Identification of hornet silk gene with a characteristic repetitive sequence in Vespa simillima xanthoptera

Vssilk 5 is a gene encoding a component protein of the silk produced by the larvae of the yellow hornet (Vespa simillima, Vespinae, Vespidae). In this study, we deduced the complete cDNA sequence of Vssilk 5. It was found that 2 silk proteins, Vssilk 5 N and Vssilk 5 C, in the cocoon of the yellow hornet are both encoded by the Vssilk 5 gene. Vssilk 5 N and 5 C are the N- and C-terminal regions, respectively, of the Vssilk 5 pro-protein (Vssilk 5p). The complete amino acid sequences of Vssilk 5 N and Vssilk 5 C were deduced. Although a non-repetitive amino acid sequence and coiled-coil structure are properties common to the major components of silk proteins produced by the larvae of the social superfamilies Apoidea and Vespoidea of the Apocrita, nearly the entire sequence of Vssilk 5 C consisted of a repeated sequence of amino acids, and the calculated coiled-coil probability for this protein was low. Vssilk 5 N is a protein without a repetitive amino acid sequence and has a low coiled-coil probability. Moreover, we found a water soluble protein, Vssilk 5S that is likely segmented from Vssilk 5 C and contains an N-terminal sequence identical to that of Vssilk 5 C.     

Film formation and structural characterization of silk of the hornet Vespa simillima xanthoptera Cameron

We extracted silk produced by the larva of the hornet Vespa simillima xanthoptera Cameron from its nest. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis of the extracted hornet silk showed four major components with molecular weights between 35 and 60 kDa. The main amino acid components of the hornet silk protein were Ala (33.5%), Ser (16.9%), Asp (8.5%) and Glu (8.1%). The hornet silk could be dissolved in hexafluoroisopropyl alcohol (HFIP) at 25 degrees C without incurring molecular degradation. A transparent film of hornet silk was obtained readily by the formation of a cast upon drying of the hornet silk in the HFIP solution. Residual HFIP solvent was removed from the film by extraction with pure water. Solid-state 13C NMR and FT-IR measurements revealed that the secondary structures of hornet silk proteins in the native state consisted of coexisting alpha-helix and beta-sheet conformations. The beta-sheet to alpha-helix ratio, which was changed by processing, was mainly responsible for the silk's thermostability.     

Evidence of α-helical coiled coils and β-sheets in hornet silk

α-Helical coiled coil and β-sheet complexes are essential structural building elements of silk proteins produced by different species of the Hymenoptera. Beside X-ray scattering at wide and small angles we applied cryo-electron diffraction and microscopy to demonstrate the presence and the details of such structures in silk of the giant hornet Vespa mandarinia japonica. Our studies on the assembly of the fibrous silk proteins and their internal organization in relation to the primary chain structure suggest a 172 Å pitch supercoil consisting of four intertwined alanine-rich α-helical strands. The axial periodicity may adopt even multiples of the pitch value. Coiled coil motifs form the largest portion of the hornet silk structure and are aligned nearly parallel to the cocoon fiber axis in the same way as the membrane-like parts of the cocoon are molecularly orientated in the spinning direction. Supercoils were found to be associated with β-crystals, predominantly localized in the l-serine-rich chain sequences terminating each of the four predominant silk proteins. Such β-sheet blocks are considered resulting from transformation of random coil molecular sequences due to the action of elongational forces during the spinning process.     

Hornet silk proteins in the cocoons produced by different Vespa species inhabiting Japan

We compared the components of hornet silk - a fibrous protein occurring in the cocoons produced by hornet larvae - among 6 species of the genus Vespa inhabiting Japan: V. simillima, V. dybowskii, V. crabro, V. mandarinia, V. ducalis, and V. analis. From the sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), N-terminal amino acid sequence analysis, and 5'-RACE, it was found that the major component proteins composing hornet silk could be divided into 6 groups. Among these 6 proteins, 5 proteins were common to the hornet silks of all 6 Vespa species. The SDS-PAGE major band corresponding to the remaining protein was observed only in the hornet silks of V. mandarinia and V. ducalis. This correspondence between V. mandarinia and V. ducalis can probably be explained in terms of the phylogenetic relationships of the Vespa species.     

Single honeybee silk protein mimics properties of multi-protein silk

Honeybee silk is composed of four fibrous proteins that, unlike other silks, are readily synthesized at full-length and high yield. The four silk genes have been conserved for over 150 million years in all investigated bee, ant and hornet species, implying a distinct functional role for each protein. However, the amino acid composition and molecular architecture of the proteins are similar, suggesting functional redundancy. In this study we compare materials generated from a single honeybee silk protein to materials containing all four recombinant proteins or to natural honeybee silk. We analyse solution conformation by dynamic light scattering and circular dichroism, solid state structure by Fourier Transform Infrared spectroscopy and Raman spectroscopy, and fiber tensile properties by stress-strain analysis. The results demonstrate that fibers artificially generated from a single recombinant silk protein can reproduce the structural and mechanical properties of the natural silk. The importance of the four protein complex found in natural silk may lie in biological silk storage or hierarchical self-assembly. The finding that the functional properties of the mature material can be achieved with a single protein greatly simplifies the route to production for artificial honeybee silk.     

