Properties of a P70 proteolytic factor of murine leukemia viruses.

Murine leukemia viruses, such as Rauscher leukemia virus (RLV), contain a proteolytic factor which becomes activated after detergent treatment of the virus. This factor specifically cleaves P70, the gag precursor polyprotein which is enriched for in preparations of immature virus core subparticles. The factor has been partially purified on Sephadex G-75 columns. It has a molecular weight of 10,000-12,000 daltons but does not coincide in elution position with the major peaks of the viral polypeptides p10 or p12. Under optimal conditions, that is 2% NP-40 (v/v), 10 mM DTT, (pH 7.2) and incubation for 16 hr at 22 degrees C, cleavage of labeled P70 occurs and increasing amounts of the four gag polypeptides p30, p15, p12 and p10 are obtained. The P70 cleavage activity is blocked by TLCK, TAME, CBZ-lysine and other lysyl-containing protease inhibitors. Further, the CBZ-lysine inhibition is reversible, while an inhibition by phenyl-methylsulfonyl fluoride (PMSF) is irreversible. These inhibition studies suggest that a similarity exists between the P70 proteolytic factor and some serine proteases, such as trypsin. The cleavage pattern of P70-rich immature cores treated with trypsin or chymotrypsin is different from that obtained with the P70 proteolytic factor. Thus murine leukemia virions apparently contain a unique, highly specific protease which is present in small amounts and cleaves P70.     

Partial characterization of a P70 proteolytic factor that is present in purified virions of Rauscher leukemia virus (RLV)

Incubation of RLV at 22°C in the presence of 2% NP40 (v/v) induces the activity of a proteolytic factor which cleaves p70, the major precursor protein of P30. The cleavage apparently occurs in two steps: first to a protein of MW app. 40–42,000 daltons (P40–42), and then to P30. In the absence of DTT (10mM), the latter step is blocked. $\text{In vitro}$ incubation of labeled immature core subparticles, enriched in P70, with a partially purified proteolytic factor fraction shows an enrichment in both P40–42 and P30. This activity is inhibited by TLCK at 1–10mM, but not TPCK nor ZPCK at concentrations ≤2mM, suggesting the factor is more trypsin than chymotrypsin-like.     

Characterization of the HIV N-terminal fusion peptide-containing region in context of key gp41 fusion conformations

Central to our understanding of human immunodeficiency virus-induced fusion is the high resolution structure of fragments of the gp41 fusion protein folded in a low energy core conformation. However, regions fundamental to fusion, like the fusion peptide (FP), have yet to be characterized in the context of the cognate protein regardless of its conformation. Based on conformation-specific monoclonal antibody recognition, we identified the polar region consecutive to the N36 fragment as a stabilizer of trimeric coiled-coil assembly, thereby enhancing inhibitory potency. This tertiary organization is retained in the context of the hydrophobic FP (N70 fragment). Our data indicate that the N70 fragment recapitulates the expected organization of this region in the viral fusion intermediate (N-terminal half of the pre-hairpin intermediate (N-PHI)), which happens to be the prime target for fusion inhibitors. Regarding the low energy conformation, we show for the first time core formation in the context of the FP (N70 core). The alpha-helical and coiled-coil stabilizing polar region confers substantial thermal stability to the core, whereas the hydrophobic FP does not add further stability. For the two key fusion conformations, N-PHI and N70 core, we find that the FP adopts a nonhelical structure and directs higher order assembly (assembly of coiled coils in N-PHI and assembly of bundles in the N70 core). This supra-molecular organization of coiled coils or folded cores is seen only in the context of the FP. This study is the first to characterize the FP region in the context of the folded core and provides a basic understanding of the role of the elusive FP for key gp41 fusion conformations.     

The cytoplasmic tail of NSP4, the endoplasmic reticulum-localized non-structural glycoprotein of rotavirus, contains distinct virus binding and coiled coil domains.

