Porcine platelet tropomyosin: Purification,characterization and paracrystal formation

Porcine platelet tropomyosin has been isolated by hydroxyapatite chromatography following isoelectric precipitation and ethanol fractionation. A single component (M_r = 30,000 on polyacrylamide gel electrophoresis in sodium dodecyl sulphate) was obtained in a variety of gel electrophoretic systems, including urea/sodium dodecyl sulphate and isoelectric focussing, suggesting the presence of a single polypeptide species. This contrasts with the observations by others using horse platelet tropomyosin or tropomyosins isolated from brain, where two polypeptides were found. The amino acid composition of porcine platelet tropomyosin was virtually identical to that of the horse platelet protein except for the presence of a single cysteine residue in the pig protein, whereas horse tropomyosin contains two. Oxidation of this sulphydryl group produced a molecule of over 60,000 M_r on polyacrylamide gels in sodium dodecyl sulphate, suggesting by analogy with skeletal muscle tropomyosin that the two chains had been linked and therefore existed in register in the coiled-coil structure. Cleavage at the cysteine produced a fragment of M_r = 19,000, indicating that this residue was located about one-third of the distance from a molecular end.Magnesium paracrystals of platelet tropomyosin were examined by electron microscopy following negative staining and found to have a repeat of 345 Å, close to that expected for an extended alpha-helical coiled-coil with an apparent M_r of 30,000. The repeating unit was centrosymmetric and the appearance of broken paracrystals suggested that the molecular ends lie on a dyad axis. Location of the sulphydryl residues in the paracrystals by labelling with N-pyrrolo-isomaleimide showed two bands separated by approximately 80 Å, which was consistent with the location of the molecular ends on a dyad.The amount of tropomyosin present was estimated as 2·2% of the total platelet protein. This implied a molar ratio of G-actin to tropomyosin of about 14:1, based on previous estimates of the actin content in porcine platelets. Assuming that one molecule of tropomyosin will bind six molecules of actin (based on the reduced molecular length of the platelet protein), there was not sufficient tropomyosin to bind to more than half the total actin in the cell.     

On the resolution of polypeptides by isoelectric focusing in polyacrylamide gels in the presence of urea and nonidet-p40.

Three model substances were used to test the resolving power of isoelectric focusing in polyacrylamide gels in the presence of 9 m urea and 2% Nonidet-P40: (1) The α subunit of RNA polymerase from Escherichia coli modified by a single covalently attached adenosine 5′-diphosphate-ribose residue can be clearly resolved from the unmodified subunit. (2) The α subunit of RNA polymerase from a mutant of E. coli in which a single leucine residue is replaced by a histidine residue can be resolved from the wild-type subunit. (3) Muscle actin presumably modified by carboxymethylation with iodoacetate at only one cysteine residue can be separated from the unmodified polypeptide.     

Purification and structural characterization of placental NAD(+)-linked 15-hydroxyprostaglandin dehydrogenase. The primary structure reveals the enzyme to belong to the short-chain alcohol dehydrogenase family

Human placental NAD(+)-linked 15-hydroxyprostaglandin dehydrogenase was purified to homogeneity according to a five-step method, with chromatography on DEAE-Sepharose, Blue Sepharose, and Mono-Q FPLC as principal steps. Final yield was 23% and purification about 13,000-fold, with a specific activity of 24,000 milliunits/mg. The subunit molecular weight is about 29,000 as determined by sodium dodecyl sulfate/polyacrylamide gel electrophoresis, and the native protein molecular weight is about 54,000 as estimated by Sephadex G-100 chromatography, establishing the enzyme to be a dimer of similar-sized protein chains. The subunit N-terminal residue is methionine, and the alpha-amino group is free. The complete primary structure was determined by peptide analysis, based essentially on four different proteolytic treatments (Lys-specific protease, Glu-specific protease, Asp-specific protease, and CNBr). The protein chain is composed of 266 residues, with C-terminal glutamine. A microheterogeneity was detected at position 217, with both Cys and Tyr, in about equal amounts, from a preparation starting with a single placenta. No other subunit heterogeneities were detected. The protein is clearly but distantly related to insect alcohol dehydrogenases, characterized bacterial dehydrogenases of sugar metabolism, and bacterial and eukaryotic steroid dehydrogenases. Together, these results establish that placental 15-hydroxyprostaglandin dehydrogenase is a member of the short-chain nonmetalloenzyme alcohol dehydrogenase protein family. The protein has four cysteine residues (five with the positional microheterogeneity), but there is no evidence for functional importance of any of these residues.(ABSTRACT TRUNCATED AT 250 WORDS)     

