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Identification of 2'-phosphodiesterase, which plays a role in the 2-5A system regulated by interferon.

The 2-5A system is one of the major pathways for antiviral and antitumor functions that can be induced by interferons (IFNs). The 2-5A system is modulated by 5'-triphosphorylated, 2',5'-phosphodiester-linked oligoadenylates (2-5A), which are synthesized by 2',5'-oligoadenylate synthetases (2',5'-OASs), inactivated by 5'-phosphatase and completely degraded by 2'-phosphodiesterase (2'-PDE). Generated 2-5A activates 2-5A-dependent endoribonuclease, RNase L, which induces RNA degradation in cells and finally apoptosis. Although 2',5'-OASs and RNase L have been molecularly cloned and studied well, the identification of 2'-PDE has remained elusive. Here, we describe the first identification of 2'-PDE, the third key enzyme of the 2-5A system. We found a putative 2'-PDE band on SDS-PAGE by successive six-step chromatographies from ammonium sulfate precipitates of bovine liver and identified a partial amino acid sequence of the human 2'-PDE by mass spectrometry. Based on the full-length sequence of the human 2'-PDE obtained by in silico expressed sequence tag assembly, the gene was cloned by reverse transcription-PCR. The recombinant human 2'-PDE expressed in mammalian cells certainly cleaved the 2',5'-phosphodiester bond of 2-5A trimer and 2-5A analogs. Because no sequences with high homology to this human 2'-PDE were found, the human 2'-PDE was considered to be a unique enzyme without isoform. Suppression of 2'-PDE by a small interfering RNA and a 2'-PDE inhibitor resulted in significant reduction of viral replication, whereas overexpression of 2'-PDE protected cells from IFN-induced antiproliferative activity. These observations identify 2'-PDE as a key regulator of the 2-5A system and as a potential novel target for antiviral and antitumor treatments.

Adenine Nucleotides↗

Coiled-coil molecular recognition: directed solution assembly of receptor ectodomains.

The high affinity interleukin-2 (IL-2) receptor is composed of at least three cell surface proteins (alpha, beta and gamma subunits), each of which is independently capable of ligand binding. Physiologically, these subunits cooperate to form dimeric and trimeric complexes that efficiently capture IL-2 and transmit the signal across the membrane. The knowledge of how each subunit functions with respect to ligand capture, signal transmission and internalization is essential for the development of ligand-based IL-2 agonists and antagonists, as well as receptor-related therapeutic and diagnostic reagents. Only one of the subunits (p55 or alpha chain) is capable of interacting with ligand in solution in a manner that resembles cell surface binding. To generate soluble multimeric complexes of the IL-2 receptor subunits that may bind ligand in solution in a fashion that mimics the same receptor complexes on the cell surface, we have added recognition sequences (coiled-coil heptad repeats) to the ectodomains of the individual receptors. Here we describe the expression and characterization of a prototype IL-2 beta receptor ectodomain-coiled-coil fusion protein and demonstrate that this is a feasible approach to the preparation of cytokine receptor solution complexes.

Amino Acid Sequence↗

The dhb operon of Bacillus subtilis encodes the biosynthetic template for the catecholic siderophore 2,3-dihydroxybenzoate-glycine-threonine trimeric ester bacillibactin.

Bacillus subtilis was reported to produce the catecholic siderophore itoic acid (2,3-dihydroxybenzoate (DHB)-glycine) in response to iron deprivation. However, by inspecting the DNA sequences of the genes dhbE, dhbB, and dhbF as annotated by the B. subtilis genome project to encode the synthetase complex for the siderophore assembly, various sequence errors within the dhbF gene were predicted and confirmed by re-sequencing. According to the corrected sequence, dhbF encodes a dimodular instead of a monomodular nonribosomal peptide synthetase. We have heterologously expressed, purified, and assayed the substrate selectivity of the recombinant proteins DhbB, DhbE, and DhbF. DhbE, a stand-alone adenylation domain of 59.9 kDa, activates, in an ATP-dependent reaction, DHB, which is subsequently transferred to the free thiol group of the cofactor phosphopantetheine of the bifunctional isochorismate lyase/aryl carrier protein DhbB. The third synthetase, DhbF, is a dimodular nonribosomal peptide synthetase of 264 kDa that specifically adenylates threonine and, to a lesser extent, glycine and that covalently loads both amino acids onto their corresponding peptidyl carrier domains. To functionally link the dhb gene cluster to siderophore synthesis, we have disrupted the dhbF gene. Comparative mass spectrometric analysis of culture extracts from both the wild type and the dhbF mutant led to the identification of a mass peak at m/z 881 ([M-H](1-)) that corresponds to a cyclic trimeric ester of DHB-glycine-threonine.