The conformation of T4 bacteriophage dihydrofolate reductase from circular dichroism

The secondary and tertiary structure of T4 bacteriophage dihydrofolate reductase is investigated by vacuum ultraviolet circular dichroism (CD) spectroscopy and probability analysis of the primary amino acid sequence. The far ultraviolet CD spectrum of the enzyme in the range of 260-178 nm is analyzed by the generalized inverse and variable selection methods developed by our laboratory. Variable selection yields an average content of 26% alpha-helix, 21% antiparallel beta-sheet, 10% parallel beta-sheet, 20% beta-turns, and 32% "other" structures within the T4 protein. The characteristic peaks of the CD spectrum indicate that the enzyme has a lot of antiparallel beta-sheet, which is typical of the alpha + beta tertiary class of globular proteins. The secondary structure of the protein is also analyzed by using four statistical methods on the amino acid sequence. Although the secondary structures predicted by each individual statistical method vary to a considerable extent, the fractions of each structure jointly predicted by a majority of the methods are in excellent agreement with our CD analysis. The alternating arrangement for some segments of alpha-helix and beta-sheet predicted from primary structure to be within the enzyme is characteristic of proteins containing parallel beta-sheet. This supports our conclusion that the protein contains both parallel and antiparallel beta-sheet structures, but finding both types of beta-sheet also means that the protein may have the variation on alpha/beta tertiary structure recently found in EcoRI endonuclease and thymidylate synthase. These observations, in conjunction with other physical properties of the T4 reductase, suggest that the enzyme perhaps shares an evolution in common with the dihydrofolate reductases derived from type I R-plasmids rather than with the host-cell protein.     

Left-handed topology of super-secondary structure formed by aligned alpha-helix and beta-hairpin.

A novel super-secondary structure common for many non-homological proteins is considered. This folding pattern, consisting of adjacent along the chain alpha-helix and beta-hairpin, has an aligned packing. It is found that one of the two possible 'mirror-symmetrical' topologies is observed in proteins. The alpha-helix + beta-hairpin structures have a similar pattern of hydrophobic residues in their amino acid sequences. The remaining part of a molecule or a domain is almost always located on the same side of the considered folding pattern. These results can be used in the prediction of three-dimensional protein structure and protein design.     

Oleosin KD 18 on the surface of oil bodies in maize. Genomic and cDNA sequences and the deduced protein structure

Oleosins are newly discovered, abundant, and small Mr hydrophobic proteins localized on the surface of oil bodies in diverse seeds. So far, most of the studies have been on the general characteristics of the proteins, and only one protein (maize KD 16) has been studied using a cDNA clone containing an incomplete coding sequence. Here, we report the sequences of a genomic clone and a cDNA clone of a new maize oleosin (KD 18). There is no intron in the gene. The 5'-flanking region contains potential regulatory elements including RY repeats, CACA consensus, and CATC boxes, which are presumably involved in the specific expression of the proteins in maturing seeds. The deduced amino acid sequence was analyzed for secondary structures. We suggest that KD 18 of 187-amino acid residues contains three major structural domains: a largely hydrophilic domain at the N terminus, a hydrophobic hairpin alpha-helical domain at the center, and an amphipathic alpha-helix domain at the C terminus. These structural domains are very similar to those of oleosin KD 16. However, the KD 18 and KD 16 amino acid sequences as well as nucleotide sequences are highly similar only at the central domain (72 and 71%, respectively). The similarities are highest at the loop region of the alpha-helical hairpin. These results suggest that KD 18 and KD 16 are isoforms, encoded by genes derived from a common ancestor gene. We propose that the hairpin domain acts as an indispensible internal signal for intracellular trafficking of oleosins during protein synthesis as well as an anchor for oleosins on the oil bodies. The other two domains can undergo relatively massive amino acid substitutions without impairing the structure/function of the oleosins or have evolved to generate oleosins having different functions.     

