Tracking the PROTAC degradation pathway in living cells highlights the importance of ternary complex measurement for PROTAC optimization

The multi-step degradation process of PROteolysis TArgeting Chimeras (PROTACs) poses a challenge for their rational development, as the rate-limiting steps that determine PROTACs efficiency remain largely unknown. Moreover, the slow throughput of currently used endpoint assays does not allow the comprehensive analysis of larger series of PROTACs. Here, we developed cell-based assays using the NanoLuciferase and HaloTag that allow measuring PROTAC-induced degradation and ternary complex formation kinetics and stability in cells. Using PROTACs developed for the degradation of WD40 repeat domain protein 5 (WDR5), the characterization of the mode of action of these PROTACs in the early degradation cascade revealed a key role of ternary complex formation and stability. Comparing a series of ternary complex crystal structures highlighted the importance of an efficient E3-target interface for ternary complex stability. The developed assays outline a strategy for the rational optimization of PROTACs using a series of live cell assays monitoring key steps of the early PROTAC-induced degradation pathway.

Macrocyclization of Quinazoline-Based EGFR Inhibitors Leads to Exclusive Mutant Selectivity for EGFR L858R and Del19

Activating mutations in the epidermal growth factor receptor (EGFR) are frequent oncogenic drivers of non-small-cell lung cancer (NSCLC). The most frequent alterations in EGFR are short in-frame deletions in exon 19 (Del19) and the missense mutation L858R, which both lead to increased activity and sensitization of NSCLC to EGFR inhibition. The first approved EGFR inhibitors used for first-line treatment of NSCLC, gefitinib and erlotinib, are quinazoline-based. However, both inhibitors have several known off-targets, and they also potently inhibit wild-type (WT) EGFR, resulting in side effects. Here, we applied a macrocyclic strategy on a quinazoline-based scaffold as a proof-of-concept study with the goal of increasing kinome-wide selectivity of this privileged inhibitor scaffold. Kinome-wide screens and SAR studies yielded 3f, a potent inhibitor for the most common EGFR mutation (EGFR Del19: 119 nM) with selectivity against the WT receptor (EGFR: >10 μM) and the kinome.

Design, Synthesis, and Evaluation of WD-Repeat-Containing Protein 5 (WDR5) Degraders

Histone H3K4 methylation serves as a post-translational hallmark of actively transcribed genes and is introduced by histone methyltransferase (HMT) and its regulatory scaffolding proteins. One of these is the WD-repeat-containing protein 5 (WDR5) that has also been associated with controlling long noncoding RNAs and transcription factors including MYC. The wide influence of dysfunctional HMT complexes and the typically upregulated MYC levels in diverse tumor types suggested WDR5 as an attractive drug target. Indeed, protein-protein interface inhibitors for two protein interaction interfaces on WDR5 have been developed. While such compounds only inhibit a subset of WDR5 interactions, chemically induced proteasomal degradation of WDR5 might represent an elegant way to target all oncogenic functions. This study presents the design, synthesis, and evaluation of two diverse WDR5 degrader series based on two WIN site binding scaffolds and shows that linker nature and length strongly influence degradation efficacy.

Scyptolin A and B, cyclic depsipeptides from axenic cultures of Scytonema hofmanni PCC 7110

Two novel cyclic depsipeptides were isolated from axenic cultures of the terrestrial cyanobacterium Scytonema hofmanni PCC 7110 and designated scyptolin A and B. Amino acid analyses in context with mass and 1H/13C NMR spectroscopies revealed a composition typical for heterologous cyanopeptolins but containing the uncommon residue 3'-chloro-N-methyl-Tyr (cmTyr) and a unique sidechain. Scyptolin A and B both consist of the N-acylated peptide But(1)-Ala(2)-Thr(3)-Thr(4)-Leu(5)-Ahp(6) (3-amino-6-hydroxy-2-oxo-1-piperidine)-Thr(7)-cmTyr(8)-Val(9), which forms a 19-membered ring by esterification of the carboxyl of Val(9) with the hydroxyl of Thr(4). In scyptolin B, the hydroxyl of the Thr(3) residue is additionally esterified with N-butyroyl-Ala. Both scyptolin A and B exhibit selective inhibition of porcine pancreatic elastase in vitro with IC(50) values of 3.1 microg/ml.

Taxonomic study of extreme halophilic archaea isolated from the "Salar de Atacama", Chile

A large number of halophilic bacteria were isolated in 1984-1992 from the Atacama Saltern (North of Chile). For this study 82 strains of extreme halophilic archaea were selected. The characterization was performed by using the phenotypic characters including morphological, physiological, biochemical, nutritional and antimicrobial susceptibility test. The results, together with those from reference strains, were subjected to numerical analysis, using the Simple Matching (S(SM)) coefficient and clustered by the unweighted pair group method of association (UPGMA). Fifteen phena were obtained at an 70% similarity level. The results obtained reveal a high diversity among the halophilic archaea isolated. Representative strains from the phena were chosen to determine their DNA base composition and the percentage of DNA-DNA similarity compared to reference strains. The 16S rRNA studies showed that some of these strains constitutes a new taxa of extreme halophilic archaea.

