Biochemical analysis of RNA particles and nucleolar RNases in eucaryotic cells]

Four types of rat liver nucleolar RNP particles with the sedimentation coefficients of 120S, 80S, 60S and 12--16S were analyzed and their chemical composition was established. The nucleolar RNP particles were found to contain a RNA set with the sedimentation coefficients of 43S, 33S, 20S and 7S. The nucleolar proteins were shown to contain endonucleases, one of which was isolated and partially purified by fractionation on DEAE-Sephadex A-50. In some of its properties this RNAse was found similar to an analogous enzyme from membrane-bound ribosomes.     

Nitrogenase of Klebsiella pneumoniae. Interaction of the component proteins studied by ultracentrifugation

Sedimentation-velocity analyses of mixtures of the component proteins of nitrogenase of Klebsiella pneumoniae at a 1:1 molar ratio, showed a single peak of sedimentation coefficient (12.4S) considerably greater than that obtained for the larger (Fe+Mo-containing) protein centrifuged alone (10.4S). When the ratio exceeded 1:1 (the smaller Fe-containing protein in excess) an additional peak corresponding in sedimentation coefficient (about 4.5S) to free Fe-containing protein appeared. When proteins, which had been inactivated by exposure to air were used, no interaction occurred. Na(2)S(2)O(4) at 2mm both reversed and prevented interaction between the two proteins; sedimentation coefficients corresponded to those of the proteins when centrifuged alone. These results demonstrate the formation of a complex between the nitrogenase proteins, and, together with data of activity titration curves, are consistent with the formulation of the nitrogenase complex of K. pneumoniae as (Fe-containing protein)-(Fe+Mo-containing protein).     

Synthesis, Transport, and Morphogenesis of Type 5 Adenovirus Capsid Proteins

During the period between 20 and 24 hr after infection of KB cells with type 5 adenovirus, at a time when approximately 85% of the proteins made were virus-specific, viral proteins were synthesized on polyribosomes with an average sedimentation coefficient of 200S. The polypeptide chains synthesized during a 1-min period of labeling with (14)C-amino acids had an average sedimentation coefficient of 3.4S in sucrose gradients containing 1% sodium dodecyl sulfate. Within 1 min after completion, the newly made polypeptide chains were released from polyribosomes, and the majority were transported into the nuclei within 6 min. Meanwhile, the immunological reactivity of the newly synthesized proteins also increased rapidly. During the same 6-min interval after synthesis, the single polypeptide chains assembled into multimeric proteins with average sedimentation coefficients of 6S, 9S, and 12S. The 6S and 12S proteins were identified immunologically as the fiber and hexon capsid proteins, respectively. The 9S protein was trypsin-sensitive and appeared to be the precursor of the penton; it was tentatively identified as the penton base. The penton had a sedimentation coefficient of about 10.5S and sedimented with the hexon in sucrose gradients. The concomitant migration of nascent proteins into the nuclei, development of the capsid proteins' immunological reactivity, and morphogenesis of the multimeric capsid proteins suggest that the single polypeptide chains or small complexes were transported into the nuclei where they assembled into mature structural proteins of the virion.     

Organization of clathrin coat structures

Clathrin (8S), when purified, polymerizes under low-pH conditions (0.1 M MES, pH 6.0-6.2) into a heterogeneous population of baskets with sedimentation coefficients ranging from 150 to 400 S. Several groups of proteins of molecular masses 180, 110, 100, 50, and 47 kDa (based on sodium dodecyl sulfate gel electrophoresis) present in the isolated coated vesicles are involved in polymerizing clathrin under physiological conditions to a homogeneous population of baskets [Zaremba, S., & Keen, J. H. (1983) J. Cell Biol. 97, 1339; Ahle, S., & Ungewickell, E. (1986) EMBO J. 5, 3143]. We now report that in 0.1 M MES, pH 6.0, where pure clathrin polymerizes by itself, the above proteins (together known as associated proteins or APs) induce polymerization of clathrin into three distinct sizes of baskets with sedimentation coefficients of 150, 220, and 300 S. Low ratios of clathrin to APs give rise to smaller sizes, whereas higher ratios give rise to predominantly the larger sizes. The smaller size baskets (150S) are intermediates in the polymerization of clathrin to larger size baskets (300S) as inferred from the dissociation of larger size baskets into smaller size baskets and the formation of larger size baskets from smaller size baskets upon the addition of pure clathrin.     

