Structural and antigenic analysis of the nucleic acid-binding proteins of bovine and feline leukemia viruses.

The nucleic acid-binding proteins of bovine leukemia virus (BLV) and feline leukemia virus (FeLV) were isolated in a high state of purity with chloroform-methanol extraction followed by reversed-phase liquid chromatography. Selective solubilization and purity of BLV p12 and FeLV p10 was confirmed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The compositions and molecular weights were determined by amino acid analysis. An abundance of lysine and arginine residues along with their size identifies both BLV p12 and FeLV p10 as small basic proteins similar to well-defined type C viral nucleoproteins. NH2-terminal degradation by the semiautomated Edman method provided the sequence of the first 40 amino acids for both proteins. The putative nucleic acid binding site found in several type C viral nucleoproteins was contained within this sequence, with the most homology centered around an eight-amino acid region involving seven identical residues and one substitution. Antisera were developed in rabbits, and specificity and titers were determined by electroblotting and immunoautoradiography. By this technique, an immunological cross-reaction was found between BLV p12 and FeLV p10. The shared antigenic determinant most likely exists in the highly conserved eight-amino acid region. Although this sequence is also highly conserved in the nucleic acid-binding proteins of murine leukemia viruses, the shared antigenic determinant is not found in these or any other type C viruses tested. It is suggested that substitution of arginine (BLV p12/FeLV p10) to lysine (murine leukemia virus p10) is sufficient to elicit a change in antibody specificity.     

Macrophage accumulation in mice is inhibited by low molecular weight products from murine leukemia viruses

Low m.w. extracts from three known oncogenic viruses, Friend, Moloney, and Rauscher, inhibited the accumulation of macrophages at sites of delayed inflammatory reactions in mice. The potential biologic significance of these proteins is suggested by their potency: as little as 1.2 ng of viral protein inhibited (p less than 0.02) macrophage accumulation when injected at a site distant to the inflammatory reaction. A virus envelope protein fraction of 15,000 daltons (p15E) was likewise found to inhibit macrophage accumulation and may in part represent the active factor of the virus extracts. Certain oncogenic viruses may thus exert their immunosuppressive activity by release of potent inhibitors of systemic macrophage function.     

Modern tools for identification of nucleic acid-binding proteins

Numerous biological mechanisms depend on nucleic acid--protein interactions. The first step to the understanding of these mechanisms is to identify interacting molecules. Knowing one partner, the identification of other associated molecular species can be carried out using affinity-based purification procedures. When the nucleic acid-binding protein is known, the nucleic acid can be isolated and identified by sensitive techniques such as polymerase chain reaction followed by DNA sequencing or hybridization on chips. The reverse identification procedure is less straightforward in part because interesting nucleic acid-binding proteins are generally of low abundance and there are no methods to amplify amino acid sequences. In this article, we will review the strategies that have been developed to identify nucleic acid-binding proteins. We will focus on methods permitting the identification of these proteins without a priori knowledge of protein candidates.     

The inhibition of nucleic acid-binding proteins by aurintricarboxylic acid

Qβ replicase, $\text{Escherichia coli}$ RNA polymerase, and T7 RNA polymerase are inhibited by low concentrations of the dye aurintricarboxylic acid (ATA). In each case initiation by the enzyme was preferentially inhibited. The elongation of initiated polynucleotide chains by Qβ replicase was insensitive to ATA in the range of concentrations required to inhibit initiation. Treatment of Qβ replicase, RNA polymerase and $\text{lac}$ repressor with ATA prevented enzymemediated binding of the templates to nitrocellulose filters. We propose that the inhibitor combines with the template binding site of these proteins to prevent initiation.     

Annotating nucleic acid-binding function based on protein structure

Many of the targets of structural genomics will be proteins with little or no structural similarity to those currently in the database. Therefore, novel function prediction methods that do not rely on sequence or fold similarity to other known proteins are needed. We present an automated approach to predict nucleic-acid-binding (NA-binding) proteins, specifically DNA-binding proteins. The method is based on characterizing the structural and sequence properties of large, positively charged electrostatic patches on DNA-binding protein surfaces, which typically coincide with the DNA-binding-sites. Using an ensemble of features extracted from these electrostatic patches, we predict DNA-binding proteins with high accuracy. We show that our method does not rely on sequence or structure homology and is capable of predicting proteins of novel-binding motifs and protein structures solved in an unbound state. Our method can also distinguish NA-binding proteins from other proteins that have similar, large positive electrostatic patches on their surfaces, but that do not bind nucleic acids.     