Mesoscopic correlation of supramolecular chirality in one-dimensional hydrogen-bonded assemblies

The ordering of 4-[trans-2-(pyrid-4-yl-vinyl)] benzoic acid, a two-dimensional chiral species, was studied by scanning tunneling microscopy at noble metal surfaces. Homochiral molecules self-assemble in supramolecular chiral hydrogen-bonded twin chains, which order in nanogratings where the supramolecular chirality is strictly correlated over the entire microm domains without intimate molecular contact. Model simulations indicate that the underlying mesoscopic chiral resolution is associated with twin chains acting as chiroselective templates for transient molecular attachment, which process mediates the gratings' evolution.

Co-occurrence of non-toxic (cyanopeptolin) and toxic (microcystin) peptides in a bloom of Microcystis sp. from a Chilean lake

A cyanobacterial bloom occurring in 1998 in lake Tres Pascualas (Concepción/Chile) was found to be dominated by Microcystis sp. The bloom contained both non-toxic (cyanopeptolin-type) and hepatotoxic (microcystin-type) peptides. Cyanopeptolin structure of the non-toxic peptides (called cyanopeptolin VW-1 and VW-2, respectively) was revealed by matrix assisted laser desorption ionization mass spectrometry (MALDI-TOF-MS) of whole cells, showing dominant molecular ions at m/z = 975 and m/z 995, respectively. On post source decay (PSD), both cyanopeptolins showed fragments deriving from Ahp-Phe-MTyr (3-amino-6-hydroxy-2-piperidone), the characteristic partial structure of cyanopeptolins. The amounts of each of the two cyanopeptolins could only roughly be estimated to be >0.1% of bloom material dry weight. In addition the blooms contained microcystins (20 microg/g bloom dry weight as determined by RP-HPLC, 13 microg/g according to ELISA determination). MALDI-TOF-MS revealed several structural variants of microcystin: MCYST-RR (microcystin with Arg and Arg, indicated by m/z 1,038 and confirmed by PSD revealing a m/z = 135 fragment deriving from the Adda side chain, MCYST-FR (microcystin with Phe and Arg, indicated by m/z = 1,015). The presence of [Asp(3)]-MCYST-LR (microcystin with Leu and Arg, Asp non-methylated, indicated by m/z 981), and [Asp(3)]-MCYST-YR (microcystin with Tyr and Arg, Asp non-methylated, indicated by m/z 1,031) were likely. The relative amounts of the peptides varied between February, April, and May. Whole cell extracts from the bloom material revealed specific enzyme inhibitory activities. The serin-proteases trypsin, plasmin, elastase were inhibited, assumable due to the cyanopeptolins found. Elastase and the cysteine-protease papain were not inhibited, inhibitions of protein kinase and glutathione S-transferase (GST) were low. Strong inhibition was observed with protein-phosphatase-1, likely due to the microcystins present in the samples.

Generation of antibodies directed against the low-immunogenic peptide-toxins microcystin-LR/RR and nodularin

The preparation of antibodies against the liver toxin microcystin, as described here, is of major importance for its detection and purification in food and water, and for a therapeutic approach to neutralize the toxin by passive immunization. Microcystin-LR (MLR) and microcystin-RR (MRR) were purified from cyanobacterial cell materials by extraction, Sephadex LH-20-, ODS silica gel-, ionic exchange and RP-HPLC-chromatography. In order to reduce the toxicity for parenteral administration, microcystins were coupled by the carbodiimide method to poly-L-lysine (PLL(50.000)). Mice and rabbits were immunized with the conjugates in the presence of two lipopeptide immunoadjuvants (P(3)CSK(4) and P(3)CS-T(h)). High MLR-specific antibody levels were observed after parenteral coadministration of antigen and lipopeptides, whereas no anti-MLR antibodies were obtained with free microcystin or the microcystin-PLL(50.000)-conjugate in the absence of lipopeptide. In oral immunization, coadministration of antigen and adjuvants resulted in an accelerated development of anti MLR-specific antibodies and high antibody levels. Using the antisera, we could detect different microcystins and nodularin down to a concentration range of 10-50 ng/ml by a competitive inhibition ELISA; detection of microcystins in crude cell preparations was also possible. Furthermore, microcystins from different sources could be detected and discriminated from cyclic cyanopeptolines.

Dynamics of surface migration in the weak corrugation regime

We report a systematic study for metal-on-metal surface migration in the weak corrugation regime, i.e., with migration barriers falling below approximately 100 meV. The migration characteristics are elucidated by variable-temperature scanning tunneling microscopy observations in the 50-200 K temperature range, which are analyzed by means of nucleation theory. The results demonstrate that, upon entering the weak corrugation regime, the dynamics of the systems are characterized by increasingly reduced effective preexponential factors, while Arrhenius behavior prevails.

Microcystin in cyanobacterial blooms in a Chilean lake

Cyanobacterial blooms dominated by Microcystis sp. occurred in lake Rocuant ("marisma", near Concepción/Chile) in February 1995 and 1996. In the bloom samples collected in both years the hepatotoxin microcystin was detected by RP-HPLC in both samples and in the sample of 1995 also by a toxicity assay using primary rat hepatocytes. In the bloom of 1995, the microcystin content of the dry bloom biomass was determined to be 130 micrograms/g on the basis of the RP-HPLC peak area and 800 micrograms/g on the basis of the rat hepatotoxicity assay, respectively. In the bloom of 1996, RP-HPLC analysis revealed a microcystin content of 8.13 micrograms/g bloom material dry weight. In this year no hepatotoxicity was measured using a concentration range up to 0.8 mg (d. w.) of bloom material per ml in the rat hepatotoxicity assay. This is the first report on the detection of microcystins in Chilean water bodies.

