Membrane protein structure determination by SAD, SIR, or SIRAS phasing in serial femtosecond crystallography using an iododetergent.

The 3D structure determination of biological macromolecules by X-ray crystallography suffers from a phase problem: to perform Fourier transformation to calculate real space density maps, both intensities and phases of structure factors are necessary; however, measured diffraction patterns give only intensities. Although serial femtosecond crystallography (SFX) using X-ray free electron lasers (XFELs) has been steadily developed since 2009, experimental phasing still remains challenging. Here, using 7.0-keV (1.771 Å) X-ray pulses from the SPring-8 Angstrom Compact Free Electron Laser (SACLA), iodine single-wavelength anomalous diffraction (SAD), single isomorphous replacement (SIR), and single isomorphous replacement with anomalous scattering (SIRAS) phasing were performed in an SFX regime for a model membrane protein bacteriorhodopsin (bR). The crystals grown in bicelles were derivatized with an iodine-labeled detergent heavy-atom additive 13a (HAD13a), which contains the magic triangle, I3C head group with three iodine atoms. The alkyl tail was essential for binding of the detergent to the surface of bR. Strong anomalous and isomorphous difference signals from HAD13a enabled successful phasing using reflections up to 2.1-Å resolution from only 3,000 and 4,000 indexed images from native and derivative crystals, respectively. When more images were merged, structure solution was possible with data truncated at 3.3-Å resolution, which is the lowest resolution among the reported cases of SFX phasing. Moreover, preliminary SFX experiment showed that HAD13a successfully derivatized the G protein-coupled A2a adenosine receptor crystallized in lipidic cubic phases. These results pave the way for de novo structure determination of membrane proteins, which often diffract poorly, even with the brightest XFEL beams.

Evaluation of diacylphospholipids as boundary lipids for bacteriorhodopsin from structural and functional aspects.

Reconstituted membranes with diverse diacylphospholipids were prepared by using bacteriorhodopsin (bR) in which the intrinsic lipid content was decreased to 24% of the original while the trimeric structure and photocycle of bR were retained. Four phospholipids with a different headgroup, phosphatidic acid (PA), phosphatidylcholine (PC), phosphatidylglycerol (PG), and phosphatidylserine (PS), were adopted for reconstitution. By varying the lipid-protein ratios, the interactions of these phospholipids with bR, as a boundary lipid, were evaluated by solid state (2)H/(31)P NMR, circular dichroism (CD), and laser-flash photolysis. The (31)P NMR results revealed that the headgroup of acidic phosphatidylglycerol (PG) interacts more strongly with bR than that of phosphatidylcholine (PC). CD analysis indicated that the trimetric structure of bR was retained in all the phospholipid-bR preparations at low and medium lipid contents. Acidic lipids PA, PG and PS restored the photocycle activity of bR to an extent comparable to (or slightly lower than) that of the purple membrane while PC caused a marked reduction of the bR photocycle efficiency. Among PGs with different fatty acyl groups, those with mono- and di-unsaturated lipids tended to preserve the photocycle efficiency, whereas the fully saturated lipid did not. These results show that acidic unsaturated phospholipids, particularly dioleoylphosphatidylglycerol (DOPG), have higher affinity for bR and efficiently restore its trimetric structure. The present study suggests that bR reconstituted in DOPG bilayers may possibly be used as a model system for spectroscopic investigations of the lipid-bR interactions with the membrane-integral α-helices, and potentially for a similar type of membrane proteins.

Correction: Stereoselective synthesis of the head group of archaeal phospholipid PGP-Me to investigate bacteriorhodopsin-lipid interactions.

Correction for 'Stereoselective synthesis of the head group of archaeal phospholipid PGP-Me to investigate bacteriorhodopsin-lipid interactions' by Jin Cui, et al., Org. Biomol. Chem., 2015, DOI: 10.1039/c5ob01252j.

Stereoselective synthesis of the head group of archaeal phospholipid PGP-Me to investigate bacteriorhodopsin-lipid interactions.

Phosphatidylglycerophosphate methyl ester (PGP-Me), a major constituent of the archaeal purple membrane, is essential for the proper proton-pump activity of bacteriorhodopsin (bR). We carried out the first synthesis of the bisphosphate head group of PGP-Me using H-phosphonate chemistry that led to the production of a simplified PGP-Me analogue with straight alkyl chains. To investigate the role of this head group in the structural and functional integrity of bR, the analogue was used to reconstitute bR into liposomes, in which bR retained the original trimeric structure and light-induced photocycle activity. Enhanced ordering of an alkyl chain of the (2)H-labelled analogue was observed in (2)H NMR spectra upon interaction with bR. These results together suggest that the bisphosphate moiety plays a role in the proper functioning of bR through the lipid-protein interaction.