Multiple species of single-stranded nucleic acid-binding proteins in Saccharomyces cerevisiae

DNA affinity chromatography has been used to identify the major single-stranded nucleic acid binding proteins (SSBs) of Saccharomyces cerevisiae. There are five abundant species having molecular masses of 50, 45, 31, 23, and 20 kDa. Four of these proteins are cytoplasmic and one is mitochondrial. To date, three of the proteins have been purified to homogeneity. The purified proteins are designated SSB-m, SSB-1, and SSB-2, with molecular masses of 20, 45, and 50 kDa, respectively. SSB-m is found only in mitochondrial subcellular fractions. SSB-1 stimulates purified yeast DNA polymerase I, while SSB-2 inhibits DNA polymerase I. An antibody against SSB-1 has been prepared in rabbits and purified by SSB-1-Sepharose affinity chromatography. The purified antibody specifically inhibits DNA synthesis in an in vitro replication system, suggesting that SSB-1 may be involved in DNA replication in vivo. SSB-2 has the highest affinity for single-stranded DNA of all three proteins. It may represent a new class of eukaryotic SSB, on the basis of molecular weight, inhibition of DNA polymerase and antigenicity. Antibodies have also been prepared against SSB-2. The immunological reagents have been used to show that SSB-1, SSB-2, and SSB-m are antigenically distinct, as well as to study the relationship of these three SSBs to other proteins in yeast.     

Difference sedimentation velocity adapted to low molecular weight proteins

The difference sedimentation velocity technique reported by Kirschner and Schachman (1971, Biochemistry10, 1900–1919) has been modified to eliminate the need for a supernatant region. The method is now applicable to the measurement of small changes in sedimentation coefficient for low molecular weight proteins and other small macromolecules. Procedural changes necessary to overcome the absence of a supernatant region until late in the run have been devised and tested. A modified double-sector centerpiece was used to match the radial positions of the two menisci. The integration of the moment of the concentration difference was carried out from the meniscus to the plateau region, rather than over the peak only. The interference baseline was measured on photographs at the start of each run and after remixing. Some instability of baseline height was noted. The calculation method adjusted the baseline height to correspond with the concentration difference in the plateau region arising from unequal radial dilution. Tests of the method have been made using D₂O to retard the sedimentation of lysozyme. The interference results at low D₂O concentration (small values of Δs) are in agreement with schlieren results at high D₂O concentrations. Changes of 0.005 S have been detected.     

Synthesis of the low molecular weight heat shock proteins in plants

Heat shock of living tissue induces the synthesis of a unique group of proteins, the heat shock proteins. In plants, the major group of heat shock proteins has a molecular mass of 15 to 25 kilodaltons. Accumulation of these proteins to stainable levels has been reported in only a few species. To examine accumulation of the low molecular weight heat shock proteins in a broader range of species, two-dimensional electrophoresis was used to resolve total protein from the following species: soybean (Glycine max L. Merr., var Wayne), pea (Pisum sativum L., var Early Alaska), sunflower (Helianthus annuus L.), wheat (Triticum aestivum L.), rice (Oryza sativa L., cv IR-36), maize (Zea mays L.), pearl millet (Pennisetum americanum L. Leeke, line 23DB), and Panicum miliaceum L. When identified by both silver staining and incorporation of radiolabel, a diverse array of low molecular weight heat shock proteins was synthesized in each of these species. These proteins accumulated to significant levels after three hours of heat shock but exhibited considerable heterogeneity in isoelectric point, molecular weight, stainability, and radiolabel incorporation. Although most appeared to be synthesized only during heat shock, some were detectable at low levels in control tissue. Compared to the monocots, a higher proportion of low molecular weight heat shock proteins was detectable in control tissues from dicots.     

Biologic and molecular characterization of two newly isolated ras-containing murine leukemia viruses.

