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Single-chain Fv multimers of the anti-neuraminidase antibody NC10: the residue at position 15 in the V(L) domain of the scFv-0 (V(L)-V(H)) molecule is primarily responsible for formation of a tetramer-trimer equilibrium.

Single-chain variable fragment of the murine monoclonal antibody NC10 specific to influenza virus N9 neuraminidase, joined directly in the V(L) to V(H) orientation (scFv-0), forms an equilibrium mixture of tetramer and trimer with the tetramer as the preferred multimeric species. In contrast, the V(H)-V(L) isomer was previously shown to exist exclusively as a trimer. Computer-generated trimeric and tetrameric scFv models, based on the refined crystal structure for NC10 Fv domain, were constructed and used to evaluate factors influencing the transition between V(L)-V(H) trimer and tetramer. These model structures indicated that steric restrictions between loops spanning amino acid residues L55-L59 and L13-L17 from the two adjacent V(L) domains within the V(L)-V(H) trimer were responsible for four scFv-0 molecules assembling to form a tetramer. In particular, leucine at position L15 and glutamate at position L57 appeared to interfere significantly with each other. To minimize this steric interference, the site-directed mutagenesis technique was used to construct several NC10 scFv-0 clones with mutations at these positions. Size-exclusion chromatographic analyses revealed that several of these mutations resulted in the production of NC10 scFv-0 proteins with significantly altered tetramer-trimer equilibrium ratios. In particular, introduction of a polar residue, such as asparagine or threonine, at position L15 generated a highly stable NC10 scFv-0 trimer.

Amino Acid Sequence↗

Surfactant protein D binds to human immunodeficiency virus (HIV) envelope protein gp120 and inhibits HIV replication.

The envelope protein (gp120) of human immunodeficiency virus (HIV) contains highly conserved mannosylated oligosaccharides. These glycoconjugates contribute to resistance to antibody neutralization, and binding to cell surface lectins on macrophages and dendritic cells. Mannose-binding lectin (MBL) binds to gp120 and plays a role in defence against the virus. In this study it is demonstrated that surfactant protein D (SP-D) binds to gp120 and inhibits HIV infectivity at significantly lower concentrations than MBL. The binding of SP-D was mediated by its calcium-dependent carbohydrate-binding activity and was dependent on glycosylation of gp120. Native dodecameric SP-D bound to HIV gp120 more strongly than native trimeric SP-D. Since one common polymorphic form of SP-D is predominantly expressed as trimers and associated with lower blood levels, these individuals may have less effective innate defence against HIV. A chimeric protein containing the N-terminal and collagen domains of SP-D linked to the neck and carbohydrate-recognition domains of MBL (called SP-D/MBL(neck+CRD)) had greater ability to bind to gp120 and inhibit virus replication than either SP-D or MBL. The enhanced binding of SP-D/MBL(neck+CRD) was dependent on assembly into higher molecular mass multimers (i.e. a trimeric form of the chimera did not bind to a greater extent than MBL). Hence, the enhanced binding of SP-D compared with MBL results from distinctive properties of its N-terminal and/or collagen domains. SP-D is present in lung and airway fluids, as well as in blood and various mucosal locations, and could, like MBL, play a role in restricting HIV transmission or replication in vivo.

HIV Envelope Protein gp120↗

Dynamic combinatorial libraries based on hydrogen-bonded molecular boxes.

This article describes two different types of dynamic combinatorial libraries of host and guest molecules. The first part of this article describes the encapsulation of alizarin trimer 2a3 by dynamic mixtures of up to twenty different self-assembled molecular receptors together with the amplification and selection of the best binder. Receptors (1a-d)3.(DEB)6 are formed by the self-assembly of six diethyl barbiturate (DEB) and calix[4]arene dimelamine derivatives 1a-d by using hydrogen bonds. The largest amplification factor (2.8) for a host assembly (1a3.(DEB)6) was observed after the addition of 2a to four-component library 1a(n).1b(3-n).(DEB)6 (n=0-3). Addition of 2a to twenty-component library 1a(n).1b(m).1c(o).1d(3-(n+m+o)).(DEB)6 (n, m, o=0-3; (n+m+o)<or=3) also showed amplification of receptor 1a3.(DEB)6. The second part of this article describes the complexation of libraries of different alizarin-like guest molecules (2a-d) and the self-assembled receptor 1a3.(DEB)6. This receptor is able to template the formation of the best-fitting guest trimer.

