely, the lowest-energy isomers of boron pentamer neutral and anionic clusters have peripheral and intra-annular sizable bonding interactions reflected in the delocalization of both π- and σ-type valence natural orbitals over the whole molecular plane, which impart large structural stability. In accordance to our calculations, the lowest energy triplet spin-state isomer of the anionic boron pentamer cluster has C2 symmetry, and consequently, it should show optical activity. Finally, we have studied the change of the geometrical structure of the boron pentamer clusters from planar to compact three-dimensional structures caused by the bonding of ligands to the boron atoms. Our explicit all-electron calculations have been rationalized in terms of the shell-closure of the delocalized valence orbitals of the clusters as predicted by the jellium model extended to nonspherical confinement potentials, circumscribing the role of the ligand to modulate the total number of valence electrons assigned to the core cluster.

The biallelic inheritance of an expanded intronic pentamer (AAGGG)A retrospective descriptive study from an ataxia database comprising 500 patients.The study was performed at the Otorhinolaryngology Department of a hospital in the north of Spain.Specific genetic testing for CANVAS was performed in 13 patients with clinical suspicion of complete or incomplete syndrome. The clinical diagnosis was supported by quantitative vestibular hypofunction, cerebellar atrophy, and abnormal sensory nerve conduction testing.Nine of 13 (69%) patients met clinical diagnostic criteria for definite CANVAS disease. The first manifestation of the syndrome was lower limb dysesthesia in 8 of 13 patients and gait imbalance in 5 of 13. Eleven of 13 (85%) patients were carriers of the biallelic (AAGGG)A genetic cause of CANVAS has recently been discovered. We propose genetic screening for biallelic expansions of the AAGGG pentamer of

The experimentally known reaction of Cp2Cr2(CO)6 with white phosphorus (P4) to give CpCr(CO)2(η3-P3), Cp2Cr2(CO)4(μ-η,2η2-P2), and the triple-decker sandwich Cp2Cr2(μ-η,5η5-P5) is of interest since the P4 reactant having a tetrahedral cluster of four phosphorus atoms is converted to products having P2, P3, and P5 ligands. The mechanism of this obviously complicated reaction can be dissected into three stages using a coupled cluster theoretical method that has been benchmarked with the P2, Mn(CO)5, and CpCr(CO)3 dimerization processes. The first stage of the Cp2Cr2(CO)6/P4 reaction mechanism generates the unsaturated singlet intermediate Cp2Cr2(CO)5 that combines with the P4 reactant. Decarbonylation of the resulting Cp2Cr2(CO)5(P4) complex provides a singlet tetracarbonyl readily fragmenting into the stable triphosphacyclopropenyl complex CpCr(CO)2(η3-P3) and the chromium phosphide CpCr(CO)2(P). The isomeric triplet tetracarbonyl Cp2Cr2(CO)4(P4), readily fragments into CpCr(CO)2(η2-P2), which can generate the stable diphosphaacetylene complex Cp2Cr2(CO)4(η,2η2-P2) as well as the pentamer [CpCr(CO)2]5(P10). Combination of the coordinately unsaturated CpCr(CO)(η3-P3) with CpCr(CO)2(η2-P2) can lead to a ring expansion. This generates the P5 pentagonal ligand in a Cp2Cr2(CO)3(P5) precursor to the experimentally observed carbonyl-free triple-decker sandwich Cp2Cr2(μ-η,5η5-P5) after three successive decarbonylations.

The aggregation of amyloid has been an important event in the pathology of amyloidogenicity. A number of small molecules have been designed for Amyloidosis treatment. Molecular tweezer CLR01, a potential drug for misfolded β-amyloids inhibition, was reportedly bind directly to Lysine residues and interrupt oligomerization. However, the disaggregation mechanism of amyloid for this inhibitor is unclear. Here we used long timescale of molecular dynamic simulation to reveal the mechanism of disaggregation for pentamer prion amyloid. Molecular docking and molecular dynamics simulation demonstrate that CLR01 is attached with Lysine222 nitrogen by π-cation interaction of its nine aromatic rings and formation of salt bridge/hydrogen bond of one of the two rotatable peripheral anionic phosphate groups. Upon CLR01 binding, we found a major shifting occurs in initial conformation of the oligomer and stretch out the N-terminal chain A from the rest of the amyloid which seems to be the first stage of disaggregated the fibrils slowly yet efficiently. Moreover, the CLR01 remodelled the pentamer Prion220-272 into a compact structure which might be the resistant conformation for further oligomerization. Our work will contribute to better understand the interaction and deterioration mechanism of molecular tweezer for prions and similar amyloids, and offer significant insights into therapeutic development for Amyloidosis treatment.

One of the most crucial characteristic traits of Envelope (E) proteins in the severe acute respiratory syndrome SARS-CoV-1 and NCOVID19 viruses is their membrane-associated oligomerization led ion channel activity, virion assembly, and replication. NMR spectroscopic structural studies of envelope proteins from both the SARS CoV-1/2 reveal that this protein assembles into a homopentamer. Proof of concept studies via truncation mutants on either transmembrane (VFLLV), glycosylation motif (CACCN), hydrophobic helical bundle (PVYVY) as well as replacing C-terminal “DLLV” segments or point mutants such as S68, E69 residues with cysteine have significantly reduced viral titers of SARS-CoV-1. In this present study, we have first developed SARS-2 E protein homology model based on the pentamer coordinates of SARS-CoV-1 E protein (86.4% structural identity) with good stereochemical quality. Next, we focused on the glycosylation motif and hydrophobic helical bundle regions of E protein shown to be important for viral replication. A four feature (4F) model comprising of an acceptor targeting S60 hydroxyl group, a donor feature anchoring the C40 residue, and two hydrophobic features anchoring the V47 L28, L31, Y55, and P51 residues formed the protein based pharmacophore model targeting the glycosylation motif and helical bundle of E protein. Database screening with this 4F protein pharmacophore, ADMET property filtering on enamine small molecule discovery collection yielded a focused library of ~7000 hits. Further molecular docking and visual inspection of docked pose interactions at the above mention V47 L28, L31, Y55, P51, S60, C40 residues led to the identification of 10 best hits. Our STD NMR binding assay results demonstrate that the ligand 3, 2-(2-amino-2-oxo-ethoxy)-N-benzyl-benzamide, binds to NCOVID19 E protein with a binding affinity (KD) of 141.7 ± 13.6 μM. Furthermore, the ligand 3 also showed binding to C-terminal peptide (NR25) as evidenced with the STD spectrums of wild type E protein would serve to confirm the involvement of C-terminal helical bundle as envisaged in this study., Graphical abstract Unlabelled Image

