Bacteriorhodopsin (bR) is a light-driven proton pump and a model membrane transport protein. We used time-resolved serial femtosecond crystallography at an x-ray free electron laser to visualize conformational changes in bR from nanoseconds to milliseconds following photoactivation. An initially twisted retinal chromophore displaces a conserved tryptophan residue of transmembrane helix F on the cytoplasmic side of the protein while dislodging a key water molecule on the extracellular side. The resulting cascade of structural changes throughout the protein shows how motions are choreographed as bR transports protons uphill against a transmembrane concentration gradient.

Many pathogenic bacteria utilise sialic acids as an energy source or use them as an external coating to evade immune detection. As such, bacteria that colonise sialylated environments deploy specific transporters to mediate import of scavenged sialic acids. Here, we report a substrate-bound 1.95 Å resolution structure and subsequent characterisation of SiaT, a sialic acid transporter from Proteus mirabilis. SiaT is a secondary active transporter of the sodium solute symporter (SSS) family, which use Na+ gradients to drive the uptake of extracellular substrates. SiaT adopts the LeuT-fold and is in an outward-open conformation in complex with the sialic acid N-acetylneuraminic acid and two Na+ ions. One Na+ binds to the conserved Na2 site, while the second Na+ binds to a new position, termed Na3, which is conserved in many SSS family members. Functional and molecular dynamics studies validate the substrate-binding site and demonstrate that both Na+ sites regulate N-acetylneuraminic acid transport.

Cytochrome c oxidase catalyses the reduction of molecular oxygen to water while the energy released in this process is used to pump protons across a biological membrane. Although an extremely well-studied biological system, the molecular mechanism of proton pumping by cytochrome c oxidase is still not understood. Here we report a method to produce large quantities of highly diffracting microcrystals of ba 3-type cytochrome c oxidase from Thermus thermophilus suitable for serial femtosecond crystallography. The room-temperature structure of cytochrome c oxidase is solved to 2.3 Å resolution from data collected at an X-ray Free Electron Laser. We find overall agreement with earlier X-ray structures solved from diffraction data collected at cryogenic temperature. Previous structures solved from synchrotron radiation data, however, have shown conflicting results regarding the identity of the active-site ligand. Our room-temperature structure, which is free from the effects of radiation damage, reveals that a single-oxygen species in the form of a water molecule or hydroxide ion is bound in the active site. Structural differences between the ba 3-type and aa 3-type cytochrome c oxidases around the proton-loading site are also described.

Resampling, full occupancy structural refinement and analysis were performed by V.A.G, G.K. and A.V. Integration within a sphere and statistical tests were performed by C.W., R.N. and P.Bå.. SVD analysis was performed by A.V. Quantum Mechanics/Molecular Mechanics analysis were performed by D.M., H.L.L and G.G.. Time-resolved IR spectroscopy measurements were performed by J.K, M.M and S.W. The manuscript was prepared by R.N.,

The effects of temperature changes and polymer addition on the behavior of droplet microemulsions of nonionic surfactant, water, and decane are reported and analyzed within polymer depletion theory. Dilution viscometry and dynamic light scattering were used to confirm that these microemulsions behave essentially as hard-sphere dispersions, providing us with an ideal reference system. Addition of poly(ethylene glycol) (PEG) lowers the emulsification failure boundary, where excess oil is expelled, which can be qualitatively understood by an analysis of the available volume for the polymer. Sufficient addition of PEG causes a fluid-fluid phase separation in qualitative accord with experiments on mixtures of rigid colloidal hard spheres and nonadsorbing polymer. Addition of PEG or raising the temperature causes the collective diffusion coefficient DC to decrease. From theory, the initial linear slope of DC versus droplet concentration can be used to discriminate between attractions and repulsions. The measured DC data for the droplets in the presence of PEG are modeled using the Asakura-Oosawa theory of depletion. Fitting the theory to the measured DC data permits for extracting the only unknown parameter, the polymer radius of gyration. Quantitative agreement is found with literature data, demonstrating that polymer depletion occurs in the system and that the Asakura-Oosawa theory provides a faithful description of the phenomenon.