Adenosine Monophosphate↗

Self-assembly of achiral and chiral macrocyclic ligands: synthesis, protonation constants, conformation and asymmetric catalysis.

New 30-membered achiral and chiral polyaza macrocyclic ligands, L1 and L2 were synthesized directly from [3 + 3] condensation of phthalic dicarboxaldehyde with cis- and (1R,2R)-diaminocyclohexane, respectively. The trimeric macrocyclic structures were confirmed by electrospray ionization mass spectrometry (ESI-MS), 1H NMR, 13C NMR spectroscopy and elemental analysis. Potentiometry was used to determine the protonation constants of the ligands. UV-vis spectrophotometric titration was employed to investigate the coordination and conformational properties of the chiral ligand (L2). Direct enantioselective aldol reaction has been successfully performed using 4-nitrobenzaldehyde and acetone in the presence of the chiral macrocycle and its zinc(II) complexes as catalysts.

Journal Article↗

Biosynthesis of human fibrinogen. Subunit interactions and potential intermediates in the assembly.

Stable transfected baby hamster kidney (BHK) cells expressing human alpha, beta, and gamma fibrinogen chains together, in various combinations of any two, or individually, were established. Several types of subunit interactions were observed in the intracellular extracts of the transfected BHK cell lines as well as in Hep G2 cells. These included: 1) formation of alpha gamma dimers linked by a disulfide bond(s), 2) formation of beta gamma dimers linked by a disulfide bond(s), 3) formation of alpha beta gamma half-molecules linked by disulfide bonds, and 4) formation of mature fibrinogen, which was also secreted into the cell culture medium. Analysis of the chain composition confirmed the stoichiometry of the alpha gamma, beta gamma, and alpha beta gamma complexes. These data are consistent with the proposal that the alpha gamma and beta gamma dimers as well as the alpha beta gamma half-molecules are intermediates in the assembly and biosynthesis of fibrinogen. In contrast, disulfide-linked alpha beta complexes were not found in transfected BHK cells or in Hep G2 cells, suggesting that the formation of disulfide bonds between these two chains most likely occurs when alpha beta gamma half-molecules are formed from alpha gamma and/or beta gamma complexes and when alpha beta gamma half-molecules dimerize to generate the mature molecule. Dimers, trimers, and larger oligomers of each individual chain linked by disulfide bonds were also identified when each chain was expressed in the absence of the other two chains. Preferential formation of alpha gamma and beta gamma complexes, rather than oligomers of individual chains, suggested that the oligomers were less likely to be intermediates in the assembly of fibrinogen. A model for fibrinogen assembly is presented based on these results.

Animals↗

Xanthophylls of the major photosynthetic light-harvesting complex of plants: identification, conformation and dynamics.

The electronic transitions of lutein and neoxanthin in the major light-harvesting complex, LHCIIb, have been identified for the first time. It was found that 0-0, 0-1 and 0-2 transitions of neoxanthin were located around 486, 457 and 430 nm, whilst those for lutein were dependent on the oligomerisation state. For the monomer, the absorption bands of lutein were found at 495, 466 and 437 nm. Trimerisation caused a decrease in lutein absorption and the parallel appearance of an additional absorption band around 510 nm, which was identified by resonance Raman excitation spectra to originate from lutein. Circular dichroism measurements together with analysis of the nu(4) resonance Raman region of xanthophylls suggested that this lutein molecule is distorted in the trimer. This feature is not predicted by the LHCIIb atomic model of Kühlbrandt and co-workers [Kühlbrandt, W., Wang, D.N. and Fugiyoshi, Y. (1994) Nature 367, 614-621] and is an important step in understanding pigment dynamics of the complex. Oligomerisation of trimers led to a specific distortion of the neoxanthin molecule. These observations suggest that the xanthophylls of LHCIIb sense the protein conformation and which may reflect their special role in the assembly and function of the light-harvesting antenna of higher plants.

