The effect of protein depletion on the rate of protein synthesis in rat liver.

In order to understand the mechanism of decreased protein synthesis in the liver of rats fed a protein-free diet, the average polypeptide chain assembly time (tc) was measured by the method of Mathews et al. (J. Biol. Chem. (1973) 248, 1329). For rats fed a normal diet, tc in liver in vivo was 1.28 min. A 10-day period of protein depletion led to a value of tc = 2.08 min, corresponding to a 38% depression in polypeptide elongation rate. Protein depletion caused an extensive breakdown of hepatic polysomes and refeeding of a complete mixture of amino acids resulted in rapid recovery of polysomal profile. But tc in the liver of the refed animals gave still depressed value of 1.95 min. The amount and size distribution of poly(A)-containing mRNA in the liver, as determined by [3H]poly(U) hybridization, were the same for normal and depleted groups. These results suggest that both initiation and elongation steps of protein synthesis are depressed in the liver of protein-depleted rats. Refeeding of amino acid mixture rapidly restores initiation but not elongation activity.     

Comparative characteristics of protein-synthesizing apparatus of diploid and aneuploid human embryo fibroblasts

The time of average polypeptide chain synthesis (tc), distribution of synthesized polypeptides according to their molecular masses, the ratio of translating and nontranslating ribosomes and polyribosomes of different size have been analyzed for diploid and aneuploid strains of fibroblasts. The magnitude of tc as well as the size of polypeptide chains synthesized were found to be similar for both kinds of fibroblasts. The relative cellular content of the translating ribosomes has been shown to decrease during the transition of cells from both strains to the stationary growth phase. The relative content of heavy polyribosomes is lower in aneuploid cells as compared with that in diploid cells. The process of translation in aneuploid fibroblasts is concluded to have no essential deviations from normal.     

High-molecular-weight kininogen from horse plasma. Isolation, characterization and comparison with bovine high-Mr kininogen

High-molecular-weight (high-Mr) kininogen was purified from horse plasma by chromatography on columns of DEAE-Sephadex A-50, CM-Sephadex C-50, p-chlorobenzylamine-Sepharose and Sephadex G-150. The yield was about 150 mg from 81 of fresh plasma. The purified material gave a single band on sodium dodecylsulfate/polyacrylamide gel electrophoresis and a single precipitin line on immunodiffusion and immunoelectrophoresis. The molecular weight of horse high-Mr kininogen was estimated to be 78000 by dodecylsulfate gel electrophoresis using the Ferguson plot. Its polypeptide content was determined to be 86% by amino acid analysis and there was a total of 581 amino acid residues/molecule of protein. The kininogen contained a total of 13.9% carbohydrates, consisting of hexoses (7.8%), glucosamine (1.9%), galactosamine (0.6%) and sialic acid (3.6%). On incubation of horse high-Mr kininogen with bovine and horse plasma kallikreins, several fragments which contained extremely high levels of histidine, were liberated, in addition to kinin. After the liberation of kinin and histidine-rich fragments, a protein free of kinin and its fragments was isolated. This protein consisted of two polypeptide chains, heavy chain and light chain, which are bridged by disulfide bonds. The molecular weight and amino acid composition of the heavy chain and the light chain from horse high-Mr kininogen were very similar to those of the heavy and light chains from bovine high-Mr kininogen, respectively. From these results, it was revealed that horse high-Mr kininogen is quite similar to bovine high-Mr kininogen in terms of their physicochemical and chemical properties, although they are immunologically distinguishable.     

Investigation of the quaternary structure of beef liver glutamate dehydrogenase with bifunctional reagents

The six identical polypeptide chains of the smallest enzymatically active unit of beef liver glutamate dehydrogenase are shown to be arranged in two trimers. Cross-linking with bifunctional reagents of varying chain length and subsequent SDS polyacrylamide gel electrophoresis of the protein shows main bands corresponding to molecular weights of 168,000 and 336,000 daltons which is three times and six times, respectively, the molecular weight of the polypeptide chain (56,000 daltons). This finding supports a model for the quaternary structure of the glutamate dehydrogenase proposed by Reisler and Eisenberg (Biopolymers $\text{9}$, 877 (1970)).     

