A One-Letter Notation for Amino Acid Sequences*. Tentative Rules

A brief history of bioinformatics

It is easy for today’s students and researchers to believe that modern bioinformatics emerged recently to assist next-generation sequencing data analysis. However, the very beginnings of bioinformatics occurred more than 50 years ago, when desktop computers were still a hypothesis and DNA could not yet be sequenced. The foundations of bioinformatics were laid in the early 1960s with the application of computational methods to protein sequence analysis (notably, de novo sequence assembly, biological sequence databases and substitution models). Later on, DNA analysis also emerged due to parallel advances in (i) molecular biology methods, which allowed easier manipulation of DNA, as well as its sequencing, and (ii) computer science, which saw the rise of increasingly miniaturized and more powerful computers, as well as novel software better suited to handle bioinformatics tasks. In the 1990s through the 2000s, major improvements in sequencing technology, along with reduced costs, gave rise to an exponential increase of data. The arrival of ‘Big Data’ has laid out new challenges in terms of data mining and management, calling for more expertise from computer science into the field. Coupled with an ever-increasing amount of bioinformatics tools, biological Big Data had (and continues to have) profound implications on the predictive power and reproducibility of bioinformatics results. To overcome this issue, universities are now fully integrating this discipline into the curriculum of biology students. Recent subdisciplines such as synthetic biology, systems biology and whole-cell modeling have emerged from the ever-increasing complementarity between computer science and biology.

obitools: a unix-inspired software package for DNA metabarcoding

DNA metabarcoding offers new perspectives in biodiversity research. This recently developed approach to ecosystem study relies heavily on the use of next-generation sequencing (NGS) and thus calls upon the ability to deal with huge sequence data sets. The obitools package satisfies this requirement thanks to a set of programs specifically designed for analysing NGS data in a DNA metabarcoding context. Their capacity to filter and edit sequences while taking into account taxonomic annotation helps to set up tailor-made analysis pipelines for a broad range of DNA metabarcoding applications, including biodiversity surveys or diet analyses. The obitools package is distributed as an open source software available on the following website: http://metabarcoding.org/obitools. A Galaxy wrapper is available on the GenOuest core facility toolshed: http://toolshed.genouest.org.

Potential-energy calculations of terminally blocked tetrapeptides from the third loop of short-chain snake venom neurotoxins

The conformational space of six tetrapeptides from the beta-bends in the third loop of short-chain snake venom neurotoxins was investigated with the aid of energy calculations. It was shown that these peptides can be divided into two groups: those with a specific preference for an alpha-helix and those that exist as an ensemble of beta-turn conformations.

A segment corresponding to amino acids Val170-Arg182 of bovine arrestin is capable of binding to phosphorylated rhodopsin

In retinal rods, photoexcited rhodopsin (R*) is inactivated upon phosphorylation by rhodopsin kinase and the subsequent binding of arrestin. We have studied the structural role of a cationic region of bovine arrestin (Val170-Arg182) using anti-peptide IgGs specifically recognizing this segment and the corresponding oligopeptide. Our results clearly indicate that amino acids Val170-Arg182 are shielded within the arrestin-rhodopsin-complex and very likely belong to a binding domain of arrestin for phosphorylated R*. The purified anti-peptide IgGs strongly reacted with isolated arrestin but did not recognize arrestin when bound to phosphorylated R*. In agreement with these experiments, the oligopeptide Val170-Arg182 was found to compete with arrestin for binding to phosphorylated R*. Increasing concentrations of this peptide caused an oligomerization of phosphorylated rhodopsin when illuminated by white light as well as in the dark. Unphosphorylated rhodopsin did not oligomerize up to a 400-fold molar ratio of peptide/rhodopsin. Limited proteolysis of the phosphorylated carboxy-terminus of rhodopsin with endoproteinase Asp-N caused a significant decrease in the peptide-induced formation of oligomers. Therefore, Val170-Arg182 of bovine arrestin probably interacts with the phosphorylated carboxy-terminus of rhodopsin. The data presented support the proposal of Palczewski et al. (1991c) considering the region Lys163-Arg182 in bovine arrestin to be a possible binding domain for phosphorylated R*.

Experimental studies and potential-energy calculations of the blocked tetrapeptide Ac-Lys-Gln-Gly-Ile-NMA from the third loop of a short-chain snake venom neurotoxin

The conformational space of the tetrapeptide Ac-Lys-Gln-Gly-Ile-NMA from the beta-bend in the third loop of a short-chain snake venom neurotoxin was investigated with the aid of energy calculations. It was shown that this peptide has a preference for an alpha-helical conformation. This result was compared with the experimentally determined conformations, as observed using NMR and CD spectroscopy. With NMR spectroscopy a random-coil conformation of the peptide is indicated in H2O, DMSO and TFE. The results from the CD experiments suggest that the peptide exists as a random coil in water, but a small population of alpha-helical conformations is present in TFE. These results indicate that additional long-range interactions also play a role in the conformation of this tetrapeptide in the protein.

