Solid-phase edman degradation: attachment of carboxyl-terminal homoserine peptides to an insoluble resin

C-terminal protein characterization by mass spectrometry: isolation of C-terminal fragments from cyanogen bromide-cleaved protein

A sample preparation method for protein C-terminal peptide isolation from cyanogen bromide (CNBr) digests has been developed. In this strategy, the analyte was reduced and carboxyamidomethylated, followed by CNBr cleavage in a one-pot reaction scheme. The digest was then adsorbed on ZipTipC18 pipette tips for conjugation of the homoserine lactone-terminated peptides with 2,2'-dithiobis (ethylamine) dihydrochloride, followed by reductive release of 2-aminoethanethiol from the derivatives. The thiol-functionalized internal and N-terminal peptides were scavenged on activated thiol sepharose, leaving the C-terminal peptide in the flow-through fraction. The use of reversed-phase supports as a venue for peptide derivatization enabled facile optimization of the individual reaction steps for throughput and completeness of reaction. Reagents were replaced directly on the support, allowing the reactions to proceed at minimal sample loss. By this sequence of solid-phase reactions, the C-terminal peptide could be recognized uniquely in mass spectra of unfractionated digests by its unaltered mass signature. The use of the sample preparation method was demonstrated with low-level amounts of a whole, intact model protein. The C-terminal fragments were retrieved selectively and efficiently from the affinity support. The use of covalent chromatography for C-terminal peptide purification enabled recovery of the depleted material for further chemical and/or enzymatic manipulation. The sample preparation method provides for robustness and simplicity of operation and is anticipated to be expanded to gel-separated proteins and in a scaled-up format to high-throughput protein profiling in complex biological mixtures.

Chemical labeling of electrochemically cleaved peptides

RATIONALE

Cleavage of peptide bonds C-terminal to tyrosine and tryptophan after electrochemical oxidation may become a complementary approach to chemical and enzymatic cleavage. A chemical labeling approach specifically targeting reactive cleavage products is presented here and constitutes a promising first step towards the development of a new proteomics workflow.

METHODS

Hexylamine was used to react with the spirolactone moieties generated after electrochemical oxidation and cleavage of tripeptides. The influence of pH and reaction time on the yield was determined and the excess of tagging reagent was optimized. Selective detection of the tagged cleavage products was achieved by precursor ion scanning in a triple quadrupole mass spectrometer.

RESULTS

Optimal labeling was reached under aqueous conditions when working at pH 10 with a reaction time of 0.5 min. The excess of hexylamine over spirolactone groups can be significantly decreased by working under non-aqueous conditions in pure acetonitrile to prevent spirolactone hydrolysis. The specific formation of hexylamine-containing y(1) reporter ions generated by collision-induced dissociation (CID) tandem mass spectrometry (MS/MS) allows for selective detection by precursor ion scanning of the cleaved and labeled peptides.

CONCLUSIONS

This work presents a method for selective labeling and detection of electrochemically cleaved Tyr- and Trp-containing peptides for which reaction conditions have been optimized with hexylamine as labeling agent. This workflow offers new possibilities for electrochemical oxidation, cleavage and labeling of peptides and proteins.

Functionalized membrane supports for covalent protein microsequence analysis

Methods were developed for high yield covalent attachment of peptides and proteins to isothiocyanate and arylamine-derivatized poly(vinylidene difluoride) membranes for solid-phase sequence analysis. Solutions of protein or peptide were dried onto 8-mm membrane disks such that the functional groups on the surface and the polypeptide were brought into close proximity. In the case of the isothiocyanate membrane, reaction between polypeptide amino groups and the surface isothiocyanate moieties was promoted by application of aqueous N-methylmorpholine. Attachment of proteins and peptides to the arylamine surface was achieved by application of water-soluble carbodiimide in a pH 5.0 buffer. Edman degradation of covalently bound polypeptides was accomplished with initial and repetitive sequence yields ranging from 33 to 75% and 88.5 to 98.5%, respectively. The yields were independent of the sample load (20 pmol to greater than 1 nmol) for either surface. Significant loss of material was not observed when attachment residues were encountered during sequence runs. Application of bovine beta-lactoglobulin A chain, staphylococcus protein A, or the peptide melittin to the isothiocyanate membrane allowed for extended N-terminal sequence identification (35 residues from 20 pmol of beta-lactoglobulin). A number of synthetic and naturally occurring peptides were sequenced to the C-terminal residue following attachment to the arylamine surface. In one example, 10 micrograms of bovine alpha-casein was digested with staphylococcal protease V8 and the peptides were separated by reverse-phase chromatography. Peptide fractions were then directly applied to arylamine membrane disks for covalent sequence analysis. From as little as 2 pmol of initial signal it was possible to determine substantial sequence information (greater than 10 residues).