Protein-lipid acyl chain interactions: Depth-dependent changes of segmental mobility of phospholipid in contact with bacteriorhodopsin.

Boundary lipids surrounding membrane proteins play an essential role in protein function and structure. These protein-lipid interactions are mainly divided into electrostatic interactions between the polar amino acids of proteins and polar heads of phospholipids, and hydrophobic interactions between protein transmembrane sites and phospholipid acyl chains. Our previous report (Kawatake et al., Biochim. Biophys. Acta 1858 [2016] 2106-2115) covered a method for selectively analyzing boundary lipid interactions and showed differences in membrane protein-peripheral lipid interactions due to differences in their head group. Interactions in the hydrophobic acyl chains of phospholipids are relatively consistent among proteins, but the details of these interactions have not been elucidated. In this study, we reconstituted bacteriorhodopsin as a model protein into phospholipid membranes labeled with 2H and 13C for solid-state NMR measurement to investigate the depth-dependent effect of the head group structure on the lipid bilayer. The results showed that the position of the phospholipid near the carbonyl carbon was affected by the head group in terms of selectivity for protein surfaces, whereas in the deep interior of the bilayer near the leaflet interface, there was little difference between the head groups, indicating that the dependence of their interactions on the head group was much reduced.

Combined effect of the head groups and alkyl chains of archaea lipids when interacting with bacteriorhodopsin.

Bacteriorhodopsin (bR), a transmembrane protein with seven α-helices, is highly expressed in the purple membrane (PM) of archaea such as Halobacterium salinarum. It is well known that bR forms two-dimensional crystals with acidic lipids such as phosphatidylglycerol phosphate methyl ester (PGP-Me)-a major component of PM lipids bearing unique chemical structures-methyl-branched alkyl chains, ether linkages, and divalent anionic head groups with two phosphodiester groups. Therefore, we aimed to determine which functional groups of PGP-Me are essential for the boundary lipids of bR and how these functionalities interact with bR. To this end, we compared various well-known phospholipids (PLs) that carry one of the structural features of PGP-Me, and evaluated the affinity of PLs to bR using the centerband-only analysis of rotor-unsynchronized spin echo (COARSE) method in solid-state NMR measurements and thermal shift assays. The results clearly showed that the branched methyl groups of alkyl chains and double negative charges in the head groups are important for PL interactions with bR. We then examined the effect of phospholipids on the monomer-trimer exchange of bR using circular dichroism (CD) spectra. The results indicated that the divalent negative charge in a head group stabilizes the trimer structure, while the branched methyl chains significantly enhance the PLs' affinity for bR, thus dispersing bR trimers in the PM even at high concentrations. Finally, we investigated the effects of PL on the proton-pumping activity of bR based on the decay rate constant of the M intermediate of a bR photocycle. The findings showed that bR activities decreased to 20% in 1,2-dimyristoyl-sn-glycero-3-phosphate (DMPA), and in 1,2-diphytanoyl-sn-glycero-3-phosphocholine (DPhPC) bilayers as compared to that in PM. Meanwhile, 1,2-Diphytanoyl-sn-glycero-3-phosphate (DPhPA) bilayers bearing both negative charges and branched methyl groups preserved over 80% of the activity. These results strongly suggest that the head groups and alkyl chains of phospholipids are essential for boundary lipids and greatly influence the biological function of bR.

A three-dimensional movie of structural changes in bacteriorhodopsin.

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.

Isolation and structure of four new ceramides from the starfish Luidia maculata.

A new sphingosine-type ceramide LMCer-1-1 (1) and three new phytosphingosine-type ceramides, LMCer-2-1 (2), LMCer-2-6 (3), and LMCer-2-7 (4), were isolated from the anti-hyperglycemic active ceramide molecular species LMCer-1 and LMCer-2, obtained from the less polar fraction of the chloroform-methanol extract of the whole bodies of Luidia maculata. The structures of these ceramides were determined on the basis of chemical and spectroscopic evidence as: (2S,3R,4E,2'R)-2-(2-hydroxyhexadecanoylamino)-16-methyl-4-octadecene-1,3-diol (1), (2S,3S,4R,2'R)-2-(2-hydroxyhexadecanoylamino)-16-methyl-octadecane-1,3,4-triol (2), (2S,3S,4R,2'R)-2-(2-hydroxydocosanoylamino)-hexadecane-1,3,4-triol (3), and (2S,3S,4R,2'R)-2-(2-hydroxydocosanoylamino)-14-methyl-hexadecane-1,3,4-triol (4).

Surface plasmon resonance analysis for the screening of anti-prion compounds.