A difference infrared spectroscopic study of gramicidin A, alamethicin and bacteriorhodopsin in perdeuterated dimyristoylphosphatidylcholine

Difference infrared spectroscopy has been used to study the way in which the intrinsic molecules gramicidin A, alamethicin and bacteriorhodopsin perturb their environment when present within a lipid bilayer structure. Dimyristoylphosphatidylcholine containing perdeuterated chains has been used to enable the lipid chain C-2H stretching absorption band to be separated from the C-H bands arising from the intrinsic polypeptide or protein. The C-2H stretching bands of the phospholipid are sensitive to two different types of chain conformation. The C-2H stretching frequency provides information about the static order of the lipid chains, whilst the half-maximum bandwidth provides a measure of chain librational and torsional motion. From the measurements it is concluded that: (1) Above the lipid phase transition temperature tc, low concentrations of either gramicidin A or alamethicin cause a small decrease in lipid chain gauche isomers whilst bacteriorhodopsin in the lipid bilayer has no effect. At higher concentrations each intrinsic molecule causes an increase to occur in lipid chain gauche isomers. (2) The lipid acyl chain motion, as deduced from the bandwidths is increased by the presence of a low concentration of gramicidin A within the lipid bilayer. The presence of the other intrinsic molecules studied have little effect. A higher concentration of alamethicin causes a decrease in chain motion whilst gramicidin A and bacteriorhodopsin have no effect. (3) Below tc each of the intrinsic molecules when present in the lipid bilayer causes an increase in gauche isomers to occur as well as an increase in the lipid chain motion. A broadening of the lipid phase transition occurs as the concentration of the polypeptide increases.     

The subunit structure of thymus leukemia antigens.

EDTA-containing buffer solubilizes thymus leukemia antigens (TLa) from crude thymocyte membrane fractions. The TL antigens consist mainly of molecules of a size similar to immunoglobulin G when gel chromatography analyses were performed under physiological conditions. A single component of TLa was apparent on sucrose density gradient ultracentrifugation of solubilized thymocyte membrane macromolecules as monitored by indirect immunoprecipitation. The sedimentation constant for the TL antigens (5.8 S) was considerably less than that for immunoglobulin G. The gel chromatography and ultracentrifugation data suggest an apparent molecular weight for TLa of about 120000. TLa isolated by indirect immunoprecipitation is composed of two types of polypeptide chains. The smaller subunit was identified as beta2-microglobulin. The larger polypeptide chain carried the alloantigenic determinants and displayed a molecular weight of about 50000 after reduction and alkylation. TLa subjected to molecular weight determination under denaturing conditions was composed of two components. The smaller component was beta2-microglobulin which evidently is linked to the larger polypeptide chain by noncovalent interactions only. The larger component had a size greater than reduced and alkylated immunoglobulin G heavy chains. Upon reduction and alkylation of the latter component its size was reduced and it appeared to have a molecular weight of about 50000. Consequently, TLa is composed of two disulfide linked heavy polypeptide chains and two beta2-microglobulin molecules. TLa solubilized by papain digestion comprises two polypeptide chains, one of which is beta2-microglobulin. The larger 37000-dalton subunit is a fragment of the heavy polypeptide chain. This was demonstrated by digesting solubilized 120000-dalton TLa with papain. The proteolytic fragments obtained were indistinguishable from those directly released from the cell surface by proteolysis. The papain-derived TLa fragment exhibited most if not all the alloantigenic determinants.     

Processing of the human heparanase precursor and evidence that the active enzyme is a heterodimer.

Human platelet heparanase has been purified to homogeneity and shown to consist of two, non-covalently associated polypeptide chains of molecular masses 50 and 8 kDa. Protein sequencing provided the basis for determination of the full-length cDNA for this novel protein. Based upon this information and results from protein analysis and mass spectrometry, we propose a scheme to define the structural organization of heparanase in relation to its precursor forms, proheparanase and pre-proheparanase. The 8- and 50-kDa chains which make up the active enzyme reside, respectively, at the NH(2)- and COOH-terminal regions of the inactive precursor, proheparanase. The heparanase heterodimer is produced by excision and loss of an internal linking segment. This paper is the first to suggest that human heparanase is a two-chain enzyme.     

A major polypeptide component of rat liver mitochondria: carbamyl phosphate synthetase.

One of the major components of rat liver mitochondria detected by gel electrophoresis in sodium dodecyl sulfate is a 165,000 molecular weight polypeptide that makes up 15 to 20% of the total mitochondrial protein. This component appears to be a single molecular species. Evidence is presented here for the identification of this protein with the polypeptide chain of a urea cycle enzyme, carbamoylphosphate synthetase I (EC 2.7.2.5). The 165,000 molecular weight polypeptide was solubilized from mitochondria with Triton X-100 and purified to 90% homogeneity by DEAE-cellulose chromatography. This component co-migrated with carbamyl phosphate synthetase activity when mitochondrial proteins were separated by gel filtration or sucrose gradient centifugation. The identification of the 165,000 molecular weight polypeptide with this activity was also supported by the presence or absence of this protein in a variety of rat tissue mitochondria, in liver and kidney mitochondria from various ureotelic and nonureotelic species, and in fetal rat liver mitochondria.     