Covalent immobilization of proteins and peptides for solid-phase sequencing using prepacked capillary columns

The use of prepacked capillary columns for immobilizing proteins and peptides for solid-phase Edman degradation is described. Capillary tubes with an internal volume of about 30 microliters are filled with glass beads bearing isothiocyanato groups (DITC-glass), aminophenyl groups (AP-glass), or aminoethylaminopropyl groups (AEAP-glass) and are sealed with porous plugs. Proteins or peptides in appropriate buffers are introduced into the columns by capillary action and are covalently coupled to the glass beads, either by reaction of lysine side-chain amino groups with DITC-glass, by carbodi-imide-mediated reaction of carboxyl groups with AP-glass, or by reaction of homoserine lactone groups with AEAP-glass. Optimization of attachment conditions is described. The capillary columns are loaded into the sequencer and, when sequencing has been completed, are discarded. This technique greatly simplifies polypeptide immobilization and is suitable for microsequencing (less than 50-1000 pmol) or macrosequencing (1-50 nmol).

The sequence of the major protein stored in ovine ceroid lipofuscinosis is identical with that of the dicyclohexylcarbodiimide-reactive proteolipid of mitochondrial ATP synthase

The ceroid lipofuscinoses are a group of neurodegenerative lysosomal storage diseases of children and animals that are recessively inherited. In diseased individuals fluorescent storage bodies accumulate in a wide variety of cells, including neurons. Previous studies of these bodies isolated from tissues of affected sheep confirmed that the storage occurs in lysosomes, and showed that the storage body is mostly made of a single protein with an apparent molecular mass of 3500 Da with an N-terminal amino acid sequence that is the same as residues 1-40 of the c-subunit (or dicyclohexylcarbodi-imide-reactive proteolipid) of mitochondrial ATP synthase. In the present work we have shown by direct analysis that the stored protein is identical in sequence with the entire c-subunit of mitochondrial ATP synthase, a very hydrophobic protein of 75 amino acid residues. As far as can be detected by the Edman degradation, the stored protein appears not to have been subject to any post-translational modification other than the correct removal of the mitochondrial import sequences that have been shown in other experiments to be present at the N-terminal of its two different precursors. No other protein accumulates in the storage bodies to any significant extent. Taken with studies of the cDNAs for the c-subunit in normal and diseased sheep, these results indicate that the material that is stored in lysosomes of diseased animals has probably entered mitochondria and has been subjected to the proteolytic processing that is associated with mitochondrial import. This implies that the defect that leads to the lysosomal accumulation concerns the degradative pathway of the c-subunit of ATP synthase. An alternative, but less likely, hypothesis is that for some unknown reason the precursors of subunit c are being directly mis-targeted to lysosomes, where they become processed to yield a protein identical with the protein that is normally found in the mitochondrial ATP synthase assembly, and which then accumulates.

Solid-phase sequence analysis of proteins electroblotted or spotted onto polyvinylidene difluoride membranes

Electroblotted proteins noncovalently bound to polyvinylidene difluoride (PVDF) membranes are typically sequenced using adsorptive sequencer protocols (gas-phase or pulsed-liquid) that do not require a covalent linkage between protein and surface. We have developed simple chemical protocols where proteins are first electroblotted onto unmodified PVDF membranes, visualized with common protein stains, and then immobilized for solid-phase sequence analysis. Adsorbed, stained proteins are first treated with phenylisothiocyanate (PITC) to modify alpha and epsilon amines. The protein is then overlayed with a solution of 1,4-phenylene di-isothiocyanate (DITC), followed by a few microliters of a basic solution containing a poly(alkylamine). As the polymer dries onto the surface both polymer and remaining protein amino groups are crosslinked by DITC. The protein is thus immobilized to the membrane surface by entrapment in a thin polymer coating. The coating is transparent to the degradation chemistry, and extensive enough to remain immobilized even in the absence of any covalent link between polymer and surface. Partial modification with PITC allows for identification of N-terminal and internal lysine residues during sequencing. The process was tested with a variety of poly(alkylamines), linear and branched, with molecular weights ranging from 600 to over 100,000. Proteins bound in this manner were successfully sequenced using covalent (solid-phase) sequencer protocols with cycle times as short as 26 min.

