An ancestral interaction module promotes oligomerization in divergent mitochondrial ATP synthases

Mitochondrial ATP synthase forms stable dimers arranged into oligomeric assemblies that generate the inner-membrane curvature essential for efficient energy conversion. Here, we report cryo-EM structures of the intact ATP synthase dimer from Trypanosoma brucei in ten different rotational states. The model consists of 25 subunits, including nine lineage-specific, as well as 36 lipids. The rotary mechanism is influenced by the divergent peripheral stalk, conferring a greater conformational flexibility. Proton transfer in the lumenal half-channel occurs via a chain of five ordered water molecules. The dimerization interface is formed by subunit-g that is critical for interactions but not for the catalytic activity. Although overall dimer architecture varies among eukaryotes, we find that subunit-g together with subunit-e form an ancestral oligomerization motif, which is shared between the trypanosomal and mammalian lineages. Therefore, our data defines the subunit-g/e module as a structural component determining ATP synthase oligomeric assemblies.

An ancestral interaction module promotes oligomerisation in divergent mitochondrial ATP synthases

Mitochondrial ATP synthase forms stable dimers arranged into oligomeric assemblies that generate the inner-membrane curvature essential for efficient energy conversion. Here, we report cryo EM structures of the intact ATP synthase dimer from trypanosomes in 10 different rotational states. The model consists of 25 subunits, including 11 lineage-specific, as well as 36 lipids. The rotary mechanism is influenced by the divergent peripheral stalk, conferring a greater conformational flexibility. Proton transfer in the lumenal half-channel occurs via a chain of five ordered water molecules. The dimerization interface is formed by subunit-g that is critical for interactions but not for the catalytic activity. Although overall dimer architecture varies among eukaryotes, we find that subunit-g and -e form a common ancestral oligomerisation motif, which is shared between the trypanosomal and mammalian lineages. Therefore, our data defines the subunit-g/e module as a structural component determining ATP synthase oligomeric assemblies.

The vibrational properties of benzene on an ordered water ice surface

We present a hybrid CCSD(T)+PBE-D3 approach to calculating the vibrational signatures for gas phase benzene and benzene adsorbed on an ordered water-ice surface. We compare the results of our method against experimentally recorded spectra and calculations performed using PBE-D3-only approaches (harmonic and anharmonic). Calculations use a proton ordered XIh water-ice surface consisting of 288 water molecules, and results are compared against experimental spectra recorded for an ASW ice surface. We show the importance of including a water ice surface into spectroscopic calculations, owing to the resulting differences in vibrational modes, frequencies and intensities of transitions seen in the IR spectrum. The overall intensity pattern shifts from a dominating ν11 band in the gas-phase to several high-intensity carriers for an IR spectrum of adsorbed benzene. When used for adsorbed benzene, the hybrid approach presented here achieves an RMSD for IR active modes of 21 cm-1, compared to 72 cm-1 and 49 cm-1 for the anharmonic and harmonic PBE-D3 approaches, respectively. Our hybrid model for gaseous benzene also achieves the best results when compared to experiment, with an RMSD for IR active modes of 24 cm-1, compared to 55 cm-1 and 31 cm-1 for the anharmonic and harmonic PBE-D3 approaches, respectively. To facilitate assignment, we generate and provide a correspondence graph between the normal modes of the gaseous and adsorbed benzene molecules. Finally, we calculate the frequency shifts, Δν, of adsorbed benzene relative to its gas phase to highlight the effects of surface interactions on vibrational bands and evaluate the suitability of our chosen dispersion-corrected density functional theory.

Atomistic insight into salinity dependent preferential binding of polar aromatics to calcite/brine interface: implications to low salinity waterflooding

This paper resolve the salinity-dependent interactions of polar components of crude oil at calcite-brine interface in atomic resolution. Molecular dynamics simulations carried out on the present study showed that ordered water monolayers develop immediate to a calcite substrate in contact with a saline solution. Carboxylic compounds, herein represented by benzoic acid (BA), penetrate into those hydration layers and directly linking to the calcite surface. Through a mechanism termed screening effect, development of hydrogen bonding between –COOH functional groups of BA and carbonate groups is inhibited by formation of a positively-charged Na+ layer over CaCO3 surface. Contrary to the common perception, a sodium-depleted solution potentially intensifies surface adsorption of polar hydrocarbons onto carbonate substrates; thus, shifting wetting characteristic to hydrophobic condition. In the context of enhanced oil recovery, an ion-engineered waterflooding would be more effective than injecting a solely diluted saltwater.