Physicochemical characterization of multimeric biomacromolecule assembly and disassembly processes is a milestone to understand the mechanisms for biological phenomena at the molecular level. Mass spectroscopy (MS) and structural bioinformatics (SB) approaches have become feasible to identify subcomplexes involved in assembly and disassembly, while they cannot provide atomic information sufficient for free-energy calculation to characterize transition mechanism between two different sets of subcomplexes. To combine observations derived from MS and SB approaches with conventional free-energy calculation protocols, we here designed a new reaction pathway sampling method by employing hybrid configuration bias Monte Carlo/molecular dynamics (hcbMC/MD) scheme and applied it to simulate the disassembly process of serum amyloid P component (SAP) pentamer. The results we obtained are consistent with those of the earlier MS and SB studies with respect to SAP subcomplex species and the initial stage of SAP disassembly processes. Furthermore, we observed a novel dissociation event, ring-opening reaction of SAP pentamer. Employing free-energy calculation combined with the hcbMC/MD reaction pathway trajectories, we moreover obtained experimentally testable observations on (1) reaction time of the ring-opening reaction and (2) importance of Asp42 and Lys117 for stable formation of SAP oligomer.

Cyclocondensation between 4,4`-bis(4-chlorobenzenesulfonyl)biphenyl and catechol, with subsequent chromatographic separation of the reaction products, led to the isolation of four novel ether-sulfone macrocycles (cyclic dimer, -trimer, -tetramer and -pentamer). Similarly, cyclocondensation of catechol with a novel seven-ring diketone/disulfone monomer allowed the isolation of the two new aromatic ether-ketone-sulfone macrocycles, a cyclic monomer and a cyclic dimer. Transannular shielding and deshielding effects in the cyclic monomer produce substantial chemical shift differences for chemically equivalent protons in the 1H NMR spectra of the cyclic monomer and -dimer. Fluoride-initiated ring-opening polymerization of the ether-sulfone cyclic trimer affords a novel, high-molecular weight poly(ether-sulfone).

A DFT-based methodology has been used to construct the potential energy surface of H2S clusters up to pentamers. Geometrical parameters and energetics show very good agreement with the existing experimental and high-level theoretical results. Distinct stable conformers of three dimers, six trimers, eleven tetramers and twenty-three pentamers have been identified. Both S–H⋯S H-bond and S⋯S interactions are identified in dimers, trimers and pentamers, while no S⋯S interactions could be found in any of the 11 tetramer conformers. The binding energies of the most stable dimer, trimer, tetramer and pentamer are −1.66, −5.21, −8.57 and −12.54 kcal mol−1, respectively. The PES has been found to be exceedingly flat and the energy gap between the most and the least stable conformers was found to be only 0.09, 2.13, 1.65 and 1.13 kcal mol−1, from the dimer to the pentamer, respectively. The proposed method has also been used for water clusters up to the pentamer. The results obtained were found to agree closely with the existing results. Only one conformer was found for the water dimer, whereas four, five and fifteen conformers were obtained for the trimer, tetramer and pentamer, respectively. Atoms in molecular calculations were found to corroborate with the geometric and energetic results for both clusters.

Thiolated gold clusters are constituted by building blocks (Au4, Au6, Au12 and so on) and protected by staple motifs (–S–Au–S–Au–S–…). In this study, we propose the structure of Au11(SR)9 and Au13(SR)11 clusters that are in the synthesis route of the ubiquitous Au15(SR)13 cluster. Our DFT-D calculations support one triangular Au3 unit as the smallest one comprising the structure of the Au11(SR)9 cluster, while it competes with the Au4 unit found in the Au13(SR)11 cluster. The ligand effects on the electronic, optical and chiroptical properties were studied by considering H, CH3, phenyl and adamantyl as protecting ligands. In the case of the Au11(SR)9 cluster, its Au3 inner core is protected by one dimer motif and one [Au6(SR)6] cyclomer when H and CH3 were considered as ligands, and the preference for Au3 over Au4 inner core was calculated to be 0.042 (H), 0.190 (CH3), and 0.117 eV (adamantyl). In contrast, the preference for one Au4 core increased when using phenyl ligands (0.23 eV energy difference) and dimer and pentamer motifs. Moreover, the Au13(SR)11 cluster (R = CH3) has one Au4 inner core and is protected by the combination of cyclomer, monomer and dimer motifs, and the isomer containing one Au3 inner core and protected by one tetramer and one [Au6(SR)6] cyclomer is 0.170 eV less stable. This implies that the Au3 unit is important in these small sizes and that the energetic preference depends on the used ligand types. Moreover, we discuss the IR/Raman, optical absorption (UV-vis), and circular dichroism (CD) spectra of our predicted new structures.

We study the earliest steps in the radiolysis of a water pentamer in an intense, 800 nm, linearlypolarized fs laser field [I = (0.1 − 50) ∙ 1014 W/cm2] through a real-space, real-time implementation of time-dependent density functional theory nonadiabatically coupled to molecular dynamics. The ionization is enhanced with increasing laser intensity, resulting in the continuous emergence of higher charge states and an increase in the ionization ratio of the deepest levels. Two different reaction pathways of the water pentamer are presented by analyzing the degree of ionization, the level depletion, the probabilities of ionic states, the time-resolved electron density, the bond lengths, and the vibrational frequencies. Both pathways exhibit fluctuations and rearrangement dynamics of the hydrogen bonding network under irradiation. The cyclic structure of the pentamer formed via five oxygen ions is distorted and opened after ionization and tends to maintain a hydronium H3O+ configuration. Proton transfer is accompanied by an oxygen–oxygen contraction and the first proton transfer rate ranges over 6–22 fs.