The final steps in the assembly of rotavirus occur in the lumen of the endoplasmic reticulum (ER). Targeting of the immature inner capsid particle (ICP) to this compartment is mediated by the cytoplasmic tail of NSP4, a non-structural virus glycoprotein located in the ER membrane. To delineate structural and functional features of NSP4, soluble fragments of the cytoplasmic tail have been expressed and purified. Our analysis combines a functional assay for ICP binding with biochemical and CD spectroscopic studies to examine the secondary and quaternary structure. The ICP-binding domain is located within the C-terminal 20 amino acids of the polypeptide. A second region, distinct from this receptor domain, adopts an alpha-helical coiled coil structure and mediates the oligomerization of the virus binding domains into a homotetramer. The domain organization of the cytoplasmic fragments of NSP4 suggests a novel structure for an icosahedral virus receptor protein in which C-terminal binding sites for immature rotavirus particles are connected to an alpha-helical coiled coil stalk which projects from the ER membrane.     

Influence of a heptad repeat stutter on the pH‐dependent conformational behavior of the central coiled‐coil from influenza hemagglutinin HA2

The coiled‐coil is one of the most common protein structural motifs. Amino acid sequences of regions that participate in coiled‐coils contain a heptad repeat in which every third then forth residue is occupied by a hydrophobic residue. Here we examine the consequences of a “stutter,” a deviation of the idealized heptad repeat that is found in the central coiled‐coil of influenza hemagluttinin HA2. Characterization of a peptide containing the native stutter‐containing HA2 sequence, as well as several variants in which the stutter was engineered out to restore an idealized heptad repeat pattern, revealed that the stutter is important for allowing coiled‐coil formation in the WT HA2 at both neutral and low pH (7.1 and 4.5). By contrast, all variants that contained idealized heptad repeats exhibited marked pH‐dependent coiled‐coil formation with structures forming much more stably at low pH. A crystal structure of one variant containing an idealized heptad repeat, and comparison to the WT HA2 structure, suggest that the stutter distorts the optimal interhelical core packing arrangement, resulting in unwinding of the coiled‐coil superhelix. Interactions between acidic side chains, in particular E69 and E74 (present in all peptides studied), are suggested to play a role in mediating these pH‐dependent conformational effects. This conclusion is partially supported by studies on HA2 variant peptides in which these positions were altered to aspartic acid. These results provide new insight into the structural role of the heptad repeat stutter in HA2. Proteins 2014; 82:2220–2228. © 2014 Wiley Periodicals, Inc.     

Hyperthermostable Surface Layer Protein Tetrabrachion from the ArchaebacteriumStaphylothermus marinus: Evidence for the Presence of a Right-handed Coiled Coil Derived from the Primary Structure

The scaffold of the surface layer covering the hyperthermophilic archaebacteriumStaphylothermus marinusis formed by an extended filiform glycoprotein complex, tetrabrachion, which is anchored in the cell membrane at one end of a 70 nm stalk and branches at the other end into four arms of 24 nm length. The arms from a canopy-like meshwork by end-to-end contacts, enclosing a “quasi-periplasmic space”. The primary structure of the complex, obtained by an approach based entirely on the polymerase chain reaction, shows that the light and the heavy chains are encoded in this order in a single gene and are generated by internal proteolytic cleavage. One light chain associates with the N-terminal part of a heavy chain to form one of the four arms of the complex, comprising about 1000 residues. Following a glycine-rich linker of about ten residues, the C-terminal 500 residues of the four heavy chains converge to form a four-stranded parallel coiled coil, which ends in a transmembrane segment. The sequence of the coiled coil is exceptional in that the heptad repeat of hydrophobic residues typical for left-handed coiled coils shifts to an undecad repeat after an internal proline residue, indicating that the C-terminal part of the sequence forms a right-handed coiled coil. Such a periodicity has not been detected in coiled coils to date. The almost flawless pattern of aliphatic residues, mainly leucine and isoleucine, throughout the hydrophobic core of the stalk provide one explanation for its exceptional stability.     