Fabrication of fluorescent nanospheres by heating PEGylated tetratyrosine nanofibers

Aromatic polypeptides have recently drawn the interest of the research community for their capability to self-assemble into a variety of functional nanostructures. Due to their interesting mechanical, electrical and optical properties, these nanostructures have been proposed as innovative materials in different biomedical, biotechnological and industrial fields. Recently, several efforts have been employed in the development of these innovative materials as nanoscale fluorescence (FL) imaging probes. In this context, we describe the synthesis and the functional properties of a novel fluorescent tyrosine (Tyr, Y)-based nanospheres, obtained by heating at 200 °C a solution of the PEGylated tetra-peptide PEG6-Y4. At room temperature, this peptide self-assembles into not fluorescent low ordered water-soluble fibrillary aggregates. After heating, the aggregation of different polyphenolic species generates Y4-based nanospheres able to emit FL into blue, green and red spectral regions, both in solution and at the solid state. The aggregation features of PEG6-Y4 before and after heating were studied using a set of complementary techniques (Fluorescence, CD, FT-IR, Small and Wide-Angle X-ray Scattering and SEM). After a deep investigation of their optoelectronic properties, these nanospheres could be exploited as promising tools for precise biomedicine in advanced nanomedical technologies (local bioimaging, light diagnostics, therapy, optogenetics and health monitoring).

Computing Binding Energies of Interstellar Molecules by Semiempirical Quantum Methods: Comparison Between DFT and GFN2 on Crystalline Ice

Interstellar Grains (IGs) spread in the Interstellar Medium (ISM) host a multitude of chemical reactions that could lead to the production of interstellar Complex Organic Molecules (iCOMs), relevant in the context of prebiotic chemistry. These IGs are composed of a silicate-based core covered by several layers of amorphous water ice, known as a grain mantle. Molecules from the ISM gas-phase can be adsorbed at the grain surfaces, diffuse and react to give iCOMs and ultimately desorbed back to the gas phase. Thus, the study of the Binding Energy (BE) of these molecules at the water ice grain surface is important to understand the molecular composition of the ISM and its evolution in time. In this paper, we propose to use a recently developed semiempirical quantum approach, named GFN-xTB, and more precisely the GFN2 method, to compute the BE of several molecular species at the crystalline water ice slab model. This method is very cheap in term of computing power and time and was already showed in a previous work to be very accurate with small water clusters. To support our proposition, we decided to use, as a benchmark, the recent work published by some of us in which a crystalline model of proton-ordered water ice (P-ice) was adopted to predict the BEs of 21 molecules relevant in the ISM. The relatively good results obtained confirm GFN2 as the method of choice to model adsorption processes occurring at the icy grains in the ISM. The only notable exception was for the CO molecule, in which both structure and BE are badly predicted by GFN2, a real pity due to the relevance of CO in astrochemistry.

Cryo-EM and MD infer water-mediated proton transport and autoinhibition mechanisms of Vo complex

Rotary vacuolar adenosine triphosphatases (V-ATPases) drive transmembrane proton transport through a Vo proton channel subcomplex. Despite recent high-resolution structures of several rotary ATPases, the dynamic mechanism of proton pumping remains elusive. Here, we determined a 2.7-Å cryo–electron microscopy (cryo-EM) structure of yeast Vo proton channel in nanodisc that reveals the location of ordered water molecules along the proton path, details of specific protein-lipid interactions, and the architecture of the membrane scaffold protein. Moreover, we uncover a state of Vo that shows the c-ring rotated by ~14°. Molecular dynamics simulations demonstrate that the two rotary states are in thermal equilibrium and depict how the protonation state of essential glutamic acid residues couples water-mediated proton transfer with c-ring rotation. Our cryo-EM models and simulations also rationalize a mechanism for inhibition of passive proton transport as observed for free Vo that is generated as a result of V-ATPase regulation by reversible disassembly in vivo.

Active Roles of Water in Aqueous Assembly of Macromolecules

Aqueous self-assembly customarily focuses on the molecular interactions of assembling building blocks; the role of water is barely studied. The hydration of hydrophobic P+X- (P+: macromolecular phosphonium cation, X-: anion) is dependent on the ionic end groups, which is responsible for the consequent assembling behavior. The water interaction with the backbone was analyzed by FT-IR, and the dynamics were measured by low field-NMR spectroscopy. The combination of these two techniques reveals the effect of X- on hydration. When X- is I-, the ionic end group ordered water molecules that exerted a detectable long-range effect de-hydrating the backbone. The consequent hydrophobic interaction drove the aqueous assembly of P+I- into micelle-like aggregates with the ionic group exposed to water. In contrast, the ion pair with a hydrophobic anion of [BPh4]- was not able to hold water and did not deplete the hydration water. The hydrated backbone of P+[BPh4]- assembled into vesicles that were driven by hydration interactions. This elucidation at the molecular level is craved to progress aqueous supramolecular chemistry.