Structural and Physicochemical Characteristics of Novel Basic Proteins Isolated from Duck Egg White

Novel basic proteins, duck basic protein small 1 (dBPS₁) and 2 (dBPS₂), were isolated from duck egg white by cation-exchange and gel filtration chromatography. Protein sequence analyses indicated that they possessed 39 amino acid residues with three disulfide bonds. The amino acid sequence of dBPS₁ showed 45% identity with dBPS₂. The amino acid sequence of dBPS₂ was the same as cygnin, a small protein from black swan, and strongly homologous with meleagrin from turkey and chicken. Phylogenic relationships implied that dBPS₁ and dBPS₂ share a common ancestry with cygnin and meleagrin. Based on MALDI-TOF mass spectra, the molecular masses of dBPS₁ and dBPS₂ were 4,373, and the 4,486 Da. pI of dBPS₁ and dBPS₂ elucidated by isoelectric focusing were 9.35 and 9.44. FT-IR spectra classified these proteins as (β) proteins. Both dBPS₁ and dBPS₂, possessed high heat stability, Td 101.2 and 98.3 °C. Indirect ELISA results showed that the dBPS₁/dBPS₂-related proteins were distributed in the oviduct and gallbladder.     

Covalent structure of a low-molecular-mass protein, meleagrin, present in a turkey (Meleagris gallopavo) ovomucoid preparation

A low-molecular-mass protein, tentatively named meleagrin, was isolated from a commercial preparation of turkey (Meleagris gallopavo) ovomucoid. This 40-amino acid protein contains 3 disulfide bonds and high concentrations of aromatic residues (2 tryptophans and 3 tyrosines). It lacks threonine, methionine, phenylalanine, and arginine residues. The complete amino acid sequence was determined to be the following: less than Glu-Val-Leu-Lys-Tyr-Cys-Pro-Lys-Ile-Gly-Tyr-Cys-Ser-Ser-Lys-Cys-Ser-Lys- Ala- Glu-Val-Trp-Ala-Tyr-Ser-Pro-Asp-Cys-Lys-Val-His-Cys-Cys-Val-Pro-Ala-Asn- Gln-Lys - Trp. One of the three disulfide bonds exists between Cys12 and Cys28, and the two others links Cys32-Cys33 with Cys6 and Cys16. The amino acid sequence of meleagrin shows a strong homology to a similar basic protein, cygnin (Simpson, G.R. & Morgan, F.J. [1983] Int. J. Pep. Protein Res. 22, 476-481), of a rather distantly related aves, black swan (Cygnus atratus), suggesting some vital role of this protein in avian eggs. Similarity to a part (exon 9) of transferrins was also recognized.     

The chicken egg white proteome

Using 1-D PAGE and LC-MS/MS and MS(3) we identified 78 chicken egg white proteins, 54 of which were identified in egg white for the first time. All proteins were quantitated by calculating their exponentially modified protein abundance index (emPAI). Some previously known egg white components not characterized by amino acid sequences before, such as alpha-2-macroglobulin, were associated to a sequence for the first time. The predicted sequence was confirmed by MS-sequenced peptides covering 42% of the entire sequence. alpha-2-Macroglobulin occurred in egg white at the same concentration as ovostatin with which it showed 35% identity. For other proteins, which were previously only characterized by partial sequences, such as beta-ovomucin or ovalbumin X, we identified and confirmed predicted complete sequences with a high coverage by MS-sequenced peptides. New proteins included a 7 kDa protein consisting of a single secretoglobin sequence (ovosecretoglobin), a 7 kDa protein with similarity to black swan cygnin and turkey meleagrin (gallin) and proteins involved in binding, modification, and possibly detoxification, of bacterial lipopolysaccaride. The list of egg white proteins provided is by far the most comprehensive at present and is intended to serve as a starting point for the isolation and functional characterization of interesting new proteins.     

Isolation and complete amino acid sequence of a basic low molecular weight protein from black swan egg white

The following complete amino acid sequence of a low molecular weight basic protein (Mr 4,454) from black swan egg white has been determined: less than Glu-Val-Arg-Lys-Tyr-Cys-Pro-Lys-Val-Gly-Tyr-Cys-Ser-Ser-Lys-Cys-Ser-Lys-Ala-Asp-Val-Trp-Ser-Leu-Ser-Ser-Asp-Cys-Lys-Phe-Tyr-Cys-Cys-Leu-Pro-Pro-Gly-Trp-Lys. There is significant homology between this protein, provisionally designated cygnin, and the NH2-terminal region of the second domain of chicken ovotransferrin. The disulfide bonds have not been assigned; however, the arrangement of half-cystines in cygnin is sufficiently different from that of the known transferrins to suggest that cygnin is derived from another gene.     