Anthraquinones↗

Characterization and structural properties of the major biliproteins of Anabaena sp.

Studies are presented of the biliproteins of Anabaena sp. This filamentous cyanobacterium contains three major biliproteins. Whereas two of these, C-phycocyanin and allophycocyanin, are common to all cyanobacteria, the third, phycoerythrocyanin (gammamax approximately 568 nm) has hitherto not been described and its distribution among cyanobacteria appears to be limited. Anabaena variabilis and Anabaena sp. 6411 allophycocyanin, C-phycocyanin, and phycoerythrocyanin were purified to homogeneity and characterized with respect to molecular weight, isoelectric point, absorption spectrum and amino acid composition. The alpha and beta subunits of each of these proteins were also purified to homogeneity and characterized in the same manner. The tetrapyrrole chromophore content was determined for each of the proteins and subunits. The alpha subunit of phycoerythrocyanin carries a novel phycobiliviolin-like chromophore. This chromophore has not previously been detected in cyanobacterial biliproteins, but has been noted as a prosthetic group of a cryptophytan phycocyanin. Sedimentation equilibrium studies show that at pH 7.0, at protein concentrations of 0.2-0.6 mg/ml, allophycocyanin, C-phycocyanin and phycoerythrocyanin, each exists as a trimeric aggregate, (alphabeta)3, of molecular weight of approximately 105000. Structrual studies of microcrystals of these three biliproteins by electron microscopy and X-ray diffraction reveal a common plan for the construction of higher assembly forms. The major building block appears to be the trimer (alphabeta)3. It is proposed that this is a disc-like structure about 3.0 X 12.0 nm. The individual alpha or beta subunits are roughly spherical, 3 nm in diameter. Allophycocyanin trimers stack to form bundles of rods which form long needles. Both phycocyanin and phycoerythrocyanin form double discs (alphabeta)6 which are visible as ring-shaped structures by electron microscopy. The mode of assembly of the biliprotein structures in the phycobilisome is, as yet, unknown.

Amino Acids↗

Role of the carboxy-terminal phenylalanine in the biogenesis of outer membrane protein PhoE of Escherichia coli K-12.

Most bacterial outer membrane proteins contain a phenylalanine at their C terminus. It has been shown that this residue has an important role in the efficient and correct assembly of PhoE protein into the Escherichia coli outer membrane, since its substitution or deletion resulted in the accumulation of trypsin-sensitive monomers of this normally trimeric protein. Here, the role of the C-terminal Phe in the assembly of PhoE was studied in further detail. Immunocytochemical labelling on ultrathin cryosections revealed that a mutant PhoE protein that lacks the C-terminal Phe accumulates in the periplasm. However, when the expression levels of the altered species were reduced, the efficiency of outer membrane incorporation was increased and the lethal effects were alleviated. The role of the C-terminal Phe in protein folding, trimerization and outer membrane incorporation was further studied in vitro. Deletion of this residue interfered with the efficiency of the formation of an assembly-competent folded monomer, and the stability of this PhoE form was affected. The in vitro trimerization and insertion into outer membranes were not affected by the mutation.

Bacterial Proteins↗

Amyloid beta -protein (Abeta) assembly: Abeta 40 and Abeta 42 oligomerize through distinct pathways.

Amyloid beta-protein (Abeta) is linked to neuronal injury and death in Alzheimer's disease (AD). Of particular relevance for elucidating the role of Abeta in AD is new evidence that oligomeric forms of Abeta are potent neurotoxins that play a major role in neurodegeneration and the strong association of the 42-residue form of Abeta, Abeta42, with the disease. Detailed knowledge of the structure and assembly dynamics of Abeta thus is important for the development of properly targeted AD therapeutics. Recently, we have shown that Abeta oligomers can be cross-linked efficiently, and their relative abundances quantified, by using the technique of photo-induced cross-linking of unmodified proteins (PICUP). Here, PICUP, size-exclusion chromatography, dynamic light scattering, circular dichroism spectroscopy, and electron microscopy have been combined to elucidate fundamental features of the early assembly of Abeta40 and Abeta42. Carefully prepared aggregate-free Abeta40 existed as monomers, dimers, trimers, and tetramers, in rapid equilibrium. In contrast, Abeta42 preferentially formed pentamerhexamer units (paranuclei) that assembled further to form beaded superstructures similar to early protofibrils. Addition of Ile-41 to Abeta40 was sufficient to induce formation of paranuclei, but the presence of Ala-42 was required for their further association. These data demonstrate that Abeta42 assembly involves formation of several distinct transient structures that gradually rearrange into protofibrils. The strong etiologic association of Abeta42 with AD may thus be a result of assemblies formed at the earliest stages of peptide oligomerization.

