Knowledge Based Membrane Protein Structure Prediction: From X-Ray Crystallography to Bioinformatics and Back to Molecular Biology

Integral membrane proteins play a key role in detecting and conveying outside signals into cells, allowing them to interact and respond to their environment in a specific manner. They form principal nodes in several signaling pathways and attract large interest in therapeutic interventions as the majority of drug targets are associated to the cell's membrane. The original human genome sequence project estimated 20% of the total gene count of 31,778 genes to code for membrane proteins[1]. Thus membrane proteins constitute a very large set of yet-to be-characterized proteins mediating all the relevant life-related functions both in prokaryotes and eukaryotes. Estimates are suggesting that in whole genomes the content of this protein type may vary from 10% to 40% of the whole proteome, depending on the organism. As of today, this may change on time, while the rough amount of protein sequences is ~ 6,000,000 (in the Non Redundant data base [http://www.ncbi.nlm.nih.gov/]), the sequences annotated as \u201cmembrane protein\u201d are just 45,281 in Swiss-Prot (http://expasy.org/sprot/ where the annotation is manually curated), and the solved atomic structures of membrane proteins are about 350 in the Protein Data Bank [http://www.rcsb.org/pdb/]. This is a very small number considering that we may consider a rough average of 30% of membrane proteins per genome (as derived from sequence similarity search) and end up with an approximate number of about 2,000,000 membrane proteins in the data bases. We can then easily evaluate that less than ~0.6% of membrane proteins are annotated and that ~0.001% of all the membrane protein sequences are known with atomic resolution , giving the idea of an enormous gap that should be filled in order to fully characterize the functioning of membrane proteins. The main reason behind these small numbers is that membrane proteins are very difficult to study as they are inserted into lipid bilayers surrounding the cell and its subcompartments, and expose to the polar outer and inner environments portions of different sizes. When isolated from membranes, membrane proteins are generally less stable than globular ones. It is therefore difficult to purify them in the native, functional form, and more difficult to crystallize them. Thus, crystallization of this type of proteins is yet a very difficult process, given the fact that they expose two different chemico-physical surfaces to the environment: water- and lipid-like. Still, in the last few years, and after great improvements in the techniques underlying X-ray crystallography, several new membrane proteins were solved in different activation states, offering to the entire scientific community a fundamental contribution to the characterization of astonishing mechanisms of signal transduction. Although the improvements in the technologies allowed the determination of several new structures in the last few years, the gap between the known membrane proteins and those with solved structures is still enormous. Thus, a deep combination of X-ray crystallography techniques, computational biology techniques and molecular biology validating experiments, is the key to face the challenge of bridging the gap existing between membrane proteins with and those without known structures. This and other issues may be resolved in the post-genomic era by taking advantage of the all the theoretical and experimental efforts aiming at developing tools based on our present knowledge that are capable of extracting selected structural/functional features from known sequences/structures and of computing the likelihood of their presence in never-seen before sequences/structures. Indeed, some of state-of-the-art tools, are based in the seminal idea that proteins are products of evolution and that their sequences contain millions of years of evolutionary information waiting to be extracted

Titanium activation in prussian blue based electrodes for Na-ion batteries: A synthesis and electrochemical study

Sodium titanium hexacyanoferrate (TiHCF, Na$_{0.86}$0 Ti$_{0.73 }$ [Fe(CN)$_{6}$]·3H$_{2}$O) is synthesized by a simple co-precipitation method in this study. Its crystal structure, chemical composition, and geometric/electronic structural information are investigated by X-ray powder diffraction (XRPD), microwave plasma-atomic emission spectroscopy (MP-AES), and X-ray absorption spectroscopy (XAS). The electroactivity of TiHCF as a host for Li-ion and Na-ion batteries is studied in organic electrolytes. The results demonstrate that TiHCF is a good positive electrode material for both Li-ion and Na-ion batteries. Surprisingly, however, the material shows better electrochemical performance as a Na-ion host, offering a capacity of 74 mAh g$^{-1}$ at C/20 and a 94.5% retention after 50 cycles. This is due to the activation of Ti towards the redox reaction, making TiHCF a good candidate electrode material for Na-ion batteries