A murine sarcoma virus (MSV) was recovered from an (NFS X NS.C58v-1) F1 mouse which developed splenic sarcoma and erythroleukemia 6 months after inoculation with a mink cell focus-inducing murine leukemia virus (MuLV) isolated from an NFS mouse infected with a wild mouse ecotropic MuLV. The MSV, designated NS.C58 MSV-1, induced foci of transformation in mouse and rat fibroblasts, and inoculation of mice of various strains 2 weeks of age or younger resulted in erythroleukemia and sarcomatous lesions in spleen, lymph node, and brain. The MSV provirus was molecularly cloned from a genomic library prepared from transformed non-producer rat cells. The 8.8-kilobase proviral DNA contained a 1.0-kilobase p21 ras coding segment which replaced most of the gp70-encoding portion of an MuLV, most likely the endogenous C58v-1 ecotropic virus. The ras oncogene is closely related to v-Ha-ras by hybridization, expression of p21 protein, and nucleotide sequence. It is nearly identical in sequence to v-bas, the only previously described transduced, activated mouse c-ras. At position 12 in the p21 coding region, arginine is substituted for the naturally occurring glycine present in c-ras. A second MSV isolate is described which is similar to NS.C58 MSV-1 except for a 100- to 200-base-pair deletion in the noncoding region of the ras-containing insert.     

p10, a low molecular weight single-stranded nucleic acid binding protein of murine leukemia retroviruses, shows stacking interactions of its single tryptophan residue with nucleotide bases

Room temperature fluorescence and low-temperature phosphorescence studies of the association of p10, a basic low molecular weight single-stranded DNA binding protein isolated from murine leukemia viruses, point to the involvement of its single tryptophan residue in a close-range interaction with single-stranded polynucleotides. Optically detected triplet-state magnetic resonance (ODMR) techniques applied to the complex of p10 protein with the heavy atom derivatized polynucleotide poly(5-HgU) demonstrate the occurrence of stacking interactions of Trp35 with nucleic acid bases, thus agreeing with earlier reports that this residue is involved in the binding process [Karpel, R. L., Henderson, L. E., & Oroszlan, S. (1987) J. Biol. Chem. 262, 4961-4967].     

Isolation of low molecular weight actin-binding proteins from porcine brain

Three new actin-binding proteins having molecular weights of 26,000, 21,000, and 19,000 were isolated from porcine brain by DNase I affinity column chromatography. These proteins were released from the DNase I column by elution with a solution of high ionic strength. They were further purified by column chromatographies using hydroxyapatite, phosphocellulose, and Sephadex G-75. All of these actin-binding proteins behaved as monomeric particles in the gel filtration chromatography. After elution of the three actin-binding proteins, actin and profilin were recovered from the DNase I column with 2 M urea solution. The eluted was further purified by a cycle of polymerization and depolymerization and finally by gel filtration. Little difference in polymerizability was detected between the purified brain actin and muscle actin. After sedimentation of the polymerized brain actin, profilin was purified by DEAE-cellulose and gel filtration column chromatographies. In the assay of the action of these actin-binding proteins, the 26K protein was found to cause a large decrease in the rate of actin polymerization, while showing little effect on the extent of polymerization. The 21K protein decreased the steady-state viscosity of actin solution in a concentration-dependent manner irrespective of whether it was added before or after actin polymerization. It reacted with actin at a 1:1 molar ratio.     

Antigenic properties and molecular weights of murine leukemia virus-binding proteins.

A murine T lymphoma cell line, WEHI-22, has been studied for the presence of murine leukemia virus-binding proteins and for the presence of cell surface molecules that share antigens with mouse immunoglobulins. With surface radioiodination, detergent disruption, and immunoprecipitation, a 60 to 70,000-dalton molecule has been described that is recognized by chicken anti-mouse immunoglobulin serum. In competition experiments this molecule cross-reacts with highly purified mouse IgM myeloma proteins. A cell surface molecule of similar size can be shown to bind to mouse leukemia viruses. Pre-precipitation of the WEHI-22 cell surface material with chicken anti-mouse immunoglobulin removes the material binding to leukemia viruses.     

Primary structure and cellular distribution of two fatty acid-binding proteins in adult rat kidneys

Fatty acid-binding proteins (FABPs) were purified from the kidneys of female and male rats and characterized by primary structure and histological distribution in the kidney. Two FABPs (14 and 15.5 kDa) were found in male rat kidney cytosol whereas only 14-kDa FABP could be recognized in female rat kidneys throughout the purification steps. The amino acid sequence of the 14-kDa FABP was identical to that of rat heart FABP deduced from the cDNA sequence (Heuckeroth, R. O., Birkenmeier, E. H., Levin, M. S., and Gordon, J. I. (1987) J. Biol. Chem. 262, 9709-9717). Structural analysis of the male-specific 15.5-kDa FABP identified this second FABP as a proteolytically modified form of alpha 2u-globulin, an 18.7-kDa major urinary protein of adult male rats (Unterman, R. D., Lynch, K. R., Nakhasi, H. L., dolan, K. P., Hamilton, J. W., Cohn, D. V., and Feigelson, P. (1981) Proc. Natl. Acad. Sci. U.S.A. 78, 3478-3482) which shares a common ancestry with a number of hydrophobic ligand-binding proteins such as serum retinol-binding proteins. Immunohistochemical investigation disclosed that heart-type FABP (14-kDa FABP) is localized in the cytoplasm of the epithelia of the distal tubules in both male and female rat kidneys whereas 15.5-kDa FABP immunostaining was observed predominantly in the endosomes or lysosomes of proximal tubules in male rat kidneys. These results suggest strongly the functional divergence of two FABPs in the rat kidney.     