Experimental studies and potential energy calculations of the blocked tetrapeptide Ac-Lys-Pro-Gly-Ile-NMA from the third loop of short-chain snake venom neurotoxins

The conformational space of the tetrapeptide Ac-Lys-Pro-Gly-Ile-NMA from the beta-bend present in the third loop of short-chain snake venom neurotoxins was investigated with the aid of energy calculations, resulting in the identification of an ensemble of beta-turn conformations. These results were compared with the experimentally determined conformations, as observed using NMR and CD spectroscopy. A random coil conformation of the peptide is indicated in polar hydrogen-bonding solvents. In less polar solvents the peptide backbone assumed a more rigid conformation, as reflected by the existence of at least a type II beta-turn conformation.

Murine and human B cell epitope mapping of the Mycobacterium tuberculosis 10-kD heat shock protein using overlapping peptides

The human immune response to the 10-kD M. tuberculosis protein was studied by a competition ELISA using monoclonal antibody (MoAb) SA-12. Twenty-five per cent of the sera from 20 patients with tuberculosis and none from 21 control subjects inhibited binding of SA-12 to the 10-kD antigen. To characterize the antigenic parts of the 10-kD antigen, overlapping decapeptides according to the amino acid sequence of the 10-kD protein were synthesized. In total, 91 sequential decapeptides, with an overlap of nine amino acids, were tested in ELISA with MoAb SA-12, human and murine sera (PEP scan). SA-12 recognized the amino acid sequence WDEDGEK (amino acid 50-56). All human sera, from patients with tuberculosis as well as from control subjects, gave almost identical undulating patterns of reactivity with the decapeptides. No relationship was found between the ability of the patients' sera to inhibit binding of MoAb SA-12 and the binding of these sera to the decapeptides comprising the epitope recognized by SA-12 in the PEP scan. Apparently, antibodies in patients' sera against the 10-kD protein are predominantly directed against discontinuous epitopes and, consequently, the continuous epitopes as presented in the PEP scan are not suitable to discriminate between patients with tuberculosis and control subjects. In the PEP scan, sera from BALB/c mice, both non-immunized and immunized with either live M. tuberculosis or the 10-kD protein gave similar patterns of reactivity, albeit different from the patterns obtained with the human sera. However, after immunization of the mice, clearly increased levels of antibodies to primary structures of the 10-kD protein were observed.

Strategies for epitope analysis using peptide synthesis

A recently developed approach to the synthesis and ELISA screening of large numbers of peptides is described. The method has created the opportunity to tackle questions about the sites and specificity of antigenic determinants which were formerly thought to be too difficult to answer. The various strategies for application of this method are described along with examples of their successful use. They include a procedure for locating all the continuous antigenic peptides of a protein antigen, and the identification of non-replaceable amino acid residues within an antigenic peptide. An approach to the determination of amino acid residues involved in the epitope for any monoclonal antibody is also described. These strategies open up the prospect of rapid mapping of the antigenic properties of hitherto poorly understood antigens.

Antigenic determinants on fimbriae of Serratia marcescens US5 analyzed using monoclonal antibodies

The antigenic sites on small thin fimbriae of Serratia marcescens strain US5 were investigated using immunoelectron microscopy and monoclonal antibodies (MAbs). Negative staining of the fimbriae after treatment with MAbs showed a regularly spaced arrangement of the antibody molecules. When the subunit peptide was subjected to immunoblotting using the MAbs, a single band with a molecular weight of approximately 19kD was evident. This binding of the MAbs to the subunit peptide was completely abrogated after treatment with 2-mercaptoethanol, thereby suggesting the important role of disulfide linkage in the maintenance of the conformation of the antigenic site reacted with MAbs. Amino acid analysis of the subunit peptide revealed two cysteine residues, and cysteine residues were absent in the N-terminal portion.

Identification of the gene encoding an RNA polymerase-binding protein of bacteriophage T4

One of five bacteriophage T4-specified proteins that bind to host RNA polymerase core has been purified and partially sequenced. A mixed oligonucleotide, based on the amino acid sequence, was used to probe genomic restriction fragments. The gene for this protein, previously designated the 15K protein, has been located between T4 genes 45 and 46 and designated rpbA.

Identification and assay of phosphoserine and tyrosine-O-sulphate in fibrinopeptides by reversed-phase high-performance liquid chromatography

A procedure utilizing reversed-phase high-performance liquid chromatography (HPLC) is described for the identification and quantitation of individual phosphorylated and sulphated fibrinopeptides present in fibrin clot supernatants. Fibrinopeptides from human, rabbit and canine fibrinogens, which have different structures and degrees of phosphorylation and sulphation, were used to demonstrate the applicability of these methods. The procedure relies on the increased peptide hydrophobicity following removal of highly charged phosphate or sulphate groups. Dephosphorylated or desulphated peptides are thus more strongly retained on the reversed-phase HPLC column and are eluted later than their corresponding phosphorylated or sulphated peptide counterparts. Dephosphorylation is achieved by treatment of fibrinopeptide-containing clot supernatants with alkaline phosphatase. Phosphorylated peptides are characterized by an increased retention time resulting from loss of phosphate, whereas non-phosphorylated peptides remain unaffected. Similarly, a prolongation of the peptide retention time resulting from desulphation by mild acid hydrolysis serves to verify sulphation of a peptide.

