Antiparallel Orientation Research Articles

Multiscale Molecular Dynamics Simulations of the Homodimer Accessory Protein ORF7b of SARS-CoV-2.

The SARS-CoV-2 ORF7b protein has drawn attention for its potential role in viral pathogenesis, but its structural details and lateral membrane associations remain elusive. In this study, we conducted multiscale molecular dynamics simulations to provide detailed molecular insights of the protein's dimerization, which is crucial for unraveling its structural model of protein-protein interface important to regulating cellular immune response. To gain a deeper understanding of homodimer configurations, we employed a machine learning algorithm for structural-based clustering. Clusters were categorized into three distinct groups for both parallel and antiparallel orientations, highlighting the influence of the initial monomer conformation on dimer configurations. Analysis of hydrogen bonding and π-π and π-cation stacking interactions within clusters revealed variations in interactions between clusters. In parallel dimers, weak stacking interactions in the transmembrane (TM) region were observed. In contrast, antiparallel dimers exhibited strong hydrogen bonding and stacking interactions contributing to tight dimeric packing, both within and outside the TM domain. Overall, our study provides a comprehensive view of the structural dynamics of ORF7b homodimerization in both parallel and antiparallel orientations. These findings shed light on the molecular interactions involved in ORF7b dimerization, which are crucial for understanding its potential roles in SARS-CoV-2 pathogenesis. This knowledge could inform future research and therapeutic strategies targeting this viral protein.

Unveiling the structural organisation of carvacrol through X-ray scattering and molecular Dynamics: A comparative study with liquid thymol

An integrated approach involving Small and Wide Angle X-ray scattering and computational tools, Molecular Dynamics (MD) and Density Functional Theory (DFT) calculations, was employed to describe the microscopic structural arrangement in carvacrol (2-methyl-5-(1-methylethyl)phenol) at 300 K and 353 K. Carvacrol is a phenol derivative, with an aromatic nature and amphiphilic features and is liquid at room temperature. Its structural organization in the liquid state was compared with the one found for its structural isomer, thymol (5-methyl-2-(1-methylethyl)phenol), at 353 K (in its liquid state), through MD simulations: significant differences between the two compounds have emerged. For carvacrol, at both 300 K and 353 K, there is an inclination for the aromatic rings to orient perpendicularly, maintaining a first neighbour separation of around 6 Å. Conversely, liquid thymol at 353 K exhibits a more heterogeneous structural organisation and is characterised by both parallel and antiparallel orientations of neighbour rings already at shorter distances of approximately 4.5 Å. On a local scale, liquid thymol tends to establish hydrogen bonds (HBs) between its hydroxyl groups, reminiscent of its solid crystalline form. Conversely, carvacrol exhibits a stronger inclination towards O-H···π hydrogen bonding interactions. On a mesoscopic scale, both carvacrol and thymol are characterised by an X-ray scattering low Q peak, which fingerprints the existence of nm-scale structural heterogeneities due to the segregation of HB-interacting polar moieties, embedded within the apolar matrix. Notably, the low Q peak is more pronounced in liquid thymol where the preferential HBs between hydroxyl groups have been observed. Overall, the different structural arrangements of liquid carvacrol and thymol have the potential to influence various bulk and macroscopic properties, including melting points and solvation capabilities. Given these differences, one might envisage the use of carvacrol as a replacement to thymol, in order to fine-tune specific chemical physical properties of applicative interest, including deep eutectic solvents formulation.

Ultrahigh spin filter efficiency and large spin Seebeck polarization of binuclear manganese phthalocyanine molecular junctions on nickel electrodes

In this paper, we investigated the spin transport properties of binuclear manganese phthalocyanine (Mn2Pc2) spintronic devices sandwiched between two nickel electrodes using the non-equilibrium Green's function method in combination with density functional theory. Based on the calculation results, the Mn2Pc2 device exhibited excellent spin-filtering capabilities, demonstrating an exceptionally high spin filter efficiency (SFE). Irrespective of the parallel or antiparallel orientation of magnetization in the electrodes, we observed that when both manganese atoms were in a spin-up state, the SFE of spin-resolved currents under finite bias and the thermoelectric currents induced by temperature gradients at fixed temperatures were both close to 100%. The large spin Seebeck polarization of the Mn2Pc2 device was also obtained at low reference temperatures. This study explores the potential for developing multifunctional spintronic single-molecule devices using Ni−Mn2Pc2.