Relationship between structure and amino acid sequence of strongly twisted and coiled β-hairpins in globular proteins

β-Hairpins are widespread in proteins, and it is possible to find them both within β-sheets and separately. In this work, a comparative analysis of amino acid sequences of β-strands within strongly twisted β-hairpins from different structural protein subclasses has been conducted. Strongly twisted and coiled β-hairpin generates in the space a right double helix out of β-strands that are connected by a loop region (connections). The frequencies of amino acid residues on the internal (concave) and external (convex) surfaces of strongly twisted β-hairpins have been determined (220 β-hairpins from nonhomologous proteins were studied). The concave surface of these β-hairpins is mainly generated by hydrophobic residues, while the convex surface by hydrophilic residues; accordingly, the alternation of hydrophobic internal and hydrophilic external residues is observed in their amino acid sequences. Amino acid residues of glycine and alanine (especially in places of the largest twisting of the strands) were anomalously frequently found in internal positions of strongly twisted and coiled β-hairpins. It was established that internal positions never contain the proline residues, while external positions in the twisting region contain them in a relatively large amount. It was demonstrated that at least one amino acid residue in α_L- or ε-conformation is required for generation of relatively short (up to 7 amino acid residues) connection. As a rule, these positions are occupied by glycines. Thus, not only the alternation of hydrophobic and hydrophilic amino acid residues, but also the presence of one or two glycine residues in the connection region and the excess of glycines and alanines in the places of the largest strand twisting on the concave surface, as well as the presence of prolines on the convex surface, are required to generate a strongly twisted and coiled β-hairpin.     

Growth of bone marrow cells of normal and Rauscher virus infected mice in suspension cultures stimulated by CSA.

Bone marrow cells of normal and Rauscher virus (RLV) infected CBA/J mice were cultured under stimulation by postendotoxin serum. Cellular morphology and the number of granulocytic committed stem cells from day 1-5 after the onset of the cultures were studied with different amounts of postendotoxin serum added. There was a good correlation between total cellularity, the number of immature granulocytopoietic cells and the number of colony forming unit cells (CFUc) in suspension with the amount of postendotoxin serum. Postendotoxin serum delayed the appearance of macrophages in the cultures for 1-2 days. Cells from RLV infected animals showed a rather normal differentiation of the morphological recognisable cells 5 and 21 days after infection, but the CFUc survival in vitro 3 and 5 weeks after infection was reduced.     

Kinetics of murine type C virus-specific DNA synthesis newly infected cells.

Replicating transforming functions of Rauscher leukemia virus (RLV) and the RLV pseudotype of Moloney sarcoma virus in mouse embryo fibroblasts were found to be most sensitive to inhibition by cytosine arabinoside (ara-C) 30 to 90 min after infection. The initiation of intracellular RLV DNA synthesis was detected by nucleic acid hybridization within this time interval. Treatment of infected cells with cytosine arabinoside abolished RLV DNA synthesis. Peak synthesis of the DNA complementary to the infecting RLV genome, the (-) strand, occurred 40 to 60 min after infection. During this interval two s two species of DNA were observed with estimated molecular weights of 0.5 X 10(5) to 1.0 X 10(5) and 3 X 10(6). Peak synthesis of the (+) strand viral DNA occurred 50 to 70 min after infection. The initial species detected had a molecular weight of 1.5 X 10(5) to 4.0 X 10(5) which shifted as a function of time to 3 X 10(6). Both (+) strand species were initially detected in the cytoplasm followed by a rapid (10-min interval) appearance of the faster-sedimenting species in the nucleus. The virus-specific (-) and (+) strand DNA species are presumably unintegrated intermediates in provirus formation.     

Freeze-fracture characterization of the outermost Golgi cisterna (OGC) in rat pancreatic acinar cells

The outermost Golgi cisterna (OGC) frequently exhibits 55 nm diameter protuberances in P fracture faces and corresponding depressions, or pits, in E faces. When these protuberances (pits) appear regularly disposed, OGC faces are recognizable at relatively low electron microscopic magnifications. The mean particle width is less in OGC (6.4 nm) than in rough ER (7.9 nm) P faces, while particle number per unit area is respectively 70% and 100% greater in OGC P and E faces than in corresponding ER faces. The rather small OGC P face particles are better resolved at a relatively low shadowing angle. These differences in particle size (for P faces) and density between OGC and rough ER faces are detectable by inspection and may be used in the recognition of OGC faces devoid of protuberances (in P faces) and pits (in E faces). Fusion of presumably rough ER-derived microvesicles form short double-bossed tubular elements which constitute the OGC initial structure. These tubules enlarge by addition of microvesicle membrane and contents forming a characteristic sheet-like bossed structure.     

Potentiation of leukemogenicity and infectivity of Rauscher leukemia virus by an enhancing factor present in egg fluids.

