An efficient method for detecting membrane protein oligomerization and complex using 05SAR-PAGE

Oligomerization is an important feature of proteins, which gives a defined quaternary structure to complete the biological functions. Although frequently observed in membrane proteins, characterizing the oligomerization state remains complicated and time-consuming. In this study, 0.05% (w/v) sarkosyl-polyacrylamide gel electrophoresis (05SAR-PAGE) was used to identify the oligomer states of the membrane proteins CpxA, EnvZ, and Ma-Mscl with high sensitivity. Furthermore, two-dimensional electrophoresis (05SAR/sodium dodecyl sulfate-PAGE) combined with western blotting and liquid chromatography-tandem mass spectrometry was successfully applied to study the complex of CpxA/OmpA in cell lysate. The results indicated that 05SAR-PAGE is an efficient, economical, and practical gel method that can be widely used for the identification of membrane protein oligomerization and the analysis of weak protein interactions.

Enabling Ultralow-Temperature (-70 °C) Lithium-Ion Batteries: Advanced Electrolytes Utilizing Weak-Solvation and Low-Viscosity Nitrile Cosolvent

Low-temperature performance of lithium-ion batteries (LIBs) has always posed a significant challenge, limiting their wide application in cold environments. In this work, the high-performance LIBs working under ultralow-temperature conditions, which is achieved by employing the weak-solvation and low-viscosity isobutyronitrile as a cosolvent to tame the affinity between solvents and lithium ions, is reported. The as-prepared electrolytes exhibit a sufficiently high conductivity (1.152 mS cm-1 ) at -70 °C. The electrolytes enable LiCoO2 cathode and graphite anode to achieve high Coulombic efficiency of >99.9% during long-term cycling at room temperature, and to respectively achieve 75.8% and 100.0% of their room-temperature capacities at -40 °C. Even the LiCoO2 //graphite pouch cells can retain 68.7% of the room-temperature capacity when discharged at -70 °C, and present stable cycling performance at -40 and 60 °C. This work provides a solution for the development of advanced electrolytes to enable LIBs working at wide-temperatures range.

aRDG Analysis of Asphaltene Molecular Viscosity and Molecular Interaction Based on Non-Equilibrium Molecular Dynamics Simulation

Understanding the noncovalent (weak) interactions between asphaltene molecules is crucial to further comprehending the viscosity and aggregation behavior of asphaltenes. In the past, intermolecular interactions were characterized indirectly by calculating the radial distribution function and the numerical distribution of distances/angles between atoms, which are far less intuitive than the average reduced density gradient (aRDG) method. This study selected three representative asphaltene molecules (AsphalteneO, AsphalteneT, and AsphalteneY) to investigate the relationship between viscosity and weak intermolecular interactions. Firstly, a non-equilibrium molecular dynamics (NEMD) simulation was employed to calculate the shear viscosities of these molecules and analyze their aggregation behaviors. In addition, the types of weak intermolecular interactions of asphaltene were visualized by the aRDG method. Finally, the stability of the weak intermolecular interactions was analyzed by the thermal fluctuation index (TFI). The results indicate that AsphalteneY has the highest viscosity. The aggregation behavior of AsphalteneO is mainly face-face stacking, while AsphalteneT and AsphalteneY associate mainly via offset stacking and T-shaped stacking. According to the aRDG analysis, the weak interactions between AshalteneT molecules are similar to those between AshalteneO molecules, mainly due to van der Waals interactions and steric hindrance effects. At the same time, there is a strong attraction between AsphalteneY molecules. Additionally, the results of the TFI analysis show that the weak intermolecular interactions of the three types of asphaltene molecules are relatively stable and not significantly affected by thermal motion. Our results provide a new method for better understanding asphaltene molecules' viscosity and aggregation behavior.

Bioinformation and Neutrino Communication

Communications among civilizations may include self-descriptive bioinformation because pathogen dynamics exist in their astrobiology and astrovirology, which could become pathogenic upon actual contact. This information is of mutual benefit, if reciprocated. However, in contrast, the strategic counter-scenario of self-hidden civilizations is also discussed. Civilizations, including extra-terrestrial civilizations have been divided and stratified into three levels, using a wide non-linear logarithmic scale. The levels are based on their energy expenditures: level 1 is at 4x10^19 erg/sec; level 2 is at 4x10^33 erg/sec; and level 3 is at 4x10^44 erg/sec. Terrestrial civilization is currently below the entry level I. Particularly advanced civilizations, which are above the highest level, may engineer interstellar travel and could move their planets across interstellar distances. Communication among civilizations has always been of keen interest. In terms of ability to communicate among advanced civilizations, neutrinos may be used for galactic and inter-galactic communication, in addition to or instead of using electromagnetic radiation. Thus, at this juncture, deliberation and debate are essential to proceed with development of civilization and communication.