Synthetic peptides and beta-chain gene rearrangements reveal a diversified T cell repertoire for a lambda light chain third hypervariable region

Twelve L3T4+ Ly-2.2- subclones, derived from 4 independent BALB/c T cell lines, responded to a combination of the I-Ed molecule and a synthetic peptide corresponding to residues 91-108 of the lambda light chain from BALB/c myeloma protein M315 (alpha, lambda 2). Peptide analogues in which the mutated residues Arg95 or Asn96 were exchanged with the corresponding germ-line-encoded Ser95 or Thr96 had an abolished or greatly reduced capacity to stimulate T cell clones. However, responses of subclones to an analogue where the mutated Phe94 was substituted with the germ-line-encoded Tyr94 revealed three specificity patterns: 5 clones reacted only with the lambda 2(315) peptide, 6 clones responded equally well to both peptides and a single clone reacted better with the Tyr94 analogue. Analysis of the T cell receptor beta-chain gene rearrangements disclosed 7 distinct rearrangements, identical rearrangements only being found for subclones originating from the same line. At least 3 different V beta genes were used. Subclones with identical or nearly identical peptide specificity, major histocompatibility complex-restriction and alloreactivity could differ in their V beta or J beta gene segment utilization.

Purification and characterization of fimbriae from Salmonella enteritidis

A human isolate of Salmonella enteritidis which displayed strong pellicle formation during static broth culture and mannose-sensitive hemagglutination produced fimbriae which were morphologically indistinguishable from type 1 fimbriae of members of the family Enterobacteriaceae. Fimbrin was purified to homogeneity, and the apparent molecular weight (Mr, 14,400) was markedly lower than that reported for the type 1 fimbrin of Salmonella typhimurium (Mr, 22,100). This fimbrin contained 40% hydrophobic amino acids and lacked cysteine. The sequence of the N-terminal 64 amino acids was determined, and sequence alignment revealed that although the 18 N-terminal residues of the S. enteritidis molecule shared considerable homology with Escherichia coli and S. typhimurium type 1 fimbrins, the S. enteritidis fimbrin lacked a 6- to 9-residue terminal sequence present in the other type 1 fimbrins and, after residue 18, shared little homology with the E. coli sequence. Antibodies raised to the purified S. enteritidis fimbrin bound to surface-exposed conformational epitopes on the native fimbriae and displayed pronounced serospecificity. These antibodies were used in the isolation of a nonfimbriated Tn10 insertion mutant which was unable to hemagglutinate.

Style proteins of a wild tomato (Lycopersicon peruvianum) associated with expression of self-incompatibility

The identification, isolation and aminoterminal sequencing of two S-genotype-associated proteins from style extracts of Lycopersicon peruvianum Mill. is reported. There is a high level of homology between these two sequences and with the amino-terminal sequences of other S-allele-associated glycoproteins isolated from Nicotiana alata Link et Otto. These sequences were obtained by a new high-sensitivity method of selected twodimensional gel analysis followed by electroelution and purification of proteins by inverse-gradient high-performance liquid chromatography before sequencing.

Use of microbore high-performance liquid chromatography for purifying subnanomole levels of polypeptides for microsequencing. Structural studies on the murine plasma cell antigen PC-1

A procedure for the purification of subnanomole levels of polypeptides has been developed. Reversed-phase high performance liquid chromatography on short (10 cm or less) microbore (1-2 mm internal diameter) columns has been used to fractionate and purify a number of tryptic peptides generated from approximately 600 pmol of purified murine plasma cell antigen PC-1, a major membrane glycoprotein on all cells secreting immunoglobulins. The use of reversed-phase microbore columns permits the recovery of subnanomole amounts of polypeptides from large volumes in high yield (greater than 90%) and in small eluent volumes (40-60 microL) which can be loaded directly onto the gas-phase sequencer without further concentration. This procedure avoids the severe sample loss which frequently occurs with other concentration procedures such as lyophilization and evaporation. The use of a photodiode-array detector for identifying tryptophan-containing peptides from on-the-fly, ultraviolet spectra is described. This procedure permits the selection of tryptophan-containing peptides from complex tryptic digests for use as candidate peptides for oligonucleotide probe construction. Automated Edman degradation was performed on seven tryptic peptides, yielding 110 unique assignments; this corresponds to approximately 11% of the molecule.