Structural effects of anomalous current densities on manganese hexacyanoferrate for Li-ion batteries

A battery management system (BMS) plays a pivotal role in providing optimal performance of lithium-ion batteries (LIBs). However, the eventual malfunction of the BMS may lead to safety hazards or reduce the remaining useful life of LIBs. Manganese hexacyanoferrate (MnHCF) was employed as the positive electrode material in a Li-ion half-cell and subjected to five cycles at high current densities (10 A g$_{MnHCF}$$^{−1}$) and to discharge at 0.1 A g$_{MnHCF}$$^{−1}$, instead of classical charge/discharge cycling with initial positive polarization at 0.01 A g$_{MnHCF}$$^{−1}$, to simulate a current sensor malfunctioning and to evaluate the electrochemical and structural effects on MnHCF. The operando set of spectra at the Mn and Fe K-edges was further analyzed through multivariate curve resolution analysis with an alternating least squares algorithm (MCR–ALS) and extended X-ray absorption fine structure (EXAFS) spectroscopy to investigate the structural modifications arising during cycling after the applied electrochemical protocol. The coulombic efficiency in the first cycle was dramatically affected; however, the local structural environment around each photo absorber recovered during charging. The identification of an additional spectral contribution in the electrochemical process was achieved through MCR-ALS analysis, and the Mn-local asymmetry was thoroughly explored via EXAFS analysis

Highlighting the Reversible Manganese Electroactivity in Na‐Rich Manganese Hexacyanoferrate Material for Li‐ and Na‐Ion Storage

The electroactivity of sodium‐rich manganese hexacyanoferrate (MnHCF) material constituted of only abundant elements, as insertion host for Li‐ and Na‐ions is herein comprehensively discussed. This material features high specific capacities (>130 mAh g−1) at high potentials when compared to other materials of the same class, i.e., Prussian blue analogs. The reversible electronic and structural modifications occurring during ion release/uptake, which are responsible for such high specific capacity, are revealed herein. The in‐depth electronic and structural analysis carried out combining X‐ray diffraction and X‐ray absorption spectroscopy (XAS), demonstrates that both Fe and Mn sites are involved in the electrochemical process, being the high delivered capacity the result of a reversible evolution in oxidation states of the metallic centers (Fe3+/Fe2+ and Mn2+/Mn3+). Along with the Mn2+/Mn3+ oxidation, the Mn local environment experiences a substantial yet reversible Jahn–Teller effect, being the equatorial Mn‐N distances shrunk by 10% (2.18 Å → 1.96 Å). Na‐rich MnHCF material offers slightly higher performance upon uptake and release of Na‐ions (469 Wh kg−1) than Li‐ions (457 Wh kg−1), being, however, the electronic and structural transformation independent of the adopted medium, as observed by XAS spectroscopy

All optical switches based on the coupling of surface plasmon polaritons

We studied the potentials of All Optical Switches (AOS) based on the intensity-dependent coupling and decoupling of light into the SPP modes (Surface Plasmon Polaritons) of a sinusoidally corrugated thin metal film (TMF), due to Kerr induced refractive index changes of the surrounding dielectrics. The ideal device has two spatially separated outputs, collecting the reflected and transmitted light and the active volume can be as small as 10(-2) mm(3). Gold and PTS (poly-(2,4-hexadiyne-1,6-diol bis(p-toluene sulfonate) are the materials considered. Losses are limited to 1.5 dB,while a 20 dB extinction ratio per gate has been theoretically demonstrated with signal pulsewidths of 5-10 ps , using a maximum optical switching peak power of 11 kW

Mapping Heterogeneity of Pristine and Aged Li‐ and N‐Mnhcf Cathode by Synchrotron‐Based Energy‐Dependent Full Field Transmission X‐ray Microscopy

Manganese hexacyanoferrate is a promising cathode material for lithium and sodium ion batteries, however, it suffers of capacity fading during the cycling process. To access the structural and functional characteristics at the nanometer scale, fresh and cycled electrodes are extracted and investigated by transmission soft X-ray microscopy, which allows chemical characterization with spatial resolution from position-dependent x-ray spectra at the Mn L-, Fe L- and N K-edges. Furthermore, soft X-rays prove to show superior sensitivity toward Fe, compare to hard X-rays. Inhomogeneities within the samples are identified, increasing in the aged electrodes, more dramatically in the Li-ion system, which explains the poorer cycle life as Li-ion cathode material. Local spectra, revealing different oxidation states over the sample with strong correlation between the Fe L-edge, Mn L-edge, and N K-edge, imply a coupling between redox centers and an electron delocalization over the host framework

