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CD40 and LMP-1 both signal from lipid rafts but LMP-1 assembles a distinct, more efficient signaling complex.

CD40, a member of the TNFR-1 receptor family, shares several features with LMP-1, an oncoprotein encoded by Epstein-Barr virus. CD40 and LMP-1 activate transcription by binding to TRAFs, JAK3 and/or TRADD. CD40's association with CD40L activates signaling. However, LMP-1 signals independently of a ligand but dependently on self-association. We demonstrate that activated CD40 and LMP-1 co-localize in lipid rafts and recruit TRAF3 there, findings consistent with signals of CD40 and LMP-1 being initiated from lipid rafts. To elucidate their signaling, we compared requirements for their aggregation and subcellular localization. Targeting CD40's monomeric C-terminal signaling domain to lipid rafts activates signaling, as does rendering it trimeric. Addition of both modifications supports signaling more efficiently. Parallel experiments with LMP-1 indicate that targeting the monomeric C-terminal signaling domain of LMP-1 to lipid rafts activates signaling, but trimerizing it does not. Fusing LMP-1's N-terminus and membrane-spanning domains to CD40's C-terminus supports signaling more efficiently than CD40 plus ligand or CD40's trimerized and/or localized derivatives. An activity of LMP-1's N-terminus and membrane-spanning domains other than trimerization must contribute to its efficient signaling.

Adaptor Proteins, Signal Transducing↗

Semliki Forest virus produced in the absence of the 6K protein has an altered spike structure as revealed by decreased membrane fusion capacity.

We examined the kinetics of membrane fusion of wild type (wt) and Delta6K mutant Semliki Forest virus in a liposomal model system. The final extent of membrane fusion of the mutant (at pH 5.5) was approximately one third that of the wt virus, although the level of E1 (fusion protein) trimerization was, in fact, greater than that of the wt. Studies on the effect of exposure of the viruses to low pH revealed that the Delta6K mutant was inactivated much more rapidly than the wt virus. It is this instability of the mutant particles which probably accounts for the lower fusion levels. Moreover, fusion of the Delta6K mutant was significantly increased by the inclusion of lipid-conjugated heparin in the target liposomes. We conclude that the presence of the 6K protein either in the particle or during the assembly process is important for the correct assembly of the fully infectious SFV particle.

Animals↗

Plasticity in the composition of the light harvesting antenna of higher plants preserves structural integrity and biological function.

Arabidopsis plants in which the major trimeric light harvesting complex (LHCIIb) is eliminated by antisense expression still exhibit the typical macrostructure of photosystem II in the granal membranes. Here the detailed analysis of the composition and the functional state of the light harvesting antennae of both photosystem I and II of these plants is presented. Two new populations of trimers were found, both functional in energy transfer to the PSII reaction center, a homotrimer of CP26 and a heterotrimer of CP26 and Lhcb3. These trimers possess characteristic features thought to be specific for the native LHCIIb trimers they are replacing: the long wavelength form of lutein and at least one extra chlorophyll b, but they were less stable. A new population of loosely bound LHCI was also found, contributing to an increased antenna size for photosystem I, which may in part compensate for the loss of the phosphorylated LHCIIb that can associate with this photosystem. Thus, the loss of LHCIIb has triggered concerted compensatory responses in the composition of antennae of both photosystems. These responses clearly show the importance of LHCIIb in the structure and assembly of the photosynthetic membrane and illustrate the extreme plasticity at the level of the composition of the light harvesting system.

Arabidopsis↗

Simultaneous assessment of conformation and aggregation of beta-amyloid peptide using electrospray ionization mass spectrometry.

Electrospray ionization mass spectrometry was used to study conformation and aggregation of the synthetic beta-amyloid peptide, residues 1-40 (betaA4), as a function of concentration and sample aging. All mass spectra showed a major envelope of peaks corresponding to charge states of 7-3 of the monomeric form of betaA4. In addition, weaker envelopes of peaks corresponding to charge states of dimeric, trimeric, and tetrameric betaA4 species were seen under gentle ionization conditions. The average charge state of the envelope associated with the monomeric form decreased by ca. 0.5 z as samples were aged, indicating that the relatively open form (likely random coil) of the peptide was modified into the more compact form (likely beta-sheet) as a function of sample aging. The aggregate forms became weaker and ultimately were absent both in the more dilute solutions and in aged aliquots of the concentrated sample. These aggregates were interpreted as assemblies of the random coil form. We interpret our inability to see an ion envelope that can be associated with aggregates of the beta-sheet form to be a consequence of the presumed very compact nature of this form. A model for the formation of betaA4 fibrils is proposed and discussed.