Poliovirus-encoded proteinase 3C: a possible evolutionary link between cellular serine and cysteine proteinase families

Here we demonstrate significant similarities between the amino acid sequences of trypsin (a serine protease) and the N-terminal piece of a specific fragment of the poliovirus polyprotein encompassing the sequence of the viral proteinase 3C, and also between cathepsin H (a cysteine protease) and the C-terminal piece of the same fragment. A coherent alignment of the sequences of the 3 proteases was obtained, in which the principal catalytically active residues occupy identical positions. A hypothesis is proposed that the viral enzyme may provide an evolutionary link between serine and cysteine protease families.

Functional receptors for VIP, GIP, glucagon-29 and -37 in the HGT-1 human gastric cancer cell line

Three separate sets of receptors sensitive to VIP, GIP and pancreatic/entero-glucagons, have been characterized in HGT-1 cells. The order of relative potencies of VIP receptor agonists was VIP greater than rh GRF-43, rh GRF-29 greater than PHI greater than hp GRF-40, secretin. G-37 was about 4 times less potent than G-29 in HGT-1 cells (G-29 greater than G-37), whereas it was about 20 times more potent than G-29 in rat fundic glands (G-37 greater than G-29). Adenylate cyclase in HGT-1 cells was stimulated by VIP, G-29, G-37 and GIP, over a concentration from 3.16 X 10(-9) to 3.16 X 10(-7) M GIP. The experimental data: (1) support the enterogastrone activity of GIP, via adenylate cyclase activation and somatostatin release by gastric D cells; (2) demonstrate that HGT-1 cells originating from a human fundic tumor are sensitive to the glucagon-like peptides G-29 and -37, as rat fundic glands; (3) indicate that the pharmacological properties of the VIP receptor in this human gastric cell line are similar to those characterized in normal human gastric glands.

Secretin receptor activity in rat gastric glands. Binding studies, cAMP generation and pharmacology

We measured 125I-secretin binding to membranes prepared from rat fundic glands and compared the abilities of natural and synthetic secretin (SN) analogs to inhibit 125I-secretin binding and to activate the cAMP generating system in glandular and subcellular preparations from the fundus and antrum. The natural peptides structurally related to porcine secretin (pSN) included: chicken secretin (cSN), vasoactive intestinal peptide (VIP), porcine peptide with N-terminal histidine and C-terminal isoleucine amide (PHI), helodermin, growth hormone releasing factors isolated from the rat hypothalamus (rhGRF-43, rhGRF-29) or from a human pancreatic tumour (hpGRF-40). These peptides inhibited the binding of 125I-secretin to rat fundic membranes: pSN greater than cSN greater than PHI, VIP and activated the cAMP generating system in fundic glands, according to the following order of potency; pSN greater than cSN greater than PHI, VIP greater than rhGRF-29 greater than rhGRF-43. Porcine peptide with N-terminal tyrosine and C-terminal tyrosine (PYY), GIP, SOM and hpGRF-40 were inactive. Structural requirements for secretin receptor activity were evaluated with four synthetic secretin analogs corresponding to porcine secretin substituted at the N-terminal end by sequence portion of VIP, GIP, GLU and SOM: Ala4-Val5-SN(VIP-SN); Tyr1-Ala2-Glu3-SN (GIP-SN); Gln3-SN (GLU-SN) and Phe1-Phe1-Trp3-Lys4-SN (SOM-SN). The relative potencies of the analogs in fundic and antral preparations were: pSN greater than VIP-SN greater than VIP, GIP-SN greater than GLU-SN greater than SOM-SN for 125I-secretin displacement and cAMP production (glandular cAMP generation and adenylate cyclase activation).(ABSTRACT TRUNCATED AT 250 WORDS)

Peptide studies using a fast atom bombardment high field mass spectrometer and data system. 4. Disulfide-containing peptides

Ten peptides containing one, two or three disulfides were examined to determine their behavior under fast atom bombardment (FAB) mass spectrometric conditions. The mass spectra for the disulfide and the reduced disulfide forms of each peptide were compared. Several factors were examined that contribute to the fast atom bombardment mass spectra of these peptides: components of the FAB matrix such as alkali cations, acids, bases and reducing agents, the intrinsic molecular properties of the intact peptide, and the effect of reducing conditions on sensitivity. The FAB mass spectra of the disulfide-containing peptides examined in this study displayed accurate molecular weight information and fragmentation which indicated the position of the disulfide in the amino acid sequence.

The amino acid sequence of a lambda light chain presenting abnormal physicochemical and antigenic features

The amino acid sequence of the light chain of a human monoclonal IgA1 (Mem) was established, in part by analogy with already known sequences. By homology its variable part was shown to belong to the V lambda I subgroup while the isotype-associated amino acid residues characterized it as Mcg+, Kern+ and Oz-. The normal primary structure of this chain was in contrast to its abnormal physical and antigenic properties: (a) its apparent molecular mass estimated by SDS/polyacrylamide gel electrophoresis, by gel filtration chromatography and by gradient ultracentrifugation was found to be lower by approximately equal to 10% than the values (23.5 kDa) of 'normal' light chain used as controls; (b) the lambda I chain Mem, when tested in native state was not antigenically reactive. These abnormalities were reverted when the chain was treated with 8 M urea. These data suggest that the abnormal behaviour of lambda I chain Mem is at a conformational level.