Covalent attachment of peptides for high sensitivity solid-phase sequence analysis

We have developed a method for the high efficiency covalent immobilization of picomole to nanomole quantities of peptides in a form compatible with high sensitivity gas-liquid or solid-phase sequence analysis. Glass fiber filter paper was derivatized with amino-phenyltriethoxysilane and peptides were applied to circular disks cut to 1-cm diameters. Peptides were covalently immobilized on the aminophenyl-glass fiber paper through their terminal alpha-carboxyl groups and amino acid side-chain carboxyl groups by activation with the water-soluble reagent N-ethyl-N'-(3-dimethylaminopropyl)carbodiimide. Disks containing the covalently attached peptide were directly inserted into the cartridge of an automated sequenator for sequence analysis by the Edman degradation. Peptides prepared in this way could be routinely sequenced through to and including the C-terminal amino acid residue, at extraordinarily low backgrounds. The covalent immobilization of peptide fragments allowed far more flexibility in sequencing conditions, including the use of polar extraction solvents to increase the yield of phenylthiohydantoin (PTH)-His and PTH-Arg and the use of alternative Edman-type sequencing reagents with enhanced detectability, such as the chromophoric compound 4- (N,N'-dimethylamino)azobenzene-4'-isothiocyanate. The potential of this high efficiency immobilization method for contributing to the development of sequencing chemistries with enhanced sensitivity is discussed.

Isolation, characterization and amino-acid sequence of gamma-seminoprotein, a glycoprotein from human seminal plasma

gamma-Seminoprotein (gamma-SM), a glycoprotein from human seminal plasma, was isolated in highly purified form by ion-exchange chromatography on a Mono Q column. The main form, fraction M, was homogeneous by PAGE at pH 8.3 and by SDS-PAGE. The complete amino acid sequence of gamma-SM was determined with the aid of fragments generated by cleavages with cyanogen bromide, clostripain, chymotrypsin and Staphylococcus aureus V8 protease. The fragments were aligned with overlapping sequences. The single polypeptide chain of gamma-SM contains 237 amino acids with a calculated Mr of 26079. A single N-linked carbohydrate side chain is attached to Asn45. The complex structure of this oligosaccharide has been determined recently [van Halbeek H. et al. (1985) Biochem. Biophys. Res. Commun. 131, 507-514]. Sequence comparison with serine proteases shows a high degree of homology, especially with the kallikrein family. The residues in the vicinity of the active site of serine proteases are also highly conserved in gamma-SM, indicating the participation of His41, Asp96 and Ser189 in its active site. gamma-SM hydrolyzed M-casein with a pH optimum at 8.0, but failed to hydrolyze any of the synthetic substrates tested. This proteolytic activity could be inhibited with diisopropylfluorophosphate, phenylmethylsulfonyl fluoride, Zn2+ or Hg2+ ions.

On the disulphide bonds of rhodopsins

Carboxymethylation using 14C- or 3H-labelled iodoacetic acid has been used to identify the cysteine residues in bovine rhodopsin involved in the formation of the two intramolecular disulphide bridges. Iodo[2-14C]acetic acid was used to modify 5.8-5.9 residues of cysteine under non-reducing conditions. After dialysis and reduction of disulphide bridges by 2-mercaptoethanol, iodo[2-3H]acetic acid was employed to covalently modify 3.3-3.6 residues of cysteine. Peptide purification and sequencing has unambiguously shown that cysteine residues 322 and 323 are only carboxymethylated after reduction of disulphide bridges. Indirect evidence presented, now coupled with the earlier finding [Findlay & Pappin (1986) Biochem. J. 238, 625-642] suggests that the other disulphide bridge is formed between cysteine residues 110 and 187. A comparison is made of all the sequences of mammalian rhodopsins and colour pigments and attention is drawn to the fact that whereas Cys-322 and Cys-323 are conserved only in three rhodopsins (bovine, ovine and human), the residues corresponding to Cys-110 and Cys-187 are found in all the visual proteins (from rods as well as human cones).

A rapid solid-phase protein microsequencer

A solid-phase protein microsequencer is described that has been designed to determine protein sequences with subnanomolar quantities of protein. Its utility has been demonstrated by the determination of many sequences in subunits of mitochondrial F1-ATPase, in a protein isolated from mouse gap junctions and in the mitochondrial phosphate-transporter protein. It has a number of advantages over liquid- and gas-phase sequencers. Firstly, the degradation cycle takes 24 min, more than twice as fast as any other sequencer. This helps to reduce exposure of proteins to inimical reagents and increases throughput of samples. Secondly, polar amino acids such as phosphoserine, and polar derivatives formed by active-site photoaffinity labelling with 8-azido-ATP, are recovered quantitatively from the reaction column and can be positively identified. In other types of sequencer these polar derivatives, being somewhat insoluble in butyl chloride, tend to remain in the reaction chamber of the instrument and so are more difficult to identify. The solid-phase protein sequencer is also more suited than the liquid-phase instrument for analysis of proteolipids from membranes. These hydrophobic proteins tend to dissolve in organic solvents during washing steps in the liquid-phase instrument and are lost. Covalent attachment as used in the solid-phase instrument solves this problem.