Amyloid beta-Peptides↗

Reconstitution, characterisation and mass analysis of the pentacylindrical allophycocyanin core complex from the cyanobacterium Anabaena sp. PCC 7120.

The phycobilisome (PBS) of Anabaena sp. PCC 7120 was allowed to dissociate into its constituents and the resulting allophycocyanin (AP) fraction was purified. Its reconstitution yielded a complex which according to negative stain electron microscopy and spectral analysis was identical to the native pentacylindrical PBS core domain. Each cylinder of the central tricylindric unit was comprised of four AP (alphabeta)3 disks. Mass analysis using the scanning transmission electron microscope (STEM) showed the presence of 16 AP trimers in the intact reconstitute, which had a total mass of 1966(+/-66) kDa. Composition analysis indicated an AP trimer distribution of (AP-II):(AP-LCM):(AP-B):(AP-I)=6:2:2:6, i.e. an addition of two AP-I and two AP-II complexes compared to a tricylindrical PBS core domain. Therefore, we suggest that each supplementary half-core cylinder found in pentacylindrical AP core domains is comprised of one AP-I and one AP-II trimer, in agreement with the current model. The structural significance of the 127 kDa core membrane linker polypeptide was further investigated by subjecting the AP core reconstitute to mild chymotryptic degradation. After isolation, the digested complex exhibited a tricylindrical appearance while STEM mass analysis confirmed the presence of only 12 AP complexes. Polypeptide analysis by SDS-PAGE and Edman degradation related the half-cylinder loss to cleavage of the Rep4 domain of the core membrane linker polypeptide. On the basis of these data, a general model for the assembly of the three hemidiscoidal PBS types known to date is discussed.

Amino Acid Sequence↗

The short tail-fiber of bacteriophage T4: molecular structure and a mechanism for its conformational transition.

Electron microscopy, image processing and computational sequence analysis were used to investigate the structure of the short tail-fiber of bacteriophage T4. This molecule, an oligomer of gp12, is an adhesin that binds the virion irreversibly to the bacterial surface. Short tail-fibers were isolated from mutant-infected cells in which gp12 is synthesized and assembled correctly, but not incorporated into virions. Visualized in negative stain, these filamentous molecules are approximately 38 nm in total length, with an arrowhead-shaped head (approximately 10 nm long by 6 nm wide), a 24-nm shaft of uniform width (approximately 3.8 nm), and a small, seemingly flexible, tail. The primary sequence contains a domain consisting of tandem quasi-repeats, each about 40 residues long, extending from approximately residue 50 to residue 320. Molecular mass analyses by scanning transmission electron microscopy confirm that the molecule is a trimer. The masses of the head, shaft, and tail domains are consistent with (trimers of) the carboxy-terminus, the repeat region, and the amino-terminus, respectively. When short tail-fibers are visualized extending from baseplates, their heads are distal, i.e., detached, implying that it is the tail that remains in contact with the baseplate. Analysis of the molecules' curvature properties detects three hinge-sites: these suggest how the short tail-fiber may be initially accommodated in a compact conformation in the "hexagon" state of the baseplate, from which it converts to the extended conformation when the baseplate switches into its "star" state.

Amino Acid Sequence↗

A look within LHCII: differential analysis of the Lhcb1-3 complexes building the major trimeric antenna complex of higher-plant photosynthesis.