Amino acid sequence of a sea anemone toxin from Parasicyonis actinostoloides

Amino-acid sequence of a toxin from sea anemone, Parasicyonis actinostoloides, is determined. The toxin consists of 31 amino acid residues and is cross-linked with four disulphide bridges. The sequence has some similarity to that of toxin III and no similarity to those of toxin I and toxin II both from sea anemone, Anemonia sulcata, or to that of Anthopleurin A from Anthopleura xanthogrammica.

A microbore high-performance liquid chromatography strategy for the purification of polypeptides for gas-phase sequence analysis. Structural studies on the murine transferrin receptor

We describe herein the use of reversed-phase high-performance liquid chromatography coupled with the novel application of short (10 cm or less) microbore columns (2 mm internal diameter) to fractionate and purify a number of tryptic peptides generated from approximately 200 pmol purified murine transferrin receptor. The use of reversed-phase microbore columns permits the recovery of submicrogram amounts of purified polypeptides in high yield (greater than 90%) in small eluent volumes (20-60 microliter). In this manner, purified polypeptides can be loaded directly onto the gas-phase sequencer without further manipulation. This procedure avoids sample loss, which frequently occurs with other forms of concentration (e.g. lyophilization, evaporation). The application of second-order-derivative ultraviolet spectroscopy, using a diode array detector, for the analysis of aromatic aminoacid-containing peptides in complex tryptic digests is described. N-terminal amino acid sequence analyses were performed on six tryptic peptides, yielding 105 unique assignments; this corresponds to approximately 14% of the molecule. A comparison of this amino acid sequence information with the primary structure of human transferrin receptor deduced from the mRNA sequence [Nature (Lond.) 311, 675-678 (1984); Cell 39, 267-274 (1984)] reveals, with the exception of one tryptic peptide, a very close sequence homology between the murine and human transferrin receptors.

The amino acid sequence of human sperm protamine P1

Human sperm protamines have been extracted from spermatozoa pooled from several donors, converted to their S-pyridylethylated derivatives and resolved into two major components, P1 and P2, by Bio-Rex 70 chromatography. Protamine P1 was further purified by Bio-Gel P-10 chromatography and sequenced directly on a gas phase protein sequencer for 43 residues. To complete the sequence, P1 was cleaved at methionine 36 and the C-terminal tetradecapeptide was purified by h.p.l.c. and sequenced completely. The 50 residue sequence is: (sequence see text) This sequence has a calculated molecular weight of 6674 and is homologous with four other published mammalian protamine sequences.

Interaction of crystallins with the cytoskeletal-plasma membrane complex of the bovine lens

The isolated lenticular plasma membrane-cytoskeleton complex, when analysed by sodium dodecylsulphate-polyacrylamide gel electrophoresis, shows reproducibly a significant amount of crystallins, mainly alpha-crystallin. Evidence is provided that purified plasma membranes from the bovine lens also associate selectively with a limited number of newly synthesized polypeptides on cell-free translation of calf lens polyribosomes and addition of the membranes to the incubation medium. This capability is retained by purified lens membrane junctions. The polypeptides that are selected comprise alpha-crystallin chains (in particular alpha A2-crystallin), actin, vimentin and beta B1a-crystallin. Sequence analysis revealed that the latter has in its N-terminal extension a characteristic Pro-Ala track. The designation 'PAPA-arm' is proposed for this N-terminal region, comprising the alternating Pro-Ala sequence, that has previously also been found in rabbit myosin and might be responsible for anchoring beta B1a-crystallin to lens membranes.

Crystallin genes: templates for lens transparency

Analysis of recombinant DNAs provides new information on the basis of crystallin evolution and diversity. All crystallin genes contain introns. Two similar, tandemly linked chicken delta-crystallin genes, which probably arose by gene duplication, contain at least 16-17 introns. In the beta-crystallins three introns are situated between exons encoding the structural motifs of the protein, thus relating gene and protein structure. The structurally similar beta- and gamma-crystallins are coded by separate gene families which apparently arose by successive duplications of a common ancestral gene. The N-termini (5' end of gene) of the beta-crystallins appear to have diverged, while the 3' ends have been conserved. In the single murine alpha A-crystallin gene, coding information (the insert exon) for the alpha Ains peptide is contained within an intron. Alternative RNA splicing of this gene gives both the alpha A2 and the alpha Ains crystallin mRNAs. Thus, molecular genetics is providing a deeper appreciation of evolutionary events and is serving to redefine the crystallins in terms of their genes. Since the crystallins are so abundant in the lens, greater understanding of their polypeptide and gene structure should contribute to our understanding of and ability to treat cataract.