A comparsion of glycopeptides from the transferrins of several species.

1. The carbohydrate compositions of human, pig and cattle transferrins and duck ovotransferrin have been determined. 2. Glycopeptides have been prepared from these transferrins and their carbohydrate compositions and amino acid sequences determined. One of the glycopeptides from human transferrin carries the C-terminal residue of the protein. 3. Each tranferrrin yielded two glycopeptides that appeared to be identical in carbohydrate composition but different in amino acid sequence. The two glycopeptides have been distinguished as type A, in which the residue following Asn(CHO)(where CHO represents a carbohydrate moiety) is a basic amino acid and type B in which Asn(CHO) is followed by a neutral aliphatic amino acid. Cattle transferrin is exceptional in having two glycopeptides in which this position is occupied by serine. 4. It is suggested that each molecule of human and cattle transferrin and duck ovotransferrin carries an average of two carbohydrate prosthetic groups. Hen and pig transferrins appear to carry only one carbohydrate group per mol of protein. 5. The N-terminal sequences of hen and duck ovotransferrins and of cattle, human and pig transferrins were also determined.     

Molecular Characterization of the Duck Enteritis Virus UL4 Gene

Duck enteritis virus (DEV) is a herpesvirus that causes an acute, contagious and fatal disease. In the present article, the DEV UL4 gene was cloned and sequenced from a vaccine virus. A degenerate oligonucleotide primer for the consensus site of herpesvirus UL3 gene and a specific primer located in UL5 were used in the polymerase chain reaction (PCR) to amplify a DNA product 2 086 bp in size. DNA sequence analysis revealed that a 714 bp open reading frame (ORF) of DEV encoding a 237 amino acid polypeptide is homologous to the family of herpesvirus UL4 proteins and therefore has been characterized as a DEV UL4 gene. Alignment of the DEV UL4 protein sequence with those of other alphaherpesviruses showed that 10 amino acid residues are completely conserved. Phylogenetic tree analysis showed that the seventeen alphaherpesviruses viruses analyzed were classified into four large groups, and the duck enteritis virus branched separately, closely related to the Mardiviruses group comprising Gallid herpesvirus 2 (GaHV-2), Gallid herpesvirus 3 (GaHV-3) and Meleagrid herpesvirus 1 (MeHV-1). The present study showed that the evolutionary relationship of the UL4 protein could be used for classification of alphaherpesviruses.     

Conformation and aggregation of bovine myelin proteins

CD and PMR spectra were obtained on three major protein fractions of bovine CNS myelin: the basic A-1 protein, the Folch-Lees proteolipid apoprotein (APL), and the Wolfgram proteolipid protein (WPP). Most PMR peaks of the A-1 broadened on going from D₂O to salt solutions or to 100% 2-Chloroethanol (2-CE). CD spectra showed no α-helix in water or salt solutions, but showed 42% in 2-CE. The APL showed no PMR in D₂O, but did show aromatic amino acid peaks in 1.5% SDS. CD spectra showed 37% α-helix in both cases. The PMR of the WPP in 1.5% SDS showed aromatic amino acids, and the CD showed <20% α-helix. All three proteins showed sharp PMR spectra in trifluoroacetic acid with α-CH chemical shifts characteristic of random coils. It was concluded that the A-1 and the APL aggregate.     

Role of paired basic residues of protein C-termini in phospholipid binding

It is a well known phenomenon that the occurrence of several distinct amino acids at the C-terminus of proteins is non-random. We have analysed all Saccharomyces cerevisiae proteins predicted by computer databases and found lysine to be the most frequent residue both at the last (-1) and at the penultimate amino acid (-2) positions. To test the hypothesis that C-terminal basic residues efficiently bind to phospholipids we randomly expressed GST-fusion proteins from a yeast genomic library. Fifty-four different peptide fragments were found to bind phospholipids and 40% of them contained lysine/arginine residues at the (-1) or (-2) positions. One peptide showed high sequence similarity with the yeast protein Sip18p. Mutational analysis revealed that both C-terminal lysine residues of Sip18p are essential for phospholipid-binding in vitro. We assume that basic amino acid residues at the (-1) and (-2) positions in C-termini are suitable to attach the C-terminus of a given protein to membrane components such as phospholipids, thereby stabilizing the spatial structure of the protein or contributing to its subcellular localization. This mechanism could be an additional explanation for the C-terminal amino acid bias observed in proteins of several species.     