Identification of the sites in opsin modified by photoactivated azido[125I]iodobenzene

Opsin labelled with photoactivated 1-azido-4-[125I]iodobenzene was proteolysed in situ with Staphylococcus aureus V8 proteinase to yield two radioactive membrane-bound fragments. These were separated, cleaved with CNBr and the resultant peptides sequenced in order to locate the radiolabelled residues. In the whole molecule, there was clear evidence for modification of at least 20 sites, identified as derivatives of cysteine, tryptophan, tyrosine, histidine and lysine residues. The probe primary reacted, therefore, with nucleophilic substituents. The positions of the modified sites relative to the confines of the phospholipid bilayer were consistent with all other studies on the disposition of the polypeptide chain. The location of these sites substantiated an earlier suggestion that not all the transmembrane segments should be regarded as continuous regular alpha-helices.

Human complement component C1s. Partial sequence determination of the heavy chain and identification of the peptide bond cleaved during activation

Human C1s proenzyme (Mr 83 000) was isolated by a rapid two-stage method involving affinity chromatography of C1 on IgG-Sepharose and isolation of subcomponent C1s by ion-exchange chromatography on DEAE-Sephacel. Single-chain C1s proenzyme was activated to two-chain C1s with self-activated C1r. After reduction and S-carboxamidomethylation the heavy chain of C1s (Mr 57 000) was isolated by ion exchange chromatography on DEAE-Sephacel. Cleavage of C1s heavy chain with CNBr yielded five fragments whose N-terminal sequences were determined. The alignment of the fragments within the heavy chain was established by tryptic peptides containing methionine. C1s heavy chain comprises about 470 amino acid residues and 42% of its sequence was determined. An intrachain sequence homology and a homology to the alpha 2 chain of human haptoglobin were identified. The C-terminal CNBr fragment comprising 44 amino acid residues was completely sequenced. From BNPS-skatole cleavage of reduced and alkylated C1s proenzyme a fragment was isolated which overlaps the C1s heavy and light chain parts and which contains the peptide bond cleaved during activation. The results show that this is an Arg-Ile bond and that under standard conditions of activation no peptide material is liberated from this portion of the molecule. The sequence data and homology to two-chain serine proteases indicate a single interchain disulfide bond in C1s.

Modification of ovine opsin with the photosensitive hydrophobic probe 1-azido-4-[125I]iodobenzene. Labelling of the chromophore-attachment domain

The hydrophobic photosensitive probe 1-azido-4-[125I]iodobenzene (AIB) partitioned preferentially into photoreceptor disc membranes and, upon u.v. irradiation, became covalently bound to opsin and phospholipid. The labelling of both protein and phospholipid was linearly related to AIB concentration. The amount of probe incorporated into protein was not significantly different when membranes were irradiated at -100 degrees, 4 degrees or 25 degrees C, but irreversible aggregation of monomeric opsin was dramatically reduced by performing the photolysis at -100 degrees C. Labelling of opsin after irradiation at -100 degrees or 4 degrees was not significantly reduced by the presence of lysine in the aqueous buffer, indicating that significant amounts of reactive species did not enter the aqueous phase. The incorporation into phospholipid, unlike that into opsin, decreased as the temperature of irradiation increased. Some labelling of opsin occurred on incubation with pre-photoactivated AIB, indicating that reaction may also occur with reactive species of longer lifetimes than the nitrene. Proteolysis of labelled opsin with Staphylococcus aureus V8 proteinase yielded two radiolabelled membrane-bound fragments. The location of the modified sites (cysteine, tryptophan, tyrosine, lysine and histidine residues: all nucleophiles) in the smaller fragment was entirely consistent with putative models for the protein derived from other studies.

Amino acid sequence of the trypsin-generated C3d fragment from human complement factor C3

Human C3d (try-C3d), prepared from trypsin-digested C3, was fragmented by cleavage with CNBr. Eight peptides were defined and separated by h.p.l.c. on reversed-phase columns. By automatic Edman degradation the complete sequences of five peptides and partial sequences of three peptides were determined. To obtain overlapping peptides the latter three fragments were digested with trypsin, chymotrypsin or Staphylococcus aureus V8 proteinase, after which the fragments were separated on reversed-phase columns. Two of the CNBr-cleavage peptides were completely sequenced, and 70% of the sequence of the remaining CNBr-cleavage peptide was determined. The non-sequenced part represents a very hydrophobic segment of try-C3d. The sequence data obtained represent 90% of the primary structure of try-C3d. Alignment of the CNBr-cleavage fragments was made easier by comparison with the cDNA sequence of mouse pro-C3 [Wetsel, Lundwall, Davidson, Gibson, Tack & Fey (1984) J. Biol. Chem. 259, 13857-13862]. Comparison of try-C3d with the equivalent part of human C4B revealed an extensive sequence homology in the N-terminal half of the molecules.