Hemocyanins Relationships in Their Structure, Function and Assembly

Hemocyanins are high molecular weight oxygen-carrying proteinsthat occur in the molluscs and arthropods. The oxygen-bindingsite in these proteins is a pair of copper atoms bound directlyto ammo acid side chains. The biscopper sites of these proteinsbind single molecules of dioxygen or carbon monoxide. In arthropodsthere are two copper atoms per approximately 70 000 daltonsof protein. This corresponds to the molecular weight of theminimum polypeptide chain. In molluscs however there are twocopper atoms per 50,000 daltons of protein. This does not correspondto the minimum polypeptide chain although it does correspondto the minimal functional unit. The minimal polypeptide chainin molluscan hemocyanins is approximately 400,000 daltons andappears to be composed of eight or more 50 000 dalton unitslinked together like a string of pearls. In the molluscs, thenative hemocyanins found in the hemolymph generally occur asgiant cylindrical molecules 350 Å in diameter, 380 Ålong, with molecular weights of 9 000,000. These large moleculesare composed of approximately 20 polypeptide chains. In thehemolymph of the arthropods depending upon the species, hemocyaminsoccur as hexamers dodecamers 24-mers and 48-mers. The molecularweight of the 48-mers is about 3 600,000. The respiratory functionsof hemocyamns show a wide range of allosteric properties. Thelarge molecules commonly show cooperativity in oxygen binding.The number of interacting subunits is in some cases dependentupon external conditions of pH and ionic composition. The oxygenaffinity is usually sensitive to pH and to low molecular weightcofactors like chloride, calcium and magnesium ions. The intrinsicoxygen binding properties of an organism s hemocyanin and itsallosteric control by modulators allow organisms possessingthese giant molecules to adapt to their environmental conditions.     

Purification and properties of tyrosyl tRNA synthetase of rat liver.

Purification of rat liver tyrosine tRNA synthetase yields two protein fractions A and B and both fractions are required for charging of tyrosine to tRNAtyr. Fraction B catalyzes the activation of tyrosine. Fractions A and B have been purified to near homogeneity and they are composed of single polypeptide chains of 62,000 daltons each. Gel filtration studies suggest a molecular weight of 120,000 for the synthetase.     

Rabbit urinary tamm-horsfall glycoprotein. Chemical composition and tentative carbohydrate structure

The urinary Tamm-Horsfall protein (THP) is the major glycoprotein secreted by the mammalian kidney. We recently isolated and immortalized thick ascending limb of Henle cells from rabbit kidney, which produce Tamm-Horsfall protein in cell culture in vitro. In order to further study the yet undefined functional role and biosynthetic pathways of this protein, we first re-examined the chemical composition and the carbohydrate structure of rabbit urinary Tamm-Horsfall protein. Using precipitation with 0.58 mol/l NaCl a protein was isolated from rabbit urine which showed extensive microheterogeneity and had an average molecular mass of 95 kDa. Deglycosylation of the protein led to a loss of microheterogeneity and yielded a molecular mass of 58-60 kDa. Amino-acid analysis of the native and deglycosylated protein revealed a lower cysteine (20 mol/mol THP) and a higher histidine (20 mol/mol THP) content than described previously. Chemical analysis of the carbohydrates showed a high glucosamine (50 mol/mol THP), galactose (43 mol/mol THP), and mannose (24 mol/mol THP) content. The amount of sialic acid was 15 mol/mol THP. Using lectins to identify the structure of the carbohydrate chains it was shown that rabbit Tamm-Horsfall protein possesses complex-type oligosaccharide chains with terminal sialic acid, beta-galactose, and probably alpha-fucose and chains of the mucin type. These results indicate that some of the cysteine residues in the polypeptide chain of THP can be replaced by histidine, suggesting a role of some cysteins in metal binding rather than intramolecular stabilization.(ABSTRACT TRUNCATED AT 250 WORDS)     

Limited proteolysis and proton n.m.r. spectroscopy of the 2-oxoglutarate dehydrogenase multienzyme complex of Escherichia coli.