Light rare earth elements stabilize G-quadruplex structure in variants of human telomeric sequences

Recently, light rare earth elements (LREEs) are gaining importance in modern-day technologies. Thus, the entry of LREEs into biochemical pathways cannot be ignored, which might affect the conformation of biomacromolecules. Herein, for the first time, we discover the G-quadruplex formation in the human telomeric variants in presence of micromolar concentrations of LREEs. Thermal melting show that the LREE-induced unimolecular G-quadruplex structure. Isothermal titration calorimetry, UV–vis, and CD spectroscopy results suggest the binding stoichiometry of lanthanide ions to telomeric variants is 2:1. The data confirms that the LREE ions coordinate between adjacent G-quartets. The excess LREE ions are most likely binding to quadruplex loops. The CD spectra revealed that the LREE-induced quadruplex in human telomere and its variant have antiparallel orientation. The binding equilibria of LREEs have been studied both in the presence and absence of competing metal cations. Addition of LREEs to the Na+ or K+-induced G-quadruplexes led to conformational change, which may be ascribed to the displacement of K+ or Na+ ions by LREE ions and formation of a more compact LREE-induced G-quadruplex structure in human telomeric variant. Moreover, the thymine in the central loop of the human telomeric sequence stabilizes LREE induced G-quadruplex.

Study of the Structural Chemistry of the Inclusion Complexation of 4-Phenylbutyrate and Related Compounds with Cyclodextrins in Solution: Differences in Inclusion Mode with Cavity Size Dependency.

4-phenylbutyrate (PB) and structurally related compounds hold promise for treating many diseases, including cancers. However, pharmaceutical limitations, such as an unpleasant taste or poor aqueous solubility, impede their evaluation and clinical use. This study explores cyclodextrin (CD) complexation as a strategy to address these limitations. The structural chemistry of the CD complexes of these compounds was analyzed using phase solubility, nuclear magnetic resonance (NMR) spectroscopic techniques, and molecular modeling to inform the choice of CD for such application. The study revealed that PB and its shorter-chain derivative form 1:1 αCD complexes, while the longer-chain derivatives form 1:2 (guest:host) complexes. αCD includes the alkyl chain of the shorter-chain compounds, depositing the phenyl ring around its secondary rim, whereas two αCD molecules sandwich the phenyl ring in a secondary-to-secondary rim orientation for the longer-chain derivatives. βCD includes each compound to form 1:1 complexes, with their alkyl chains bent to varying degrees within the CD cavity. γCD includes two molecules of each compound to form 2:1 complexes, with both parallel and antiparallel orientations plausible. The study found that αCD is more suitable for overcoming the pharmaceutical drawbacks of PB and its shorter-chain derivative, while βCD is better for the longer-chain derivatives.

Chemically Fueled Communication Along a Scaffolded Nanoscale Array of Squaramides.

Relaying conformational change over several nanometers is central to the function of allosterically regulated proteins. Replicating this mechanism artificially would provide important communication tools, but requires nanometer-sized molecules that reversibly switch between defined shapes in response to signaling molecules. In this work, 1.8 nm long rigid rod oligo(phenylene-ethynylene)s are scaffolds for switchable multi-squaramide hydrogen-bond relays. Each relay can adopt either a parallel or an antiparallel orientation relative to the scaffold; the preferred orientation is dictated by a director group at one end. An amine director responded to proton signals, with acid-base cycles producing multiple reversible changes in relay orientation that were reported by a terminal NH, which is 1.8 nm distant. Moreover, a chemical fuel acted as a dissipative signal. As the fuel was consumed, the relay reverted to its original orientation, illustrating how information from out-of-equilibrium molecular signals can be communicated to a distant site.