In vitro labeling of proteins by reductive methylation: Application to proteins involved in supramolecular structures

Actin and tropomyosin, purified from both muscle and brain, and α-actinin, purified from muscle, have been labeled in vitro by reductive methylation to specific activities of greater than 10⁵ dpm/μg protein. Actin so modified bound DNase I and polymerized identically to unmodified actin. Furthermore, the spectral properties of actin did not change after labeling. The interactions of labeled tropomyosin and α-actinin with F-actin were nearly identical to those of the unmodified proteins. These modified proteins comigrated with their unmodified counterparts in both SDS-containing polyacrylamide gels and isoelectric focusing gels. The labeled actin was quantitatively extracted from SDS-containing polyacrylamide gels (yield > 98% of radioactivity applied demonstrating that all of the radioactivity was protein bound. The reductive methylation procedure worked well at pH 8.0–8.5 in either pyrophosphate buffer or Bicine buffer using formaldehyde with [³H]-sodium borohydride as the reducing agent. The procedure could also be performed at pH 7.0 in phosphate buffer using [¹⁴C]-formaldehyde with sodium cyanoborohydride as the reducing agent. Proteins so labeled are ideal for use in quantitative experiments involving protein-protein interactions.     

Mapping the cofilin binding site on yeast G-actin by chemical cross-linking

Cofilin is a major cytoskeletal protein that binds to both monomeric actin (G-actin) and polymeric actin (F-actin) and is involved in microfilament dynamics. Although an atomic structure of the G-actin-cofilin complex does not exist, models of the complex have been built using molecular dynamics simulations, structural homology considerations, and synchrotron radiolytic footprinting data. The hydrophobic cleft between actin subdomains 1 and 3 and, alternatively, the cleft between actin subdomains 1 and 2 have been proposed as possible high-affinity cofilin binding sites. In this study, the proposed binding of cofilin to the subdomain 1/subdomain 3 region on G-actin has been probed using site-directed mutagenesis, fluorescence labeling, and chemical cross-linking, with yeast actin mutants containing single reactive cysteines in the actin hydrophobic cleft and with cofilin mutants carrying reactive cysteines in the regions predicted to bind to G-actin. Mass spectrometry analysis of the cross-linked complex revealed that cysteine 345 in subdomain 1 of mutant G-actin was cross-linked to native cysteine 62 on cofilin. A cofilin mutant that carried a cysteine substitution in the α3-helix (residue 95) formed a cross-link with residue 144 in actin subdomain 3. Distance constraints imposed by these cross-links provide experimental evidence for cofilin binding between actin subdomains 1 and 3 and fit a corresponding docking-based structure of the complex. The cross-linking of the N-terminal region of recombinant yeast cofilin to actin residues 346 and 374 with dithio-bis-maleimidoethane (12.4 Å) and via disulfide bond formation was also documented. This set of cross-linking data confirms the important role of the N-terminal segment of cofilin in interactions with G-actin.     