Mapping of functional domains of human high molecular weight and low molecular weight kininogens using murine monoclonal antibodies

Thirty-four monoclonal antibodies directed against human high molecular weight (HMW) and low molecular weight (LMW) kininogens and their derivatives were obtained, and the specificities of the antibodies were assayed by enzyme-linked immunosorbent assay (ELISA). By use of HMW kininogen, kinin-free HMW kininogen, kinin-free and fragment 1.2 (fr 1.2) free HMW kininogen, fr 1.2-light chain of HMW kininogen, LMW kininogen, kinin-free LMW kininogen, heavy chain of LMW kininogen, and light chain of LMW kininogen, the monoclonal antibodies were characterized and classified into four groups: (A) 20 monoclonal antibodies reacting with only the heavy chain, a common region of HMW and LMW kininogens; each of these monoclonal antibodies possessed the specificity to domain 1 (2 monoclonal antibodies), domain 2 (2 monoclonal antibodies), domain 3 (7 monoclonal antibodies), and both domains 2 and 3 (7 monoclonal antibodies) of the heavy chain; (B) 7 monoclonal antibodies reacting with fr 1.2, a unique histidine-rich region; (C) 5 monoclonal antibodies reacting with the light chain of HMW kininogen; (D) 2 monoclonal antibodies reacting with the light chain of LMW kininogen. Two monoclonal antibodies in the first group (group A), designated HKG H7 and H12, effectively suppressed the thiol proteinase inhibitor activity of HMW kininogen to papain and calpains and of LMW kininogen to papain, but the others did not affect it. Further, all the monoclonal antibodies which recognized the fr 1.2 or light chain of HMW kininogen (groups B and C) suppressed the clotting activity.(ABSTRACT TRUNCATED AT 250 WORDS)     

Size and structure of the hydrophobic low molecular weight surfactant-associated polypeptide

The most abundant low molecular weight protein of pulmonary surfactant has unusual properties. Its primary structure has now been determined by analysis at the protein level. The highly hydrophobic polypeptide is resistant to cleavage with proteolytic enzymes, but it was possible to generate fragments by limited cleavage with concentrated HCl or with sodium in liquid ammonia. Acid hydrolysis of the peptide required exceptional conditions for release of all residues. The N-terminus is heterogeneous, and in its longest form the primary structure consists of 35 residues. This analysis establishes that the size of the major native hydrophobic surfactant polypeptide is considerably smaller than previously proposed. Biological effects of the polypeptide recombined with phospholipids are confirmed in vitro by using a pulsating bubble system and in vivo by using premature newborn rabbits. The molecule has branched-chain amino acid residues at about two-thirds of all positions and lacks nine types of residue. The middle third is composed entirely of hydrophobic residues, and fragments from this part are sparingly soluble even in organic solvents. The hydrophobic region is preceded by a more hydrophilic, N-terminal segment. Thus, the molecule has two contrasting parts, like a detergent, which may explain its essential role in the pulmonary surfactant system.     

The molecular structure of low and high molecular weight levans synthesized by levansucrase

The levan synthesized by Bacillus subtilis levansucrase in the presence of alcohols was of only high molecular weight, while in solutions of high ionic strength only low molecular weight (MW) levan was produced. The addition of low MW levan to the enzyme reaction mixture at low ionic strength stimulated synthesis of a high MW levan, but the levan added was not incorporated into this high MW levan. Methylation analysis revealed that low MW levans contained glucose, which was isolated as 2,3,46-tetra-O-methyl alditol acetate showing that the glucose units existed as terminal residues. The molecular weight of levan estimated on the basis of glucose content coincided with that determined by the gel filtration method. Methylation analysis also revealed that the number of fructose residues of the linear fraction linked by leads to 6(F)2 leads to type bonds was 22 for levan with a molecular weight of (8.4(-22)) x 10(3), while it was 11 for that of 2,000 x 10(3). The number of (formula: see text) type branched residues increased with increase in the molecular weight of the levan synthesized.