Ribonucleic Acid Species of Intracellular Nucleocapsids and Released Virions of Vesicular Stomatitis Virus

Infection of chicken embryo cells with vesicular stomatitis (VS) virus resulted in variable production of three classes of intracellular viral ribonucleocapsids with sedimentation coefficients of approximately 140S, 110S, and 80S, as well as three corresponding classes of released virions designated B, LT, and T. Intracellular nucleocapsids of each class contained three proteins of which the major N protein was firmly bound, and the minor L and NS1 proteins were readily dissociated with 0.5 m NaCl. The ribonucleic acid (RNA) species extracted from B, LT, and T virions, and from corresponding intracellular nucleocapsids, contained RNA species with approximate molecular weights of 3.2 x 10(6), 2.0 x 10(6), and 10(6), respectively, as determined by polyacrylamide gel electrophoresis. These values are roughly equivalent to sedimentation coefficients of 42S, 28S, and 23S for each of the virion and nucleocapsid RNA species. Cells infected at high multiplicity with undiluted passage VS virus gave rise primarily to virions and nucleocapsids containing 23S RNA, whereas cells productively infected with purified B virions produced predominantly B and LT virions and nucleocapsids. At late stages in the productive cycle of infection, more virions containing 42S RNA were produced, but the intracellular pool of nucleocapsids containing 28S and 23S RNA remained relatively constant. Additional studies by more refined techniques are required to test the hypothesis that nucleocapsids containing 28S and 23S RNA are precursors of the 42S RNA in infectious VS-B virions and that production of defective T and LT virions results from failure of ligation of the RNA precursors.     

Skeletal structure of clathrin triskelion in solution: experimental and theoretical approaches

The physicochemical properties of the clathrin triskelion were determined by dynamic and static light-scattering and sedimentation analyses in Tris and triethanolamine (TEA) buffers of about pH 8, in which the clathrin triskelion has been found to be in different conformational states by electron microscopy [Heuser, J., & Kirchhausen, T. (1985) J. Ultrastruct. Res. 92, 1-27]. Dynamic light-scattering measurements provided diffusion coefficients (D0(20,w)) of 1.22 x 10(-7) and 1.23 x 10(-7) cm2/s, and ultracentrifugal analysis gave sedimentation coefficients (S0(20,w)) of 8.39 and 8.32 S in Tris and TEA buffer, respectively. The average Stokes radius of the protein was determined to be 175 A from its diffusion and sedimentation coefficients and its molecular weight. Static light-scattering analysis provided molecular weights of 6.58 x 10(5) and 6.41 x 10(5) and radii of gyration of 311 and 301 A in the respective buffers. These results indicate that the clathrin triskelion has a similar conformation in the two buffers. For clarification of the skeletal structure of the clathrin triskelion in solution, the physicochemical parameters were calculated by using two models in which the clathrin arms are bent at various angles in a plane, on the basis of the Bloomfield approximation and a formula derived to estimate the radius of gyration of proteins consisting of various structural units. Values for the Stokes radius, diffusion and sedimentation coefficients, and radius of gyration in the ranges of 178-170 A, (1.20-1.26) x 10(-7) cm2/s, 8.26-8.66 S, and 316-266 A, respectively, were obtained with these models with the arms bent in the range of 0-60 degrees.(ABSTRACT TRUNCATED AT 250 WORDS)     

Comparison of 7S nerve growth factor and nerve growth factor I from mouse submandibular glands