First report on the identification of microcystin in a water bloom collected in Belgium

A toxic cyanobacterial bloom dominated by Microcystis aeruginosa occurred in 1995 in three adjacent ponds near Liège (Belgium) where at the same time conspicuous bird deaths were observed. The toxicity assay using primary rat hepatocytes indicated a high hepatoxicity. A 4 h incubation yielded a LD50 of 0.23 mg bloom material (dry weight)/ml cell culture medium. Toxicity was due to hepatotoxins of the microcystin class, microcystin-LR and-RR being the major microcystins present as determined by RP-HPLC absorption spectra, 1H NMR, and ESMS spectra. Additionally, the bloom sample contained small amounts of microcystin-YR. The microcystin content of the dry bloom biomass was 870 micrograms/g (on the basis of the hepatotoxicity assay) and 556 micrograms/g (on the basis of the RP-HPLC peak area). A higher yield of microcystins was obtained by acetic acid extraction instead of methanol extraction, whereas different extraction temperatures (20 degrees C, 40 degrees C) had no effect on the yield.

Characterization of porin from Roseobacter denitrificans

Porin from Roseobacter denitrificans was isolated and purified to homogeneity. The pore characteristics from this marine bacterium were compared to those of its phylogenetically closely related freshwater bacteria Rhodobacter capsulatus, Rhodobacter sphaeroides and Rhodopseudomonas blastica. The porin formed weakly cation-selective, general diffusion pores in lipid bilayer membranes. High transmembrane potentials caused channel closing in steps that were of one or two thirds of the initial on-steps indicating that the porin of R. denitrificans comprised three more or less independent channels similar to PhoE and OmpC of Escherichia coli and the porin of Rhodobacter capsulatus. 37b4 Prediction of the secondary structure of the 36 N-terminal amino acid residues indicated two transmembrane beta-strands similar to those of the porins of Rhodobacter capsulatus 37b4 and Rhodopseudomonas blastica. Differences of the single channel conductivities between the porin of R. denitrificans and those of the related freshwater bacteria show that R. denitrificans evolved porin channels that are well adapted to the marine habitat.

Porin from the halophilic species Ectothiorhodospira vacuolata: cloning, structure of the gene and comparison with other porins

The gene coding for the anion-specific porin of the halophilic eubacterium Ectothiorhodospira (Ect.) vacuolata was cloned and sequenced, the first such gene so analyzed from a purple sulfur bacterium. It encodes a precursor protein consisting of 374 amino acid (aa)-residues including a signal peptide of 22-aa residues. Comparison with aa sequences of porins from several other members of the Proteobacteria revealed little homology. Only two regions showed local homology with the previously sequenced porins of Neisseria species, Comamonas acidovorans, Bordetella pertussis, Alcaligenes eutrophus, and Burkholderia cepacia. Genomic Southern blot hybridization studies were carried out with a probe derived from the 5' end of the gene coding for the porin of Ect. vacuolata. Two related species, Ect. haloalkaliphila and Ect. shaposhnikovii, exhibited a clear signal, while the extremely halophilic bacterium Halorhodospira (Hlr.) halophila (formerly Ect. halophila) did not show any cross-hybridization even at low stringency. This result is in good accordance with a recently proposed reassignment within the family Ectothiorhodospiraceae, which included the separation of the extremely halophilic species into the new genus Halorhodospira.

Drug specific antibodies: T-cell epitope-lipopeptide conjugates are potent adjuvants for small antigens in vivo and in vitro

To generate conventional or monoclonal antibodies for the serological detection of drugs, antibiotics, toxins and other low molecular mass substances, a suitable and effective adjuvant is needed. Lipopeptides derived from a major component of the bacterial cell wall constitute potent nontoxic and nonpyrogenic immunoadjuvants when mixed with conventional antigens. Here we demonstrate that the synthetic lipopeptide N-palmitoyl-S-[2,3-bis(palmitoyloxy)-(2R,S)-propyl]-(R)-cysteinyl- serine (P3CS) coupled to a Th-cell epitope (P3CS-Th) can efficiently enhance the specific immune response against low molecular weight compounds in different species. In the presence of the synthetic lipopeptide P3CS-Th, the peptides which are per se non-immunogenic stimulated a specific humoral immune response in mice after intraperitoneal application. Mixtures containing adjuvants without the Th sequence showed no significant antibody induction. A marked enhancement of the humoral immune response was obtained with the low molecular mass antigens Iturin AL, Herbicolin A and Microcystin (MLR) coupled to poly-l-lysin (MLR-PLL), in rabbits and in chickens. Lipopeptide-Th cell epitope conjugates also constituted adjuvants for the in vitro immunization of either human mononuclear cells or mouse B-cells with MLR-PLL; after fusion of the immunized cultures with the heteromyeloma cell lines CB-F7 or the mouse myeloma cell line SP 2/0, respectively, we observed a significantly increased yield of antibody secreting hybridomas.