The major antenna complex of higher-plant photosynthesis, LHCII, is composed by the products of three genes, namely, Lhcb1-2-3. In this paper, the biochemical and spectroscopic properties of each of the three gene products were investigated. The three complexes were obtained by overexpression of the apoproteins in bacteria and refolding in vitro with purified pigments, thus allowing detection of differences in the structure/function of the pigment-binding gene products. The analyses showed that Lhcb1 and Lhcb2 complexes have similar pigment binding properties, although not identical, while Lhcb3 is clearly different with respect to both pigment binding and spectral properties and cannot produce homotrimers in vitro. Heterotrimers containing Lhcb3 together with Lhcb1 and/or -2 proteins were obtained upon assembly with Lhcb proteins purified from thylakoids. The major functional characteristics of Lhcb3 with respect to Lhcb1 and -2 consisted in (i) a red-shift of one specific chlorophyll a chromophore, strongly affecting the red-most region of the absorption spectrum and (ii) a different specificity for xanthophylls binding to sites L2 and N1. These properties make Lhcb3 a relative sink for excitation energy in isolated heterotrimers with Lhcb1 + Lhcb2, and potentially, a preferential site of regulation of the antenna function in excess light conditions.

Amino Acid Sequence↗

S-layer protein from Thermus thermophilus HB8 assembles into porin-like structures.

The cells of the extreme thermophile Thermus thermophilus are surrounded by a regular layer (S-layer) built up by a protein with an apparent molecular mass of 100 kDa (P100). From purified membrane fractions, three different class of two-dimensional crystals can be obtained by following alternative extractive procedures. One of these crystals, with p6 symmetry, clearly represents the native S-layer detected by freeze etching on whole cells, while the other two, showing p2 and p3 symmetries respectively, closely resemble aggregates of bacterial porins. We demonstrate here by limited proteolysis and Western blotting the surprising fact that the protein component of the three crystals is the P100 protein. Our biochemical data also show how this protein forms Ca(2+)-stabilized trimers in each crystal, which support the structural analysis that points to p3 units as the common structural block in all of them, and again resembles the situation found in bacterial porins.

Blotting, Western↗

Distinct physicochemical characteristics of human mannose binding protein expressed by individuals of differing genotype.

Mannose binding protein (MBP) is a serum collectin (collagenous lectin) believed to be of importance in innate immunity. Three point mutations, in codons 52, 54 and 57 of exon 1 of the human MBP gene, have been predicted to affect the tertiary structure of the collagenous region of the protein, and are known to be associated with low serum concentrations of MBP. However, other groups working with recombinant mutant proteins have claimed that the proteins are expressed and assembled normally. The aim of the present investigation was to characterize the effects of these mutations on the physicochemical nature of MBP that is present in the circulation in vivo, and for this we used polyacrylamide gel electrophoresis, gel filtration and sucrose density gradient centrifugation, followed by immunoblotting and enhanced chemiluminescence. The circulating wild-type MBP appeared to comprise a mixture of polymers formed from two to eight subunits (each based on three identical 32,000 MW polypeptide chains) of apparent molecular weights 200,000-700,000, with dimers and trimers constituting the predominant forms. Individuals homozygous for the codon 54 or 57 mutation had dramatically reduced concentrations of serum MBP, mainly comprising material of an apparent molecular weight of 120,000-130,000. Heterozygous individuals showed characteristics of both phenotypes. In contrast to the results obtained with artificial expression systems, our data suggest that individuals homozygous for the MBP mutations have very little circulating protein and that this comprises mainly low molecular weight material.

Carrier Proteins↗

Tetrameric N(5)-(L-1-carboxyethyl)-L-ornithine synthase: guanidine. HCl-induced unfolding and a low temperature requirement for refolding.

Guanidine x HCl (GdnHCl)-induced unfolding of tetrameric N(5)-(L-1-carboxyethyl)-L-ornithine synthase (CEOS; 141,300 M(r)) from Lactococcus lactis at pH 7.2 and 25 degrees C occurred in several phases. The enzyme was inactivated at approximately 1 M GdnHCl. A time-, temperature-, and concentration-dependent formation of soluble protein aggregates occurred at 0.5-1.5 M GdnHCl due to an increased exposure of apolar surfaces. A transition from tetramer to unfolded monomer was observed between 2 and 3.5 M GdnHCl (without observable dimer or trimer intermediates), as evidenced by tyrosyl and tryptophanyl fluorescence changes, sulfhydryl group exposure, loss of secondary structure, size-exclusion chromatography, and sedimentation equilibrium data. GdnHCl-induced dissociation and unfolding of tetrameric CEOS was concerted, and yields of reactivated CEOS by dilution from 5 M GdnHCl were improved when unfolding took place on ice rather than at 25 degrees C. Refolding and reconstitution of the enzyme were optimal at </=15 degrees C and yields of active tetramer increased as the concentration of unfolded subunits decreased. Refolding of unfolded subunits and active tetramer assembly upon 100-fold dilution from 5 M GdnHCl at 0 degrees C also was increased two- or fourfold (to 44 or 28% reactivation for 0.08 or 0.28 microM subunit, respectively) when incubated at 15 degrees C, pH 7.2, for 4 h with the Escherichia coli molecular chaperonin GroEL, ATP, MgCl(2), and KCl.