The AD 365 Crete Earthquake/Tsunami Submarine Impact on the Mediterranean Region

The Calabrian and Hellenic subduction systems accommodate the African Eurasian plate convergence in the Mediterranean Sea and are the site of large earthquakes in the forearc region facing the northern African coasts. Some of the historical earthquakes were associated with the generation of tsunami waves affecting the entire Mediterranean basin. We investigated the submarine effects of the AD 365 Crete earthquake on the sedimentary records through the integrated analysis of geophysical data, turbidite deposits, and tsunami modelling. Seismic reflection images show that some turbidite beds are thick and marked by acoustic transparent layers at their top. Radiometric dating of the most recent of such mega-beds, the Homogenite/Augias turbidite (HAT), provide evidence for synchronous basin-wide sedimentation during a catastrophic event which has occurred in the time window of AD 364–415, consistent with the AD 365 Mw = 8.3–8.5 Crete earthquake/tsunamis. The HAT (up to 25 m thick) contains components from different sources, implying remobilization of material from areas very far from the epicentre. Utilizing the expanded stratigraphy of the HAT and the heterogeneity of the sediment sources of the Mediterranean margins, we reconstructed the relative contribution of the Italian, Maltan and African margins to the turbidite deposition. Our sedimentological reconstructions combined with tsunami modelling suggest that the tsunami following the Crete earthquake produced giant turbidity currents along a front over 2000 km long, from northern Africa to Italy. Our cores suggests that during the last 15,000 years, only two similar turbidites have been deposited in the deep basins, pointing to a large recurrence time of such extreme sedimentary events

HighSTEPS. A high strain temperature pèressure and speed apparatus to study earthquake mechanics

We present a state of-the-art biaxial apparatus able to study both earthquake rupture nucleation and propagation at conditions typical of the seismogenic crust. The HighSTEPS, High Strain TEmperature Pressure Speed, apparatus simulates fault deformation in a wide range of slip velocities, i.e., from 10-5m/s to 0.25 m/s. Within this velocity range, it is possible to study, the rate-and-state friction, the fault dynamic weakening, and healing under unique boundary conditions, i.e., normal stress up to 100 MPa, confining pressure up to 100 MPa, pore fluid pressure up to 100 MPa and temperature up to 120 °C. The apparatus consists of a hydraulic system integrated with four linear motors. The hydraulic system allows for the application of normal stress, confining pressure and pore fluid pressure. The main peculiarity of this apparatus is the system of four linear motors that are mounted in series in order to apply shearing velocities up to 0.25 m/s, accelerations up to 10 m/s2 and shear stresses up to 200 MPa. Moreover, both experiments in sliding velocity control or shear stress control on the experimental faults are possible. Preliminary experiments on carbonate and silicate bearing rocks are coherent with the previous literature. The investigation of fault friction under a wide range of velocities, normal stresses, confining pressures and pore fluid pressures will provide insights into the mechanics of earthquakes and reduce the gap between natural and laboratory observations

Disclosing the Redox Pathway Behind the Excellent Performance of CuS in Solid‐State Batteries

Copper sulfide has attracted increasing attention as conversion-type cathode material for, especially, solid-state lithium-based batteries. However, the reaction mechanism behind its extraordinary electroactivity is not well understood, and the various explanations given by the scientific community are diverging. Herein, the CuS reaction dynamics are highlighted by examining the occurring redox processes via a cutting-edge methodology combining X-ray absorption fine structure spectroscopy, and chemometrics to overcome X-ray diffraction limitations posed by the poor material\u27s crystallinity. The mathematical approach rules out the formation of intermediates and clarifies the direct conversion of CuS to Cu in a two-electron process during discharge and reversible oxidation upon delithiation. Two distinct voltage regions are identified corresponding to Cu- as well as the S-redox mechanisms occurring in the material