Neural stem cells (NSCs) represent significant potential and promise in the treatment of neurodegenerative diseases and nerve injuries. An efficient methodology or platform that can help in specifically directing the stem cell fate is important and highly desirable for future clinical therapy. In this study, a biodegradable electrical conductive film composed of an oxidative polymerized carboxyl-capped aniline pentamer (CCAP) and ring-opening polymerized tetra poly(d,l-lactide) (4a-PLA) was designed with the addition of the dopant, namely chondroitin sulfate. This conductive film acts as a biological substrate for the exogenous/endogenous electric field transmission in tissue, resulting in the control of NSC fate, as well as improvement in neural tissue regeneration. The results show that CCAP is successfully synthesized and then conjugated onto 4a-PLA to form a network structure with electrical conductivity, cell adhesion capacity, and biodegradability. The neuronal differentiation of NSCs can be induced on 4a-PLAAP, and the neuronal maturation process can be facilitated by the manipulation of the electrical field. This biocompatible and electroactive material can serve as a platform to determine the cell fate of NSCs and be employed in neural regeneration. For future perspectives, its promising performance shows potential in applications, such as electrode-tissue integration interfaces, coatings on neuroprosthetics devices and neural probes, and smart drug delivery system in neurological systems.

Single-molecule DNA/RNA sequencing based on single-molecule measurement is a prominent method for higher throughput sequencing. In a previous report, the single-molecule DNA/RNA sequencing method has applied to detect each base-conductance difference in the tunneling current time profiles, and determined the sequence. However, discrimination of identical base lengths has not yet been achieved. The number of the identical contiguous bases has importance in biology because some homopolymers of nucleic acid control gene expression. In this study, we aimed to develop a method for discriminating the length of homopolymer of nucleic acids of adenosine monophosphate (AMP) using a single-molecule sequencing technique. We carried out single-molecule conductance measurements of adenine pentamer, hexamer and heptamer. The single-molecule signals of the oligomers are not distinguishable from current and duration time histograms. The three oligomers were discriminated by our developed machine learning-based analysis with accuracy of 0.54 for a single signal, and 99% for 40 signals. This method will be applied to the single signals and identify the contiguous bases in the sequence and provide new biological insights.

Background: Gangliosides are an essential component of eukaryotic plasma membranes implicated in multiple physiological processes. Little is known about molecular mechanisms underlying the distribution and functions of membrane gangliosides. The overwhelmingly complex organization of glycocalyx impedes the structural analysis on cell surface and the interplay between the lipid components. Advanced X-ray analytical tools applicable to studying biological interfaces call for the simplistic models that mimic ganglioside-enriched cellular membranes. Objective: To summarize the mechanistic evidences of ganglioside interactions with lipid environment and biologically active ligands using high-resolution synchrotron X-ray scattering. Methods: A comprehensive review of studies published over the last decade was done to discuss recent accomplishments and future trends. Results: Langmuir monolayers represent an adequate model system to assess the effect of gangliosides on membrane structure. Grazing incidence X-ray diffraction reveals a condensation effect by gangliosides on zwitterionic phospholipids with the cooperative packing of sialo- and phosphate groups. In turn, the arrangement of negatively charged lipids in ganglioside mixture remains unchanged due to the stretched conformation of carbohydrate moieties. Upon interaction with biological ligands, such as cholera toxin and galectins, the ganglioside redistribution within the ordered regions of monolayer follows distinct mechanistic patterns. The cholera toxin pentamer attached to the oligosaccharide core induces local transition from oblique to the hexagonal lattice resulting in phase coexistence. The incorporation of the A subunit responsible for endocytosis is further promoted by the acidic environment characteristic for endosomal space. X-ray reflectivity shows in-plane orientation of galectin dimers with the spatial mismatch between the lectin binding sites and ganglioside carbohydrates to perturb ceramide alkyl chains. Recent data also demonstrate sialic acid groups to be potential targets for novel peptide mimicking anticancer therapeutics. Conclusion: Coupled with surface X-ray scattering, the membrane mimetic approach allows for better understanding the biological role of gangliosides and their potential applications.

The residue 2-thiouridine (s2U) provides a remarkable example for the "modified wobble" hypothesis, which postulates that some post-transcriptional modifications at the wobble position of tRNAs restrict recognition of degenerate codons. Through extensive molecular dynamics simulations using our χIDRP force field parameters, we demonstrate how this modification shifts the conformational ensemble from a predominantly disordered, as in the case of an RNA pentamer (GUUUC), to a substantially ordered population in Gs2UUUC. Our simulations clearly showed that the van der Waals interaction of sulfur played a major role in driving the disorder-to-order transition. The conformational redistribution and the slowing down of the transition between the clusters within the population in the presence of s2U suggest ensemble allostery to be a key mechanism that may play a general role in the functioning of the wobble modifications of tRNAs.

Human Papillomavirus (HPV) is the leading cause of cervical cancer, with only some HPV types prevented with vaccines and no treatments for the viral infection itself. One way to target viral infect...

In 1995 we extrapolated the so-called “effective conjugation length” in (para-phenylene) ladder polymers by relating the optical absorption energy to the reciprocal chain length of ladder-type oligo-(para-phenylene)s, but only based on three short-chain oligomers (a trimer, a pentamer, and a heptamer). The resulting value of 11–12 benzene rings was distinctly lower than the numbers reported for corresponding single-stranded, soluble poly(para-phenylene)s. Here, we report a series of elongated (para-phenylene)-type ladder oligomers that were isolated via repeated recycling size exclusion chromatography steps from an oligomer mixture. Now we are able to extrapolate the length of the “effectively conjugated segment” with much more precision to be 19 ± 2 benzene rings.

The human immunodeficiency virus (HIV) capsid is a cone-shaped capsule formed from the viral capsid protein (CA), which is arranged into a lattice of hexamers and pentamers. The capsid comprises multiple binding interfaces for the recruitment of host proteins and macromolecules used by the virus to establish infection. Here, we coassembled CA proteins engineered for pentamer cross-linking and fluorescence labeling, into spherical particles. The CA spheres, which resemble the pentamer-rich structure of the end caps of the native HIV capsid, were immobilized onto surfaces as biorecognition elements for fluorescence microscopy-based quantification of host protein binding. The capsid-binding host protein cyclophilin A (CypA) is bound to CA spheres with the same affinity as CA tubes but at a higher CypA/CA stoichiometry, suggesting that the level of recruitment of CypA to the HIV capsid is dependent on curvature.