The interaction of anti-prion compounds and amyloid binding dyes with a carboxy-terminal domain of prion protein (PrP121-231) was examined using surface plasmon resonance (SPR) and compared with inhibition activities of abnormal PrP formation in scrapie-infected cells. Most examined compounds had affinities for PrP121-231: antimalarials had low affinities, whereas Congo red, phthalocyanine and thioflavin S had high affinities. The SPR binding response correlated with the inhibition activity of abnormal PrP formation. Several drugs were screened using SPR to verify the findings: propranolol was identified as a new anti-prion compound. This fact indicates that drug screenings by this assay are useful.

Isolation and structure determination of six glucocerebrosides from the starfish Luidia maculata.

Two new glucocerebrosides, luidiacerebroside A (2) and B (6), were isolated from the cerebroside molecular species obtained from the less polar fraction of the CHCl3/MeOH extract of the starfish Luidia maculata using HPLC. Four known cerebrosides, CE-2b (1), astrocerebroside B (3), acanthacerebroside B (4), and CE-3-2 (5) have also been isolated and characterized. The structures of these cerebrosides were determined on the basis of chemical and spectroscopic evidence. Mass spectrometry of dimethyl disulfide derivatives was useful for the determination of the double-bond position in the long-chain base.

Isolation and structure of a GD3-Type ganglioside molecular species possessing neuritogenic activity from the starfish Luidia maculata.

A GD3-type ganglioside molecular species, LMG-4 (1), has been obtained from the polar lipid fraction of the chloroform/methanol extract of the starfish Luidia maculata. The structure of this ganglioside has been determined on the basis of chemical and spectroscopic evidence to be 1-O-[(N-acetyl-alpha-D-neuraminosyl)-(2-->8)-(N-acetyl-alpha-D-neuraminosyl)-(2-->3)-beta-D-galactopyranosyl-(1-->4)-beta-D-glucopyranosyl]-ceramide. The ceramide moiety was composed of heterogeneous 2-hydroxy fatty acid and phytosphingosine units. This is the first report on the isolation and structure elucidation of GD3-type ganglioside from echinoderms. Moreover, 1 exhibited neuritogenic activity toward the rat pheochromocytoma PC12 cells in the presence of nerve growth factor.

Isolation and structure of monomethylated GM3-type ganglioside molecular species from the starfish Luidia maculata.

Two monomethylated GM(3)-Type ganglioside molecular species, 1 and 2, have been obtained from the polar lipid fraction of the chloroform/methanol extract of the starfish Luidia maculata. The structures of these gangliosides have been determined on the basis of chemical and spectroscopic evidence as 1-O-[8-O-methyl-(N-acetyl-alpha-D-neuraminosyl)-(2-->3)-beta-D-galactopyranosyl-(1-->4)-beta-D-glucopyranosyl]-ceramide (1) and 1-O-[8-O-methyl-(N-glycolyl-alpha-D-neuraminosyl)-(2-->3)-beta-D-galactopyranosyl-(1-->4)-beta-D-glucopyranosyl]-ceramide (2). The ceramide moieties were composed of heterogeneous unsubstituted fatty acid, 2-hydroxy fatty acid, sphingosine and phytosphingosine units. Compound 1, designated as LMG-3, represents new ganglioside molecular species. Compound 2 was a known ganglioside molecular species.

Quinoline derivatives are therapeutic candidates for transmissible spongiform encephalopathies.

We previously reported that quinacrine inhibited the formation of an abnormal prion protein (PrPres), a key molecule in the pathogenesis of transmissible spongiform encephalopathy, or prion disease, in scrapie-infected neuroblastoma cells. To elucidate the structural aspects of its inhibiting action, various chemicals with a quinoline ring were screened in the present study. Assays of the scrapie-infected neuroblastoma cells revealed that chemicals with a side chain containing a quinuclidine ring at the 4 position of a quinoline ring (represented by quinine) inhibited the PrPres formation at a 50% inhibitory dose ranging from 10(-1) to 10(1) micro M. On the other hand, chemicals with a side chain at the 2 position of a quinoline ring (represented by 2,2'-biquinoline) more effectively inhibited the PrPres formation at a 50% inhibitory dose ranging from 10(-3) to 10(-1) micro M. A metabolic labeling study revealed that the action of quinine or biquinoline was not due to any alteration in the biosynthesis or turnover of normal prion protein, whereas surface plasmon resonance analysis showed a strong binding affinity of biquinoline with a recombinant prion protein. In vivo studies revealed that 4-week intraventricular infusion of quinine or biquinoline was effective in prolonging the incubation period in experimental mouse models of intracerebral infection. The findings suggest that quinoline derivatives with a nitrogen-containing side chain have the potential of both inhibiting PrPres formation in vitro and prolonging the incubation period of infected animals. These chemicals are new candidates for therapeutic drugs for use in the treatment of transmissible spongiform encephalopathies.