The 2-oxoglutarate dehydrogenase multienzyme complex of Escherichia coli was treated with trypsin at pH 7.0 at 0 degrees C. Loss of the overall catalytic activity was accompanied by rapid cleavage of the lipoate succinyltransferase polypeptide chains, this apparent Mr falling from 50 000 to 36 000 as judged by sodium dodecyl sulphate/polyacrylamide-gel electrophoresis. A slower shortening of the 2-oxoglutarate decarboxylase chains was also observed, whereas the lipoamide dehydrogenase chains were unaffected. The inactive trypsin-treated enzyme had lost the lipoic acid-containing regions of the lipoate succinyltransferase polypeptide chains, yet remained a highly assembled structure, as judged by gel filtration and electron microscopy. The lipoic acid-containing regions are therefore likely to be physically exposed in the complex, protruding from the structural core formed by the lipoate succinyltransferase component between the subunits of the other component enzymes. Proton nuclear magnetic resonance spectroscopy of the 2-oxoglutarate dehydrogenase complex revealed the existence of substantial regions of polypeptide chain with remarkable intramolecular mobility, most of which were retained after removal of the lipoic acid-containing regions by treatment of the complex with trypsin. By analogy with the comparably mobile regions of the pyruvate dehydrogenase complex of E. coli, it is likely that the highly mobile regions of polypeptide chain in the 2-oxoglutarate complex are in the lipoate succinyltransferase component and encompass the lipoyl-lysine residues. It is clear, however, that the mobility of this polypeptide chain is not restricted to the immediate vicinity of these residues.     

Purification of phospholipid methyltransferase from rat liver microsomal fraction.

Phospholipid methyltransferase, the enzyme that converts phosphatidylethanolamine into phosphatidylcholine with S-adenosyl-L-methionine as the methyl donor, was purified to apparent homogeneity from rat liver microsomal fraction. When analysed by SDS/polyacrylamide-gel electrophoresis only one protein, with molecular mass about 50 kDa, is detected. This protein could be phosphorylated at a single site by incubation with [alpha-32P]ATP and the catalytic subunit of cyclic AMP-dependent protein kinase. A less-purified preparation of the enzyme is mainly composed of two proteins, with molecular masses about 50 kDa and 25 kDa, the 50 kDa form being phosphorylated at the same site as the homogeneous enzyme. After purification of both proteins by electro-elution, the 25 kDa protein forms a dimer and migrates on SDS/polyacrylamide-gel electrophoresis with molecular mass about 50 kDa. Peptide maps of purified 25 kDa and 50 kDa proteins are identical, indicating that both proteins are formed by the same polypeptide chain(s). It is concluded that rat liver phospholipid methyltransferase can exist in two forms, as a monomer of 25 kDa and as a dimer of 50 kDa. The dimer can be phosphorylated by cyclic AMP-dependent protein kinase.     

Molecular basis for the effect of urea and guanidinium chloride on the dynamics of unfolded polypeptide chains

Chemical denaturants are frequently used to unfold proteins and to characterize mechanisms and transition states of protein folding reactions. The molecular basis of the effect of urea and guanidinium chloride (GdmCl) on polypeptide chains is still not well understood. Models for denaturant--protein interaction include both direct binding and indirect changes in solvent properties. Here we report studies on the effect of urea and GdmCl on the rate constants (k(c)) of end-to-end diffusion in unstructured poly(glycine-serine) chains of different length. Urea and GdmCl both lead to a linear decrease of lnk(c) with denaturant concentration, as observed for the rate constants for protein folding. This suggests that the effect of denaturants on chain dynamics significantly contributes to the denaturant-dependence of folding rate constants for small proteins. We show that this linear dependency is the result of two additive non-linear effects, namely increased solvent viscosity and denaturant binding. The contribution from denaturant binding can be quantitatively described by Schellman's weak binding model with binding constants (K) of 0.62(+/-0.01)M(-1) for GdmCl and 0.26(+/-0.01)M(-1) for urea. In our model peptides the number of binding sites and the effect of a bound denaturant molecule on chain dynamics is identical for urea and GdmCl. The results further identify the polypeptide backbone as the major denaturant binding site and give an upper limit of a few nanoseconds for residence times of denaturant molecules on the polypeptide chain.     

Capsid Polypeptides of Mouse Elberfeld Virus I. Amino Acid Compositions and Molar Ratios in the Virion

The four major polypeptide chains (alpha, beta, gamma, delta) constituting the capsid protein of mouse Elberfeld (ME) virus were isolated by preparative electrophoresis on polyacrylamide gels, and the amino acid composition of each chain was determined. In addition, the molecular weights of the smallest chains of ME virus, mengovirus, and poliovirus, which had previously been determined by gel electrophoretic methods, were redetermined by gel filtration chromatography in 6 m guanidine hydrochloride. Each was found to have a molecular weight about 7,300. Using the reevaluated molecular weights and the known amino acid compositions of the chains, the molar ratio of each chain in the ME virion was determined by quantitative analysis of the distribution of radioactivity in the electrophoretically separated chains of virus which had been specifically radiolabeled with leucine or with methionine. Equimolar proportions of all four chains were found in the virion.     

