Ion mobility mass spectrometry of two tetrameric membrane protein complexes reveals compact structures and differences in stability and packing

Here we examined the gas-phase structures of two tetrameric membrane protein complexes by ion mobility mass spectrometry. The collision cross sections measured for the ion channel are in accord with a compact configuration of subunits, suggesting that the native-like structure can be preserved under the harsh activation conditions required to release it from the detergent micelle into the gas phase. We also found that the quaternary structure of the transporter, which has fewer transmembrane subunits than the ion channel, is less stable once stripped of detergents and bulk water. These results highlight the potential of ion mobility mass spectrometry for characterizing the overall topologies of membrane protein complexes and the structural changes associated with nucleotide, lipid, and drug binding.     

Theoretical investigation of the ultrafast dissociation of core-ionized water and uracil molecules immersed in liquid water

We present a series of ab initio density functional based calculations of the fragmentation dynamics of core-ionized biomolecules. The computations are performed for pure liquid water, aqueous and isolated Uracil. Core ionization is described by replacing the 1s ² pseudopotential of one atom of the target molecule (C, N or O) with a pseudopotential for a 1s ¹ core-hole state. Our results predict that the dissociation of core-ionized water molecules may be reached during the lifetime of inner-shell vacancy (less than 10 fs), leading to OH bond breakage as a primary outcome. We also observe a second fragmentation channel in which total Coulomb explosion of the ionized water molecule occurs. Fragmentation pathways are found similar for pure water or when the water molecule is in the primary hydration shell of the uracil molecule. In the latter case, the proton may be transferred towards the uracil oxygen atoms. When the core hole is located on the uracil molecule, ultrafast dissociation is only observed in the aqueous environment and for nitrogen-K vacancies, resulting in proton transfers towards the hydrogen-bonded water molecule.     

Alpha clustering in 4n nuclei from 4He to 40Ca

The α clustering in nuclei from ⁴He to ⁴⁰Ca has been presented on a systematic footing which depicts the similarities from nucleus to nucleus. Here, the isomorphic shell model has been employed, which is a hybrid between the conventional shell model and liquid drop model in conjunction with the nucleon finite size and which, in addition, uses no adjustable parameters. In the framework of the model an α-like particle is defined as four close-by nucleons (two neutrons and two protons) in relative angular momentum zero. Thus, up to ⁴⁰Ca nine such α-like particles and two deuterons are formed whose average positions are well specified in the model. Hence, each time an α-like particle is formed (following the aforementioned definition), this could have an average position only at one of the above nine available positions for such particles. Any 4n nucleus arranges its n α-like particles in the same way and any such arrangement corresponds to the ground state or to an excited state of this nucleus and serves as the band head of a rotational band. For ²⁰Ne nine such bands have been found, while for ¹²C and ²⁸Si two and five bands, respectively. The linear α-chain for ¹²C and persisting α-planar structures for heavier nuclei appear in a natural way in the framework of the model and are supported by many observables. The real novelty of this presentation is the fact that the axis of rotation and the number of rotating nucleons inside the same rotational band may change in such a way that the relevant moment of inertia increases monotonically in steps forming for each step a new branch of the band. Thus, several such bands have the same band head, a fact which closely resembles the phenomenon of superdeformation. This phenomenon here is the result of existence of several axes of symmetry and of several axes of rotation which, by changing the axis of rotation, permit the moment of inertia to increase up to the solid body limit.     

Statistical and Criticality Analysis of the Lower Ionosphere Prior to the 30 October 2020 Samos (Greece) Earthquake (M6.9), Based on VLF Electromagnetic Propagation Data as Recorded by a New VLF/LF Receiver Installed in Athens (Greece)