Understanding viral assembly pathways is of critical importance to biology, medicine, and nanotechology. Here, we study the assembly path of a system with various structures, the simian vacuolating virus 40 (SV40) polymorphs. We simulate the templated assembly process of VP1 pentamers, which are the constituents of SV40, into icosahedal shells made of N = 12 pentamers (T = 1). The simulations include connections formed between pentamers by C-terminal flexible lateral units, termed here "C-terminal ligands", which are shown to control assembly behavior and shell dynamics. The model also incorporates electrostatic attractions between the N-terminal peptide strands (ligands) and the negatively charged cargo, allowing for agreement with experiments of RNA templated assembly at various pH and ionic conditions. During viral assembly, pentamers bound to any template increase its effective size due to the length and flexibility of the C-terminal ligands, which can connect to other VP1 pentamers and recruit them to a partially completed capsid. All closed shells formed other than the T = 1 feature the ability to dynamically rearrange and are thus termed "pseudo-closed". The N = 13 shell can even spontaneously "self-correct" by losing a pentamer and become a T = 1 capsid when the template size fluctuates. Bound pentamers recruiting additional pentamers to dynamically rearranging capsids allow closed shells to continue growing via the pseudo-closed growth mechanism, for which experimental evidence already exists. Overall, we show that the C-terminal ligands control the dynamic assembly paths of SV40 polymorphs.

Here we report a synthetic protocol toward a merocyanine (MC) pentamer 1 which represents the first merocyanine oligomer longer than a dimer. By continuously decreasing the solvent polarity, we demonstrate the stepwise folding from partially folded monomeric and dimeric MC subunits (in chloroform) up to the full pentamer π-stack (in 75% methylcyclohexane/25% chloroform) and a subsequent self-assembly of pentamer 1 into larger aggregates (in 80% methylcyclohexane/20% chloroform). This hierarchical structure formation process became possible due to the predominant dipole-dipole interactions among MC dyes that allowed for a precise modulation of the energy landscape by the solvent polarity. This unprecedented stepwise control of dye assembly via hierarchical dipole-dipole interactions opens the door for a more precise control of dye-dye interactions in artificial multichromophoric ensembles.

The advancement of nanoscience and technology relies on the development and utility of innovative techniques. Precise manipulation of photonic microcavities is one of the fundamental challenges in nanophotonics. This challenge impedes the construction of optoelectronic and photonic microcircuits. As a proof-of-principle, we demonstrate here that an atomic force microscopy cantilever and confocal microscopy can be used together to mechanically micromanipulate polymer-based whispering gallery mode microcavities or microresonators into well-ordered geometries. The micromanipulation technique efficiently assembles or disassembles resonators and also produces well-ordered dimer, trimer, tetramer, and pentamer assemblies of resonators in linear and bent geometries. Interestingly, an intricate L-shaped coupled-resonator optical waveguide (CROW) comprising a pentamer assembly effectively transduces light through a 90° bend angle. The presented new research direction, which combines mechanical manipulation and nanophotonics, is also expected to open up a plethora of opportunities in nano and microstructure-based research areas including nanoelectronics and nanobiology.

To inhibit hIAPP aggregation and reduce toxicity of its oligomers are one of the potential strategies for the treatment of Type 2 diabetes (T2D). It has been reported that there is an effective inhibitory effect on hIAPP aggregation by five natural flavonoids, including Genistein, Rutin, Quercetin, Epigallocatechin gallate (EGCG), and Silibinin, which are widely found in our daily food. However, the detailed mechanisms to inhibit hIAPP aggregation remain unclear. Here, we explore the mechanisms of the five flavonoids against hIAPP aggregation by molecular docking and molecular dynamics simulations. We show that these flavonoids can disaggregate Chain A and Chain B of hIAPP to reduce the extended conformation by binding with two regions of hIAPP, Leu12–Ala13–Asn14 and Asn31–Val32–Gly33–Ser34–Asn35, with the inhibitory ability of Genistein > Rutin > Quercetin > EGCG > Silibinin. These five compounds exhibit a common mechanism for disaggregation of the hIAPP pentamer; that is, they loosen the two nearest peptide chains to potentially destroy the hIAPP oligomer. Mutations of eight key residues remarkably affected by the flavonoids indicate that the secondary structures of the hIAPP pentamer change from β-sheet to be random coil, thereby to destroy its structural stability; moreover, the 28th (Ser), 12th (Leu) and 32nd (Val) amino acids exhibit significant effects on structural stability of the hIAPP pentamer, providing an important hint that these amino acids can be considered as potential targets for design of new candidate inhibitors against hIAPP oligomers. This work is beneficial to understanding of mechanism of these inhibits against hIAPP aggregation and will facilitate screening, modification, and design of new inhibitors.

Reactions of deprotonated (E)-3-(quinolin-4-yl) acrylic acid (QCA) with Cu(NO3)2 in different solvents/templates gave three supramolecular isomers: [Cu(QCA)2]2·6H2O·(CH3)2CO (1), [Cu(QCA)2]·5H2O·CH3OH (2) and [Cu(QCA)2]·DMSO (3). Single-crystal X-ray diffraction analyses revealed that 1, 2 and 3 are all 2D square grid networks, but with different metal fragments and ligand conformations, based on the remarkable effect of solvents. Interestingly, a catenarian water pentamer and a water tape composed of cyclic water pentamers were observed in the crystal lattice of 1 and 2 respectively, which played a crucial role in not only the stabilization but also the template direction of the formation of the 3D stacking crystal host. Moreover, because of the different coordination modes and intramolecular interactions, 1, 2 and 3 showed different magnetic properties.

We apply the semiclassical instanton method to calculate all feasible tunnelling pathways in the water pentamer. Similarly to the water trimer, there are labile flip dynamics as well as a number of different bifurcation pathways coupled to flips. In contrast to the trimer, the puckering motion of the oxygen ring makes the ring-polymer instanton approach difficult to converge, a problem which is resolved by using a recently developed time-independent formalism of the method. We use the results to predict the complete ground-state tunnelling splitting pattern of 320 states, which should help in the continuing effort to assign the experimental spectrum. A comparison between the rearrangement pathways in the water trimer and pentamer sheds light on the many-body cooperative effects of hydrogen bonding which are important for a full understanding of the liquid state.