Chemically Fueled Communication Along a Scaffolded Nanoscale Array of Squaramides

AbstractRelaying conformational change over several nanometers is central to the function of allosterically regulated proteins. Replicating this mechanism artificially would provide important communication tools, but requires nanometer‐sized molecules that reversibly switch between defined shapes in response to signaling molecules. In this work, 1.8 nm long rigid rod oligo(phenylene‐ethynylene)s are scaffolds for switchable multi‐squaramide hydrogen‐bond relays. Each relay can adopt either a parallel or an antiparallel orientation relative to the scaffold; the preferred orientation is dictated by a director group at one end. An amine director responded to proton signals, with acid‐base cycles producing multiple reversible changes in relay orientation that were reported by a terminal NH, which is 1.8 nm distant. Moreover, a chemical fuel acted as a dissipative signal. As the fuel was consumed, the relay reverted to its original orientation, illustrating how information from out‐of‐equilibrium molecular signals can be communicated to a distant site.

Tetrachromophoric Derivatives of Dibenzoylmethanatoboron Difluoride Based on Stereoregular Cyclotetrasiloxanes: Synthesis and Properties.

A series of new tetrachromophoric systems based on stereoregular tetracyclosiloxanes and dibenzoylmethanatoboron difluoride derivatives have been synthesized and characterized by a complex of physicochemical methods. The photophysical properties of the synthesized compounds are studied by electronic absorption, steady-state, and time-resolved fluorescence spectroscopy. In the synthesized compounds, four dibenzoylmethanatoboron difluoride (DBMBF2)-based fluorophores are in an all-cis arrangement with respect to a cyclotetrasiloxane scaffold. DFT calculations predict that they can form H-type dimers, trimers, or tetramers with an antiparallel orientation of their ground-state dipole moments. Under UV excitation, solutions of these compounds in polar and nonpolar solvents exhibit complex fluorescence consisting of monomer- and excimer-like emissions with different lifetimes. Global fitting analysis reveals the presence of at least four kinetically distinguishable species in the excited state. The studied compounds in solutions have CIE chromaticity coordinates very close to the white color point and are promising objects for the development of next-generation single-emission materials for white illumination.

Structure Guiding Supramolecular Assemblies in Metal-Organic Multi-Component Compounds of Mn(II): Experimental and Theoretical Studies

Two multi-component coordination compounds of Mn(II), viz. [Mn(H2O)6](2-Mepy)2(4-NO2bz)2·2H2O (1) and [Mn(H2O)6][Mn(2,3-PDCH)3]2 (2) (where, 2-Mepy = 2-methylpyridine, 4-NO2bz = 4-nitrobenzoate, 2,3-PDC = 2,3-pyridinedicarboxylate), have been synthesized and characterized using elemental, spectroscopic (FT-IR and electronic), TGA and single-crystal X-ray diffraction analyses. Complex 1 is a co-crystal hydrate of Mn(II) involving uncoordinated 2-Mepy, 4-NO2bz and water molecules; while compound 2 is a multi-component molecular complex salt of Mn(II) comprising cationic [Mn(H2O)6]2+ and anionic [Mn(2,3-PDCH)3]−complex moieties. The uncoordinated 2-Mepy and 4-NO2bz moieties of 1 are involved in lone-pair (l.p)-π and C–H⋯π interactions which stabilize the layered assembly of the compound. The crystal structure of compound 2 has been previously reported. However, we have explored the unusual enclathration of complex cationic moieties within the supramolecular host cavities formed by the molecular assembly of complex anionic moieties. The supramolecular assemblies obtained in the crystal structure have been further studied theoretically using DFT calculations, quantum theory of atoms-in-molecules (QTAIM) and non-covalent interaction plot (NCI plot) computational tools. Theoretical studies reveal that the combination of π-staking interactions (l.p-π, π-π and C–H···π) have more structure-guiding roles compared to the H-bonds. The large binding energy of π-stacking interactions in 2 is due to the antiparallel orientation of aromatic rings and their coordination to the metal centers, thereby increasing the contribution of the dipole–dipole interactions.

Probing the Protein Folding Energy Landscape: Dissociation of Amyloid-β Fibrils by Laser-Induced Plasmonic Heating.