Amino Acid Oxidoreductases↗

Role of precursor translocation in coordination of murein and phospholipid synthesis in Escherichia coli.

Inhibition of phospholipid synthesis in Escherichia coli by either cerulenin treatment or glycerol starvation of a glycerol-auxotrophic mutant resulted in a concomitant block of murein synthesis. The intracellular pool of cytoplasmic and lipid-linked murein precursors was not affected by an inhibition of phospholipid synthesis, nor was the activity of the penicillin-binding proteins. In addition, a decrease in the activity of the two lipoprotein murein hydrolases, the lytic transglycosylases A and B, could not be demonstrated. The indirect inhibition of murein synthesis by cerulenin resulted in a 68% decrease of trimeric muropeptide structures, proposed to represent the attachment points of newly added murein. Importantly, inhibition of phospholipid synthesis also inhibited O-antigen synthesis with a sensitivity and kinetics similar to those of murein synthesis. It is concluded that the step common for murein and O-antigen synthesis, the translocation of the respective bactoprenolphosphate-linked precursor molecules, is affected by an inhibition of phospholipid synthesis. Consistent with this assumption, it was shown that murein synthesis no longer depends on ongoing phospholipid synthesis in ether-permeabilized cells. We propose that the assembly of a murein-synthesizing machinery, a multienzyme complex consisting of murein hydrolases and synthases, at specific sites of the membrane, where integral membrane proteins such as RodA and FtsW facilitate the translocation of the lipid-linked murein precursors to the periplasm, depends on ongoing phospholipid synthesis. This would explain the well-known phenomenon that both murein synthesis and antibiotic-induced autolysis depend on phospholipid synthesis and thereby indirectly on the stringent control.

Ampicillin↗

Crystal structure of a designed, thermostable, heterotrimeric coiled coil.

Electrostatic interactions are often critical for determining the specificity of protein-protein complexes. To study the role of electrostatic interactions for assembly of helical bundles, we previously designed a thermostable, heterotrimeric coiled coil, ABC, in which charged residues were employed to drive preferential association of three distinct, 34-residue helices. To investigate the basis for heterotrimer specificity, we have used multiwavelength anomalous diffraction (MAD) analysis to determine the 1.8 A resolution crystal structure of ABC. The structure shows that ABC forms a heterotrimeric coiled coil with the intended arrangement of parallel chains. Over half of the ion pairs engineered to restrict helix associations were apparent in the experimental electron density map. As seen in other trimeric coiled coils, ABC displays acute knobs-into-holes packing and a buried anion coordinated by core polar amino acids. These interactions validate the design strategy and illustrate how packing and polar contacts determine structural uniqueness.

Amino Acid Sequence↗

Partial characterization of the C-terminal non-collagenous domain (NC1) of collagen type X.

Collagen type X is composed of three identical alpha 1(X) chains of 59 kDa, each containing a triple-helical region of 45 kDa flanked by a short N-terminal sequence and a larger non-collagenous C-terminal (NC1) domain of approx. 15 kDa. Collagen type X molecules can associate via their C-termini to form a regular hexagonal lattice in vitro, which in vivo may provide a modified extracellular matrix for the events of endochondral ossification. The NC1 domain of chick collagen type X was isolated and purified from a highly purified bacterial collagenase digest of hypertrophic chondrocyte medium proteins. The structure and aggregation properties of the NC1 domain of collagen X were investigated, independently of the triple helix. A trimer, a dimer and a monomer of the individual alpha-chain NC1 polypeptides were identified from a bacterial collagenase digest of cartilage collagens using [14C]tyrosine labelling, N-chlorosuccinimide peptide mapping and N-terminal sequencing. The trimer (50 kDa) remained intact in Laemmli sample buffer unless boiled, upon which it dissociated into the dimer (38 kDa) and the monomer (20 kDa). The dimer persisted even after prolonged periods of heating or reduction with beta-mercaptoethanol, and in preparations obtained from chondrocyte cultures treated with beta-aminoproprionitrile, indicating the presence of non-reducible, non-lysine-derived, covalent cross-links. Hexamers of the individual C-termini were observed in rotary-shadowed preparations of purified NC1 domain, reflecting the ability of collagen type X to self-assemble via its C-termini under appropriate conditions.