The sequential rise and fall of cytosolic calcium underlies the contraction-relaxation cycle of muscle cells. While contraction is initiated by the release of calcium from the sarcoplasmic reticulum, muscle relaxation involves the active transport of calcium back into the sarcoplasmic reticulum. This re-uptake of calcium is catalysed by the sarco-endoplasmic reticulum Ca2+-ATPase (SERCA), which plays a lead role in muscle contractility. The activity of SERCA is regulated by small membrane protein subunits, most well-known being phospholamban (PLN) and sarcolipin (SLN). SLN physically interacts with SERCA and differentially regulates contractility in skeletal and atrial muscle. SLN has also been implicated in skeletal muscle thermogenesis. Despite these important roles, the structural mechanisms by which SLN modulates SERCA-dependent contractility and thermogenesis remain unclear. Here, we functionally characterized wild-type SLN and a pair of mutants, Asn4-Ala and Thr5-Ala, which yielded gain-of-function behavior comparable to what has been found for PLN. Next, we analyzed twodimensional crystals of SERCA in the presence of wild-type SLN by electron cryo-microscopy. The fundamental units of the crystals are anti-parallel dimer ribbons of SERCA, known for decades as an assembly of calcium-free SERCA molecules induced by the addition of decavanadate. A projection map of the SERCA-SLN complex was determined to a resolution of 8.5 Å, which allowed the direct visualization of a SLN pentamer. The SLN pentamer was found to interact with transmembrane segment M3 of SERCA, though the interaction appeared to be indirect and mediated by an additional density consistent with a SLN monomer. This SERCA-SLN complex correlated with the ability of SLN to decrease the maximal activity of SERCA, which is distinct from the ability of PLN to increase the maximal activity of SLN. Protein-protein docking and molecular dynamics simulations provided models for the SLN pentamer and the novel interaction between SERCA and a SLN monomer.STATEMENT OF SIGNIFICANCEThis research article describes a novel complex of the sarcoplasmic reticulum calcium pump SERCA and its regulatory subunit sarcolipin. Given the potential role of sarcolipin in skeletal muscle non-shivering thermogenesis, the interactions between SERCA and sarcolipin are of critical importance. Using complementary approaches of functional analysis, electron crystallography, and molecular dynamics simulations, we demonstrate an inherent interaction between SERCA, a sarcolipin monomer, and a sarcolipin pentamer. The interaction involves transmembrane segment M3 of SERCA, which allows sarcolipin to decrease the maximal activity or turnover rate of SERCA. Protein-protein docking and molecular dynamics simulations provided models for the SLN pentamer and the novel interaction between SERCA and a SLN monomer.

Rationale Clerodendranthi Spicati Herba (CSH) is often used to treat urinary stones, urinary tract infections and nephritis in China. Much literature has reported that polymeric phenolic acids and flavonoids are the major bioactive components in CSH. Therefore, it is very meaningful to identify the polymeric phenolic acids and flavonoids in CSH. Methods Ultrahigh-performance liquid chromatography coupled to quadrupole time-of-flight tandem mass spectrometry (UHPLC/QTOF-MS/MS) analysis with target and nontarget data mining strategy was proposed to rapidly profile the polymeric phenolic acids and flavonoids in CSH. Diagnostic product ions and neutral loss filter were beneficial for identifying the polymeric phenolic acids and flavonoids from complex compounds in CSH. Results A total of 118 compounds, including 85 polymeric phenolic acids and 33 flavonoids, were reasonably identified in CSH by comparing their main fragmentation pathways with literature data, and 85 of them were discovered in CSH firstly by nontarget analysis. Nine potential compounds were characterized tentatively as new pentameric and hexameric phenolic acids in CSH. Six types of polymeric phenolic acids (monomer, dimer, trimer, tetramer, pentamer and hexamer) and four types of flavonoids (apigenin, kaempferol, luteolin and quercetin) were identified in CSH. Conclusions The results indicated that the UHPLC/QTOF-MS/MS method coupled with target and nontarget data mining strategy was feasible and rational for identifying the polymeric phenolic acids and flavonoids in complex chemical constituents of CSH. The findings will be conducive to the discovery of the active ingredients of CSH and the establishment of quality standards.

Bdellovibrio bacteriovorus is a predator bacterial species of the Deltaproteobacteria class that requires flagellum-mediated motility to initiate the parasitization of other gram-negative bacteria. The flagellum is capped by FliD, which polymerizes flagellin into a flagellar filament. FliD has been reported to function as a species-specific oligomer, such as a tetramer, a pentamer, or a hexamer, in members of the Gammaproteobacteria class. However, the oligomeric state and structural features of FliD from bacterial species outside the Gammaproteobacteria class are unknown. Based on structural and biochemical analyses, we report here that B. bacteriovorus FliD (bbFliD) forms a tetramer. bbFliD tetramerizes in a circular head-to-tail arrangement by inserting the D2 domain of one subunit into the concave surface of the second subunit generated between the D2 and D3 domains as observed in Serratia marcescens FliD. However, bbFliD adopts a more compact and flat oligomeric structure, which exhibits a more extended tetramerization interface flanked by two additional surfaces due to different intersubunit and interdomain organizations as well as an elongated loop. In conclusion, FliD from B. bacteriovorus, which belongs to the Deltaproteobacteria class, also produces a tetramer similar to FliD from Gammaproteobacterial species but adopts a unique species-specific oligomeric structure.

The analysis of data on genomic DNA sequences in the binding sites of human ribosomal protein uS3 in vivo, obtained earlier by ChIP-Seq method, was carried out; the presence of significant content of TGGAA repeats, belonging to the type III of human satellites, was found. The dependence of the affinity of the corresponding recombinant protein uS3 to single-stranded DNA and its AP lyase activity on the DNA sequence in vitro, in particular on the presence of TGGAA pentamer repeats, was investigated. It was shown that the presence of these repeats in the model DNAs did not provide an increased affinity to the isolated ribosomal protein uS3. The presence of TCC and TTC motifs in DNA complementary to the corresponding pentamer triplets only slightly increased the affinity of DNA to this protein. It was established that the AP lyase activity of the uS3 protein was also not increased when DNA containing abasic (AP) site contained TGGAA repeats and was independent on the position of the AP site in it. It was shown that the efficiency of single-stranded DNA cleavage at the AP site as a whole correlated with the affinity of uS3 protein to this DNA. It was concluded that the high content of the above repeats in the ribosomal protein uS3 binding sites on chromatin relate to high content of (TGGAA)n repeats in single-stranded DNA regions physically accessible for the protein binding but not to its higher affinity to the pentamer or DNA motifs complementary to it.