Actin Depolymerizing Factor Is a Component of Slow Axonal Transport

We examined the low molecular weight proteins transported with actin in the chicken sciatic nerve after injection of [35S]methionine into the lumbar spinal cord. A prominent component of slow axonal transport with apparent molecular mass 19 kDa comigrated on two-dimensional gels with chicken actin depolymerizing factor (ADF), previously shown to be a major actin-binding protein in brain. There was comparatively little radioactivity associated with the actin monomer sequestering proteins, profilin or cofilin, and examination of the rapid component of axonal transport failed to reveal appreciable quantities of actin, ADF, profilin, or cofilin. These results show that both actin and ADF are carried by slow axonal transport and raise the possibility that actin travels within the axon in an unpolymerized form in a complex with ADF.     

Intermediates in the refolding of reduced ribonuclease A.

The intermediates with one, two, three or four disulphide bonds which accumulate during unfolding of native ribonuclease and refolding of the reduced protein have been trapped by rapid alkylation with iodoacetate and separated by ionexchange chromatography. They have been characterized to varying extents by their enzymic activity, electrophoretic mobility through polyacrylamide gels, disulphide bonds between cysteine residues, the environments of the six tyrosine residues as indicated by ultraviolet absorption and fluorescence spectra, interaction with antibodies directed against either the trapped unfolded reduced protein or the native folded protein, and for the disruption by urea of any stable conformation producing a change in molecular shape.Correctly refolded ribonuclease was indistinguishable from the original native protein, but virtually all the intermediates with up to four disulphide bonds formed directly from the reduced protein were enzymically inactive and unfolded by these criteria. Unfolding of native ribonuclease was an all-or-none transition to the fully reduced protein, with no accumulation of disulphide intermediates. The intermediates in refolding are separated from the fully folded state by the highest energy barrier in the folding transition; they may be considered rapidly interconvertible, relatively unstable microstates of the unfolded protein. The measured elements of the final conformation are not acquired during formation of the first three disulphide bonds, but appear simultaneously with formation of the fourth native disulphide bond.These observations with ribonuclease are qualitatively similar to those made previously in greater detail with pancreatic trypsin inhibitor and suggest a possible general pattern for the kinetic process of protein unfolding and refolding.     

Isolation and some structural and functional properties of macrophage tropomyosin

Tropomyosin purified from rabbit lung macrophages is very similar in structure to other nonmuscle cell tropomyosins. Reduced and denatured, the protein has two polypeptides which migrate during electrophoresis in sodium dodecyl sulfate on polyacrylamide gels with slightly different mobilities corresponding to apparent Mr's of about 30 000. Following cross-linking by air oxidation in the presence of CuCl2, electrophoresis under nonreducing conditions reveals a single polypeptide of Mr 60 000. Macrophage tropomyosin has an isoelectric point of 4.6 and an amino acid composition similar to other tropomyosins. It contains one cysteine residue per chain. In the electron microscope, macrophage tropomyosin molecules rotary shadowed with platinum and carbon are slender, straight rods, 33 nm in length. Macrophage tropomyosin paracrystals grown in high magnesium concentrations have an axial periodicity of 34 nm. On the basis of yields from purification and from two-dimensional electrophoretic analyses of macrophage extracts, tropomyosin comprises less than 0.2% of the total macrophage protein, a molar ratio of approximately 1 tropomyosin molecule to 75 actin monomers in the cell. Macrophage tropomyosin binds to actin filaments. Macrophage, skeletal muscle, and other nonmuscle cell tropomyosins inhibit the fragmentation of actin filaments by the Ca2+-gelsolin complex. The finding implies that tropomyosin may have a role in stabilizing actin filaments in vivo.     

Two zinc finger proteins from Xenopus laevis bind the same region of 5S RNA but with different nuclease protection patterns.