Isolation and partial characterization of human parotid basic proteins

Methods are presented for the isolation of basic proteins (Pb proteins) from human parotid saliva collected from humans possessing different alleles at the Pb locus. The proteins were found to be extremely basic, with an isoelectric point above 9.5. They contain approximately 45% of the basic amino acids histidine, lysine, and arginine, and are devoid of cysteine, proline, threonine, valine, methionine, and tryptophan. They are free of carbohydrate. A comparison of the amino acid sequence data of Pb protein to all available amino acid sequences revealed that no sequence similarities exist between the Pb proteins and any other proteins reported, although proteins of similar amino acid compositions have been reported by others. A model is presented with accounts for the several forms of allelic proteins based on observed amino acid sequence differences.     

A de novo designed protein protein interface

As an approach to both explore the physical/chemical parameters that drive molecular self-assembly and to generate novel protein oligomers, we have developed a procedure to generate protein dimers from monomeric proteins using computational protein docking and amino acid sequence design. A fast Fourier transform-based docking algorithm was used to generate a model for a dimeric version of the 56-amino-acid beta1 domain of streptococcal protein G. Computational amino acid sequence design of 24 residues at the dimer interface resulted in a heterodimer comprised of 12-fold and eightfold variants of the wild-type protein. The designed proteins were expressed, purified, and characterized using analytical ultracentrifugation and heteronuclear NMR techniques. Although the measured dissociation constant was modest ( approximately 300 microM), 2D-[(1)H,(15)N]-HSQC NMR spectra of one of the designed proteins in the absence and presence of its binding partner showed clear evidence of specific dimer formation.     

Amino acid sequence of the smaller basic protein from rat brain myelin

1. The complete amino acid sequence of the smaller basic protein from rat brain myelin was determined. This protein differs from myelin basic proteins of other species in having a deletion of a polypeptide of 40 amino acid residues from the centre of the molecule. 2. A detailed comparison is made of the constant and variable regions in a group of myelin basic proteins from six species. 3. An arginine residue in the rat protein was found to be partially methylated. The ratio of methylated to unmethylated arginine at this position differed from that found for the human basic protein. 4. Three tryptic peptides were isolated in more than one form. The differences between the two forms of each peptide are discussed in relation to the electrophoretic heterogeneity of myelin basic proteins, which is known to occur at alkaline pH values. 5. Detailed evidence for the amino acid sequence of the protein has been deposited as Supplementary Publication SUP 50029 at the British Library (Lending Division) (formerly the National Lending Library for Science and Technology), Boston Spa, Yorks. LS23 7BQ, U.K., from whom copies may be obtained on the terms given in Biochem. J. (1973) 131, 5.     

Production and characterization of a plant alpha-hydroxynitrile lyase in Escherichia coli

The coding sequence of the cyanogenic alpha-hydroxynitrile lyase gene of Manihot esculenta Crantz (cassava) was cloned in the plasmid vector pMal-c2 and expressed in Escherichia coli strain JM105. DNA sequencing showed that the recombinant plasmid contained the same sequence as the cDNA clone pHNL10. Peptide sequencing of the recombinant protein showed that the N-terminus was heterogeneous, with either four or six additional amino acid residues compared with the native protein. Circular dichroism spectra indicated similar secondary structure contents for both proteins. Enzyme assays showed that specific activity of native and recombinant proteins were 0.24 and 0.26 mmol CN(-)/mg/min, respectively; that both proteins had optimal activity at 40 degrees C and pH 5.5; and that both proteins were inhibited by the serine protease inhibitor phenyl-methane sulfonyl flouride (PMSF). Isoelectric focusing of native and recombinant protein revealed multiple isoforms for both proteins; the recombinant protein had a more basic mean isoelectric point (pl) (5.1) than the native protein (4.5). (c) 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 53: 332-338, 1997.     

Serological analysis of species specificity in the high mobility group chromosomal proteins.

The non-histone chromosomal protein of the high mobility group (HMG-1) present in mouse liver was purified to homogeneity. Antibodies against this protein as well as pure HMG-1 derived from calf thymus and HMG-E purified from duck erythrocytes were elicited in rabbits. The interaction between the antibodies and the immunogens was measured by passive hemoagglutination and by quantitative microcomplement fixation. Quantitative microcomplement fixation assays revealed that the immunological distance between HMG-1 from calf thymus and HMG-1 from mouse liver and duck erythrocytes was 15. This corresponds to 3% sequence differences. It was estimated that amino acid substitution occurred at about seven positions in the polypeptide chain. Thus, HMG-1 proteins display remarkable evolutionary conservation in their primary sequence, similar to that displayed by histones H4 and H3, suggesting that their biological function is dependent on stringent structural requirements. HMG-E protein is significantly different from both HMG-1 and HMG-2 derived from calf thymus. As such, it is a protein unique to avian erythrocytes.     