7S nerve growth factor (7S NGF) and nerve growth factor I (NGFI) are NGF-containing protein complexes isolated from mouse submandibular glands by different protocols, and reports suggest that the molecules differ chemically. In this study, we compared the molecular properties and subunit compositions of the two proteins. Purified 7S NGF and NGFI electrophoresed to identical positions on polyacrylamide gels in nondissociating buffers, with electrophoretic mobilities indistinguishable from that of unpurified NGF in salivary gland extracts. Ultraviolet absorption curves were identical, and sedimentation coefficients were similar (7.3 +/- 0.25 S for 7S NGF; 7.2 +/- 0.2 S for NGFI) as determined by sedimentation velocity analysis. By sedimentation equilibrium analysis, molecular weights of 135 000-140 000 were obtained for both complexes at protein concentrations in the centrifuge cell greater than 85 micrograms/mL; when protein concentrations within the centrifuge cell ranged from approximately 30 to 100 micrograms/mL at equilibrium, both complexes dissociated. Molecular weight values determined by gel filtration on Bio-Gel P300 and Sephadex G200 resins were similar for both proteins, and the values determined on Sephadex agreed with those obtained by ultracentrifugation. The subunit compositions of the complexes were also similar as determined by nonequilibrium isoelectric focusing, NGFI being composed of proteins that migrated to positions identical with those of the alpha, beta, and gamma subunits of 7S NGF. Furthermore, the stoichiometry of the subunits was similar in the two complexes as determined by radioimmunoassays to each of the subunits and by densitometric analysis of electrophoretic gels. Both methods showed that the complexes contain approximately 2 mol of the alpha and gamma subunits per mole of beta-NGF.(ABSTRACT TRUNCATED AT 250 WORDS)     

Heterogeneity in the physicochemical properties of deoxycholate-solubilized benzodiazepine receptors from calf cerebral cortex

The hydrodynamic behaviour of benzodiazepine receptors solubilized by deoxycholate from calf cerebral cortex reveals two molecular forms. The Stokes radii are 46.5 A and 67.2 A, and the sedimentation coefficients are 10.9 S and 14.6 S. The calculated apparent molecular weights and frictional ratios suggest either two nearly globular proteins of ca. 200K and 400K daltons each, or two ca. 300K daltons proteins which differ significantly in their degree of asymmetry. The benzodiazepine binding site is located on ca. 51K daltons component(s) in both forms.     

Proteins of Vasicular Stomatitis Virus: I. Polyacrylamide Gel Analysis of Viral Antigens

Infection of L cells with vesicular stomatitis virus results in the release, into the cell-free fluid, of four antigenic components separable by rate zonal centrifugation on sucrose gradients. The largest antigens are the infectious (B) particle and a shorter noninfectious, autointerfering (T) particle. The two small antigens are characterized by sedimentation coefficients of approximately 20S and 6S. Treatment of purified B or T particles with sodium deoxycholate results in the release from the particle of a nucleoprotein core which can be purified on sucrose gradient and which has a sedimentation coefficient characteristic of the virus from which it arose. Utilizing purified antigens labeled with (14)C-amino acids during growth, we examined the protein constituents of each antigen by acrylamide-gel electrophoresis. The proteins of B and T particles are identical, each containing one minor (virus protein 1) and three major (virus proteins 2, 3, and 4) proteins, numbered in order of increasing mobility. Virus protein 3 originates from the nucleoprotein core, whereas proteins 2 and 4 come from the coat. The origin of virus protein 1 is not known. The 20S antigen contains a single protein equivalent to virus protein 3, whereas the 6S antigen shows a single protein which is similar to, but probably distinct from, virus protein 2.     

Physical and chemical properties of the NH2-terminal glutamic acid and lysine forms of human plasminogen and their derived plasmins with an NH2-terminal lysine heavy (A) chain.