Alzheimer Disease↗

Modularization of the type II secretion gene cluster from Xanthomonas euvesicatoria facilitates the identification of a structurally conserved XpsCLM assembly platform complex.

Many bacterial pathogens depend on a type II secretion (T2S) system to secrete virulence factors from the periplasm into the extracellular milieu. T2S systems consist of an outer membrane secretin channel, a periplasmic pseudopilus and an inner membrane-associated assembly platform including a cytoplasmic ATPase. The components of T2S systems are often conserved in different bacterial species, however, the architecture of the assembly platform is largely unknown. Here, we analysed predicted assembly platform components of the Xps-T2S system from the plant-pathogenic bacterium Xanthomonas euvesicatoria. To facilitate these studies, we generated a modular xps-T2S gene cluster by Golden Gate assembly of single promoter and gene fragments. The modular design allowed the efficient deletion and replacement of T2S genes and the insertion of reporter fusions. Mutant approaches as well as interaction and crosslinking studies showed that the predicted assembly platform components XpsC, XpsL and XpsM form a trimeric complex which is essential for T2S and associates with the cytoplasmic ATPase XpsE and the secretin XpsD. Structural modeling revealed a similar trimeric architecture of XpsCLM homologs from Pseudomonas, Vibrio and Klebsiella species, despite overall low amino acid sequence similarities. In X. euvesicatoria, crosslinking and fluorescence microscopy studies showed that the formation of the XpsCLM complex is independent of the secretin and vice versa, suggesting that the assembly of the T2S system is a dynamic process which involves the association of preformed subcomplexes.

Xanthomonas↗

Human immunodeficiency virus type 1 matrix protein assembles on membranes as a hexamer.

The membrane-binding matrix (MA) domain of the human immunodeficiency virus type 1 (HIV-1) structural precursor Gag (PrGag) protein oligomerizes in solution as a trimer and crystallizes in three dimensions as a trimer unit. A number of models have been proposed to explain how MA trimers might align with respect to PrGag capsid (CA) N-terminal domains (NTDs), which assemble hexagonal lattices. We have examined the binding of naturally myristoylated HIV-1 matrix (MyrMA) and matrix plus capsid (MyrMACA) proteins on membranes in vitro. Unexpectedly, MyrMA and MyrMACA proteins both assembled hexagonal cage lattices on phosphatidylserine-cholesterol membranes. Membrane-bound MyrMA proteins did not organize into trimer units but, rather, organized into hexamer rings. Our results yield a model in which MA domains stack directly above NTD hexamers in immature particles, and they have implications for HIV assembly and interactions between MA and the viral membrane glycoproteins.

Gene Products, gag↗

Design and crystal structure of bacteriophage T4 mini-fibritin NCCF.

Fibritin is a fibrous protein that forms "whiskers" attached to the neck of bacteriophage T4. Whiskers interact with the long tail fibers regulating the assembly and infectivity of the virus. The fibritin trimer includes the N-terminal domain responsible for attachment to the phage particle and for the collar formation, the central domain forming a 500 A long segmented coiled-coil structure, and the C-terminal "foldon" domain. We have designed a "mini" fibritin with most of the coiled-coil domain deleted, and solved its crystal structure. The non-helical N-terminal part represents a new protein fold that tightly interacts with the coiled-coil segment forming a single domain, as revealed by calorimetry. The analysis of the crystal structure and earlier electron microscopy data on the collar-whisker complex suggests the necessity of other proteins to participate in the collar formation. Crystal structure determination of the N-terminal domain of fibritin is the first step towards elucidating the detailed structure and assembly mechanism of the collar-whisker complex.

Amino Acid Motifs↗

The legumin precursor from white lupin seed. Identity of the subunits, assembly and proteolysis.