Murine bone marrow-derived macrophages constitute feeder cells for human B cell hybridomas

Murine bone marrow-derived macrophages (BMDM), a homogeneous cell population easily obtainable in large quantities and at reproducible quality by in vitro differentiation, were used as feeder cells for human B cell hybridomas after fusion or during recloning. We used as antigens for the in vitro immunization of human B lymphocytes from peripheral blood as well as from tonsils: (i) synthetic peptides representing immunogenic sequences of gp160 and Nef of HIV-1, coupled to the lipopeptide carrier N-palmitoyl-S-[2,3-bis(palmitoyloxy)-(2 RS)-propyl]-(R)-cysteinyl(-seryl-seryl) (P3 CSS-[gp160(303-329)] and P3C-nef24), (ii) the toxins saxitoxin and microcystin, coupled to BSA (BSA-STX and BSA-MCYST). After fusion with the mouse-human heteromyeloma CB-F7, we could demonstrate that BMDM exert a strong growth supporting effect on post-fusion cultures, resulting in 81.6% versus 23.6% growth-positive wells for P3C-nef24, and 100% versus 71.2% growth-positive wells for BSA-STX stimulated cells in cultures with and without BMDM, respectively. Furthermore, clones in wells with BMDM grew much more rapidly, resulting in 24.3% versus 3.6%, 98.1% versus 42.2% and 56.7% versus 6.7% of cultures ready for screening 2 weeks after fusion of P3C-nef24, P3CSS-[gp160(303-329)], and BSA-STX stimulated lymphocytes, respectively. Apart from their effect on cell growth, murine BMDM also increased the percentage of immunoglobulin (Ig)-producing cultures after fusion, as shown for BSA-STX stimulated lymphocytes (47.8% versus 6.7%), as well as the percentage of cultures producing specific antibodies, as demonstrated with BSA-MCYST activated cells (42% versus 10%). Finally, recloning efficiencies of two human B cell hybridomas (E 10 and F 2) were raised profoundly by BMDM, resulting in 100% versus 64.2% and 90.9% versus 44.2% growth-positive wells after recloning on a ten cells/well level. As murine BMDM can also be stored in liquid nitrogen without loss of activity, they constitute ideal feeder cells for the establishment of human B cell hybridomas.

The porins from the halophilic species Ectothiorhodospira shaposhnikovii and Ectothiorhodospira vacuolata

Major outer membrane proteins with porin activity were isolated from cell envelopes of the halophilic strains Ectothiorhodospira shaposhnikovii N1 and Ectothiorhodospira vacuolata beta1. The porins were obtained as oligomers. They dissociated into monomers by heat or EDTA treatment. The molecular masses of the monomers were determined by mass spectrometry to be 39,285 and 37,160 Da for E. shaposhnikovii N1 and E. vacuolata beta1, respectively. Both were shown by analytical ultracentrifugation to be trimers of about 112, 000 Da. Circular dichroism spectra indicated predominantly beta-sheet structure. The 18 N-terminal amino acid sequences of the two porins were identical except for the amino acids in positions 12 and 14. No sequence similarity with the primary structure of known porins was found. In reconstitution experiments with lipid bilayers, the porins of E. shaposhnikovii N1 and E. vacuolata beta1 formed channels with a single-channel conductance of 1.5 and 0.7 nS, respectively, in 1 M KCl. The single-channel conductance saturated with increasing salt concentration, indicating a putative binding-site for anions in the channel since both porins exhibited anion-selectivity. For the porin of E. vacuolata beta1, but not for that of E. shaposhnikovii N1, an influence of detergent concentration on the single-channel conductance was observed.

X-ray crystallographic and mass spectrometric structure determination and functional characterization of succinylated porin from Rhodobacter capsulatus: implications for ion selectivity and single-channel conductance

The role of charges near the pore mouth has been discussed in theoretical work about ion channels. To introduce new negative charges in a channel protein, amino groups of porin from Rhodobacter capsulatus 37b4 were succinylated with succinic anhydride, and the precise extent and sites of succinylations and structures of the succinylporins determined by mass spectrometry and X-ray crystallography. Molecular weight and peptide mapping analyses using matrix-assisted laser desorption-ionization mass spectrometry identified selective succinylation of three lysine-epsilon-amino groups (Lys-46, Lys-298, Lys-300) and the N-terminal alpha-amino group. The structure of a tetra-succinylated porin (TS-porin) was determined to 2.4 A and was generally found unchanged in comparison to native porin to form a trimeric complex. All succinylated amino groups found in a mono/di-succinylated porin (MS-porin) and a TS-porin are localized at the inner channel surface and are solvent-accessible: Lys-46 is located at the channel constriction site, whereas Lys-298, Lys-300, and the N-terminus are all near the periplasmic entrance of the channel. The Lys-46 residue at the central constriction loop was modeled as succinyl-lysine from the electron density data and shown to bend toward the periplasmic pore mouth. The electrical properties of the MS-and TS-porins were determined by reconstitution into black lipid membranes, and showed a negative charge effect on ion transport and an increased cation selectivity through the porin channel. The properties of a typical general diffusion porin changed to those of a channel that contains point charges near the pore mouth. The single-channel conductance was no longer a linear function of the bulk aqueous salt concentration. The substantially higher cation selectivity of the succinylated porins compared with the native protein is consistent with the increase of negatively charged groups introduced. These results show tertiary structure-selective modification of charged residues as an efficient approach in the structure-function evaluation of ion channels, and X-ray crystallography and mass spectrometry as complementary analytical tools for defining precisely the chemically modified structures.