Porin from bacterial and mitochondrial outer membranes

The outer membrane of gram-negative bacteria acts as a molecular filter with defined exclusion limit for hydrophilic substances. The exclusion limit is dependent on the type of bacteria and has for enteric bacteria like Escherichia coli and Salmonella typhimurium a value between 600 and 800 Daltons, whereas molecules with molecular weights up to 6000 can penetrate the outer membrane of Pseudomonas aeruginosa. The molecular sieving properties result from the presence of a class of major proteins called porins which form trimers of identical subunits in the outer membrane. The porin trimers most likely contain only one large but well-defined pore with a diameter between 1.2 and 2 nm. Mitochondria are presumably descendents of gram-negative bacteria. The outer membrane of mitochondria contains in agreement with this hypothesis large pores which are permeable for hydrophilic substances with molecular weights up to 6000. The mitochondrial porins are processed by the cell and have molecular weights around 30,000 Daltons. There exists some evidence that the pore is controlled by electric fields and metabolic processes.

The identification of tRNA isoacceptors fractionated by polyacrylamide gel electrophoresis

A method is described by which specific tRNA isoacceptors may be identified in small amounts of bulk tRNA. The strategy relies on the retention of aminoacyl-tRNA by CNBr-Sepharose through covalent coupling of the alpha-NH2 group of the amino acid to the matrix. After removing unbound material by thorough washing, the bound specific isoacceptors are released by cleavage of the labile aminoacyl-tRNA ester bond through mild alkaline treatment. The product is analysed by two-dimensional gel electrophoresis and the spots obtained may be correlated with the pattern from bulk tRNA. Optimum sensitivity is achieved by combining the method with the recently introduced silver staining technique (Igloi, G.L. (1983) Anal. Biochem. 134, 184-188) for tRNA.

Gene encoding a hybrid OmpF--PhoE pore protein in the outer membrane of Escherichia coli K12

To study the structure-function relationship of outer membrane pore proteins of E. coli K12, a hybrid gene was constructed in which the DNA encoding amino acid residues 2-73 of the mature PhoE protein is replaced by the homologous part of the related ompF gene. The product of this gene is incorporated normally into the outer membrane. It was characterized with respect to its pore activity and its phage receptor and colicin receptor properties. It is concluded that the preference of the PhoE protein pore for negatively charged solutes is partly determined by the amino terminal 73 amino acids, that part of the receptor site of PhoE protein for phage TC45 is located in this part of the protein, that colicin N uses OmpF protein as (part of) its receptor, that the specificity of OmpF protein as a colicin N receptor is completely located within the 80 amino terminal amino acid residues, whereas the specificity of this protein as a colicin A receptor is completely located within the 260 carboxy terminal amino acid residues, and that the amino terminal 73 amino acid residues of PhoE protein span the membrane at least once.

Nucleotide sequence of the marmoset herpesvirus thymidine kinase gene and predicted amino acid sequence of thymidine kinase polypeptide

The nucleotide sequence of a 2549-bp DNA fragment containing the entire coding region of the marmoset herpesvirus (MarHV) thymidine kinase gene (tk) and the flanking sequences was determined by the dideoxynucleotide chain termination method. The MarHV thymidine kinase polypeptide predicted from the nucleotide sequence contained 376 amino acids and had a molecular weight of 41,281. The sequencing data also reveal that the coding portion of another MarHV gene probably begins only 292 nucleotides downstream from the stop codon of the MarHV tk gene. There was relatively little nucleotide sequence homology between the MarHV tk gene and that of the herpes simplex virus (HSV) types 1 and 2 tk genes. Comparisons of the predicted amino acid sequences of the MarHV thymidine kinase polypeptide with that of the HSV-1 and HSV-2 thymidine kinase polypeptides, however, revealed clear, but interrupted, homology within several regions of the polypeptide chains. Amino acid sequence homology was particularly striking at residues 10 to 27 of the MarHV thymidine kinase polypeptide and residues 49 to 66 of the HSV-1 and HSV-2 thymidine kinase polypeptides. These same amino acid residues exhibit noticeable sequence homology to the mitochondrial beta subunit ATPase, oncogene p21 protein, adenylate kinase, and to other nucleotide-binding proteins. It has been proposed that the indicated regions of homology are elements of a nucleotide-binding pocket in ATPase, p21, and adenylate kinase, raising the possibility that amino acid residues 15 to 25 of the MarHV thymidine kinase and 54 to 64 of the HSV-1 and HSV-2 enzymes are likewise parts of nucleotide-binding sites.