Independent gradient model based on Hirshfeld partition: A new method for visual study of interactions in chemical systems

The powerful independent gradient model (IGM) method has been increasingly popular in visual analysis of intramolecular and intermolecular interactions in recent years. However, we frequently observed that there is an evident shortcoming of IGM map in graphically studying weak interactions, that is its isosurfaces are usually too bulgy; in these cases, not only the graphical effect is poor, but also the color on some areas on the isosurfaces is inappropriate and may lead to erroneous analysis conclusions. In addition, the IGM method was originally proposed based on promolecular density, which is quite crude and does not take actual electronic structure into account. In this article, we propose an improvement version of IGM, namely IGM based on Hirshfeld partition of molecular density (IGMH), which replaces the free-state atomic densities involved in the IGM method with the atomic densities derived by Hirshfeld partition of actual molecular electron density. This change makes IGM have more rigorous physical background. A large number of application examples in this article, including molecular and periodic systems, weak and chemical bond interactions, fully demonstrate the important value of IGMH in intuitively understanding interactions in chemical systems. Comparisons also showed that the IGMH usually has markedly better graphical effect than IGM and overcomes known problems in IGM. Currently IGMH analysis has been supported in our wavefunction analysis code Multiwfn (http://sobereva.com/multiwfn). We hope that IGMH will become a new useful method among chemists for exploring interactions in wide variety of chemical systems.

Weak cis and trans Interactions of the Hemagglutinin with Receptors Trigger Fusion Proteins of Neuropathogenic Measles Virus Isolates

Measles virus (MeV) is an enveloped RNA virus bearing two envelope glycoproteins, the hemagglutinin (H) and fusion (F) proteins. Upon receptor binding, the H protein triggers conformational changes of the F protein, causing membrane fusion and subsequent virus entry. MeV may persist in the brain, infecting neurons and causing fatal subacute sclerosing panencephalitis (SSPE). Since neurons do not express either of the MeV receptors, signaling lymphocytic activation molecule (SLAM; also called CD150) and nectin-4, how MeV propagates in neurons is unknown. Recent studies have shown that specific substitutions in the F protein found in MeV isolates from SSPE patients are critical for MeV neuropathogenicity by rendering the protein unstable and hyperfusogenic. Recombinant MeVs possessing the F proteins with such substitutions can spread in primary human neurons and in the brains of mice and hamsters and induce cell-cell fusion in cells lacking SLAM and nectin-4. Here, we show that receptor-blind mutant H proteins that have decreased binding affinities to receptors can support membrane fusion mediated by hyperfusogenic mutant F proteins, but not the wild-type F protein, in cells expressing the corresponding receptors. The results suggest that weak interactions of the H protein with certain molecules (putative neuron receptors) trigger hyperfusogenic F proteins in SSPE patients. Notably, where cell-cell contacts are ensured, the weak cis interaction of the H protein with SLAM on the same cell surface also could trigger hyperfusogenic F proteins. Some enveloped viruses may exploit such cis interactions with receptors to infect target cells, especially in cell-to-cell transmission.IMPORTANCE Measles virus (MeV) may persist in the brain, causing incurable subacute sclerosing panencephalitis (SSPE). Because neurons, the main target in SSPE, do not express receptors for wild-type (WT) MeV, how MeV propagates in the brain is a key question for the disease. Recent studies have demonstrated that specific substitutions in the MeV fusion (F) protein are critical for neuropathogenicity. Here, we show that weak cis and trans interactions of the MeV attachment protein with receptors that are not sufficient to trigger the WT MeV F protein can trigger the mutant F proteins from neuropathogenic MeV isolates. Our study not only provides an important clue to understand MeV neuropathogenicity but also reveals a novel viral strategy to expand cell tropism.