Comparative physical and chemical data are described for the human NH2-terminal Glu-plasminogen and Lys-plasminogen forms in order to determine the exact relationship between these two types of the zymogen. The molecular weights of Glu-plasminogen and Lys-plasminogen were similar and were determined to be 83, 800 plus or minus 4, 500 and 82, 400 plus or minus 3, 300, respectively, by sedimentation equilibrium methods. The molecular weights were identical in dodecyl sulfate solutions, approximately 83, 000, by sedimentation equilibrium methods. The sedimentation coefficients, s-020, w of Glu-plasminogen and Lys-plasminogen were determined to be 5.0 S, and 4.4 S, respectively. These two plasminogen forms had different partial specific volumes, and calculations of the frictional coefficients from sedimentation coefficients and molecular weights indicated conformation differences. Glu-plasminogen appeared to be larger in size than Lys-plasminogen in acrylamide gel-dodecyl sulfate electrophoresis. The amino acid compositions of Glu-plasminogen and Lys-plasminogen, and their major isolated isoelectric forms, were found to be similar, but several amino acid residues (glutamic acid, alanine, isoleucine, phenylalanine, and lysine) were found to be significantly higher in the Glu-plasminogen forms. The derived plasmins from both the Glu- and Lys-plasminogens with an nh2-terminal Lys- heavy (A) chain were found to have identical molecular weights of 76, 500 plus or minus 2, 500, and sedimentation coefficients, s-020, w of 4.3 S.     

Proteins of Soybean Seeds: II. Accumulation of the Major Protein Components during Seed Development and Maturation

Fresh weight and dry weight as well as quantitative and qualitative protein changes in the developing soybean (Glycine max) seed were described from 12 days after flowering until maturity. The seed proteins were separated on sucrose density gradients into three major fractions, having average sedimentation coefficients of 2.2S, 7.5S, and 11.8S. The 2.2S sedimenting proteins predominated at very early stages of development (12 days after flowering) and decreased proportionately throughout maturation. The 7.5S and 11.8S components appeared to be synthesized later in maturity and in larger amounts than the 2.2S proteins. Electrophoretic studies on extracts from whole seeds and on isolated protein fractions confirmed the early abundance of proteins in the 2.2S fraction and revealed temporal differences in the accumulation of three components of the 7.5S fraction. The 11.8S sedimenting fraction appeared throughout seed development as a homogeneous protein which accumulated in the seed with a time course similar to that of the total 7.5S protein fraction.     

Intracellular adenosine 3',5'-phosphate binding proteins in Dictyostelium discoideum: partial purification and characterization in aggregation competent cells

Three adenosine 3',5'-phosphate (cAMP) binding proteins were separated and partially purified from cytoplasmic extracts of Dictyostelium discoideum cells developed to aggregation competence. Two species, A and B, representing respectively 50% and 20% of the total activity, bind cAMP with very rapid kinetics and high specificity. Species A (Kd = 7.5 nM) is a monomeric protein of 36 000 daltons with a sedimentation coefficient of 2.3 S. Species B, which binds cAMP with positive cooperativity, also displays a high affinity for the ligand (Kd = 3.2 nM). This protein is present in the extracts as an equilibrium between monomeric, dimeric, and tetrameric forms with respective sedimentation coefficients of 2.4, 4.5, and 6.5 S; binding of cAMP to the monomer induces the appearance of the multimeric forms. A third cAMP binding protein (species C, Kd - 9.5 nM) was characterized as a larger protein (Mr 190 000, sedimentation coefficient of 9.2 S) which also binds adenosine and adenosyl derivatives. Species C represents 30% of the activity in the extracts and resemble the "adenosine analogue binding proteins" described in mammalian cells. The relevance of the properties of these proteins to the developmental process of D. discoideum amoebas is discussed.     