Complete amino acid sequence of bovine plasminogen. Comparison with human plasminogen

The amino acid sequence of the single polypeptide chain of bovine plasminogen (786 residues, Mr 88092) was determined. Cleavage with CNBr yielded 13 fragments of which six originated from cleavage sites different from human plasminogen. Digestion with elastase gave three major fragments: kringles (1 + 2 + 3) and kringle 4, both with intact lysine binding sites, and mini-plasminogen. Subfragmentation was achieved mainly with 2-(2-nitrophenylsulfenyl)-3-methyl-3'-bromoindolenine (BNPS-skatole), Staphylococcus aureus V8 protease and trypsin. The sequences of fragments which were determined by automated Edman degradation, were aligned with overlapping sequences, or, in a few instances, by homology with the known sequence of human plasminogen. Sequence comparison with the human protein showed varying degrees of homology in the different functional and structural domains. The overall identity (78%) is practically the same as that found in those regions corresponding to the heavy (79%) and the light chain (80%) of plasmin. The average degree of identity among the kringles is 83%. Outside the kringle structures the extent of identity decreases, to 65% in the N-terminal region and to about 50% in the connecting strands between the kringles except for the strand between kringles 2 and 3, where only one out of 12 residues is exchanged. The results reported show that bovine plasminogen apparently contains the same structural and functional domains as human plasminogen. Bovine plasminogen also contains two carbohydrate moieties. The only partially substituted N-glycosidic site, Asn289, corresponds to partially glycosylated Asn288 in human plasminogen, whereas the O-glycosidic site of the human sequence, Thr345, is shifted to Ser339 in bovine plasminogen.

Multiple-copy genes: production and modification of monomeric peptides from large multimeric fusion proteins

A vector system has been designed for obtaining high yields of polypeptides synthesized in Escherichia coli. Multiple copies of a synthetic gene encoding the neuropeptide substance P (SP) (Arg-Pro-Lys-Pro-Gln-Gln-Phe-Phe-Gly-Leu-Met-NH2) have been linked and fused to the lacZ gene. Each copy of the SP gene was flanked by codons for methionine to create sites for cleavage by cyanogen bromide (CNBr). The isolated multimeric SP fusion protein was converted to monomers of SP analog, each containing a carboxyl-terminal homoserine lactone (Hse-lactone) residue (Arg-Pro-Lys-Pro-Gln-Gln-Phe-Phe-Gly-Leu-Hse-lactone), upon treatment with CNBr in formic acid. The Hse-lactone moiety was subjected to chemical modifications to produce an SP Hse amide. This method permits synthesis of peptide amide analogs and other peptide derivatives by combining recombinant DNA techniques and chemical methods.

Solid-phase protein and peptide sequencing using either 4-N,N-dimethylaminoazobenzene 4'-isothiocyanate or phenylisothiocyanate

Automated solid-phase sequencing using 4-N,N-dimethylaminoazobenzene 4'-isothiocyanate (DABITC) double coupling or regular phenylisothiocyanate (PITC) degradation procedures have been investigated. Employing sensitive high-performance liquid chromatography for the identification of amino acid thiohydantoin derivatives (PTH and DABTH), both methods were capable of sequencing immobilized peptides or proteins at the subnanomole levels. In the sequencing program using DABITC, alternate methanol and dichloroethane washes and automated conversion using methanolic HCl containing dithiothreitol were introduced to obtain clean thiazolinones and to ensure high recovery yields of the thiohydantoins. Using regular PITC degradation with a 59-min program, the background peaks of the side products could be reduced to enhance HPLC identification. Peptides or proteins attached to the glass beads or resins via the carboxyl terminii or epsilon-amino groups of lysyl residues could be readily sequenced up to 30 identifiable degradation cycles, where the sequencing is generally terminated due to the increased background components.

The amino acid sequence of GTP:AMP phosphotransferase from beef-heart mitochondria. Extensive homology with cytosolic adenylate kinase

The amino acid sequence of GTP:AMP phosphotransferase (AK3) from beef-heart mitochondria has been determined, except for one segment of about 33 residues in the middle of the polypeptide chain. The established sequence has been unambiguously aligned to the sequence of cytosolic ATP:AMP phosphotransferase (AK1) from pig muscle, allowing for six insertions and deletions. With 30% of all aligned residues being identical, the homology between AK3 and AK1 is well established. As derived from the known three-dimensional structure of AK1, the missing segment is localized at a small surface area of the molecule, far apart from the active center. The pattern of conserved residues demonstrates that earlier views on substrate binding have to be modified. The observation of three different consecutive N-termini indicates enzyme processing.