Selective Adsorption and Separation of Xylene Isomers and Benzene/Cyclohexane with Microporous Organic Polymers POP-1

The separation of chemical substances with analogous chemical structures and physical properties remains a great challenge. In this work, triptycene-like microporous organic polymers (MOPs), POP-1, was synthesized via choosing 1,4-dimethoxybenzene (DMB) and triptycene as external cross-linkers and building blocks, respectively, and POP-1 was employed to separate xylene isomers and benzene (Bz)/cyclohexane (Cy). Results show that POP-1 has a higher uptake for m-xylene (0.29 g/g) and Bz (1.02 g/g); more intriguingly, their complete separation can be realized within 0.6 min using a column packed with POP-1. The interaction between POP-1 networks and adsorbates was also investigated using theoretical (density functional theory together with noncovalent interaction analysis) and experimental (inverse gas chromatography) approaches. Especially, both results present a good agreement, that is, weak interactions such as CH/π interactions play a dominant role in defining the separation performance of POP-1 for xylene isomers and Bz/Cy mixtures. Our findings suggest that MOPs may open up a new route for separating the chemicals that are similar in structure and size.

Potential oscillators and keystone modules in food webs

Food web theory suggests that the placement of a weak interaction is critical such that under some conditions even one well-placed weak interaction can stabilise multiple strong interactions. This theory suggests that complex stable webs may be built from pivotal weak interactions such that the removal of even one to a few keystone interactions can have significant cascading impacts on whole system diversity and structure. However, the connection between weak interactions, derived from the theory of modular food web components, and keystone species, derived from empirical results, is not yet well understood. Here, we develop numerical techniques to detect potential oscillators hidden in complex food webs, and show that, both in random and real food webs, keystone consumer-resource interactions often operate to stabilise them. Alarmingly, this result suggests that nature frequently may be dangerously close to precipitous change with even the loss of one or a few weakly interacting species.

Molecular structures of 3-[(2,2,3,3-tetrafluoropropoxy)methyl]- and 3-[(2,2,3,3,3-pentafluoropropoxy)methyl]pyridinium saccharinates

The salts 3-[(2,2,3,3-tetrafluoropropoxy)methyl]pyridinium saccharinate, C₉H₁₀F₄NO⁺·C₇H₄NO₃S^-, (1), and 3-[(2,2,3,3,3-pentafluoropropoxy)methyl]pyridinium saccharinate, C₉H₉F₅NO⁺·C₇H₄NO₃S^-, (2), i.e. saccharinate (or 1,1-dioxo-1λ⁶,2-benzothiazol-3-olate) salts of pyridinium with -CH₂OCH₂CF₂CF₂H and -CH₂OCH₂CF₂CF₃ meta substituents, respectively, were investigated crystallographically in order to compare their fluorine-related weak interactions in the solid state. Both salts demonstrate a stable synthon formed by the pyridinium cation and the saccharinate anion, in which a seven-membered ring reveals a double hydrogen-bonding pattern. The twist between the pyridinium plane and the saccharinate plane in (2) is 21.26 (8)° and that in (1) is 8.03 (6)°. Both salts also show stacks of alternating cation-anion π-interactions. The layer distances, calculated from the centroid of the saccharinate plane to the neighbouring pyridinium planes, above and below, are 3.406 (2) and 3.517 (2) Å in (1), and 3.409 (3) and 3.458 (3) Å in (2).

Three pairs of weak interactions precisely regulate the G-loop gate of Kir2.1 channel

Kir2.1 (also known as IRK1) plays key roles in regulation of resting membrane potential and cell excitability. To achieve its physiological roles, Kir2.1 performs a series of conformational transition, named as gating. However, the structural basis of gating is still obscure. Here, we combined site-directed mutation, two-electrode voltage clamp with molecular dynamics simulations and determined that H221 regulates the gating process of Kir2.1 by involving a weak interaction network. Our data show that the H221R mutant accelerates the rundown kinetics and decelerates the reactivation kinetics of Kir2.1. Compared with the WT channel, the H221R mutation strengthens the interaction between the CD- and G-loops (E303-R221) which stabilizes the close state of the G-loop gate and weakens the interactions between C-linker and CD-loop (R221-R189) and the adjacent G-loops (E303-R312) which destabilizes the open state of G-loop gate. Our data indicate that the three pairs of interactions (E303-H221, H221-R189 and E303-R312) precisely regulate the G-loop gate by controlling the conformation of G-loop. Proteins 2016; 84:1929-1937. © 2016 Wiley Periodicals, Inc.