Immature oocytes from Xenopus laevis contain a 42S ribonucleoprotein particle (RNP) containing 5S RNA, tRNA, a 43 kDa protein, and a 48 kDa protein. A particle containing 5S RNA and the 43 kDa protein (p43-5S) liberated from the 42S particle upon brief treatment with urea can be purified by anion exchange chromatography. The purified p43-5S RNA migrates as a distinct species during electrophoresis on native polyacrylamide gels. Radiolabeled 5S RNA can be incorporated into the p43-5S complex by an RNA exchange reaction. The resulting complexes containing labeled 5S RNA have a mobility on polyacrylamide gels identical to that of purified p43-5S RNPs. RNP complexes containing 5S RNA labeled at either the 5' or 3' end were probed with a variety of nucleases in order to identify residues protected by p43. Nuclease protection assays performed with alpha-sarcin indicate that p43 binds primarily helices I, II, IV, and V of 5S RNA. This is the same general binding site observed for TFIIIA on 5S RNA. Direct comparison of the binding sites of p43 and TFIIIA with T1 and cobra venom nucleases reveals striking differences in the protection patterns of these two proteins.     

p-NN''-phenylenebismaleimide, a specific cross-linking agent for F-actin.

Covalent cross-links can be inserted between the subunits of F-actin by using p-NN'-phenylenebismaleimide. Cross-linking reaches its maximum value when one molecule of reagent has reacted with each actin subunit. p-NN'-Phenylenebismaleimide reacts initially with a cysteine residue on one subunit, the slower cross-linking reaction involving a lysine residue on a neighbouring subunit. Hydrolysis of the actin-bound reagent limits the extent of cross-linking. Quantitative analysis of the amounts of cross-linked oligomers seen on polyacrylamide gels containing sodium dodecyl sulphate suggests that neither the binding of the reagent to actin nor the formation of cross-links introduces strain into the structure. The cross-links do not join together different F-actin filaments, and evidence is presented that suggests that the cross-links join subunits of the same long-pitched helix.     

Inhibition of deoxyribonuclease I activity by actin covalently cross-linked to chick brain actin depolymerizing factor through exposed sulfhydryls

All but one of the six free sulfhydryl groups of chick brain actin depolymerizing factor (ADF) are protected from modification when ADF forms a 1:1 complex with actin. This exposed sulfhydryl can be cross-linked to cys 374 of actin with N,N'-phenylenedimaleimide. The cross-linked complex inhibits the hydrolytic activity of pancreatic deoxyribonuclease (DNase I) to an identical extent as both the untreated complex and an equivalent amount of free actin. These data indicate that ADF binds to actin at a site which does not overlap with the DNase I binding site.     

Isolation and characterization of a regulated form of actin depolymerizing factor

Actin depolymerizing factor (ADF) is an 18.5-kD protein with pH- dependent reciprocal F-actin binding and severing/depolymerizing activities. We previously showed developing muscle down-regulates ADF (J. R. Bamburg and D. Bray. 1987. J. Cell Biol. 105: 2817-2825). To further study this process, we examined ADF expression in chick myocytes cultured in vitro. Surprisingly, ADF immunoreactivity increases during the first 7-10 d in culture. This increase is due to the presence of a new ADF species with higher relative molecular weight which reacts identically to brain ADF with antisera raised against either brain ADF or recombinant ADF. We have purified both ADF isoforms from myocytes and have shown by peptide mapping and partial sequence analysis that the new isoform is structurally related to ADF. Immunoprecipitation of both isoforms from extracts of cells prelabeled with [32P]orthophosphate showed that the new isoform is radiolabeled, predominantly on a serine residue, and hence is called pADF. pADF can be converted into a form which comigrates with ADF on 1-D and 2-D gels by treatment with alkaline phosphatase. pADF has been quantified in a number of cells and tissues where it is present from approximately 18% to 150% of the amount of unphosphorylated ADF. pADF, unlike ADF, does not bind to G-actin, or affect the rate or extent of actin assembly. Four ubiquitous protein kinases failed to phosphorylate ADF in vitro suggesting that ADF phosphorylation in vivo is catalyzed by a more specific kinase. We conclude that the ability to regulate ADF activity is important to muscle development since myocytes have both pre- and posttranslational mechanisms for regulating ADF activity. The latter mechanism is apparently a general one for cell regulation of ADF activity.     