Structural analysis of the Ss sialoglycoprotein specific for Henshaw blood group from human erythrocyte membranes

The N-terminal structures of the MN and Ss erythrocyte membrane sialoglycoproteins (glycophorins A, B) from two Henshaw (He) blood-group heterozygotes were determined by manual sequencing of tryptic glycopeptides and various secondary fragments. No structural alteration of the MN glycoprotein could be detected. The He-specific portion of the Ss glycoprotein was found to exhibit the N-terminal sequence Trp-Ser+-Thr+-Ser+-Gly-(+ = glycosylation). Thus it differs at three positions from its normal counterpart which possesses 'N' activity and exhibits the N-terminal structure Leu-Ser+-Thr+-Thr+-Glu-. Analysis of the Ss glycoprotein from 15 He-negative erythrocyte samples did not reveal any of the three He-specific structural alterations. The presence of a glycine residue at the fifth position of the blood-group-M-active MN glycoprotein as well as in the He-specific Ss glycoprotein provides an explanation for the occurrence of antisera (anti-Me) reacting with the M and He antigens.

Complete primary structure of the collagen-binding domain of bovine fibronectin

The complete amino acid sequence of the collagen-binding domain of bovine plasma fibronectin has been determined. The fragment, generated by digestion of fibronectin with plasmin and chymotrypsin, contains 340 residues (260-599 of fibronectin) with threonine and tryptophan as the amino-terminal and carboxyl-terminal amino acids, respectively. 24 half-cystines and no cysteines are present in the sequence. Three glucosamine-based oligosaccharide groups are attached to Asn-399, Asn-497 and to Asn-511, respectively. Two of the three types (I and II) [Petersen et al. (1983) Proc. Natl Acad. Sci. USA 80, 137-141] of internal homology occur in the fragment, namely four of the at least twelve stretches of type I sequence homology, 'fingers', and two stretches of type II homology. The type I homology is present in two other plasmic fragments from fibronectin, while the type II homology has been found in the collagen-binding domain only.

Amino acid sequence of rat submaxillary tonin reveals similarities to serine proteases

Tonin, an esteroprotease isolated from rat submaxillary gland, is a serine protease with trypsin- and chymotrypsin-like activity. The substrate specificity of tonin shows that it differs from kallikreins and is definitely not a renin-like enzyme or an angiotensin-converting enzyme. Tonin can produce directly the vasoactive peptide angiotensin II, from angiotensin I, angiotensinogen and the synthetic tetradecapeptide substrate of renin by cleavage of a Phe-His bond. It has also been found to cleave some Phe and Arg bonds in various substrates such as beta-lipotropin (beta-LPH), adrenocorticotropin (ACTH), pro-opiomelanocortin (POMC) and substance P. Here we describe the complete amino acid sequence of rat submaxillary gland, tonin. Comparison of the sequence of 219 amino acids with other serine proteases, particularly kallikreins, gamma-subunit of nerve growth factor (NGF) and the recently described gamma-renin, reveals extensive similarities. More interestingly, it also reveals the substitution of an Asp residue always found in the serine protease active site triad (Asp, His, Ser) by a Leu residue. This unusual substitution does not seem to affect the proteolytic activity of the enzyme.

Structures of Miltenberger class I and II specific major human erythrocyte membrane sialoglycoproteins

The N-terminal structures of the Miltenberger (Mi-) blood group class I and II specific human MN erythrocyte membrane sialoglycoproteins were determined by manual sequencing of tryptic glycopeptides and various secondary fragments. The Mi-I and Mi-II active glycoproteins were found to exhibit a threonine leads to methionine and threonine leads to lysine exchange, respectively, at position 28 which prevents N-glycosylation of asparagine 26. Due to the absence of the N-glycosidic oligosaccharide chain, the monomeric form of the Mi-I and Mi-II specific glycoproteins possesses a slightly increased sodium dodecyl sulfate/polyacrylamide gel electrophoretic mobility, in comparison to its normal counterpart. Serological studies suggest that antibodies, specific for Mi-I or Mi-II red cells, react with the structurally altered region of the MN glycoprotein.

The complete primary structure of phospholipase A2 from human pancreas

The complete amino acid sequence of phospholipase A2 (phosphatide 2-acylhydrolase, EC 3.1.1.4) from human pancreas was determined. The protein consists of a single polypeptide chain of 125 amino acids and has a molecular weight of 14003. The chain is cross-linked by seven disulfide bridges. The main fragmentation of the polypeptide chain was accomplished by digestion of the reduced and thialaminated derivative of the protein with clostripain, yielding three fragments. The largest fragment (residues 7-100) was further degraded both with staphylococcal proteinase and chymotrypsin. The sequence was determined by automated Edman degradation of the intact protein and of several large peptide fragments. Phospholipase A2 from human pancreas contains the same number of amino acids (125) as the enzyme from horse, while the enzymes from pig and ox contain 124 and 123 residues, respectively. The enzymes show a high degree of homology; human phospholipase differs from the other enzymes by substitutions of 26 (porcine), 28 (bovine) and 32 (equine) residues, respectively.