Sequential intraperitoneal administration of a low molecular-weight-enhancing factor, isolated from egg fluids, in mice infected with Rauscher leukemia virus (RLV) significantly stimulated viral replication. This was evidenced by elevated levels of viral DNA-polymerase in mouse sera. This stimulation of viral replication correlated with aggrevation of viral leukemogenicity, as reflected by increment of splenomegalic response and shortening of survival time. The in vivo potentiation of replication and leukemogenicity of RLV is achieved at least partly by the enhancing factor at the cellular level, since RLV replication was found to be stimulated also in an in vitro system. We assume that the stimulatory effect of the enhancing factor on viral replication is connected with its stimulatory effect on the synthesis of cellular DNA.     

Exploring alternate states and oligomerization preferences of coiled‐coils by de novo structure modeling

Homomeric coiled‐coils can self‐assemble into a wide range of structural states with different helix topologies and oligomeric states. In this study, we have combined de novo structure modeling with stability calculations to simultaneously predict structure and oligomeric states of homomeric coiled‐coils. For dimers an asymmetric modeling protocol was developed. Modeling without symmetry constraints showed that backbone asymmetry is important for the formation of parallel dimeric coiled‐coils. Collectively, our results demonstrate that high‐resolution structure of coiled‐coils, as well as parallel and antiparallel orientations of dimers and tetramers, can be accurately predicted from sequence. De novo modeling was also used to generate models of competing oligomeric states, which were used to compare stabilities and thus predict the native stoichiometry from sequence. In a benchmark set of 33 coiled‐coil sequences, forming dimers to pentamers, up to 70% of the oligomeric states could be correctly predicted. The calculations demonstrated that the free energy of helix folding could be an important factor for determining stability and oligomeric state of homomeric coiled‐coils. The computational methods developed here should be broadly applicable to studies of sequence‐structure relationships in coiled‐coils and the design of higher order assemblies with improved oligomerization specificity. Proteins 2015; 83:235–247. © 2014 Wiley Periodicals, Inc.     

Effect of Polymyxin on the Bacteriophage Receptors of the Cell Walls of Gram-Negative Bacteria

Treatment of gram-negative bacteria with lethal doses of polymyxin B and colistin resulted in the formation of projections of the outer layer of the cell wall. Phages T3, T4, and T7, which use wall lipopolysaccharide as receptors, were specifically prevented from adsorbing to Escherichia coli B cells treated with polymyxin, whereas phages T1, T2, T5, and T6 were not. In the systems of phage P22C-Salmonella typhimurium LT2 and phage C21-S. typhimurium variant SL1069, the phage were prevented from adsorbing to the host cell treated with the antibiotics. Electron microscopic observations show that phage T2 adsorbed irreversibly to the normal smooth surface between the projections on the outer layer caused by the drug treatment. These results indicate that lipopolysaccharide is affected by polymyxin functionally and morphologically, but lipoprotein is not. The purified lipopolysaccharide showed a ribbon-like structure when viewed face on and showed trilamellar structure when viewed edge on. The lipopolysaccharide from E. coli B was irreversibly adsorbed by phages T3, T4, and T7, but not phage T2. Often, phage T4 adsorbed to both sides of the lipopolysaccharide strand at comparable distances. Phage P22C adsorbed through the spikes of the tail-plates to the lipopolysaccharide from S. typhimurium LT2. Lipopolysaccharide which was treated with low doses of the drug (2.5 to 6.25 mug of polymyxin B per ml to 100 mug of lipopolysaccharide per ml) turned into the coiled form and was partially broken down into short segments with coiled form. The loosely coiled lipopolysaccharide retains both its function as the receptor and its trilamellar structure. Treatment with high doses of the drug (12.5 to 25 mug of polymyxin B per ml to 100 mug of lipopolysaccharide per ml) caused the collapse of the trilamellar structure of the strand. These collapsed lipopolysaccharides became flat and fused with each other, making an amorphous mass, and finally they were broken into small collapsed fragments.     