A peptidoglycan binding domain in the porin-associated protein (PAP) of Rhodospirillum rubrum FR1

The porin-associated protein of Rhodospirillum rubrum FR1 was found to contain a peptidoglycan binding motif. A partial fragment of 179 amino acids, obtained by cleavage of PAP with trypsin, Asp-N protease, and CNBr, was sequenced. Substantial sequence homology was found of the C-terminal part (residues 126-179) of porin-associated protein with OmpA, the peptidoglycan-associated lipoprotein of several bacteria, protein F of Pseudomonas aeruginosa, and PIII of Neisseria gonorrhoeae, the latter being also a porin-associated protein. The 179 amino acid fragment comprised about 67% of the mass spectrometrically determined total mass of PAP of 27850 Da.

Purification, characterization, crystallization, and preliminary X-ray results from Paracoccus denitrificans porin

The porin from Paracoccus denitrificans ATCC 13543 was purified and crystallized. Two crystal forms were obtained from porin solutions with beta-d-octylglucopyranoside as detergent. Crystals of form I belong to the monoclinic spacegroup C2 with unit cell dimensions a = 112.2 A, b = 193.8 A, c = 100.5 A and beta = 129.2 degrees. There is 1 trimer per asymmetric unit. Crystals of form II are triclinic with a = 89.7 A, b = 98.8 A, c = 112.5 A, alpha = 112.5 degrees, beta = 101.8 degrees, gamma = 106.7 degrees (2 trimers per asymmetric unit). Both crystal forms diffract to 3 A.

Lipopolysaccharide of Rhodospirillum salinarum 40: structural studies on the core and lipid A region

The structural elucidation of lipid A of the cell wall lipopolysaccharide (LPS) of Rhodospirillum salinarum 40 by chemical methods and laser desorption mass spectrometry revealed the presence of a mixed lipid A composed of three different 1,4'bisphosphorylated beta (1 --> 6)-linked backbone hexosaminyl-hexosamine disaccharides, i.e. those composed of GlcN --> GlcN, 2,3-diamino-2,3-dideoxy-D-Glc-(DAG --> DAG, and DAG --> GlcN. Lipid A of R. salinarum contained preferentially 3-OH-18:0 and 3-OH-14:0 as amide-linked and cis delta 11-18:1 and c19:0 as ester-linked fatty acids. The mass spectra of the liberated acyl-oxyacyl residues proved the concomitant presence of 3-O-(cis delta 11-18:1)-18:0 and 3-O-(c19:0)-14:0 as the predominating diesters in this mixed lipid A. The glycosidically linked and the ester-linked phosphate groups of the backbone disaccharide were neither substituted by ethanolamine, phosphorylethanolamine, nor by 4-amino-4-deoxy-L-arabinose, in contrast to most of the enterobacterial lipid As. In the core oligosaccharide fraction, a HexA (1 --> 4)HexA(1 --> 5)Kdo-trisaccharide was identified by methylation analysis. The terminal HexA (hexuronic acid) is possibly 4-OMe-GalA, a component described here as an LPS constituent for the first time. LPS of R. salinarum showed a lethality in C57BL/10 ScSN (LPS-responder)-mice) of an order of 10(-1)-10(-2) of that reported for Salmonella abortus equi LPS, and it was also capable of inducing TNF alpha and IL6 in macrophages of C57BL/10ScSN mice.

Cyanopeptolin S, a sulfate-containing depsipeptide from a water bloom of Microcystis sp

A new sulfated, cyclic depsipeptide, called cyanopeptolin S, from Microcystis sp. was isolated from a water bloom in the Auensee/Leipzig (Germany). The depsipeptide had a relative molecular mass of 925 and contained L-arginine, L-threonine, L-isoleucine, N-methyl-L-phenylalanine, a L-glutamic acid-delta-aldehyde ring system and a sulfated D-configurated glyceric acid as a side chain. The structure was elucidated by means of two-dimensional 1H and 13C nuclear magnetic resonance spectroscopy, fast atom bombardment mass spectroscopy. Fourier transformed infrared spectroscopy and combined gas-liquid chromatography/mass spectrometry. Cyanopeptolin S inhibited trypsin with an IC50 < or = 0.2 micrograms ml-1.

Structure of the membrane channel porin from Rhodopseudomonas blastica at 2.0 A resolution

The crystal structure of a membrane channel, homotrimeric porin from Rhodopseudomonas blastica has been determined at 2.0 A resolution by multiple isomorphous replacement and structural refinement. The current model has an R-factor of 16.5% and consists of 289 amino acids, 238 water molecules, and 3 detergent molecules per subunit. The partial protein sequence and subsequently the complete DNA sequence were determined. The general architecture is similar to those of the structurally known porins. As a particular feature there are 3 adjacent binding sites for n-alkyl chains at the molecular 3-fold axis. The side chain arrangement in the channel indicates a transverse electric field across each of the 3 pore eyelets, which may explain the discrimination against nonpolar solutes. Moreover, there are 2 significantly ordered girdles of aromatic residues at the nonpolar/polar borderlines of the interface between protein and membrane. Possibly, these residues shield the polypeptide conformation against adverse membrane fluctuations.