Insoluble amyloid fibrils made from proteins and peptides are difficult to be degraded in both living and artificial systems. The importance of studying their physical stability lies primarily with their association with human neurodegenerative diseases, but also owing to their potential role in multiple bio-nanomaterial applications. Here, gold nanorods (AuNRs) were utilized to investigate the plasmonic heating properties and dissociation of amyloid-β fibrils formed by different peptide fragments (Aβ16-22/Aβ25-35/Aβ1-42) related to the Alzheimer's disease. It is demonstrated that AuNRs were able to break mature amyloid-β fibrils from both the full length (Aβ1-42) and peptide fragments (Aβ16-22/Aβ25-35) within minutes by triggering ultrahigh localized surface plasmon resonance (LSPR) heating. The LSPR energy absorbed by the amyloids to unfold and move to higher levels in the protein folding energy landscape can be measured directly and in situ by luminescence thermometry using lanthanide-based upconverting nanoparticles. We also show that Aβ16-22 fibrils, with the largest persistence length, displayed the highest resistance to breakage, resulting in a transition from rigid fibrils to short flexible fibrils. These findings are consistent with molecular dynamics simulations indicating that Aβ16-22 fibrils possess the highest thermostability due to their highly ordered hydrogen bond networks and antiparallel β-sheet orientation, hence affected by an LSPR-induced remodeling rather than melting. The present results introduce original strategies for disassembling amyloid fibrils noninvasively in liquid environment; they also introduce a methodology to probe the positioning of amyloids on the protein folding and aggregation energy landscape via nanoparticle-enabled plasmonic and upconversion nanothermometry.

Electronic properties of the Mn<sub>3</sub>Z (Z = Ga, Ge) alloys: first-principles studies

The structural and electronic properties of Mn3Z alloys (Z = Ga, Ge) are studied ab initio. It is shown that in the cubic and tetragonal phases, the configuration with antiparallel orientation of magnetic moments of Mn atoms on different sublattices is energetically favorable. Calculations of the electronic densities of states show that the spin polarization of the tetragonal phase is about 60%. The results obtained are in good agreement with the experimental data.

Investigation of dynamic solution interactions between NET-1 and UNC-5B by multi-wavelength analytical ultracentrifugation.

NET-1 is a key chemotropic ligand that signals commissural axon migration and change in direction. NET-1 and its receptor UNC-5B switch axon growth cones from attraction to repulsion. The biophysical properties of the NET-1 + UNC-5B complex have been poorly characterized. Using multi-wavelength-AUC by adding a fluorophore to UNC-5B, we were able to separate the UNC-5B sedimentation from NET-1. Using both multi-wavelength- and single-wavelength AUC, we investigated NET-1 and UNC-5B hydrodynamic parameters and complex formation. The sedimentation velocity experiments show that NET-1 exists in a monomer-dimer equilibrium. A close study of the association shows that NET-1 forms a pH-sensitive dimer that interacts in an anti-parallel orientation. UNC-5B can form equimolar NET-1 + UNC-5B heterocomplexes with both monomeric and dimeric NET-1.

Ultrasound features for prediction of long-term outcomes of women with primary breast cancer

Some women die despite the favorable prognosis of small breast cancers. Breast ultrasound features may reflect pathological and biological characteristics of a breast tumor. This study aimed to explore whether ultrasound features could identify small breast cancers with poor outcomes. This retrospective study examined confirmed breast cancers with a size of <20mm diagnosed in our hospital between 02/2008 and 08/2019. Clinicopathological and ultrasound features were compared between alive and deceased breast cancer patients. Survival was analyzed using the Kaplan-Meier curves. Multivariable Cox proportional hazards models were used to examine the factors associated with breast cancer-specific survival (BCSS) and disease-free survival (DFS). Among the 790 patients, the median follow-up was 3.5 years. The deceased group showed higher frequencies of spiculated (36.7% vs. 11.2%, P<0.001), anti-parallel orientation (43.3% vs. 15.4%, P<0.001), and spiculated morphology combined with anti-parallel orientation (30.0% vs. 2.4%, P<0.001). Among 27 patients with spiculated morphology and anti-parallel orientation, nine cancer-specific deaths and 11 recurrences occurred, for a 5-year BCSS of 77.8% and DFS of 66.7%, while 21 breast-cancer deaths and 41 recurrences occurred among the remaining patients with higher 5-year BCSS (97.8%, P<0.001) and DFS (95.4%, P<0.001). Spiculated and anti-parallel orientation (HR=7.45, 95%CI: 3.26-17.00; HR=6.42, 95%CI: 3.19-12.93), age ≥55 years (HR=5.94, 95%CI: 2.24-15.72; HR=1.98, 95%CI: 1.11-3.54), and lymph nodes metastasis (HR=3.99, 95%CI: 1.89-8.43; HR=2.99, 95%CI: 1.71-5.23) were independently associated with poor BCSS and DFS. Spiculated and anti-parallel orientation at ultrasound are associated with poor BCSS and DFS in patients with primary breast cancer <20mm.