Molecular characterization of nuclear basic protein HPI1, a putative precursor of human sperm protamines HP2 and HP3

The largest intermediate basic protein HPI1 (101 residues) from human sperm chromatin was isolated and characterized. The amino acid composition and sequence analysis of the protein and of tryptic peptides together with peptide mapping of endoproteinases Lys-C and Glu-C hydrolysates showed that the C-terminal region (residues 45-101) of HPI1 is identical to protamine HP2. These structural data strongly suggest that protein HPI1 is a precursor of human sperm protamines HP2 and HP3 (57 and 54 residues, respectively) as well as of two other intermediate basic proteins HPS1 and HPS2 (69 and 66 residues, respectively) sequenced previously.     

The amino terminal sequence of the developmentally regulated Ch21 protein shows homology with amino terminal sequences of low molecular weight proteins binding hydrophobic molecules

Ch21 protein, a developmentally regulated chick embryo protein of 21,000 apparent molecular weight, was purified from culture medium of hypertrophic chondrocytes. The purification method included a DEAE cellulose chromatography column, a CM cellulose chromatography column and a HPLC molecular sieve column. The amino acid sequence of the amino terminal end of the protein was determined. Computer assisted analysis showed significant homology between this sequence and the amino terminal sequences of proteins that belong to the superfamily of the low molecular weight binding proteins sharing a basic framework for the binding and transport of small hydrophobic molecules. Determination of the amino terminal sequence of the chicken retinol binding protein excluded identity between this protein and the Ch21.     

A cDNA homologue of Schizosaccharomyces pombe cdc5(+) from the mushroom Lentinula edodes: characterization of the cDNA and its expressed product

A cDNA homologue of Schizosaccharomyces pombe cdc5(+) was isolated from the basidiomycete mushroom Lentinula edodes and it was named Le.cdc5 cDNA. The deduced Le.CDC5 (842 amino acid residues) possessed N-terminal amino acid sequence highly homologous to those of S. pombe cdc5(+) gene product (Sp.cdc5p) and Sp.cdc5p-related proteins (SPCDC5RPs). The N-terminal 185 amino acid peptide of Le.CDC5 (Le.CDC5(1-185) peptide) produced in Escherichia coli was subjected to random binding-site selection analysis, revealing that Le.CDC5(1-185) peptide binds to a 7-bp sequence with the consensus sequence of 5'GCAATGT3' (complementary; 5'ACATTGC3'). Genomic binding-site (GBS) cloning by using Le.CDC5(1-185) peptide resulted in an isolation of the DNA fragment that contained three sets of 7-bp consensus-like sequence and TATA box. The Le.CDC5 protein contained two putative phosphorylation sites of cAMP-dependent protein kinase (A kinase) in its C-terminus. There exists a possible leucine zipper between the two phosphorylation sites. The Le.CDC5 fragment containing the two phosphorylation sites was actually phosphorylated by commercially available A kinase. Yeast two-hybrid analysis suggested the homodimerization of Le.CDC5 protein probably through the leucine zipper. Northern blot analysis showed that Le.cdc5 gene is most actively transcribed in primordia and small immature fruiting bodies of L. edodes, implying that Le.cdc5 may play a role in the beginning and early stage of fruiting-body formation.     

Nucleotide sequence and expression of a maize H1 histone cDNA.

The first complete amino acid sequence of a H1 histone of a monocotyledonous plant was deduced from a cDNA isolated from a maize library. The encoded H1 protein is 245 amino acid-long and shows the classical tripartite organization of this class of histones. The central globular region of 76 residues shows 60% sequence homology with H1 proteins from dicots but only 20% with the animal H1 proteins. However, several of the amino acids considered as being important in the structure of the nucleosome are conserved between this protein and its animal counterparts. The N-terminal region contains an equal number of acidic and basic residues which appears as a general feature of plant H1 proteins. The 124 residue long and highly basic C-terminal region contains a 7-fold repeated element KA/PKXA/PAKA/PK. Southern-blot hybridization showed that the H1 protein is encoded by a small multigene family. Highly homologous H1 gene families were also detected in the genomes of several more or less closely related plant species. The general expression pattern of these genes was not significantly different from that of these genes encoding the core-histones neither during germination nor in the different tissues of adult maize.