Influence of the supramolecular structure of free lipid A on its biological activity

The three-dimensional supramolecular structures and the states of order of the acyl chains of lipid A from different Gram-negative species were investigated at 40 degrees C, high water content (80-90%), and different [lipid A]/[Mg2+] molar ratios using synchrotron radiation X-ray diffraction and Fourier-transform infrared spectroscopy. Measurements were made on free lipid A from Salmonella minnesota R595, mono- and bi-phosphoryl, as well as those from the non-enterobacterial strains Rhodobacter capsulatus 37b4, Rhodopseudomonas viridis F, and Rhodocyclus gelatinosus 29/1. Parallel to differences in their chemical primary structure, the structural polymorphisms and states of order at 37 degrees C of the non-enterobacterial lipid A were found to be different from those of enterobacterial lipid A. A clear correlation between the supramolecular structure and previously determined biological activities was found. Lipid A with a strong preference for lamellar structures (Rb. capsulatus and Rp. viridis) are endotoxically inactive and lack cytokine-inducing capacity; the compounds assuming a mixed lamellar/nonlamellar structure (monophosphoryl lipid A from S. minnesota) are of lower toxicity in vivo, but may induce cytokines in vitro; those lipid A with a strong tendency to form non-lamellar inverted structures (lipid A from S. minnesota and Rc. gelatinosus) exhibit full endotoxicity in vitro and in vivo. In contrast, anti-complementary activity is most pronounced for compounds with lamellar and least expressed for those with inverted structures. The states of order at 37 degrees C vary non-systematically, exhibiting the highest values for lipid A of S. minnesota and the lowest for that of Rc. gelatinosus. We propose to extend the term 'endotoxic conformation', which is used to describe the conformation of a single lipid A molecule required for optimal triggering of biological effects, to 'endotoxic supramolecular conformation' which denotes the particular organization of lipid A aggregates in physiological fluids causing biological activity.

Cyanopeptolins, new depsipeptides from the cyanobacterium Microcystis sp. PCC 7806

Four depsipeptides (peptide lactones), called cyanopeptolins A, B, C and D, have been isolated from the cyanobacterium Microcystis sp. PCC 7806. They possess identical structures consisting of cyclic L-glutamic acid-gamma-aldehyde, L-leucine, N-methyl-phenylalanine, L-valine, L-threonine, L-aspartic acid, hexanoic acid and a variable basic amino acid. This variable amino acid can be L-arginine (cyanopeptolin A), L-lysine (cyanopeptolin B), N epsilon-methyl-L-lysine (cyanopeptolin C) and N epsilon,N epsilon-dimethyl-L-lysine (cyanopeptolin D), respectively. The L-glutamic acid-gamma-aldehyde and the amino group of L-leucine form an unusual 3-amino-6-hydroxy-2-oxo-1-piperidine system. L-Threonine is connected to L-valine via its hydroxy-group forming an ester bonding. The hexanoic acid residue is attached to the N-terminal aspartic acid residue which is not a part of the ring structure. The isolation procedure of the four cyanopeptolins as well as structure elucidation are described. Amino acid analysis, GC/MS analysis, FAB-MS and several NMR techniques were used to reveal the structures.

7-Desmethyl-microcystin-RR, a hepatotoxin from a waterbloom of Microcystis aeruginosa

A peptide toxin was isolated from a waterbloom of Microcystis aeruginosa from Lake Frøylandsvatn in Norway. The isolation procedure included liquid and solid phase extraction and reversed phase high performance liquid chromatography. Amino acid analysis yielded D-glutamic acid, D-erythro-beta-methylaspartic acid and D-alanine in equimolar and L-arginine in twofold molar ratios. The presence of dehydroalanine was confirmed by hydrogenation and subsequent amino acid analysis with combined gas liquid chromatography/mass spectrometry. Investigation of the toxin with fast atom bombardment mass spectrometry showed a nominal relative molecular mass of 1023. 3-Amino-9-methoxy-2,6,8-trimethyl-10-phenyl- 4,6-decadienoic acid (Adda) was identified by 1H NMR and 1H, 1H COSY spectroscopy. The structure of the toxin was elucidated as 7-desmethyl-microcystin-RR.

Molecular architecture and electrostatic properties of a bacterial porin

The integral membrane protein porin from Rhodobacter capsulatus consists of three tightly associated 16-stranded beta barrels that give rise to three distinct diffusion channels for small solutes through the outer membrane. The x-ray structure of this porin has revealed details of its shape, the residue distributions within the pore and at the membrane-facing surface, and the location of calcium sites. The electrostatic potential has been calculated and related to function. Moreover, potential calculations were found to predict the Ca2+ sites.

Prediction of the general structure of OmpF and PhoE from the sequence and structure of porin from Rhodobacter capsulatus. Orientation of porin in the membrane

By comparing the hydrophilicity profiles and sequences of porin from Rhodobacter capsulatus with those of OmpF and PhoE from Escherichia coli, a set of insertions and deletions for alignment of the sequences has been deduced. With this alignment a similar folding of OmpF and PhoE has been predicted as found by X-ray structure analysis of porin from Rhodobacter capsulates. Furthermore, the orientation of the porin trimer in the outer membrane was inferred from topological data on PhoE. According to this result a single channel of approx. 30 A diameter starts at the outer surface. Near the middle of the outer membrane bilayer this channel branches out into three separate channels, each running within a single porin monomer to the periplasmic surface.