Utility of the gas-phase sequencer for both liquid- and solid-phase degradation of proteins and peptides at low picomole levels

The utility of the commercially available gas-phase sequencer for complete analysis of peptide samples was investigated. Using the program supplied with the instrument, significant extractive loss of samples in Polybrene was observed, even at input levels up to 500 pmol. In order to reduce this loss, the sequencer program was modified by increasing the phenylisothiocyanate (PITC)-coupling steps from two to three and lengthening the duration of ethyl acetate (S2) delivery while reducing the delivery rate. These changes gave improved results with peptides, e.g., all eight residues of angiotensin II were identified at the 25-pmol level. In addition, background contamination was decreased and repetitive yields were increased. The instrument was also found to function well with samples coupled to solid supports; however, some of the methodologies that work adequately for covalent attachment of peptides to solid supports at the level 1-10 nmol were found to give unacceptable coupling/sequenceable yields at or below the 100-pmol level. The coupling methods tried were (1) reaction of homoserine lactone with aminopropyl (AP)-glass, (2) reaction of alpha- and epsilon-NH2 groups with p-phenylenediisothiocyanate (DITC)-glass, and (3) reaction of alpha-COOH groups with aminoaryl (AA)-glass via EDAC (1-ethyl-3,3'-dimethylaminopropyl-carbodiimide). Of these, the first method gave combined yields of 42-94% while the latter two were only 9-35% efficient. The covalently bound samples provided sequence information even at the resulting low levels, e.g., 9/13 residues of dynorphin including Lys-13 at 11 pmol. In general, sequencer runs on solid-phase samples gave "cleaner" analyses and slightly higher repetitive yields (1-2%). Sequence information has also been obtained on peptides made by solid-phase synthesis prior to cleavage from the polystyrene support. With improved coupling efficiencies, solid-phase techniques would provide an alternative to immobilization of peptides in Polybrene films for low picomole level gas-phase sequencing.

The complete amino acid sequence of aspartate aminotransferase from Escherichia coli: sequence comparison with pig isoenzymes

The amino acid sequence of aspartate aminotransferase from E. coli B was determined by the alignment of seven cyanogen bromide peptides. The established sequence of the subunit was composed of 396 amino acid residues, and the molecular weight was calculated to be 43,573. The sequence was compared with those of the pig cytoplasmic and mitochondrial isoenzymes, showing that nearly 30% of all residues were invariant and that the E. coli enzyme exhibited the same degree of homology (about 40%) with either of them. Although majority of the residues were substituted, the functional residues constituting the active site structure were conserved.

Mitochondrial adenylate kinase (AK2) from bovine heart. Homology with the cytosolic isoenzyme in the catalytic region

The adenylate kinase isoenzyme located in the intermembrane space of mitochondria, AK2, is a monomeric protein of Mr 30000 which catalyzes the reaction ATP + AMP + AMP in equilibrium 2 ADP. The protein was reduced and S-carboxymethylated with iodo[14C2]acetate. Using a Laursen sequenator, the N-terminal sequence of S-carboxymethylated AK2 was determined as Ala-Pro-Asn-; in some batches of the isolated protein the N-terminal dipeptide portion was missing. The C-terminus of AK2 was found to be Met. Cleavage with CNBr yielded eight fragments which could be isolated in one step using high-performance size-exclusion chromatography. They ranged in size over 4-88 amino acid residues, the total being approximately 270 residues. All CNBr fragments were overlapped with Met-containing tryptic peptides of AK2. The N-terminal 111 residues of AK2 were sequenced. Except for an N-terminal extension of nine residues, this segment of AK2 could be aligned with the sequence 1-104 of cytosolic AK1. Allowing for two deletions in AK2, 43 of the 102 aligned residues are identical. Since this section contains the catalytic residues such as His-36 and Asp-93, we conclude that AK1 can serve as a three-dimensional model of AK2 in mechanistic and drug-designing studies. preliminary sequence results on AK2 beyond position 104 show that AK2 here contains a wing of approximately 50 residues which has no counterpart in AK1. The chain folds of the adenylate kinase isoenzymes are similar again from a position corresponding to residue 115 of AK1 onwards. The additional structural motifs of AK2 are probably related to the location of this isoenzyme in the mitochondrion.

Primary sequence differences between Chido and Rodgers variants of tryptic C4d of the human complement system

Human tryptic C4d of the Chido and Rodgers variant was fragmented by cyanogen bromide and trypsin. The fragments were characterized by amino acid analysis and sequence determination. Polymorphism between the two genetic variants was detected in 5 positions. Four were closely located (residues 141, 142, 145, 146), where Leu, Ser, Ile, His occurred in the Chido variant and Pro, Cys, Leu, Asp in the Rodgers variant, respectively. In position 94 Gly was found in Chido and Asp in Rodgers. Alignment of the fragments was performed and it is concluded that tryptic C4d of both variants contains 346 residues.

Chemical characterization of cyanogen bromide fragments from the beta-chain of human complement factor C3

The isolated beta-chain of human complement factor C3 (C3 beta) was fragmented by cyanogen bromide. Nine fragments were defined by gel filtration and high-pressure liquid chromatography, and characterized with respect to their Mr, amino acid composition and N-terminal amino acid sequence. Approx. 30% of the primary structure of C3 beta was determined. Alignment of the 3 N-terminal fragments allowed determination of 61 of the amino terminal residues of C3 beta. This region demonstrated 40% homology with the sequence in the N-terminal segment of the alpha-chain of the cobra venom factor.