Conformational isomers of insect odorant-binding proteins.

We have identified and cloned the cDNAs encoding odorant-binding proteins (OBPs) from the large black chafer, Holotrichia parallela, and the yellowish elongate chafer, Heptophylla picea. Each species possess two OBPs, the proteins migrating faster in native gels (OBP1) showed high amino acid identity (>88%) to previously identified pheromone-binding proteins (PBPs) from scarab beetles. HparOBP1 and HpicOBP1 have 116 amino acids and six highly conserved cysteine residues. In contrast to OBP1 that gave a single band, both HparOBP2 and HpicOBP2 separated each into two bands in native gels (15%). The N-terminal amino acid sequences for the two bands from each species were indistinguishable, and they had the same molecular masses. Although we sequenced several clones from each species, they all encode only one protein for each species, indicating they are different conformational isomers of the same protein. HparOBP2 and HpicOBP2 have 133 amino acids and cysteine residues are conserved in proteins of the same family.     

A chemical interference study on the interaction of ribosomal protein L11 from Escherichia coli with RNA molecules containing its binding site from 23S rRNA.

The interaction between ribosomal protein L11 from Escherichia coli and in vitro synthesized RNA containing its binding site from 23S rRNA was characterized by identifying nucleotides that interfered with complex formation when chemically modified by diethylpyrocarbonate or hydrazine. Chemically modified RNA was incubated with L11 under conditions appropriate for specific binding of L11 and the resulting protein-RNA complex was separated from unbound RNA on Mg(2+)-containing polyacrylamide gels. The ability to isolate L11 complexes on such gels was affected by the extent of modification by either reagent. Protein-bound and free RNAs were recovered and treated with aniline to identify their content of modified bases. Exclusion of RNA containing chemically altered bases from L11-associated material occurred for 29 modified nucleotides, located throughout the region corresponding to residues 1055-1105 in 23S rRNA. Ten bases within this region did not reproducibly inhibit binding when modified. Multiple bands of RNA were consistently observed on the nondenaturing gels, suggesting that significant intermolecular RNA-RNA interactions had occurred.     

The interaction of caldesmon with the COOH terminus of actin

Caldesmon interacts with the NH2-terminal region of actin. It is now shown in airfuge centrifugation experiments that modification of the penultimate cysteine residue of actin significantly weakens its binding to caldesmon both in the presence and absence of tropomyosin. Furthermore, as revealed by fluorescence measurements, caldesmon increases the exposure of the COOH-terminal region of actin to the solvent. This effect of caldesmon, like its inhibitory effect on actomyosin ATPase activity, is enhanced in the presence of tropomyosin. Proteolytic removal of the last three COOH-terminal residues of actin, containing the modified cysteine residue, restores the normal binding between caldesmon and actin. These results establish a correlation between the binding of caldesmon to actin and the conformation of the COOH-terminal region of actin and suggest an indirect rather than direct interaction between caldesmon and this part of actin.     

In-gel derivatization of proteins for cysteine-specific cleavages and their analysis by mass spectrometry

As a potential tool for proteomics and protein characterization, in-gel cysteine- and arginine-specific cleavage is demonstrated by means of trypsin or endoproteinase Lys-C for six model proteins (lysozyme, alpha-lactalbumin, beta-lactoglobulin, ribonuclease A, albumin, and transferrin), ranging in size from 14 kDa to 79 kDa. Chemical modifications of cysteine (aminoethylation with bromoethylamine or N-(iodoethyl)-trifluoroacetamide, and subsequent guanidination) and lysine (acetylation) prior to tryptic digestion releases peptides delineated by cysteine or arginine residues. Peptide products are analyzed by MALDI-TOF-MS, ESI-MS, and ESI- and MALDI-MS/MS (with a quadrupole time-of-flight instrument). Complications induced by acrylamide alkylations of cysteines were avoided by substituting lower pH bis-tris polyacrylamide gels for tris-glycine. Sequence coverages from 35 to 86% were obtained and amino acid compositions of generated peptides could be confirmed by comprehensive y- and b-ion series. Detailed information about, in particular, cysteine rich proteins after gel electrophoresis were obtained. The chemistries for modification and cleavage specificities at cysteine residues provide an alternative means to characterize and identify proteins separated by gel electrophoresis.     