Biopolymers↗

N- and C-domains of HIV-1 gp41: mutation, structure and functions.

Recent studies demonstrated that the N- and C-domains of HIV-1 gp41 is involved in virus-mediated membrane fusion resulting in HIV-entry into the target cells. Up to now, viral mutation baffled many scientists to develop effective vaccines and drugs against HIV-1. To acquire more information of mutation of gp41 and to reveal the relationship of structure and function of the N- and C-domains, we compared and analyzed amino acid sequences of the gp41 ectodomain (aa 512-681) of 862 isolates from most HIV-1 clades (including A, B, C, D, E, F, G, H, I, J and O clades). A consensus sequence of the ectodomain with the highest frequency emerging on each position is constituted. The fusion domain and the N-domain belong to the most conserved regions in gp41, and most variable residues assemble partial to the C terminal of gp41. The hydrophobicity of each position is also calculated. The a and d positions in the N-domain for maintaining stabilization of the trimeric coiled coil interactions are highly conservative, and the e and g positions in the C-domain to retain the interaction show also highly conservative. The strange high conservation of the c residues may have an implication in the coiled coil structure. The highly conserved residues form the lining of the hydrophobic cavity and the deep cavity is an ideal target for small molecular inhibitors. On the C-terminal of the C-domain there is a highly conserved segment GIVQQQ. They are intimately involved in forming the three interfaces between neighboring helices. The function of the N- and C-domains, such as binding to the potential cellular receptor and inducing protective activities, are also discussed. These studies on the mutation, structure and functions of the N- and C-domains suggested that both domains become a new focus to develop effective vaccine and antiviral drugs in the new strategies.

Amino Acid Sequence↗

Folding of coliphage T4 short tail fiber in vitro. Analysing the role of a bacteriophage-encoded chaperone.

The morphogenesis of the Escherichia coli bacteriophage T4 depends on the presence of helper proteins which are not components of the mature virion. Two bacteriophage-encoded proteins, p57 and p38, are required for the assembly of the bacteriophage T4 tail fibers. In the absence of p57, two polypeptides of the long fiber (p34 and p37) and that of the short tail fiber (p12) fail to trimerize. Instead they form water-insoluble aggregates. Co-expression of the genes 12 and 57 in vivo caused the formation of only trimeric, water-soluble p12. The function of g57 cannot be replaced by overexpression of the host proteins GroEL/ES or parvulin. The mechanism of action of this helper protein has remained unknown, mainly because it has not been possible to determine its activity in vitro. Purified p12, denatured in 7 M urea, trimerized spontaneously in a slow reaction (half-time approximately 6 h) and with low yield. Upon renaturation, p12 forms native SDS-resistant trimers as indicated by spectroscopic and hydrodynamic measurements. Addition of p57 increased the rate of folding threefold and nearly doubled the yield. These experiments demonstrate that p57 acts as a molecular chaperone during folding of T4 tail fibers.

Bacteriophage T4↗

An enzyme that removes clathrin coats: purification of an uncoating ATPase.

Uncoating ATPase, an abundant 70,000-mol-wt polypeptide mediating the ATP-dependent dissociation of clathrin from coated vesicles and empty clathrin cages, has been purified to virtual homogeneity from calf brain cytosol. Uncoating protein is present in cells in amounts roughly stoichiometric with clathrin. This enzyme is isolated as a mixture of monomers and dimers, both forms being active. ATP can support protein-facilitated dissociation of clathrin at micromolar levels; all other ribotriphosphates as well as deoxy-ATP are inactive. The clathrin that is released from cages consists of trimers (triskelions) in a stoichiometric complex with uncoating ATPase. These complexes with clathrin have little tendency to self-associate at neutral pH, and at acidic pH they interfere with the assembly of free clathrin. The possible existence and function of these complexes as clathrin carriers in cells would explain why uncoating protein is made in quantities equivalent to clathrin.

Adenosine Triphosphatases↗

Small molecules that bind the inner core of gp41 and inhibit HIV envelope-mediated fusion.