Group-directed modification of bacteriorhodopsin by arylisothiocyanates. Labeling, identification of the binding site and topology

Group-directed hydrophobic modification of membrane-integrated protein segments by arylisothiocyanates is applied to bacteriorhodopsin. Labeling of purple membrane with phenylisothiocyanate and 4-N,N'-dimethylamino-azobenzene-4'-isothiocyanate results in covalent modification of a unique lysine epsilon-amino group of bacteriorhodopsin. Lysine residue 41, located in the amino-terminal chymotryptic fragment, has been identified as the arylisothiocyanate binding site by established sequencing techniques. The phenylisothiocyanate binding site is not accessible for the aqueously soluble analog p-sulfophenylisothiocyanate. Furthermore, the acid-induced bathochromic shift of the bound chromophore reagent is not observed following acidification of 4-N,N'-dimethylamino-azobenzene-4'-isothiocyanate-labeled purple membrane. The modification thus occurs in the hydrophobic membrane domain, providing further evidence for intramembraneous disposition of the modified protein segment. Light-induced proton translocation is preserved in reconstituted vesicles containing either phenylisothiocyanate-modified or 4-N,N'-dimethylamino-azobenzene-4'-isothiocyanate-modified bacteriorhodopsin.

The primary sequence of human pancreatic colipase

The amino acid sequence of an activated colipase purified from human pancreas was determined. The protein consists of a single polypeptide chain of 86 amino acids (human colipase86) and has a molecular weight of 9289. The sequence was determined by automated Edman degradation of the reduced and S-carboxymethylated protein and of two CNBr peptides. Sequence determination of porcine procolipase II was also performed, which showed that in the original sequence determination apparently two residues were missed. These residues were determined to be a leucine at position 37 and a serine in position 50. For comparison with porcine and equine procolipases, the residues composing human colipase are numbered from 6 to 91. No human procolipase has been isolated so far. The colipases from man, pig, horse and chicken show a high degree of homology: human colipase differs from the other proteins by substitutions of 19 (porcine), 24 (equine A) and 21 (equine B) residues, respectively.

Complete amino acid sequence of mouse prolactin

The complete primary structure of mouse prolactin has been established on the basis of tryptic peptides from cyanogen-bromide-treated, S-carboxymethylated mouse prolactin and Staphylococcus-aureus-protease-cleaved overlaps, which were sequenced by manual liquid-phase and solid-phase Edman degradation. Three disulfide bonds were assigned to Cys-4-Cys-9, Cys-56-Cys-172, and Cys-189-Cys-197 by digestion of intact prolactin with S. aureus protease. One of the characteristics to date is replacement of Trp-89, which is commonly present among prolactin, growth hormone and choriomammotropin, by serine. It was suggested, by comparison with five other prolactins, five growth hormones and human choriomammotropin, that Asp-18, His-25, Ser-60 and Thr-63 are essential to lactogenic activity.

Identification of the initially NBD-labeled essential tyrosine residue in bovine heart MF1-ATPase

Bovine heart MF1-ATPase was labeled with limiting amounts of [14C]NBD-C1[( 14C]4-chloro-7-nitro-2,1,3-benzoxadiazole) and the resulting radioactive label on the essential Tyr was stabilized by reduction with zinc in the presence of multidentate ligand EDTA and redox mediator 4,4'-dipyridyl. Subsequent treatment of the labeled protein with cyanogen bromide and separation of the reaction mixture by ion-exchange chromatography yielded essentially only one radioactive polypeptide. Further cleavage of this polypeptide with TPCK-trypsin, lactonization of the terminal homoserine residue and reaction with derivatized polystyrene resin gave a shorter peptide attached to the solid support which contained all the radioactivity. Edman degradation showed that the amino acid sequence of this peptide was Glu . Gly . Asn . Asp . Leu . Tyr . His . Glu . Met, which corresponds to residues 192-200 in the beta subunit of bovine heart MF1-ATPase as determined by Runswick and Walker (1983). Since this specifically labeled Tyr-197 is separated by only one amino acid residue from the essential Glu-199 which was labeled specifically with dicyclohexylcarbodiimide by Yoshida et al. (1982) it seems most likely that both Tyr-197 and Glu-199 play direct roles in the catalytic hydrolysis and synthesis of ATP.

The identification by sequence homology of stage-specific sea urchin embryo histones H1

The histone H1 fraction from gastrula of the sea urchin Parechinus angulosus consists of a multitude of polypeptides with different electrophoretic mobilities. The synthesis of these proteins is programmed. Amino acid composition, electrophoretic properties and sequence homologies identify these as isohistones H1. One of these isohistones atypically binds the non-ionic detergent Triton X-100.