Foot-and-mouth disease virus (FMDV) exhibits broad antigenic diversity with poor intraserotype cross-neutralizing activity. Studies of the determinant involved in this diversity are essential for the development of broadly protective vaccines. In this work, we isolated a bovine antibody, designated R55, that displays cross-reaction with both FMDV A/AF/72 (hereafter named FMDV-AAF) and FMDV A/WH/09 (hereafter named FMDV-AWH) but only has a neutralizing effect on FMDV-AWH. Near-atomic resolution structures of FMDV-AAF-R55 and FMDV-AWH-R55 show that R55 engages the capsids of both FMDV-AAF and FMDV-AWH near the icosahedral 3-fold axis and binds to the βB and BC/HI-loops of VP2 and to the B-B knob of VP3. The common interaction residues are highly conserved, which is the major determinant for cross-reaction with both FMDV-AAF and FMDV-AWH. In addition, the cryo-EM structure of the FMDV-AWH-R55 complex also shows that R55 binds to (VP3)E70 located at the VP3 BC-loop in an adjacent pentamer, which enhances the acid and thermal stabilities of the viral capsid. This may prevent capsid dissociation and genome release into host cells, eventually leading to neutralization of the viral infection. In contrast, R55 binds only to the FMDV-AAF capsid within one pentamer due to the (VP3)E70G variation, which neither enhances capsid stability nor neutralizes FMDV-AAF infection. The (VP3)E70G mutation is the major determinant involved in the neutralizing differences between FMDV-AWH and FMDV-AAF. The crucial amino acid (VP3)E70 is a key component of the neutralizing epitopes, which may aid in the development of broadly protective vaccines. IMPORTANCE Foot-and-mouth disease virus (FMDV) causes a highly contagious and economically devastating disease in cloven-hoofed animals, and neutralizing antibodies play critical roles in the defense against viral infections. Here, we isolated a bovine antibody (R55) using the single B cell antibody isolation technique. Enzyme-linked immunosorbent assays (ELISA) and virus neutralization tests (VNT) showed that R55 displays cross-reactions with both FMDV-AWH and FMDV-AAF but only has a neutralizing effect on FMDV-AWH. Cryo-EM structures, fluorescence-based thermal stability assays and acid stability assays showed that R55 engages the capsid of FMDV-AWH near the icosahedral 3-fold axis and informs an interpentamer epitope, which overstabilizes virions to hinder capsid dissociation to release the genome, eventually leading to neutralization of viral infection. The crucial amino acid (VP3)E70 forms a key component of neutralizing epitopes, and the determination of the (VP3)E70G mutation involved in the neutralizing differences between FMDV-AWH and FMDV-AAF could aid in the development of broadly protective vaccines.

Phenalenyl (PLY) and its derivatives could form one-dimensional π-aggregates through pancake π–π bonding, which would lead to exotic optoelectronic properties. We will highlight the key aspects of the PLY derivatives from the design strategies to exploration of the electronic properties. Here, we primarily construct alternating boron (B)- and nitrogen (N)-doped PLY π-aggregates: dimer[12], trimer[12-1], trimer[12-2], tetramer[12]2, pentamer[12]2-1, pentamer[12]2-2, and hexamer[12]3. The geometric and electronic structures show that the short intermolecular distances of the π-aggregates drive the formation of pancake π–π bonding. Significantly, the molecular structures show periodic changes in the π-aggregates, but the first hyperpolarizabilities (βtot) present unexpected changes, which are found to increase sharply with increasing even layer thickness due to intermolecular charge transfer. The βtot value of hexamer[12]3 (5.72 × 104 a.u.) is 6.4 times that of tetramer[12]2 (8.95 × 103 a.u.), and is 22.4 times that of dimer[12] (2.55 × 103 a.u.). Thus, constructing π-aggregates can significantly improve the second-order NLO response, which is mainly due to intermolecular charge transfer through pancake π–π bonding of the interlayers.

Cyclic-di-guanosine monophosphate (c-di-GMP) is an important effector associated with acute-chronic infection transition in Pseudomonas aeruginosa. Previously, we reported a signaling network SiaABCD, which regulates biofilm formation by modulating c-di-GMP level. However, the mechanism for SiaD activation by SiaC remains elusive. Here we determine the crystal structure of SiaC-SiaD-GpCpp complex and revealed a unique mirror symmetric conformation: two SiaD form a dimer with long stalk domains, while four SiaC bind to the conserved motifs on the stalks of SiaD and stabilize the conformation for further enzymatic catalysis. Furthermore, SiaD alone exhibits an inactive pentamer conformation in solution, demonstrating that SiaC activates SiaD through a dynamic mechanism of promoting the formation of active SiaD dimers. Mutagenesis assay confirmed that the stalks of SiaD are necessary for its activation. Together, we reveal a novel mechanism for DGC activation, which clarifies the regulatory networks of c-di-GMP signaling.

The prevailing opinion is that prefibrillar beta-amyloid (A beta) species, rather than end-stage amyloid fibrils, cause neuronal dysfunction in Alzheimers disease, although the mechanisms behind A beta neurotoxicity remain to be elucidated. Luminescent conjugated oligothiophenes (LCOs) exhibit spectral properties upon binding to amyloid proteins and have previously been reported to change the toxicity of A beta(1- 42) and prion protein. In a previous study, we showed that an LCO, pentamer formyl thiophene acetic acid (p-FTAA), changed the toxicity of A beta(1-42). Here we investigated whether an LCO, heptamer formyl thiophene acetic acid (h-FTAA), could change the toxicity of A beta(1-42) by comparing its behavior with that of p-FTAA. Moreover, we investigated the effects on toxicity when A ss with the Arctic mutation (A beta Arc) was aggregated with both LCOs. Cell viability assays on SH-SY5Y neuroblastoma cells demonstrated that h-FTAA has a stronger impact on A beta(1-42) toxicity than does p-FTAA. Interestingly, h-FTAA, but not p-FTAA, rescued the A beta(Arc)-mediated toxicity. Aggregation kinetics and binding assay experiments with A beta(1-42) and A beta(Arc) when aggregated with both LCOs showed that h-FTAA and p-FTAA either interact with different species or affect the aggregation in different ways. In conclusion, h-FTAA protects against A beta(1-42) and A beta(Arc) toxicity, thus showing h-FTAA to be a useful tool for improving our understanding of the process of A beta aggregation linked to cytotoxicity. Funding Agencies|Torsten Soderberg Foundation; Apotekare Hedbergs Foundation; Stohnes stiftelse

1,4-bis[2-(5-thiophen-2-yl)-1-benzothiophene]-2,5-dioctyloxybenzene (BOBzBT 2 ) is a functionalized organic pentamer that was used to modify the carbon working electrode surface to be used as a biosensor for creatinine detection. BOBzBT 2 has good solubility characteristics in common organic solvents. Although it is insoluble in water, BOBzBT 2 is able to be stored in a relatively stable condition. In addition, the hydrophobic property of BOBzBT 2 enables it to be reusable. This is especially useful for the non-destructive sensing application besides ensuring stability even in environments with high humidity. The BOBzBT 2 modified sensor was compared to the unmodified sensor to see the improvements in charge transfer. A repeatability test was performed on the modified sensor to determine whether the modified sensor can be used repetitively or only for single use. A reproducibility test was also performed on the modified sensor to determine whether the modified sensor can be used to reproduce consistent data. The BOBzBT 2 modified sensor was compared to the unmodified sensor to see the improvements in charge transfer.