Chickpea seed proteins: Modification during germination

Changes in the proteins of chickpea during a 12-day germination period are reported using techniques of gel filtration, DEAE-cellulose chromatography, polyacrylamide gel (PAG) electrophoresis and ultracentrifugation. In the ultracentrifuge, the total proteins of dormant seeds resolve into 3 components which have the sedimentation coefficients of 2.2 S, 6.9 S and 10.3 S respectively. On germination, the presence of fractions of lower sedimentation coefficient indicates possible degradation of these components; in the early stages, the degradation rate of the 7 S fraction is higher, while the 10 S fraction is broken down faster in the later stages. Gel filtration experiments indicate the possibility of degradation of high polymer into intermediary products. Increase in the relative mobility of protein components on PAG and elution constant on DEAE-cellulose chromatographs indicates an increase in the net negative charge of the protein fractions. The accumulation of subunits of the proteins is negligible during the germination period.     

Determination of sedimentation coefficients for small peptides.

Direct fitting of sedimentation velocity data with numerical solutions of the Lamm equations has been exploited to obtain sedimentation coefficients for single solutes under conditions where solvent and solution plateaus are either not available or are transient. The calculated evolution was initialized with the first experimental scan and nonlinear regression was employed to obtain best-fit values for the sedimentation and diffusion coefficients. General properties of the Lamm equations as data analysis tools were examined. This method was applied to study a set of small peptides containing amphipathic heptad repeats with the general structure Ac-YS-(AKEAAKE)nGAR-NH2, n = 2, 3, or 4. Sedimentation velocity analysis indicated single sedimenting species with sedimentation coefficients (s(20,w) values) of 0.37, 0.45, and 0.52 S, respectively, in good agreement with sedimentation coefficients predicted by hydrodynamic theory. The described approach can be applied to synthetic boundary and conventional loading experiments, and can be extended to analyze sedimentation data for both large and small macromolecules in order to define shape, heterogeneity, and state of association.     

Sedimentation velocity properties of catenated DNA molecules from HeLa cell mitochondria

Catenated molecules of closed circular DNA have been isolated from the mitochondrial DNA of HeLs cells. The sedimentation coefficients of several purified species have been investigated. The catenated dimer, made up of two interlocked duplex circles, sediments at 51 S in its superhelical (closed) form. Treatment with pancreatic DNase to relax the duplex circles converts the 51 S doubly closed dimer to a 42 S singly open species, then to a 36 S doubly open catenated dimer. The triply closed trimer sediments at 63 S and is converted to a 45 S triply open form by DNase. Electron microscopy of the DNA samples before and after DNase treatment shows that under the conditions used DNase does not change the catenated nature of the DNA. The measured sedimentation coefficients, have been compared with those estimated from previously proposed correlations of sedimentation coefficient and molecular weight, and with the sedimentation coefficients for catenated DNA presented by Wang. When all the interlocked circles in a catenane are relaxed, the DNA sediments about 5–10% faster than a relaxed multiple-length circular molecule of the same molecular weight. The sedimentation coefficient, 36 S, of the fully relaxed catenated dimer is 1.4 times that of the relaxed monomer.     

Study on mammalian ribosomal protein reactivity in situ. III. Effect of trypsin on 40S and 60S subunits.

Rat liver 40S and 60S ribosomal subunits were treated with increasing concentrations of trypsin. The activity of both trypsin-treated subunits, when assayed for polyphenylalanine synthesis, progressively decreased, but the 60S subunits were inactivated at much lower trypsin concentrations than were the 40S ones. The sedimentation coefficients of trypsin-treated subunits were identical to those of control subunits when sucrose gradients containing 0.5 M KCl were used. When the sucrose gradients were prepared with a low salt buffer (80 mM KCl), dimer formation was observed with control subunits, but not with trypsin-treated ones. Two-dimensional gel electrophoresis analysis of the proteins extracted from trypsin-treated subunits revealed that all ribosomal proteins in the subunits were accessible to the enzyme. However, several proteins were more resistant to trypsin in compact subunits than when they were free or in unfolded subunits. Proteins of the 60S subunits were generally digested by lower trypsin concentrations than those of the 40S subunits. From the quantitative measurements of the undigested proteins, a classification of the proteins from both subunits according to their trypsin sensitivity was established. These results were compared with those previously obtained concerning ribosomal protein reactivity to chemical reagents.     