Segmentation and additive approach: A reliable technique to study noncovalent interactions of large molecules at the surface of single-wall carbon nanotubes

This investigation explores a new protocol, named Segmentation and Additive approach (SAA), to study exohedral noncovalent functionalization of single-walled carbon nanotubes with large molecules, such as polymers and biomolecules, by segmenting the entire system into smaller units to reduce computational cost. A key criterion of the segmentation process is the preservation of the molecular structure responsible for stabilization of the entire system in smaller segments. Noncovalent interaction of linoleic acid (LA, C18 H32 O2 ), a fatty acid, at the surface of a (10,0) zigzag nanotube is considered for test purposes. Three smaller segmented models have been created from the full (10,0)-LA system and interaction energies were calculated for these models and compared with the full system at different levels of theory, namely ωB97XD, LDA. The success of this SAA is confirmed as the sum of the interaction energies is in very good agreement with the total interaction energy. Besides reducing computational cost, another merit of SAA is an estimation of the contributions from different sections of the large system to the total interaction energy which can be studied in-depth using a higher level of theory to estimate several properties of each segment. On the negative side, bulk properties, such as HOMO-LUMO (highest occupied molecular orbital - lowest occupied molecular orbital) gap, of the entire system cannot be estimated by adding results from segment models. © 2016 Wiley Periodicals, Inc.

An unusual conformation of gabapentin (Gpn) in Pyr-Gpn-NH-NH-Pyr stabilized by weak interactions

The crystal structure of N-[(1-{2-oxo-2-[2-(pyrazin-2-ylcarbonyl)hydrazin-1-yl]ethyl}cyclohexyl)methyl]pyrazine-2-carboxamide monohydrate (Pyr-Gpn-NN-NH-Pyr·H2O), C19H23N7O3·H2O, reveals an unusual trans-gauche (tg(-)) conformation for the gabapentin (Gpn) residue around the C(γ)-C(β) (θ1) and C(β)-C(α) (θ2) bonds. The molecular conformation is stabilized by intramolecular N-H...N hydrogen bonds and weak C-H...O interactions. The packing of the molecules in the crystal lattice shows a network of strong N-H...O and O-H...O hydrogen bonds together with weak C-H...O and π-π inteactions.

Multiple fuzzy interactions in the moonlighting function of thymosin-β4

Thymosine β4 (Tß4) is a 43 amino acid long intrinsically disordered protein (IDP), which was initially identified as an actin-binding and sequestering molecule. Later it was described to have multiple other functions, such as regulation of endothelial cell differentiation, blood vessel formation, wound repair, cardiac cell migration, and survival.1 The various functions of Tβ4 are mediated by interactions with distinct and structurally unrelated partners, such as PINCH, ILK, and stabilin-2, besides the originally identified G-actin. Although the cellular readout of these interactions and the formation of these complexes have been thoroughly described, no attempt was made to study these interactions in detail, and to elucidate the thermodynamic, kinetic, and structural underpinning of this range of moonlighting functions. Because Tβ4 is mostly disordered, and its 4 described partners are structurally unrelated (the CTD of stabilin-2 is actually fully disordered), it occurred to us that this system might be ideal to characterize the structural adaptability and ensuing moonlighting functions of IDPs. Unexpectedly, we found that Tβ4 engages in multiple weak, transient, and fuzzy interactions, i.e., it is capable of mediating distinct yet specific interactions without adapting stable folded structures.

Neutron Measurements and the Weak Nucleon-Nucleon Interaction

The weak interaction between nucleons remains one of the most poorly-understood sectors of the Standard Model. A quantitative description of this interaction is needed to understand weak interaction phenomena in atomic, nuclear, and hadronic systems. This paper summarizes briefly what is known about the weak nucleon-nucleon interaction, tries to place this phenomenon in the context of other studies of the weak and strong interactions, and outlines a set of measurements involving low energy neutrons which can lead to significant experimental progress.

Measurement of the Parity-Violating Neutron Spin Rotation in (4) He

In the meson exchange model of weak nucleon-nucleon (NN) interactions, the exchange of virtual mesons between the nucleons is parameterized by a set of weak meson exchange amplitudes. The strengths of these amplitudes from theoretical calculations are not well known, and experimental measurements of parity-violating (PV) observables in different nuclear systems have not constrained their values. Transversely polarized cold neutrons traveling through liquid helium experience a PV spin rotation due to the weak interaction with an angle proportional to a linear combination of these weak meson exchange amplitudes. A measurement of the PV neutron spin rotation in helium (φ PV ( n ,α)) would provide information about the relative strengths of the weak meson exchange amplitudes, and with the longitudinal analyzing power measurement in the p + α system, allow the first comparison between isospin mirror systems in weak NN interaction. An earlier experiment performed at NIST obtained a result consistent with zero: φ PV ( n ,α) = (8.0 ±14(stat) ±2.2(syst)) ×10(-7) rad / m[1]. We describe a modified apparatus using a superfluid helium target to increase statistics and reduce systematic effects in an effort to reach a sensitivity goal of 10(-7) rad/m.