A series of merocyanine (MC) oligomers with a varying number of chromophores from two to six has been synthesized via a peptide synthesis strategy. Solvent-dependent UV/vis spectroscopic studies reveal folding processes for the MC oligomers driven by strong dipole–dipole interactions resulting in well-defined π-stacks with antiparallel orientation of the dyes. Whilst even-numbered tetramer 4 and hexamer 6 only show partial folding into dimeric units, odd-numbered trimer 3 and pentamer 5 fold into π-stacks of three and five MC units upon decreasing solvent polarity. In-depth 2D NMR studies provided insight into the supramolecular structure. For trimer 3, an NMR structure could be generated revealing the presence of a well-defined triple π-stack in the folded state. Concomitant with folding, the fluorescence quantum yield is increased for all MC oligomers in comparison to the single chromophore. Based on radiative and non-radiative decay rates, this fluorescence enhancement can be attributed to the rigidification of the chromophores within the π-stacks that affords a pronounced decrease of the non-radiative decay rates. Theoretical investigations for the double and triple dye stacks based on time-dependent density functional theory (TD-DFT) calculations indicate for trimer 3 a pronounced mixing of Frenkel and charge transfer (CT) states. This leads to significant deviations from the predictions obtained by the molecular exciton theory which only accounts for the Coulomb interaction between the transition dipole moments of the chromophores., A series of merocyanine (MC) oligomers with a varying number of chromophores from two to six has been synthesized via a peptide synthesis strategy.

Bacterial flagella are the best-known rotational organelles in the biological world. The spiral-shaped flagellar filaments that extending from the cell surface rotate like a screw to create a propulsive force. At the base of the flagellar filament lies a protein motor that consists of a stator and a rotor embedded in the membrane. The stator is composed of two types of membrane subunits, PomA(MotA) and PomB(MotB), which are energy converters that assemble around the rotor to couple rotation with the ion flow. Recently, stator structures, where two MotB molecules are inserted into the center of a ring made of five MotA molecules, were reported. This structure inspired a model in which the MotA ring rotates around the MotB dimer in response to ion influx. Here, we focus on the Vibrio PomB plug region, which is involved in flagellar motor activation. We investigated the plug region using site-directed photo-crosslinking and disulfide crosslinking experiments. Our results demonstrated that the plug interacts with the extracellular short loop region of PomA, which is located between transmembrane helices 3 and 4. Although the motor stopped rotating after crosslinking, its function recovered after treatment with a reducing reagent that disrupted the disulfide bond. Our results support the hypothesis, which has been inferred from the stator structure, that the plug region terminates the ion influx by blocking the rotation of the rotor as a spanner. Importance The biological flagellar motor resembles a mechanical motor. It is composed of a stator and a rotor. The force is transmitted to the rotor by the gear-like stator movements. It has been proposed that the pentamer of MotA subunits revolves around the axis of the B subunit dimer in response to ion flow. The plug region of the B subunit regulates the ion flow. Here, we demonstrated that the ion flow was terminated by crosslinking the plug region of PomB with PomA. These findings support the rotation hypothesis and explain the role of the plug region in blocking the rotation of the stator unit.

α-Synuclein (α-syn) aggregates into cytotoxic amyloid fibrils, which are recognized as the defining neuropathological feature of Parkinson's disease (PD). Therefore, inhibiting α-syn fibrillogenesis and disrupting the preformed fibrils are both considered attractive strategies to cure PD. We discovered that a safe food additive, fast green FCF, is capable of inhibiting α-synuclein fibrillogenesis and reducing the related cytotoxicity. Thioflavin T fluorescence assays demonstrated that fast green FCF could inhibit the fibrillogenesis α-synuclein. In the presence of 100 μM fast green FCF, amorphous aggregates were formed and observed by atomic force microscopy. Toxicity assays in cell cultures revealed that fast green FCF significantly reduced the cytotoxicity of α-syn. Molecular dynamics simulations revealed the potential mechanism of the interactions between fast green FCF and α-synuclein. Fast green FCF greatly disrupted the α-synuclein pentamer and reduced the β-sheet content by reducing both nonpolar and polar interactions. Furthermore, two binding sites were identified, named region I (Y39-K45) and region II (H50-Q62). Our data reveal that electrostatic interactions, hydrogen bonds, and π–π interactions synergistically contribute to the binding of fast green FCF to the α-synuclein pentamer. These results indicate that fast green FCF is a candidate prototype for the development of drugs against the aggregation of amyloid fibrils in PD.

We report on an accelerated molecular dynamics investigation of surface transport mechanisms on W surfaces. These mechanisms likely influence the formation of nano-fuzz in fusion plasma-facing conditions. The simulations use an embedded-atom potential to investigate the diffusion mechanisms of W clusters (Wn, n = 2–9) on W(1 1 0) and W(1 0 0) surfaces at 1000 K, reaching timescales beyond 10 microseconds. A number of fast moving adatom species, Wn (n = 2–6), were observed. In contrast, slightly larger clusters Wn (n = 7–9), especially W8, exhibit significantly lower diffusivities. The diffusion mechanisms of Wn clusters on the W(1 1 0) surface are complex, with the most common elementary steps involving hops of monomers and dimers. Moreover, we observe tetramer hopping in the diffusion processes of Wn (n = 4–7), trimer hopping in Wn (n = 5, 6, 8), and pentamer hopping in W5 on the W(1 1 0) surface. Wn (n ≤ 3) and metastable Wn (n > 3) clusters on the W(1 0 0) surface diffuse predominantly through monomer exchange with surface atoms. However, W clusters containing square tetramers are essentially immobile on the W(1 0 0) surface at 1000 K.