In this work we present the statistical and criticality analysis of the very low frequency (VLF) sub-ionospheric propagation data recorded by a VLF/LF radio receiver which has recently been established at the University of West Attica in Athens (Greece). We investigate a very recent, strong (M6.9), and shallow earthquake (EQ) that occurred on 30 October 2020, very close to the northern coast of the island of Samos (Greece). We focus on the reception data from two VLF transmitters, located in Turkey and Israel, on the basis that the EQ’s epicenter was located within or very close to the 5th Fresnel zone, respectively, of the corresponding sub-ionospheric propagation path. Firstly, we employed in our study the conventional analyses known as the nighttime fluctuation method (NFM) and the terminator time method (TTM), aiming to reveal any statistical anomalies prior to the EQ’s occurrence. These analyses revealed statistical anomalies in the studied sub-ionospheric propagation paths within ~2 weeks and a few days before the EQ’s occurrence. Secondly, we performed criticality analysis using two well-established complex systems’ time series analysis methods—the natural time (NT) analysis method, and the method of critical fluctuations (MCF). The NT analysis method was applied to the VLF propagation quantities of the NFM, revealing criticality indications over a period of ~2 weeks prior to the Samos EQ, whereas MCF was applied to the raw receiver amplitude data, uncovering the time excerpts of the analyzed time series that present criticality which were closest before the Samos EQ. Interestingly, power-law indications were also found shortly after the EQ’s occurrence. However, it is shown that these do not correspond to criticality related to EQ preparation processes. Finally, it is noted that no other complex space-sourced or geophysical phenomenon that could disturb the lower ionosphere did occur during the studied time period or close after, corroborating the view that our results prior to the Samos EQ are likely related to this mainshock.     

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Light exotic nuclei: A new explanation of halo

The experimental Tanihata density distributions for both protons and neutrons in ^6,8He are very well reproduced here without an increase of the 1p neutron orbital size. Instead, an internal collective rotation, due to the invalidity of the adiabatic approximation, leads to the same measurable increase in the radius and to a simultaneous decrease in the separation energy of the nucleons participating in this rotation. Further support of the approach presented is gained by the reproduction of the ground-state properties of ^7–11Be and of the excited (particle and rotational) states of ¹¹Be.     

Photoemission investigation of the high temperature superconductors La2−x Sr x CuO4

Photoemission spectra of the La_2–x Sr _x CuO₄ system which recently has been demonstrated of being capable to produce high temperature (T _c >35 K) superconducting compounds are reported. The photoemission spectra of the basic system (La₂CuO₄) and of samples which contain up to 20% Sr are not significantly different. The density of states at the Fermi energy is small (smaller than that of metallic Cu) and the samples show a possible small shift of the Cu 2p lines towards the trivalent position with increasing tendency to superconductivity. From the Sr 3d spectra a considerable amount of oxygen defects coordinated to the Sr ions is estimated.     

Charge-state dependent compaction and dissociation of protein complexes: insights from ion mobility and molecular dynamics

Collapse to compact states in the gas phase, with smaller collision cross sections than calculated for their native-like structure, has been reported previously for some protein complexes although not rationalized. Here we combine experimental and theoretical studies to investigate the gas-phase structures of four multimeric protein complexes during collisional activation. Importantly, using ion mobility-mass spectrometry (IM-MS), we find that all four macromolecular complexes retain their native-like topologies at low energy. Upon increasing the collision energy, two of the four complexes adopt a more compact state. This collapse was most noticeable for pentameric serum amyloid P (SAP) which contains a large central cavity. The extent of collapse was found to be highly correlated with charge state, with the surprising observation that the lowest charge states were those which experience the greatest degree of compaction. We compared these experimental results with in vacuo molecular dynamics (MD) simulations of SAP, during which the temperature was increased. Simulations showed that low charge states of SAP exhibited compact states, corresponding to collapse of the ring, while intermediate and high charge states unfolded to more extended structures, maintaining their ring-like topology, as observed experimentally. To simulate the collision-induced dissociation (CID) of different charge states of SAP, we used MS to measure the charge state of the ejected monomer and assigned this charge to one subunit, distributing the residual charges evenly among the remaining four subunits. Under these conditions, MD simulations captured the unfolding and ejection of a single subunit for intermediate charge states of SAP. The highest charge states recapitulated the ejection of compact monomers and dimers, which we observed in CID experiments of high charge states of SAP, accessed by supercharging. This strong correlation between theory and experiment has implications for further studies as well as for understanding the process of CID and for applications to gas-phase structural biology more generally.