Amino Acid Sequence↗

Cross-linking of Newcastle disease virus (NDV) proteins.

The proxomity and spatial relationships of the structural proteins of Newcastle disease virus (NDV) were studied by chemical cross-linking with a series of imidoesters. When the virions were reacted by the cross-linker with a distance 6.1A or longer between the functional groups and analyzed by polyacrylamide gel electrophoresis, remarkable changes were observed in the migration patterns of the viral proteins. The most striking one was the extensive decrease in the intensity of the M protein band, and although not so strikingly, glycoprotein and nucleocapsid protein bands were reduced significantly. Instead, several protein complexes appeared at and near the top of the gels. The protein complexes formed by a reversible cross-linker, dimethyl-3,3'-dithiobispropionimidate (DTBP), were analyzed by two dimensional electrophoresis; the complexes on the first-dimension cylindrical gels were cleaved by reduction with 2-mercaptoethanol and electrophoresed laterally on the second-dimension slab gels. The results indicated that homodimers of glycoprotein, nucleocapsid protein and M protein were generated under the condition of the most gentle cross-linking employed. At the same time, however, trimer and higher homopolymers of M protein were already detectable. Under the more extensive conditions, the bulk of M protein was cross-linked to form a large protein complex with very high molecular weight. Further, small but significant amounts of glycoprotein and nucleocapsid protein were always detected in this complex. These results suggest that M protein may be present in the virion in close enough proximity to interact with each other and may further have some interactions with glycoprotein and nucleocapsid protein. On the basis of these findings possible roles of M protein in virus assembly were discussed.

Dimethyl Adipimidate↗

Topological investigations of the FomA porin from Fusobacterium nucleatum and identification of the constriction loop L6.

Porin FomA in the outer membrane of Fusobacterium nucleatum is a trimeric protein, which exhibits permeability properties similar to that of the well-known enterobacterial diffusion porins. The proposed topology model of the FomA monomer depicts the beta-barrel motif typical of diffusion porins, consisting of 16 antiparallel beta-strands. To investigate the accuracy of the FomA model and assess the topological relationship with other porins, individual deletions of variable size in seven of the eight surface-exposed regions of the porin were genetically engineered. Deletions in the predicted loops L1 to L7 were tolerated by the FomA porins, as judged by a normal assembly in the outer membrane of Escherichia coli and a sustained pore-forming ability. Deletions in the largest proposed external region, loop L6, made the FomA porins considerably more permeable to antibiotics, indicating larger pore channels. The distinctly increased uptake rates and size exclusion limits displayed by the L6 deletion mutant porins, suggest that loop L6 folds back into the beta-barrel thereby constricting the native FomA channel. Thus, the position of the channel constriction loop appears to be shifted towards the C terminus in the FomA porin, as compared to the crystal structures of five non-specific diffusion porins.

Amino Acid Sequence↗

Molecular modelling study of HIV p17gag (MA) protein shell utilising data from electron microscopy and X-ray crystallography.