The structure of porin from Rhodobacter capsulatus at 1.8 A resolution

The structure of the porin from Rhodobacter capsulatus was determined at a resolution of 1.8 A. The analysis started from a closely related crystal structure that had been solved at a medium resolution of 3 A using multiple isomorphous replacement and solvent flattening. The new structure contains the complete sequence of 301 amino acid residues. Refinement of the model is under way; the present R-factor is 22% with good geometry. Except for the lengths of several loops, the resulting chain fold corresponds to the medium resolution model. The membrane channel is lined by a large number of ionogenic side chains with characteristic segregation of differently charged groups.

Crystals of an integral membrane protein diffracting to 1.8 A resolution

A new crystal form of porin from Rhodobacter capsulatus has been obtained. The crystals are rhombohedral, space group R3, with hexagonal axes a = b = 92.3 A, c = 146.2 A. They contain one monomer in the asymmetric unit and diffract to a resolution of at least 1.8 A.

Fine-structural and chemical analyses on inner and outer sheath of the cyanobacterium Gloeothece sp. PCC 6909

Cells of the unicellular cyanobacterium Gloeothece sp. PCC 6909 are surrounded by an inner (enclosing 1-2 cells) and an outer (enclosing cell groups) sheath. Using conventional Epon-embedding in combination with ruthenium-red staining, the inner and outer sheaths appeared similar and displayed multiple bands of electron-dense subunits. However, embedding in Nanoplast resin to avoid shrinkage led to the detection of two distinct zones (inner and outer zone) each with several distinct layers. The zone delimited by the electron-dense thick inner sheath layer, and the zone enclosed by the thin electron-dense outer sheath layer, are composed of a homogeneous material of little electron-contrast. Whereas the outer zone appears to be of even contrast, the inner zone is characterized by a distinct electron-transparent layer. Element distribution analysis revealed that the electron-transparent layer contained relatively large amounts of sulfur, carbon, and oxygen but only little nitrogen. Inner and outer sheath fractions were isolated by differential mechanical cell breakage and centrifugation. The outer sheath fraction was less hydrated than the inner one. The two fractions differed little in their contents of uronic acids, carbohydrate and protein, although the outer sheath fraction contained less sulfate. A soluble polysaccharide with a chemical composition similar to that of inner and outer sheath fractions was also obtained from the culture supernatant.

Cytokine induction by lipopolysaccharide (LPS) corresponds to lethal toxicity and is inhibited by nontoxic Rhodobacter capsulatus LPS

Many pathological effects of gram-negative bacteria are produced by their cell wall-derived lipopolysaccharides (LPSs). Differing pathogenicity of gram-negative LPSs, however, may depend on their capacities to induce cytokines. Thus, we studied the lethal toxicity of four nonenterobacterial LPSs and compared it with their capacity to induce mononuclear cell (MNC)-derived interleukin-1 (IL-1), interleukin-6 (IL-6), and tumor necrosis factor (TNF). Unstimulated MNC did not release these cytokines. LPS from the phototrophic strain Rhodobacter capsulatus 37b4 elaborated little toxicity in galactosamine-treated mice (10 micrograms of LPS per mouse was the 100% lethal dose [LD100]) and induced IL-1 and IL-6 release only at high concentrations (10 to 50 micrograms of LPS per ml). R. capsulatus LPS failed to induce TNF activity even at the highest concentration tested (100 micrograms of LPS per ml). In contrast, LPS derived from Pseudomonas diminuta NCTC 8545 or the nodulating species Bradyrhizobium lupini DSM 30140 and Rhizobium meliloti 10406 expressed lethal toxicity (LD100, 1,000, 100, and 10 ng per mouse, respectively) and induced IL-1 or IL-6 (10 to 100, 10, and 1 ng of LPS per ml, respectively) at concentrations 1,000- to 10,000-fold lower than effective levels of R. capsulatus LPS. LPSs from P. diminuta, B. lupini, and R. meliloti also stimulated TNF production and release. MNC accumulated cell-associated IL-1 activities under circumstances in which released activity was readily detected. The cells contained only scant IL-6 activity, indicating release of this mediator rather than intracellular accumulation. Antisera to the respective cytokines inactivated biological activities of the samples selectively. The R. capsulatus LPS inhibited cytokine induction by LPS from P. diminuta, B. lupini, and R. meliloti in coincubation experiments. These results show that the in vivo lethality of the LPSs tested correlates with the induction of monocyte-derived cytokines in vitro. The results of this study suggest that the different lethality of various LPSs from gram-negative bacteria may be due to the differential ability of these LPSs to induce cytokine production.

The three-dimensional structure of porin from Rhodobacter capsulatus at 3 A resolution

The crystal structure of porin from Rhodobacter capsulatus strain 37b4 has been solved at 3.0 A (1 A = 0.1 nm) resolution by multiple isomorphous replacement and solvent-flattening. The three pores of the trimer are well defined in the electron density map. Each pore consists of a 16-stranded beta-barrel which traverses the membrane as a tube. Near its center the tube is narrowed by chain segments protruding from the inner wall of the barrel that form an eye-let with an irregular cross-section of about 6 A by 10 A. The eye-let has an axial length of about 10 A; it defines the exclusion limit for diffusing particles.