The precursors of the legumin-like storage protein from developing white lupin seeds (35 days after flowering) are trimers composed of protomers of M(r) 72,000 or 67,000. Some subunits of these oligomers contain processed precursor polypeptides, namely alpha polypeptides of either 52,000 or 44,000 linked through disulphide bonds to a beta polypeptide of 21,000, typical of the mature legumin. The prolegumin is glycosylated. Legumin oligomers purified from the same seeds are both trimers and hexamers; some of their subunits are still made of precursor polypeptides. The hexamer contains less precursor polypeptide than the trimer. A low level or absence of precursor appears to be a condition of hexamer assembly. The heterogenous prolegumin and legumin oligomers represent intermediates in the processing of the prolegumin to mature legumin. Hydrophobic-interaction chromatography on TSK-phenyl-5PW and titration with the hydrophobic probe 8-anilino-1-naphthalenesulphonate indicate that the legumin is less hydrophobic than the prolegumin. This is attributed to structural rearrangements at processing of the propolypeptide, made evident by the behaviour in CD and by the second-derivative ultraviolet spectra of the two proteins. The total protein extract of developing cotyledons at 40 days after flowering contains endopeptidases, similar to those existing in the resting seeds, which cause a limited cascade degradation of the prolegumin and legumin.

Blotting, Western↗

Triply fused Zn(II)-porphyrin oligomers: synthesis, properties, and supramolecular interactions with single-walled carbon nanotubes (SWNTs).

The photophysical, electrochemical, and self-assembly properties of a novel triply fused Zn(II)-porphyrin trimer were investigated and compared to the properties of a triply fused porphyrin dimer and the analogous monomer. The trimer exhibited significantly red-shifted absorption bands relative to the corresponding monomer and dimer. Electrochemical investigations indicated a clear trend in redox properties amongst the three porphyrin structures, with the lowest oxidation potential and the lowest HOMO-LUMO gap exhibited by the triply fused trimer. This electrochemical behavior is attributed to the extensive pi-electron delocalization in the trimeric structure relative to the monomer and dimer. Additionally, it was found that the trimer forms extremely strong and nearly irreversible supramolecular interactions with single-walled carbon nanotubes (SWNTs), resulting in stable solutions of porphyrin-nanotube complexes in THF. Formation of these complexes required the addition of trifluoroacetic acid (TFA) to the solvent. This allowed the oligomers to make close contact with the nanotubes, enabling the formation of stable supramolecular assemblies. Atomic force microscopy (AFM) was used to observe the supramolecular porphyrin-nanotube complexes and revealed that the porphyrin trimer formed a uniform coating on the SWNTs. Height profiles indicated that nanotube bundles could be exfoliated into either individual tubes or very small bundles by exposure to the porphyrin trimer during sonication.

Journal Article↗

Structure and mechanism of imidazoleglycerol-phosphate dehydratase.

The structure of A. thaliana imidazoleglycerol-phosphate dehydratase, an enzyme of histidine biosynthesis and a target for the triazole phosphonate herbicides, has been determined to 3.0 A resolution. The structure is composed of 24 identical subunits arranged in 432 symmetry and shows how the formation of a novel dimanganese cluster is crucial to the assembly of the active 24-mer from an inactive trimeric precursor and to the formation of the active site of the enzyme. Molecular modeling suggests that the substrate is bound to the manganese cluster as an imidazolate moiety that subsequently collapses to yield a diazafulvene intermediate. The mode of imidazolate recognition exploits pseudosymmetry at the active site arising from a combination of the assembly of the particle and the pseudosymmetry present in each subunit as a result of gene duplication. This provides an intriguing example of the role of evolution in the design of Nature's catalysts.

Amino Acid Sequence↗

Mechanism of the self-assembly of apoferritin from horse spleen. Cross-linking and spectroscopic analysis.