Metal selective adsorbent (MCPP-SA-MCC) was synthesized by the reaction of macrocyclic pyridone pentamer (MCPP) with succinic acid anhydride modified microcrystalline cellulose (SA-MCC). Selectivity of the tailor-made adsorbent to metal cations was studied by measuring its competitive adsorption ability to nine metal cations (Ba2+, Pb2+, Cd2+, Mn2+, Cu2+, Co2+, Ni2+, and Cr3+). It was found that MCPP-SA-MCC exhibited a patterned recognition of metal cations remarkably correlated with the metal cation radius. In the simulated wastewater effluent containing nine metal cations, MCPP-SA-MCC dominantly adsorbed Ba2+, which has a larger ion radius than others, and 75% of Ba2+ was removed while others less than 18%. These features indicated the promise of MCPP-SA-MCC as a candidate to remove heavy metal cations from aqueous solution selectively.

Synthesis of functionalized pentamer metallonanobelts was accomplished by using a series of triptycene ligands, which were synthesized by quinoxaline formation from 2,3,6,7,14,15-hexaaminotriptycene (1) as a common precursor. It was also found that two kinds of template-bound metal complexes were selectively formed by changing the ratio of Pd2+/ligand.

Ragulator is a pentamer composed of p18, MP1, p14, C7orf59, and hepatitis B virus X‐interacting protein (HBXIP; LAMTOR 1—5) which acts as a lysosomal scaffold of the Rag GTPases in the amino acid sensitive branch of TORC1 signaling. Here, we present the crystal structure of human HBXIP‐C7orf59 dimer (LAMTOR 4/5) at 2.9 Å and identify a phosphorylation site on C7orf59 which modulates its interaction with p18. Additionally, we demonstrate the requirement of HBXIP‐C7orf59 to stabilize p18 and allow further binding of MP1‐p14. The structure of the dimer revealed an unfolded N terminus in C7orf59 (residues 1–15) which was shown to be essential for p18 binding. Full‐length p18 does not interact stably with MP1‐p14 in the absence of HBXIP‐C7orf59, but deletion of p18 residues 108–161 rescues MP1‐p14 binding. C7orf59 was phosphorylated by protein kinase A (PKA) in vitro and mutation of the conserved Ser67 residue to aspartate prevented phosphorylation and negatively affected the C7orf59 interaction with p18 both in cell culture and in vitro. C7orf59 Ser67 was phosphorylated in human embryonic kidney 293T cells. PKA activation with forskolin induced dissociation of p18 from C7orf59, which was prevented by the PKA inhibitor H‐89. Our results highlight the essential role of HBXIP‐C7orf59 dimer as a nucleator of pentameric Ragulator and support a sequential model of Ragulator assembly in which HBXIP‐C7orf59 binds and stabilizes p18 which allows subsequent binding of MP1‐p14.

C-reactive protein (CRP) is a non-specific diagnostic marker of inflammation and an evolutionarily conserved protein with roles in innate immune signaling. Natural CRP is composed of five identical globular subunits that form a pentamer, but the role of pentameric CRP (pCRP) during inflammatory pathogenesis remains controversial. Emerging evidence suggests that pCRP can be dissociated into monomeric CRP (mCRP) that has major roles in host defenses and inflammation. Here, we discuss our current knowledge of the dissociation mechanisms of pCRP and summarize the stepwise conformational transition model to mCRP to elucidate how CRP dissociation contributes to proinflammatory activity. These discussions will evoke new understanding of this ancient protein.

Photochemical damage of DNA is initiated by absorption of ultraviolet light, and the photoproducts are formed as a result of excited-state structural and electronic dynamics. We have used UV resonance Raman spectroscopy to measure the initial excited-state structural dynamics of homopentamers of adenosine monophosphate (3'-dApdApdApdApdAp-5') and thymidine monophosphate (3'-dTpdTpdTpdTpdTp-5') and compare them to those of the monomeric nucleobases. The resonance Raman spectra of the homopentamers are similar to those of the corresponding monomers. Initial excited-state slopes, homogeneous and inhomogeneous broadening, and other excited-state parameters were extracted by self-consistent simulation of the resonance Raman excitation profiles and absorption spectra with a time-dependent formalism and are also similar to the initial excited-state slopes and broadening in the nucleotide monomers. The lack of differences between the initial excited-state structural dynamics of the nucleotides within the pentamer and the isolated nucleobases is consistent with a model in which the formation of photochemical products in oligonucleotides and DNA is dependent on the formation of the transition-state structure within these polymers, dictated by their large-scale dynamics. These results are discussed in light of the known photochemistry of DNA and the nucleobases.

Summary Molecular Kekule diradicals have been demonstrated to show unique optoelectronic properties as a function of their diradical character. A series of thienoquinoidal oligothiophenes from dimer to pentamer and substituted with an odd and even number of pyrrolo-dione groups have been prepared and proven to be n-dopable materials showing outstanding ambient stability and excellent electrical and thermoelectric behavior. Going from dimer to pentamer, a progressive change in the diradical character and aggregation mode is observed, with the tetramer showing an optimal diradical character that allows favorable intermolecular contacts with π−π multi-bonding features, while the presence of the two dione groups promotes a cholesteric-like π−π stacking. Both features synergistically contribute to form a material with exceptional ambient stability for an n-doped system exhibiting high electrical conductivities and thermoelectric performance.

Uranyl-peroxide capsules are the newest family of polyoxometalates. Although discovered 13 years previously with over 70 topologies reported, there is a lack in the fundamental understanding of assembly mechanisms, particularly the role of the alkali counterions. Herein, the reaction pathway and assembly of uranyl peroxide capsules is reported by tracking the conversion from K+ uranyl triperoxide monomer to the K+ uranyl-peroxide U28 capsule by means of small-angle X-ray scattering and Raman spectroscopy. For the first time, the K+ uranyl-peroxide pentamer face is isolated and structurally characterized, giving credence to the long-held belief that these geometric faces serve as building blocks to the fully formed capsules. Once isolated and re-dissolved, the pentamer face undergoes rapid conversion to capsule forms, underlining its high reactivity that challenges its isolation. Calorimetric measurements of the studied species confirms the pentamer lies on the energy landscape between the monomer and capsule.