The preparation and characterization of an antimicrobial polypeptide from the loach,Misgurnus anguillicaudatus

Using Sephadex G-50 gel filtration, DEAE-52 cellulose ion-exchange chromatography, and an improved polyacrylamide gel electrophoresis together with electroelution, a novel polypeptide with antimicrobial activity in vitro was isolated and characterized from loach, Misgurnus anguillicaudatus. The polypeptide, named MAPP, contains about 94 residues containing l0 different amino acids, of which cysteine was the most abundant. No alkaline residue was found in MAPP. MAPP is a single-chain polypeptide with Mw of about 9800Da and pI of about 4.78; the N-terminus of MAPP was CFGWN. MAPP showed good inhibition of various bacteria including Bacillus subtilis, Escherichia coli, and Staphylococcus aureus. MAPP is thermally stable with more than 70% inhibitory bioactivity remaining after treatment at 60 degrees C for 30min. In addition, MAPP could inhibit the autoxidation of pyrogallol with a high efficiency. Similarity searches by comparing amino acid composition, MS-fingerprint, and the N-terminus of MAPP demonstrated that no protein exactly matched MAPP in databases around the world.     

Isolation and characterization of des(Ala-Lys)calmodulin in porcine brain

A calmodulin-like protein -des(Ala-Lys)calmodulin- was isolated from porcine brain extract, and was characterized in comparison to porcine brain calmodulin. Des(Ala-Lys)calmodulin was distinguishable from calmodulin by its slightly faster mobility in 10% polyacrylamide gels without sodium dodecyl sulfate. The protein gave an amino acid composition very similar to calmodulin, and contained one ?-N-trimethyllysyl residue. Comparative peptide mapping of calmodulin and des(Ala-Lys)calmodulin by high performance anion-exchange liquid chromatography, and the subsequent analyses of the isolated peptides, have indicated that des(Ala-Lys)calmodulin lacks the Ala(147)-Lys (148) sequence at the C-terminus of calmodulin. The content of des(Ala-Lys)-calmodulin was about one-tenth of calmodulin.     

Purification and properties of methylmalonyl coenzyme A mutase from human liver

Methylmalonyl coenzyme A (CoA) mutase has been purified to apparent homogeneity from human liver by a procedure involving column chromatography on DEAE-cellulose, Matrex-Gel Blue A, hydroxylapatite, and Sephadex G-150. The overall purification achieved is 500- to 600-fold, yield 3–5%. Electrophoresis of the native purified protein on nondenaturing polyacrylamide gels shows a single diffuse band coincident with the enzyme activity; dodecyl sulfate/polyacrylamide gels show a single protein band with an apparent molecular weight of 77,500. The native protein has a molecular weight of approximately 150,000 by Sephadex G-150 chromatography, suggesting that it is composed of two identical subunits. The activity of the purified enzyme is stimulated only slightly (10–20%) by the addition of its cofactor, adenosylcobalamin, indicating that the purified enzyme is largely saturated with coenzyme. The spectrum of the enzyme is consistent with the presence of about 1 mole of adenosylcobalamin per mole of subunit. The enzyme displays complex kinetics with respect to dl-methylmalonyl CoA; substrate inhibition by l-methylmalonyl CoA appears to occur. The enzyme activity is stimulated by polyvalent anions (PO₄^3? > SO₄^2? > Cl^?); monovalent cations are without effect, but high concentrations of divalent cations are inhibitory. The enzyme activity is insensitive to N-ethylmaleimide, is rapidly destroyed at temperatures > 50 °C, and shows a broad pH optimum around pH 7.5.