HIV-1 enters cells by membrane fusion, mediated by the trimeric viral envelope glycoprotein gp160, which is processed by a single proteolytic cleavage into stably associated gp120 and gp41. The gp120/gp41 trimer can be triggered to undergo an irreversible conformational change. Using a protein-based assay designed to mimic the gp41 conformational change, we screened for small molecules that prevent the formation of postfusion gp41. Several compounds were identified. One set of structurally related molecules inhibited formation of a postfusion-like assembly with an IC50 of approximately 5 microM. The compounds also inhibited envelope-mediated membrane fusion in both cell-cell fusion and viral infectivity assays. Thus, our screen identifies effective fusion inhibitors. Tested against a panel of envelope proteins from primary HIV-1 isolates, the compounds inhibited fusion across a broad range of clades, including both M and T tropic strains. They bind in a highly conserved, hydrophobic pocket on the inner core of the gp41 trimer, a region previously identified as a potential inhibitor site.

Amino Acid Sequence↗

The molecular interactions of heat shock protein 47 (Hsp47) and their implications for collagen biosynthesis.

Heat shock protein 47 (Hsp47) is a procollagen/collagen-specific molecular chaperone protein derived from the serpin family of proteins and essential for the early stages of collagen biosynthesis. In this paper, the results of an extensive biophysical analysis of mature recombinant mouse Hsp47 show the existence of both a structurally mesostable monomer with a 5-strand A-sheet and/or a hyperstable trimer; both states have biological activity. It is also demonstrated that Hsp47 is able to bind to a monomeric and partially folded conformation collagen mimic peptide (PPG)(10). Upon peptide binding Hsp47 has the capacity to induce the peptide backbone to fold into a polyproline type II conformation. Induction of this conformation results in (PPG)(10) peptides associating into higher order assemblies with increased stability compared with the monomeric peptide alone. These assemblies are similar to those observed by others (Go, N., and Suezaki, Y. (1973) Biopolymers 12, 1927-1930; Engel, J., Chen, H. T., Prockop, D. J., and Klump, H. (1977) Biopolymers 16, 601-622) when the peptide is dissolved at high concentration and are proposed to be long chains of peptides in a collagen-like configuration. Examination of the biophysical characteristics of both monomeric and trimeric Hsp47-(PPG)(10) complexes is also used to determine that the peptide-binding site does not reside in strand 4 position of sheet A, as observed for other serpins (Skinner, R., Chang, W. S. W., Jin, L., Pei, X., Huntington, J. A., Abrahams, J. P., Carrell, R. W., and Lomas, D. A. (1998) J. Mol. Biol. 283, 9-14), leaving earlier proposals of a binding site near helix A viable.

Animals↗

The RMA-S lymphoma mutant; consequences of a peptide loading defect on immunological recognition and graft rejection.

Experiments with mutant cell lines have underscored the role for peptide in maintenance of the structure of major histocompatibility complex (MHC) class-I molecules. The class-I molecules act as receptors for antigenic and "self" peptides derived from degraded intracellular synthesized proteins. The class-I/peptide trimeric complex is transported to the cell surface where it is scrutinized by cytotoxic T lymphocytes (CTL). The murine RMA-S mutant cell lines have a defect in class-I assembly and express markedly reduced levels of class-I molecules at the cell surface. The mutation is consistent with a defect in peptide transport from the cytosol to the place of assembly with class-I molecules. Addition of synthetic peptides to RMA-S cells and RMA-S cell lysates stimulates assembly of the class-I molecules and indicates that peptide plays a crucial role in attaining the class-I structure. Recent findings have demonstrated that class-I heavy clains (HCs) and beta 2 microglobulin (beta 2m) can assemble in absence of synthetic peptides, forming presumably "empty" (non-peptide-containing) class-I dimeric complexes, in RMA-S cells cultured at reduced temperature. The few class-I molecules present on RMA-S cultured at physiological temperature share the phenotype of "empty" class-I molecules induced at reduced temperature. This finding has allowed the re-interpretation of earlier studies and opened new ways to analyze the interaction between MHC-class-I molecules and different effector cells such as allo-specific CTLs, class-I-restricted CTLs and natural killer (NK) cells. In addition, recent data also suggest that RMA-S represents an attractive model for examining direct class-I-peptide interactions on intact cells or in cell lysates.