Conformation-dependent molecular association and spectral properties of 4-pentyl-4′-cyanobiphenyl liquid crystal in different phases

The 4-pentyl-4′-cyanobiphenyl (5CB) molecule conformation and structure alignment have been investigated by means of temperature variable Fourier transform infrared (FTIR) and photoluminescence (PL) spectroscopy in a wide temperature range (from −90 to 50 °C) covering the 5CB glass-like, metastable and stable crystalline, nematic and isotropic phases defined by differential scanning calorimetry measurements. The corresponding FTIR absorption and PL emission bands reflect a strong dipolar association and a formation of at least two types of 5CB dimeric structures with antiparallel or parallel orientation in the planar configuration. No formation of hydrogen bonds between the cyano groups and hydrogen atoms of the adjacent benzene ring has been found. Besides, a small amount of the 5CB monomer structure has been shown to be present in all phases. The observed temperature-induced changes in the IR and PL spectra can be used as an independent source of experimental information on conformational equilibria and structure alignment of 5CB in different states under the phase transitions.

Revealing the Key Packing Features Determining the Stability of Peptide Bilayer Membrane.

Short surfactant-like amphiphilic peptide, A3K, resembling a surfactant with a hydrophobic tail (A3) and a polar headgroup (K), is experimentally determined to form a membrane. Although the peptides are known to exist as β-strands, the exact packing architecture stabilizing the membrane is unknown. Earlier simulation studies have reported successful packing configurations through trial and error. In this work, we present a systematic protocol to identify the best peptide configurations for different packing patterns. The influence of stacking peptides in square and hexagonal packing geometry with the neighboring peptides in parallel and antiparallel orientations was explored. The best peptide configurations were determined from the free energy of bringing 2-4 peptides together as a bundle that can be stacked into a membrane. The stability of the assembled bilayer membrane was further investigated through molecular dynamics simulation. The role of peptide tilting, interpeptide distance, the nature and the extent of interactions, and the conformational degrees of freedom on the stability of the membrane is discussed. The consistency with the experimental findings suggests hexagonal antiparallel as the most relevant molecular architecture.

Interisland-Distance-Mediated Growth of Centimeter-Scale Two-Dimensional Magnetic Fe3O4 Arrays with Unidirectional Domain Orientations.

Two-dimensional (2D) nanosheet arrays with unidirectional orientations are of great significance for synthesizing wafer-scale single crystals. Although great efforts have been devoted, the growth of atomically thin magnetic nanosheet arrays and single crystals is still unaddressed. Here we design an interisland-distance-mediated chemical vapor deposition strategy to synthesize centimeter-scale atomically thin Fe3O4 arrays with unidirectional orientations on mica. The unidirectional alignment of nearly all the Fe3O4 nanosheets is driven by a dual-coupling-guided growth mechanism. The Fe3O4/mica interlayer interaction induces two preferred antiparallel orientations, whereas the interisland interaction of Fe3O4 breaks the energy degeneracy of antiparallel orientations. The room-temperature long-range ferrimagnetic order and thickness-tunable magnetic domain evolution are uncovered in atomically thin Fe3O4. This strategy to tune the orientations of nanosheets through the an interisland interaction can guide the synthesis of other 2D transition-metal oxides, thereby laying a solid foundation for future spintronic device applications at the integration level.