Topological disposition of UDP-glucuronyltransferase in rat liver microsomes.

The topological disposition of a form of UDP-glucuronyltransferase (called GT-1) in rat liver microsomes was examined. Concanavalin A-Sepharose failed to bind microsomal vesicles even though GT-1 has sugar chains of "high mannose" type, indicating that mannose-containing sugar chains of microsomal glycoproteins including GT-1 are not exposed to the outer surface of microsomal vesicles. Polyclonal antibodies raised against purified GT-1 could bind to microsomal vesicles, indicating that at least part of the GT-1 polypeptide chain is extruded to the outside of the microsomal membrane. Intact microsomal vesicles were digested with carboxypeptidase Y and then subjected to immunoblot analysis using the anti-GT-1 antibodies. It was thus found that the digestion resulted in cleavage of a C-terminal, 2-kDa fragment, leaving a 52-kDa fragment of GT-1 still tightly bound to the membrane. From these results, it is concluded that GT-1 is a transmembrane protein, which extrudes its C-terminal end (at least 2 kDa) to the outside of the membrane, whereas most of its polypeptide chain together with the sugar chains are located on the luminal side of the membrane.     

Polypeptide-chain stoicheiometry and lipoic acid content of the pyruvate dehydrogenase complex of Escherichia coli.

The pyruvate dehydrogenase multienzyme complex was isolated from Escherichia coli grown in the presence of [35S]sulphate. The three component enzymes were separated by sodium dodecyl sulphate/polyacrylamide-gel electrophoresis and the molar ratios of the three polypeptide chains were determined by measurement of the radioactivity in each band. The chain ratio of lipoamide dehydrogenase to lipoate acetyltransferase approached unity, but there was a molar excess of chains of the pyruvate decarboxylase component. The 35S-labelled complex was also used in a new determination of the total lipoic acid content. It was found that each polypeptide chain of the lipoate acetyltransferase component appears to bear at least three lipoyl groups.     

Dynamics of unfolded polypeptide chains as model for the earliest steps in protein folding

The rate of formation of intramolecular interactions in unfolded proteins determines how fast conformational space can be explored during folding. Characterization of the dynamics of unfolded proteins is therefore essential for the understanding of the earliest steps in protein folding. We used triplet-triplet energy transfer to measure formation of intrachain contacts in different unfolded polypeptide chains. The time constants (1/k) for contact formation over short distances are almost independent of chain length, with a maximum value of about 5 ns for flexible glycine-rich chains and of 12 ns for stiffer chains. The rates of contact formation over longer distances decrease with increasing chain length, indicating different rate-limiting steps for motions over short and long chain segments. The effect of the amino acid sequence on local chain dynamics was probed by using a series of host-guest peptides. Formation of local contacts is only sixfold slower around the stiffest amino acid (proline) compared to the most flexible amino acid (glycine). Good solvents for polypeptide chains like EtOH, GdmCl and urea were found to slow intrachain diffusion and to decrease chain stiffness. These data allow us to determine the time constants for formation of the earliest intrachain contacts during protein folding.     

Cellular retinol-binding protein from rat liver. Purification and characterization

Cellular retinol-binding protein has been purified to homogeneity from rat liver. The procedures utilized in the purification included acid precipitation, gel filtration on Sephadex G-75 and G-50, and chromatography on DEAE-cellulose. The binding protein was purified approximately 3,500-fold, based on total soluble liver protein. The protein is a single polypeptide chain with a molecular weight of 14,600 based on information obtained by the techniques of sedimentation equilibrium analysis, gel filtration, and sodium dodecyl sulfate-polyacrylamide electrophoresis. The protein binds retinol with high affinity; the appparent dissociation constant was determined by fluorometric titration to be 1.6 X 10(-8) M. Retinol bound to the protein has an absorption spectrum (lambdamax, 350 nm) considerably altered from the spectrum of retinol in ethanol (lambdamax, 325 nm).     

Complete Amino Acid Sequence of the Sweet Protein Monellin

The sweet protein monellin consists of two noncovalently associated polypeptide chains, the A chain of 44 amino acid residues and the B chain of 50 residues. Two different primary structures have been reported for each of these chains. The complete amino acid sequence of monellin was determined by a combination of FAB- and ESI-mass spectrometry, and by automatic Edman degradation.