Apoferritin from horse spleen can be reversibly dissociated at pH2 or in 7.2 M G-HCl (pH 3.5). Reconstitution of the native icositetramer in 0.1 M TEA buffer (pH 7.9) in the presence of 1 mM EDTA and 3 mM dithioerythritol leads to yields higher than 80%. To monitor the kinetic mechanism, intrinsic fluorescence, far-UV circular dichroism, and covalent cross-linking with glutaraldehyde were applied. The overall mechanism of assembly is characterized by a sequence of concentration-dependent association reactions involving "structured monomers" and a dimeric intermediate as the most prominent species, apart from trimers and dodecamers. The parallel decrease in monomers, dimers and trimers indicates that association equilibria precede the formation of the final assembly product. The assembly reaction is accompanied by characteristic changes in fluorescence emission and dichroic absorption. To a first approximation, renaturation and reassociation may be quantitatively described by one single rate-determining second-order process, subsequent to fast folding steps at the monomer level.

Animals↗

The assembly pathway of outer membrane protein PhoE of Escherichia coli.

The assembly of the wild-type and several mutant forms of the trimeric outer membrane porin PhoE of Escherichia coli was investigated in vitro and in vivo. In in vivo pulse-chase experiments, approximately half of the wild-type PhoE molecules assembled within the 30-s pulse in the native conformation in the cell envelope. The other half of the molecules followed slower kinetics, and three intermediates in this multistep assembly process were detected: a soluble trypsin-sensitive monomer, a trypsin-sensitive monomeric form that was loosely associated with the cell envelope and a metastable trimer, which was integrated into the membranes and converted to the stable trimeric configuration within minutes. The metastable trimers disassembled during sample preparation for standard SDS/PAGE into folded monomers. In vitro, the isolated PhoE protein could efficiently be folded in the presence of N,N-dimethyldodecylamine-N-oxide (LDAO). A mutant PhoE protein, DeltaF330, which lacks the C-terminal phenylalanine residue, mainly followed the slower kinetic pathway observed in vivo, resulting in increased amounts of the various assembly intermediates. It appears that the DeltaF330 mutant protein is intrinsically able to fold, because it was able to fold in vitro with LDAO with similar efficiencies as the wild-type protein. Therefore, we propose that the conserved C-terminal Phe is (part of) a sorting signal, directing the protein efficiently to the outer membrane. Furthermore, we analysed a mutant protein with a hydrophilic residue introduced at the hydrophobic side of one of the membrane-spanning amphipathic beta strands. The assembly of this mutant protein was not affected in vivo or in vitro in the presence of LDAO. However, it was not able to form folded monomers in a previously established in vitro folding system, which requires the presence of lipopolysaccharides and Triton. Hence, a folded monomer might not be a true assembly intermediate of PhoE in vivo.

Biochemistry↗

Dimeric and trimeric antibodies: high avidity scFvs for cancer targeting.

Recombinant antibody fragments can be engineered to assemble into stable multimeric oligomers of high binding avidity and specificity to a wide range of target antigens and haptens. This review describes the design and expression of diabodies (dimers), triabodies (trimers) and tetrabodies (tetramers). In particular we discuss the role of linker length between V-domains and the orientation of the V-domains to direct the formation of either diabodies (60 kDa), triabodies (90 kDa) or tetrabodies (120 kDa), and how the size, flexibility and valency of each molecules is suited to different applications for in vivo imaging and therapy. Single chain Fv antibody fragments joined by polypeptide linkers of at least 12 residues irrespective of V-domains orientation predominantly form monomers with varying amounts of dimer and higher molecular mass oligomers in equilibrium. A scFv molecule with a linker of 3-12 residues cannot fold into a functional Fv domain and instead associates with a second scFv molecule to form a bivalent dimer (diabody, approximately 60 kDa). Reducing the linker length below three residues can force scFv association into trimers (triabodies, approximately 90 kDa) or tetramers ( approximately 120 kDa) depending on linker length, composition and V-domain orientation. A particular advantage for tumour targeting is that molecules of 60-100 kDa have increased tumour penetration and fast clearance rates compared with the parent Ig (150 kDa). We highlight a number of cancer-targeting scFv diabodies that have undergone successful pre-clinical trials for in vivo stability and efficacy. We also briefly review the design of multi-specific Fv modules suited to cross-link two or more different target antigens. Bi-specific diabodies formed by association of different scFv molecules have been designed as cross-linking reagents for T-cell recruitment into tumours (immunotherapy), viral retargeting (gene therapy) and as red blood cell agglutination reagents (immunodiagnostics). The more challenging trispecific multimers (triabodies) remain to be described.

Antibodies, Monoclonal↗

Conformational suppression of inter-receptor signaling defects.