Animals↗

Metal-directed self-assembly of cavitand frameworks.

The self-assembly between bidentate cavitand ligands and mono/dinuclear metal precursors to give cavitand frameworks has been explored. For this purpose, two new cavitands bearing AB and AC phenylpyridyl moieties at the upper rim have been synthesized. A series of self-assembled molecular dimers featuring fac-Re(CO)(3)Br as metal corners have been prepared and characterized. Two possible dimeric structures (C-shaped and S-shaped) are possible when AB cavitand 2 is used in the self-assembly reaction; only one is obtained in the case of AC cavitand 3. In addition, the self-assembly of AB-dibridged cavitand 2 with dinuclear Pd/Pt metal precursors 5a and 5b has been studied. At this level of complexity, the self-assembly can lead to more than one structure. Several different final structures have been envisioned and their formation analyzed in silico and in solution. Out of the three possible cyclic structures (dimer, trimer, and tetramer), only the entropically favored dimer 6a (6b) is formed, as predicted from molecular modeling and demonstrated by PGSE NMR experiments.

Journal Article↗

The alpha1.alpha2 network of collagen IV. Reinforced stabilization of the noncollagenous domain-1 by noncovalent forces and the absence of Met-Lys cross-links.

Collagen IV networks are present in all metazoa and underlie epithelia as a component of basement membranes. The networks are essential for tissue function and are defective in disease. They are assembled by the oligomerization of triple-helical protomers that are linked end-to-end. At the C terminus, two protomers are linked head-to-head by interactions of their trimeric noncollagenous domains, forming a hexamer structure. This linkage in the alpha1.alpha2 network is stabilized by a putative covalent Met-Lys cross-link between the trimer-trimer interface (Than, M. E., Henrich, S., Huber, R., Ries, A., Mann, K., Kuhn, K., Timpl, R., Bourenkov, G. P., Bartunik, H. D., and Bode, W. (2002) Proc. Natl. Acad. Sci. U. S. A. 99, 6607-6612) forming a nonreducible dimer that connects the hexamer. In the present study, this cross-link was further investigated by: (a) comparing the 1.5-A resolution crystal structures of the alpha1.alpha2 hexamers from bovine placenta and lens capsule basement membranes, (b) mass spectrometric analysis of monomer and nonreducible dimer subunits of placenta basement membrane hexamers, and (c) hexamer dissociation/re-association studies. The findings rule out the novel Met-Lys cross-link, as well as other covalent cross-links, but establish that the nonreducible dimer is an inherent structural feature of a subpopulation of hexamers. The dimers reflect the reinforced stabilization, by noncovalent forces, of the connection between two adjoining protomers of a network. The reinforcement extends to other types of collagen IV networks, and it underlies the cryptic nature of a B-cell epitope of the alpha3.alpha4.alpha5 hexamer, implicating the stabilization event in the etiology and pathogenesis of Goodpasture autoimmune disease.

Animals↗

Targeting of an abundant cytosolic form of the protein import receptor at Toc159 to the outer chloroplast membrane.

Chloroplast biogenesis requires the large-scale import of cytosolically synthesized precursor proteins. A trimeric translocon (Toc complex) containing two homologous GTP-binding proteins (atToc33 and atToc159) and a channel protein (atToc75) facilitates protein translocation across the outer envelope membrane. The mechanisms governing function and assembly of the Toc complex are not yet understood. This study demonstrates that atToc159 and its pea orthologue exist in an abundant, previously unrecognized soluble form, and partition between cytosol-containing soluble fractions and the chloroplast outer membrane. We show that soluble atToc159 binds directly to the cytosolic domain of atToc33 in a homotypic interaction, contributing to the integration of atToc159 into the chloroplast outer membrane. The data suggest that the function of the Toc complex involves switching of atToc159 between a soluble and an integral membrane form.

Arabidopsis↗

Cell wall chemical composition of Enterococcus faecalis in the viable but nonculturable state.