Inactivation of MS-2 phage and poliovirus in groundwater

Since temperature affects the inactivation rate of viruses in natural water systems, the aim of this study was to determine if a temperature shift could influence the structural integrity of model viruses. When crude lysates of MS-2 phage were seeded into groundwater microcosms and incubated at 27 degrees C, complete virus inactivation took place in eight days. The temperature was then shifted to 4 degrees C. Three days after the temperature shift, a two-log increase in virus titer (reactivation) occurred. However, when purified MS-2 lysates were added to groundwater microcosms, no reactivation was obtained. No reactivation of poliovirus took place when similar microcosm experiments were done. The sedimentation coefficients of MS-2 shifted from 80S to 58S, 48S, 37S, 32S, and 18S as inactivation proceeded in groundwater and distilled water controls. Similarly, the sedimentation coefficients of polioviruses changed from 156S to 142S, 135S, 117S, 105S, 95S, and 80 S as inactivation took place. There was no correlation between % virus inactivation and % decrease in virions with intact sedimentation coefficients, as reported earlier for poliovirus inactivated by chlorine. The results presented support our hypothesis that virus inactivation proceeds gradually, involving the rearrangement and (or) loss of capsomere components that may eventually lead to the ejection of nucleic acids. The intermediate particles generated as inactivation proceeds may be in a reversibly inactivated state, and may revert back to a fully infectious state when chemical components stabilize the virus particle.     

Porcine serum cobalophilin and transcobalamin. Identification, isolation and properties including electrofocusing patterns

Pooled porcine serum was found to contain cobalophilin (also called transcobalamin I) and transcobalamin (also called transcobalamin II). The two proteins were harvested by batchwise absorption with vitamin B-12 covalently coupled to Sepharose, and then separated from each other either by gel filtration or using an immunoadsorbent. Both proteins were finally isolated as single proteins using a second vitamin B-12-Sepharose chromatography step. Cobalophilin and transcobalamin complexed with vitamin B-12 had molecular weights by gel filtration of 135 000 and 38 000 and by the formula of Svedberg 104 000 and 44 000, Stokes radii 4.97 nm and 2.65 nm, and sedimentation coefficients 5.39 S and 3.75 S, respectively. Electrofocusing resolved the cobalophilin complex into three main isoproteins isoelectric at pH 3.23, 3.42 and 3.69, and transcobalamin into only the main component isoelectric at a value as low as pH 3.47. Neither protein was capable of binding to the ileal intrinsic factor receptor.     

Sedimentation velocity analysis of flexible macromolecules: self-association and tangling of amyloid fibrils

A novel bead modeling technique has been developed for the analysis of the sedimentation velocity behavior of flexible fibrils. The method involves the generation of a family of bead models representing a sample of the conformations available to the molecule and the calculation of the sedimentation coefficients of these models by established techniques. This approach has been used to investigate the size distribution of amyloid fibrils formed by human apolipoprotein C-II (apoC-II). ApoC-II fibrils have a simple and homogeneous ribbon morphology with no evidence of amorphous aggregation. Freshly prepared apoC-II forms fibrils with systematically larger sedimentation coefficients upon increasing protein concentration (modes of 100, 300, and 800 for apoC-II concentrations of 0.3, 0.7, and 1.0 mg/mL, respectively). The sedimentation coefficient distributions are not affected by rotor speed, and are not significantly changed by dilution once the fibrils are formed. The kinetics of aggregation (1 mg/mL apoC-II) as assessed using thioflavin T and preparative pelleting assays reveal that monomeric apoC-II is depleted after approximately 12 h incubation at room temperature. In contrast, the sedimentation coefficient distribution of fibrils continues to grow larger over a period of 48 h to an average value of 800 S. Calculations using the bead modeling procedure suggest maximum sedimentation coefficients for individual apoC-II fibrils to be around 100 S. The larger experimentally observed sedimentation coefficients for apoC-II fibrils indicate an extensive and time-dependent tangling or association of the fibrils to form specific networks.