Isolation and characterization of the CNBr peptides from the proteolytically derived N-terminal fragment of ovine opsin

Ovine rhodopsin may be cleaved in situ by Staphylococcus aureus V8 proteinase into two membrane-bound fragments designated V8-L (27 000 mol.wt.) and V8-S (12 000 mol.wt.). After purification of the proteolysed complex by affinity chromatography in detergent using concanavalin A immobilized on Sepharose 4B, the two polypeptide fragments may be separated by gel-permeation chromatography on Sephadex LH-60. Digestion of the N-terminal-derived V8-L fragment with CNBr in 70% (v/v) trifluoroacetic acid resulted in a peptide mixture that could be fractionated by procedures involving gel-permeation chromatography in organic and aqueous solvents and the use of differential solubility. The complete or partial sequences of all ten peptides are reported.

Preparation of the alkali and P light chains of chicken gizzard myosin. Amino acid sequence of the alkali light chain

1. A simple method is described for the purification of the alkali and P light chains from chicken gizzard myosin. 2. The sequence of the alkali light chain has been unequivocally determined, except for the N-terminal dipeptide, by using the tryptic and CNBr peptides. 3. No evidence was obtained for any specific high-affinity Ca2+-binding sites on the alkali light chain. 4. Detailed evidence on which the sequence is based has been deposited as Supplementary Publication SUP 50120 (14 pages) at the British Library Lending Division, Boston Spa, Wetherby, West Yorkshire LS23 7QB, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1983) 209, 5.

Characterization and partial sequence of di-iodosulphophenyl isothiocyanate-binding peptide from human erythrocyte anion-transport protein

We investigated the presumed anion-binding domain of the anion-transport protein from human erythrocyte membranes, using 2,6-di-iodo-4-sulphophenyl isothiocyanate, an inhibitor of anion transport. The 125I-labelled reagent binds covalently to the protein with a half-maximal inhibitory concentration of 86 microM. Treatment of unsealed erythrocyte 'ghosts' with chymotrypsin yielded a membrane-bound fragment (mol.wt. 14 500 +/- 1000) that contained all the protein-bound radioactivity. The binding of the inhibitor to this peptide gave a pattern very similar to that obtained for the effect of the compound on phosphate transport into erythrocytes. The peptide is therefore presumed to be intimately involved in the mediation of anion exchange. Cleavage of the 14 500-mol.wt. transmembrane fragment with CNBr resulted in the production of two peptides with apparent molecular weights of 8800 and 4700. The 4700-mol.wt. peptide is the N-terminal portion of the 14 500-mol.wt. peptide. The attachment site for 2,6-di-iodo-4-sulphophenyl isothiocyanate is situated near the C-terminal of the 8800-mol.wt. peptide. This locates the inhibitor-binding site near the chymotrypsin cleavage point at the extracellular surface of the membrane. A partial sequence (residues 1--38) of the 8800-mol.wt. peptide was obtained.

Solid-phase sequence analysis of polypeptides eluted from polyacrylamide gels. An aid to interpretation of DNA sequences exemplified by the Escherichia coli unc operon and bacteriophage lambda

An approach to sequencing proteins by the solid-phase method combined with isolation of proteins and polypeptides by gel electrophoresis is described. Mixtures of proteins or polypeptides resulting from digests are fractionated in the presence of dodecylsulphate in polyacrylamide gels. They are detected with Coomassie blue, eluted, selectively reacted with porous glass derivatives and sequenced in their amino-terminal regions with the aid of a new microsequencer. Alternatively they can be analysed or digested with enzymes and fingerprinted. It is a relatively rapid method of purifying proteins for sequence analysis which we have used to provide partial protein sequence data to complement DNA sequences. Nine genes, four from the unc operon of Escherichia coli encoding the alpha, beta, gamma and epsilon subunits of ATP synthase and five for capsid proteins of bacteriophage lambda, have been identified by this method.

A hydrophobic tryptic peptide from bovine white matter proteolipid

A hydrophobic, chloroform-soluble tryptic peptide with a molecular weight of approximately 4000 has been purified from the bovine white matter proteolipid protein. Its primary structure was obtained by a combination of solid-phase Edman degradation and mass spectrometry. A major part of the tryptic peptide appears to be inaccessible to the action of proteolytic enzymes. The peptide spans the three cyanogen bromide peptides located by Jollès et al. (Biochem. Biophys. Res. Commun. (1979) 87, 619--626) at the COOH-terminal region of the intact protein. Secondary structure calculations for this region indicate a segregation into discrete domains, with most of the tryptic peptide corresponding to a highly ordered, hydrophobic domain; an equal probability for alpha-helical or beta-structure is predicted for this region.