Structural mapping of the coiled‐coil domain of a bacterial condensin and comparative analyses across all domains of life suggest conserved features of SMC proteins

The structural maintenance of chromosomes (SMC) proteins form the cores of multisubunit complexes that are required for the segregation and global organization of chromosomes in all domains of life. These proteins share a common domain structure in which N‐ and C‐ terminal regions pack against one another to form a globular ATPase domain. This “head” domain is connected to a central, globular, “hinge” or dimerization domain by a long, antiparallel coiled coil. To date, most efforts for structural characterization of SMC proteins have focused on the globular domains. Recently, however, we developed a method to map interstrand interactions in the 50‐nm coiled‐coil domain of MukB, the divergent SMC protein found in γ‐proteobacteria. Here, we apply that technique to map the structure of the Bacillus subtilis SMC (BsSMC) coiled‐coil domain. We find that, in contrast to the relatively complicated coiled‐coil domain of MukB, the BsSMC domain is nearly continuous, with only two detectable coiled‐coil interruptions. Near the middle of the domain is a break in coiled‐coil structure in which there are three more residues on the C‐terminal strand than on the N‐terminal strand. Close to the head domain, there is a second break with a significantly longer insertion on the same strand. These results provide an experience base that allows an informed interpretation of the output of coiled‐coil prediction algorithms for this family of proteins. A comparison of such predictions suggests that these coiled‐coil deviations are highly conserved across SMC types in a wide variety of organisms, including humans. Proteins 2015; 83:1027–1045. © 2015 Wiley Periodicals, Inc.     

Ecological physiology of Pereskia guamacho, a cactus with leaves

The specialized physiology of leafless, stem-succulent cacti is relatively well understood. This is not true, however, for Pereskia (Cactaceae), the 17 species of leafy trees and shrubs that represent the earliest diverging lineages of the cacti. Here we report on the water relations and photosynthesis of Pereskia guamacho, a small tree of the semiarid scrubland of Venezuela's Caribbean coast. Sapwood-specific xylem conductivity (Ksp) is low when compared to other vessel-bearing trees of tropical dry systems, but leaf-specific xylem conductivity is relatively high due to the high Huber value afforded by P. guamacho's short shoot architecture. P. guamacho xylem is not particularly vulnerable to drought-induced cavitation, especially considering the high leaf water potentials maintained year round. This is confirmed by the lack of significant variation exhibited in Ksp between wet and dry seasons. In the rainy season, P. guamacho exhibited C3-like patterns of stomatal conductance, but during a prolonged drought we documented nocturnal stomatal opening with a concomitant accumulation of titratable acid in leaves. This suggests that P. guamacho can perform drought-induced crassulacean acid metabolism (CAM photosynthesis), although delta 13C values imply that most carbon is assimilated via the C3 pathway. P. guamacho leaves display very low stomatal densities, and maximum stomatal conductance is low whether stomata open during the day or night. We conclude that leaf performance is not limited by stem hydraulic capacity in this species, and that water use is conservative and tightly regulated at the leaf level.     

Stoichiometry in aboveground and fine roots of <Emphasis Type="Italic">Seriphidium korovinii</Emphasis> in desert grassland in response to artificial nitrogen addition

Nitrogen (N) input by atmospheric deposition and human activity enhances the availability of N in various ecosystems, which may further affect N and phosphorus (P) cycling and use by plants. However, the internal use of N, P, and N:P stoichiometry by plants in response to N supply, particularly for grass species in a desert steppe ecosystem, remains unclear. In this work, a field experiment was conducted at an infertile area in a desert steppe to investigate the effects of N fertilizer addition rates on the stoichiometry of N and P in a dominant grass species, Seriphidium korovinii. Results showed that for both aboveground and fine roots of S. korovinii, N inputs exponentially increased the N concentration and N:P ratios while P concentrations decreased. Meanwhile, the relationships between N and P concentrations for both aboveground and fine roots were significantly negative. Furthermore, while the N concentrations in the plants were relatively low, P concentrations were higher than the global means, resulting in a relatively low N:P ratio. These results suggest that the stoichiometric characteristics of N were different from that of P for this desert plant species. Results also show that the intraspecific variations in the main element traits (N, P, and N:P ratios) were consistent at the whole-plant level. Our results also suggest that N should be part of any short-term fertilization plan that is part of a management strategy designed to restore degraded desert grassland. These findings highlight that nutrient addition by atmospheric N deposition and human activity can have significant effects on the internal use of N and P by plants. Therefore, establishing a nutrient-conservation strategy for desert grasslands is important.