The viable but nonculturable (VBNC) state is a survival mechanism adopted by many bacteria (including those of medical interest) when exposed to adverse environmental conditions. In this state bacteria lose the ability to grow in bacteriological media but maintain viability and pathogenicity and sometimes are able to revert to regular division upon restoration of normal growth conditions. The aim of this work was to analyze the biochemical composition of the cell wall of Enterococcus faecalis in the VBNC state in comparison with exponentially growing and stationary cells. VBNC enterococcal cells appeared as slightly elongated and were endowed with a wall more resistant to mechanical disruption than dividing cells. Analysis of the peptidoglycan chemical composition showed an increase in total cross-linking, which rose from 39% in growing cells to 48% in VBNC cells. This increase was detected in oligomers of a higher order than dimers, such as trimers (24% increase), tetramers (37% increase), pentamers (65% increase), and higher oligomers (95% increase). Changes were also observed in penicillin binding proteins (PBPs), the enzymes involved in the terminal stages of peptidoglycan assembly, with PBPs 5 and 1 being prevalent, and in autolytic enzymes, with a threefold increase in the activity of latent muramidase-1 in E. faecalis in the VBNC state. Accessory wall polymers such as teichoic acid and lipoteichoic acid proved unchanged and doubled in quantity, respectively, in VBNC cells in comparison to dividing cells. It is suggested that all these changes in the cell wall of VBNC enterococci are specific to this particular physiological state. This may provide indirect confirmation of the viability of these cells.

Bacterial Proteins↗

Partitioning conformational intermediates between competing refolding and aggregation pathways: insights into transthyretin amyloid disease.

Amyloid diseases are caused by the aberrant assembly of a protein in the extracellular space. Folded proteins are not amyloidogenic; however, the native state is generally in equilibrium with a minor population of unfolded or partially folded aggregation-competent conformers outside of the cell. Understanding how the partially unfolded conformers kinetically partition between the competing refolding and aggregation pathways provides insight into how misfolding, which occurs continuously, becomes pathogenic. Towards this end, we have previously studied the amyloidogenicity of transthyretin (TTR), a human beta-sheet-rich homotetrameric protein that must undergo rate-limiting tetramer dissociation and partial monomer unfolding to misassemble into amyloid and other aggregates. We demonstrate herein that TTR homotetramers reassemble by an unusual monomer-dimer-trimer-tetramer (MDRT) pathway. Therefore, the rate of every step in the reassembly pathway is dependent on the concentration of folded TTR monomer. Partitioning soluble TTR monomers between the reassembly pathway and the aggregation pathway should therefore depend on the relative concentrations of aggregates and assembly intermediates. Aggregate clearance is envisioned to play an important role in the partitioning of protein in vivo, where partitioning to the aggregation pathway becomes increasingly favorable under conditions where the concentration of aggregates is increased because aggregate clearance is slow relative to the rate of aggregation. This shift from efficient to inefficient aggregate clearance could occur with aging, offering an explanation for the age-associated nature of these neurodegenerative diseases.

Amyloidosis↗

Invariant chain trimers are sequestered in the rough endoplasmic reticulum in the absence of association with HLA class II antigens.

HLA class II antigens are heterodimeric cell surface glycoproteins that interact with antigenic peptides to form complexes recognizable by CD4-positive T cells. During their biosynthesis, class II antigens are retained in a post-Golgi compartment in association with the invariant chain, which dissociates before class II cell surface expression. To address whether the invariant chain mediates this post-Golgi retention, its transport and assembly were examined in cells that do not express HLA class II antigens. Pulse-chase analysis and endoglycosidase digestions showed that very little invariant chain proceeded as far as the trans-Golgi in class II-negative cell lines. Immunofluorescence studies suggested that in these cells the invariant chain is sequestered in the RER. Gel filtration and cross-linking data showed that RER-localized invariant chain is present as trimers or aggregated trimers. Multimerization is mediated by lumenal interactions; a proteolytic fragment of the invariant chain corresponding to the lumenal domain remained trimeric as determined by cross-linking analysis. Similar transport and structural characteristics were observed for a pool of excess invariant chain in class II-positive cells, suggesting that an excess of invariant chain in the ER may be important for class II antigen function. These results have important implications for the transport of cellular proteins in general and for the role of the invariant chain in class II antigen biosynthesis.

B-Lymphocytes↗