The matrix protein p17gag (MA) is a product of proteolytic cleavage of the gag gene encoded polyprotein (pr55gag) and is formed when HIV particles undergo the process of maturation. The MA protein is associated with the inner surface of the viral membrane and determines the overall shape of the virion. Previous studies have shown the existence of trimers of MA in solution and in the crystalline state. Here, we used molecular modelling methods to identify feasible interactions between pairs of MA trimers and have related this to structural data from electron microscopy. A systematic search docking procedure was able to identify many energetically favourable conformations for a pair of trimers, including some which have been previously reported. These conformations were used to generate several networks of MA trimers, which were then evaluated against structural observations of the MA network. The model suggested here provides a good match with experimental data such as the spacing between gag protein rings, the number and disposition of glycoprotein (gp41-gp120) knobs and the number of copies of MA in a virus particle. It also rationalizes the observed distribution of sizes of virus particles and is consistent with the presence of icosahedral organisation in mature HIV. Energy minimisation performed with explicit water and counter ions, was used to identify residues participating in inter-trimer interactions. The nature of these interactions is discussed in relation to the conservation of these residues in reported variants of the HIV and SIV MA protein sequences.

Computer Simulation↗

Molecular pathogenesis of Sindbis virus encephalitis in experimental animals.

In general, the analysis of a number of strains of Sindbis virus has revealed amino acid differences of potential importance for virulence at relatively few positions in the E2-glycoprotein. Only 10 amino acid changes are potentially implicated, and 9 of these 10 lie in the N-terminal half of the protein (Fig. 1.). Currently, there is strong evidence to implicate 3 of these positions (E2-55, -114, and -172) in virulence (Table V). As more recombinant viruses are prepared and analyzed, the evidence for or against the relevance of other changes should become apparent. As is generally true in alphaviruses, the E1 gene is more invariant than E2 and analysis of several strains has revealed amino acid changes at only four positions (Fig. 2). Two, 72, and 75, are just N-terminal to the hydrophobic segment postulated to be the site of fusion activity, suggesting the possibility that virus entry into the host cell could be affected by amino acid differences at these locations. The other two changes (at 237 and 313) are distant from the fusion site on the linear molecule, but changes at 313 do affect the pH fusion suggesting participation of this site in providing stability to the glycoprotein trimers. The mechanism of altered virulence associated with any amino acid change in the E1- or E2-glycoproteins has yet to be determined. The change at E2-114 associated with reduced virulence in mice shows reduced latency and increased virulence in BHK-21 cells in vitro. This suggests that some changes result in enhanced replication that is host cell-specific. There are several points in the replication cycle of Sindbis virus where the glycoproteins and their ability to undergo conformational changes play an important role in efficiency of replication. These include attachment, fusion, transport through the Golgi, assembly, and budding from the cell surface. Some steps in replication involve host cell proteins (Baric et al., 1983), so that there may be unique, unexplored interactions with neurons or ependymal cells leading to increased neurovirulence for mice that are not represented in the typical BHK, Vero, or chick embryo fibroblast cell culture system. The task now will be to determine why specific amino changes in the proteins of Sindbis virus cause such dramatic changes in the biological properties of the virus.

Age Factors↗

Biochemical and physiological studies of the small heat shock protein Lo18 from the lactic acid bacterium Oenococcus oeni.

The small heat shock protein (smHSP) family has been extensively studied in eukaryotic cells. SmHSP assemble into large multimeric structures and possess chaperone activity that can prevent protein aggregation in vitro. Few studies on prokaryotic smHSP are actually available and no smHSP from lactic acid bacteria has been characterized at a biochemical level to date. Here we report on the Lo18 membrane-associated smHSP from the lactic acid bacterium Oenococcus oeni. Using size exclusion chromatography, nondenaturing pore-exclusion PAGE and in vitro and in vivo cross-linking experiments, the multimeric structure of Lol8 from O. oeni or expressed in Escherichia coli was investigated. In vitro, Lo18 is able to form a trimer and a higher oligomer which could be a dodecamer. Experiments strongly suggest that the same structures exist in vivo. First, Lo18 prevented thermal aggregation of citrate synthase and lactate dehydrogenase even at 60degreesC. These findings showed that the prokaryotic smHSP Lo18 can function as a molecular chaperone in vitro. Second, Lo18 did not protect lactate dehydrogenase from thermal inactivation and did not assist in enzymatic activity restoration after thermal aggregation, suggesting that other components may be needed for the refolding of the enzyme in an active conformation. Third, we showed that membrane association of Lo18 depends on the temperature upshift. Moreover, expression of this smHSP was induced by administration of a membrane fluidiser, the benzyl alcohol, suggesting that Lo18 expression could be regulated by the level of membrane fluidity.

Bacterial Proteins↗