Motile bacteria follow gradients of attractant and repellent chemicals with high sensitivity. Their chemoreceptors are physically clustered, which may enable them to function as a cooperative array. Although native chemoreceptor molecules are typically transmembrane homodimers, they appear to associate through their cytoplasmic tips to form trimers of dimers, which may be an important architectural element in the assembly and operation of receptor clusters. The five receptors of Escherichia coli that mediate most of its chemotactic and aerotactic behaviors have identical trimer contact residues and have been shown by in vivo crosslinking methods to form mixed trimers of dimers. Mutations at the trimer contact sites of Tsr, the serine chemoreceptor, invariably abrogate Tsr function, but some of those lesions (designated Tsr*) are epistatic and block the function of heterologous chemoreceptors. We isolated and characterized mutations (designated Tar()) in the aspartate chemoreceptor that restored function to Tsr* receptors. The suppressors arose at or near the Tar trimer contact sites and acted in an allele-specific fashion on Tsr* partners. Alone, many Tar() receptors were unable to mediate chemotactic responses to aspartate, but all formed clusters with varying efficiencies. Most of those Tar() receptors were epistatic to WT Tsr, but some regained Tar function in combination with a suppressible Tsr* partner. Tar()-Tsr* suppression most likely occurs through compensatory changes in the conformation or dynamics of a mixed receptor signaling complex, presumably based on trimer-of-dimer interactions. These collaborative teams may be responsible for the high-gain signaling properties of bacterial chemoreceptors.

Bacterial Proteins↗

The giant extracellular hemoglobin from the polychaete Neanthes diversicolor. The cDNA-derived amino acid sequence of linker chain L2 and the exon/intron boundary conserved in linker genes.

The 4000 kDa extracellular hemoglobin from the polychaete Neanthes diversicolor consists of three types of subunits; three 15 kDa monomers (chains M1, M2 and M3), a 45 kDa disulfide-bonded trimer of chains T1, T2 and T3, and two 50-55 kDa disulfide-bonded homodimeric linkers (chains L1 and L2). The latter linker subunits are essential for the assembly of the other heme-containing subunits, monomers and a trimer. The cDNA encoding the linker chain L2 was amplified by polymerase chain reaction (PCR), and the cDNA-derived amino acid sequence of 235 residues has been determined. The sequence showed 22-75% identity with other linker chains. All of the linker sequences examined so far have a highly conserved cysteine-rich segment at positions 89-130: Xaa3-Cys-Xaa6-Cys-Xaa6-Cys-Xaa6-Cys-Asp-Gly-X aa2-Asp-Cys-Xaa4-Asp-Glu-Xaa4-Cys, and the motif corresponds exactly to the cysteine-rich repeats of the ligand-binding domains of vertebrate low-density lipoprotein (LDL) receptors (Suzuki, T. and Riggs, A.F. (1993) J. Biol. Chem. 268, 13548-13555). A 287 bp intron interrupts the coding sequence of Neanthes L2 gene just at the N-terminal boundary of this motif, and the position of the splice junction was exactly conserved in Neanthes and Lumbricus linker genes. This suggests that the intron has been conserved for at least 450 million years in annelid linker genes. The evolutionary origin of the remaining parts of linker chains is unclear, but it is noteworthy that the topology of the two intrachain disulfide bridges in the C-terminal segment of linker chains is homologous with that of the carbohydrate-recognition domain of animal C-type lectin.

Amino Acid Sequence↗

Self-complementary peptides for the formation of collagen-like triple helical supramolecules.

Collagen is acknowledged as one of the most prominent biomaterials on account of its high biocompatibility and biostability. The development of artificial collagens to replace the animal-derived collagens presents a challenge in the formation of safer and highly functionalized biomaterials. Here, a novel peptide-based system for obtaining collagen-like supramolecules via a spontaneous self-assembling process is described. The designed collagen-like peptides are self-complementary trimers in which each of the 24-mer peptide strands is tethered by two cystine knots forming a staggered arrangement. Their self-assembling ability in aqueous solution was analyzed by circular dichroism, ultrafiltration, and laser diffraction particle size estimation. The obtained results indicate that the staggered trimers form large supramolecular architectures through intermolecular triple helix-formation.

Amino Acid Sequence↗