Porin of Rhodobacter capsulatus: biochemical and functional characterization

The major outer membrane protein of Rhodobacter capsulatus 37b4 (capsule-free) was isolated. Strong porin-activity was observed after reconstitution into artificial lipid bilayer membranes with a single channel conductance of 3.15 nS in 1 M KCl. The porin migrated as a broad, single band (Mr above 90,000) on sodium dodecyl sulfate polyacrylamide gel electrophoresis and dissociated into a single species of polypeptides (Mr 36,000) on treatment with EDTA (10 mM at 30 degrees C, 20 min) or by heating (100 degrees C, 5 min). Analytical ultracentrifugation studies demonstrated the native porin to be a trimer. The monomers chromatofocused as a single, sharp peak on fast performance liquid chromatography and only one band, corresponding to an isoelectric point of about 4.0, was obtained on isoelectric focusing. Gas-phase sequencing of the 23 N-terminal residues revealed Glu-Val-Lys-Leu-Ser-Gly-Asp-Ala-Arg-Met-Gly-Val-Met-Tyr-Asn-Gly-Asp-Asp- X-Asn- Phe-Ser-Ser.

Rapid purification of the peptide toxins microcystin-LR and nodularin

An isolation procedure was developed to provide within one day microcystin-LR, a cyclic heptapeptide toxin from Microcystis aeruginosa PCC 7806. After ODS (octadecylsilyl) solid phase extraction, the crude toxin fraction was chromatographed using a strong anion exchange column. The toxin was eluted with 0.02 M ammonium bicarbonate. An at least 95% purity was revealed on HPLC separation by monitoring at 214 nm. Application of the procedure to the cyclic pentapeptide toxin nodularin from Nodularia spumigena AV2 was examined.

Porin from Thiobacillus versutus

The porin of Thiobacillus versutus IFO 14567 was isolated by extraction of cell-envelopes with sodium dodecyl sulfate. It exhibited strong porin-activity after reconstitution into artificial lipid bilayer membranes. The diameter of the pore was determined as 1.6 nm, with a weak selectivity for cations being observed. The porin migrated as a single band (Mr 35 kDa) on SDS-polyacrylamide gel-electrophoresis after heating (100 degrees C, 5 min). The porin oligomer was not sensitive towards EDTA. Analytical ultracentrifugation studies demonstrated the native oligomer to be a trimer.

Cell wall constituents of Microcystis sp. PCC 7806

Cell walls of Microcystis sp. PCC 7806 were purified from cell homogenates by sucrose density centrifugation and Triton X-100 extraction. The outer membrane contained carotenoids, two major peptidoglycan-associated proteins (Mr 49,000 and 52,000), and lipopolysaccharide (LPS) as indicated by the presence of 3-hydroxy fatty acids (3-OH-14:0, 3-OH-16:0, 3-OH-18:0), 4-oxo-18:0 fatty acid, and GlcN as lipid A components in addition to rare O-methyl sugars (2-O-methyl-6-deoxyhexoses I and II). The peptidoglycan (A1 gamma-type) was found to be covalently linked to a wall polysaccharide composed of GlcN, ManN, Man, Glc, and phosphate.

Nontoxic and toxic oligopeptides with D-amino acids and unusual residues in Microcystis aeruginosa PCC 7806

Toxic and nontoxic peptides were isolated from the cyanobacterium Microcystis aeruginosa PCC 7806 by a procedure including extraction of cells with water-saturated 1-butanol, chromatography of the extract on silica gel plates and high performance liquid chromatography (HPLC) on Partisil-5. The toxin was shown to be only a minor constituent, being negatively charged and thus separable by electrophoresis, within the HPLC-purified fraction. It contained erythro-beta-methyl-D-Asp, D-Glu, D-Ala, L-Leu, and L-Arg known to be part of the Microcystis peptide-toxin with Mr 994. The major part of the HPLC-purified fraction was assigned, however, to a nontoxic peptide with a Mr of 956. Partial hydrolysis studies of the nontoxic peptide(s) revealed amino acid sequences composed of D-Glu, N-methyl-Phe, and 3,4-dehydro-Pro, aside from the common L-amino acids. Cyclic linkage in the nontoxic peptide(s) appears likely.

Structural analysis of the nontoxic lipid A of Rhodobacter capsulatus 37b4

Lipid A from Rhodobacter capsulatus 37b4 consists of a D-glucosaminyl-(beta 1-6)-D-glucosamine disaccharide backbone, carrying diphosphorylethanolamine at C-1 of the reducing glucosamine and phosphorylethanolamine at C-4' of the nonreducing glucosamine. 1,4'-Bisphosphorylated lipid A, lacking the polar head groups, was also encountered and contributed to the observed microheterogeneity in the phosphate substitution. The amino functions of both glucosamines are substituted almost entirely by the rare 3-oxotetradecanoic acid, which is a characteristic constituent of lipid A in the genus Rhodobacter. 3-Hydroxydecanoic acid is ester-bound at C-3 and C-3' of the glucosamine disaccharide and the one at the nonreducing glucosamine (C-3') is partially substituted by dodecenoic acid to form an ester-bound diester. In free lipid A, hydroxy groups at C-4 and C-6' of the glucosamine disaccharide are unsubstituted. C-6' being the putative attachment point of the lipopolysaccharide core. The nontoxic Rhodobacter capsulatus lipid A shows extensive serological cross-reaction with the toxic Salmonella lipid A. Structural similarities in the hydrophilic part of both types of lipid A, dissimilarities in the hydrophobic part and their impacts on serologic properties are discussed.