Complete nucleotide sequence of phoE, the structural gene for the phosphate limitation inducible outer membrane pore protein of Escherichia coli K12

The complete nucleotide sequence of the gene phoE, which codes for the phosphate limitation inducible outer membrane pore protein of Escherichia coli K12 was established. The results show that PhoE protein is synthesized in a precursor form with a 21 amino acid residue amino-terminal extension. This peptide has the general characteristics of a signal sequence. The promoter region of phoE has no homology with the consensus sequence of E. coli promoter regions, but homologous sequences with the promoter region of phoA, the structural gene for alkaline phosphatase, were observed. The deduced amino acid sequence showed that the mature PhoE protein is composed of 330 amino acid residues with a calculated molecular weight of 36,782. A number of 81 charged amino acids was found scattered throughout the protein while no large stretches of hydrophobic amino acids were observed. Hydrophobicity and hydration profiles of PhoE protein showed five pronounced hydrophilic maxima which are all located in the region from the amino terminus to residue 212. When the deduced amino acid sequence of PhoE protein was compared with the established sequence of the OmpF pore protein, a number of 210 identical residues was found. Some aspects of the structure-function relationship of PhoE protein are discussed in view of the hydrophobicity and hydration profiles, and the homology between PhoE protein and OmpF protein.

Partial amino-acid sequence of the epidermal growth-factor-binding protein

The partial amino acid sequence of the epidermal growth-factor-binding protein was determined. Residues in 108 unique positions, corresponding to 45% of the molecule, were identified. The protein is a serine protease, closely related to the nerve growth factor gamma subunit. It is suggested that the epidermal growth-factor-binding protein, like other serine protease, is synthesized as a single polypeptide chain which undergoes limited endoproteolysis. The isolated material also contained minor amounts of a second serine protease. This protease is closely related to the epidermal growth-factor-binding protein, differing from it in 7 out of the 45 amino acid positions available for comparison. The latter protease may be identical to the previously described protease A.

Human low-molecular-weight urinary urokinase. Partial characterization and preliminary sequence data of the two polypeptide chains

Low-molecular-weight urokinase (molecular weight 33100) was separated by analytical and preparative isoelectric focusing into five major subforms with isoelectric points between 8.7 and 9.6. These subforms are very similar in molecular weight, specific activity, amino acid composition and content of amino sugar and their N-terminal sequence constellation is identical. Low-molecular-weight urokinase consists of two polypeptide chains connected by a single disulfide bridge. The N-terminal region of the heavy chain (calculated Mr 30700) exhibits homology within the first 46 residues analyzed, with the known primary structure of other serine proteases. The mini chain (Mr 2426), whose complete sequence was determined, consists of 21 residues which show homology with the primary structure of the C-terminal region of the plasmin heavy chain. Based on sequence data and homology criteria with serine proteases a single-chain urokinase precursor is postulated having a peptide bond constellation between heavy and light chain region compatible with the requirements for serine protease activation.

N-terminal amino acid sequence of sialoglycoprotein D (glycophorin C) from human erythrocyte membranes

The amino acid sequence of the N-terminal tryptic glycopeptide from a minor human erythrocyte membrane sialoglycoprotein (component D or glycophorin C) was determined by manual sequencing. The glycosylation sites were identified by a new procedure for the detection of the glycosylated derivatives released by Edman degradation. The fragment, comprising 47 residues, was found to contain an average of about 12 O-glycosidically linked oligosaccharides and one asparagine-linked carbohydrate chain. An identical hexapeptide sequence occurring in two regions of the glycopeptide provides evidence that it has developed by an internal gene duplication during evolution. In addition, a part of its structure shows a striking similarity to the sequence of a certain region of the MN and Ss erythrocyte membrane sialoglycoproteins (glycophorins A and B), suggesting that the molecules might be related.

Cell-free synthesis, proteolytic processing, core glycosylation, and amino terminal sequence of rabbit pre-alpha-lactalbumin

Two different forms of alpha-lactalbumin were isolated from rabbit milk and partially characterized. The major and the minor species had apparent molecular weights of 18000 and 14000, respectively, according to their electrophoretic mobilities on SDS polyacrylamide gels. Analyses of their amino acid compositions and amino-and carboxy-terminal sequences did not reveal any difference, but sugar analysis showed the occurrence of carbohydrates in the major species. Rabbit alpha-lactalbumin was synthesized in a cell-free translation system as a precursor with an amino terminal extension of 19 amino acid residues whose primary structure is rather different from those of its ovine and porcine counterparts, in contrast with the extensive similarity so far observed between the known signals of homologous milk proteins. When mammary microsomal membranes were added during translation, the preprotein was converted to authentic alpha-lactalbumin, as demonstrated by amino terminal sequence analyses. However, one of the two processed forms migrated more slowly than pre-alpha-lactalbumin on SDS polyacrylamide gels and this was related to the occurrence of carbohydrates: only the "slower moving" polypeptide was specifically adsorbed on concanavalin A Sepharose and its electrophoretic mobility was enhanced after treatment with endoglycosidase H, an enzyme known to remove clustered mannosyl residues linked to di-N-acetylchitobiose. It was also observed that the rate of translocation of alpha-lactalbumin across the microsomal membrane was lower than that of beta-casein.