Cytokinesis in Trypanosoma brucei relies on an orphan kinesin that dynamically crosslinks microtubules

Many single-celled eukaryotes have complex cell morphologies defined by microtubules arranged into higher-order structures. The auger-like shape of the parasitic protist Trypanosoma brucei (T.brucei) is mediated by a parallel array of microtubules that underlies the plasma membrane. The subpellicular array must be partitioned and segregated using a microtubule-based mechanism during cell division. We previously identified an orphan kinesin, KLIF, that localizes to the ingressing cleavage furrow and is essential for the completion of cytokinesis. We have characterized the biophysical properties of a truncated KLIF construct invitro to gain mechanistic insight into the function of this novel kinesin. We find that KLIF is a non-processive dimeric kinesin that dynamically crosslinks microtubules. Microtubules crosslinked by KLIF in an antiparallel orientation are translocated relative to one another, while microtubules crosslinked parallel to one another remain static, resulting in the formation of organized parallel bundles. In addition, we find that KLIF stabilizes the alignment of microtubule plus ends. These features provide a mechanistic understanding for how KLIF functions to form a new pole of aligned microtubule plus ends that defines the shape of the new cell posterior, which is an essential requirement for the completion of cytokinesis in T.brucei.

Intermolecular-Type Conical Intersections in Benzene Dimer.

The equilibrium and conical intersection geometries of the benzene dimer were computed in the framework of the conventional, linear-response time-dependent and spin-flipped time-dependent density functional theories (known as DFT, TDDFT and SF-TDDFT) as well as using the multiconfigurational complete active space self-consistent field (CASSCF) method considering the minimally augmented def2-TZVPP and the 6-31G(d,p) basis sets. It was found that the stacking distance between the benzene monomers decreases by about 0.5 Å in the first electronic excited state, due to the stronger intermolecular interaction energy, bringing the two monomers closer together. Intermolecular-type conical intersection (CI) geometries can be formed between the two benzene molecules, when (i) both monomer rings show planar deformation and (ii) weaker (approximately 1.6-1.8 Å long) C-C bonds are formed between the two monomers, with parallel and antiparallel orientation with respect to the monomer. These intermolecular-type CIs look energetically more favorable than dimeric CIs containing only one deformed monomer. The validity of the dimer-type CI geometries obtained by SF-TDDFT was confirmed by the CASSCF method. The nudged elastic band method used for finding the optimal relaxation path has confirmed both the accessibility of these intermolecular-type CIs and the possibility of the radiationless deactivation of the electronic excited states through these CI geometries. Although not as energetically favorable as the previous two CI geometries, there are other CI geometries characterized by the relative rotation of monomers at different angles around a vertical C-C axis.

Photo-induced crosslinking uncovers an antiparallel strand orientation in heterodimeric (EIAALEK)3/(KIAALKE)3 and (EIAALEK)3/(RIAALRE)3 coiled-coil systems.

We describe for the first time the co-existence of the parallel and antiparallel conformation of the heterodimeric E3/K3 and E3/R3 coiled-coil systems in solution. The introduction of a furanylated amino acid in the (EIAALEK)3 sequence allowed, upon photo-induced covalent crosslinking, freezing of the respective coiled-coil complexes present in solution. The occurrence of both parallel and antiparallel conformations in solution was supported by computational simulations and further confirmed by fluorescence experiments based on pyrene-pyrene stacking.

Ultrafast Two-Electron Orbital Swap in Li Initiated by Attosecond Pulses

A universal mechanism of ultrafast 2-electron orbital swap is discovered through 2-photon sequential double ionization of Li. After a 1s electron in Li is ionized by absorbing an extreme ultraviolet photon, the other 2 bound electrons located on 2 different shells have either parallel or antiparallel spin orientations. In the latter case, these 2 electrons are in the superposition of the singlet and triplet states with different energies, forming a quantum beat and giving rise to the 2-electron orbital swap with a period of several hundred attoseconds. The orbital swap mechanism can be used to manipulate the spin polarization of photoelectron pairs by conceiving the attosecond-pump attosecond-probe strategy and thus serves as a knob to control spin-resolved multielectron ultrafast dynamics.