Structural homology among four nodaviruses as deduced by sequencing and X-ray crystallography

The genomic RNA2s of nodaviruses encode a single gene, that of protein alpha, the precursor of virion proteins beta and gamma. We compared the sequences of the RNA2s of the nodaviruses, black beetle virus (BBV), flock house virus, boolarra virus and nodamura virus, with the objective of identifying homologies in the primary and secondary structure of these RNAs and in the structure of their encoded protein. The sequences of the four RNAs were found to be similar, so that homologous regions relating to translation and RNA replication were readily identified. However, the overall, secondary structures in solution, deduced from calculations of optimal Watson-Crick base-pairing configurations, were very different for the four RNAs. We conclude that a particular, overall, secondary structure in solution within host cells is not required for virus viability. The partially refined X-ray structure of BBV (R = 26.4% for the current model) was used as a framework for comparing the structure of the encoded proteins of the four viruses. Mapping of the four protein sequences onto the BBV capsid showed many amino acid differences on the outer surface, indicating that the exteriors of the four virions are substantially different. Mapping in the beta-barrel region showed an intermediate level of differences, indicating that some freedom in choice of amino acid residues is possible there although the basic framework of the capsids is evidently conserved. Mapping onto the interior surface of the BBV capsid showed a high degree of conservation of amino acid residues, particularly near the protein cleavage site, implying that that region is nearly identical in all four virions and has an essential role in virion maturation, and also suggests that all four capsid interior surfaces have similar surfaces exposed to the viral RNA. Apart from a small portion of the C promoter, the amino terminus of the BBV protein (residues 1 to 60) is crystallographically disordered and the amino acid residues in that region are not well conserved. The disordered portion of the BBV protein clearly projects from the capsid inner surface into the interior of the virion, the region occupied by the viral RNA. In all four viruses, residues 1 to 60 had a high proportion of basic residues, suggesting a virus-specific interaction of the amino terminus with the virion RNA.     

Standard conformations of a polypeptide chain in irregular protein regions

A detailed stereochemical analysis of known protein structures has been made which shows that: (1) irregular regions of proteins consist of a limited number of standard structures formed by three, four of more residues; (2) an amino acid residue of a protein can adopt one of the six sterically allowed conformations designated here as alpha, alpha L, beta, gamma, delta, and epsilon. It is shown that there are two allowed conformations of a polypeptide chain at the N-end of an alpha-helix, beta alpha n- and beta gamma alpha n-conformations, where n is a number of residues in the alpha-helix. At the C-end of the alpha-helix there are two conformations as well, alpha n gamma beta- and alpha n gamma alpha L beta-ones. Two beta-strands in a beta-hairpin can be joined, for example, by standard structures with beta beta alpha L beta-, beta alpha gamma alpha L beta-, beta alpha alpha gamma alpha L beta-conformations which are referred to as turns. In the regions where a polypeptide chain passes from one layer to another there are standard structures with beta gamma beta-, beta alpha beta beta-, beta alpha gamma beta-conformations etc., referred to as cross-overs. A structure of any protein irregular region can be represented as a combination of these and other standard turns and cross-overs considered in the paper. The major part of the turns and cross-overs has residues in alpha L- or epsilon-conformations which must be glycine or other residues with small or flexible side chains. Massive hydrophobic residues must not occupy the first beta-positions of the most standard structures. The results obtained can be successfully applied for prediction of the location of the turns and cross-overs in proteins from their amino acid sequences and for interpretation of electron density maps.     

Protein as an edited random copolymer

It is widely believed that the unique primary structure of a given protein is quite necessary for its folding into a certain three-dimensional structure as well as for its functioning and is a result of a directed selection in the course of biological evolution. The present paper provides arguments in favour of an alternative point of view according to which typical three-dimensional structures of globular proteins are characteristic even for random sequences of amino acid residues. Therefore it may be possible that primary structures of proteins are mainly examples of random amino acid sequences slightly edited in the course of biological evolution to impart them some additional (functional) meaning.     

Design, expression and solid-state NMR characterization of silk-like materials constructed from sequences of spider silk, Samia cynthia ricini and Bombyx mori silk fibroins

Silk has a long history of use in medicine as sutures. To address the requirements of a mechanically robust and biocompatible material, basic research to clarify the role of repeated sequences in silk fibroin in its structures and properties seems important as well as the development of a processing technique suitable for the preparation of fibers with excellent mechanical properties. In this study, three silk-like protein analogs were constructed from two regions selected from among the crystalline region of Bombyx mori silk fibroin, (GAGSGA)(2), the crystalline region of Samia cynthia ricini silk fibroin, (Ala)(12), the crystalline region of spider dragline silk fibroin, (Ala)(6), and the Gly-rich region of spider silk fibroin, (GGA)(4). The silk-like protein analog constructed from the crystalline regions of the spider dragline silk and B. mori silk fibroins, (A(6)SCS)(8), that constructed from the crystalline regions of the S. c.ricini and B. mori silk fibroins, (A(12)SGS)(4), that constructed from and the crystalline region of S. c.ricini silk fibroin and the glycine-rich region of spider dragline silk fibroin, (A(12)SGS)(4),were expressed their molecular weights being about 36.0 kDa, 17.0 kDa and 17.5 kDa, respectively in E. coli by means of genetic engineering technologies. (A(12)SCS)(4) and (A(12)SGS)(4 )undergo a structural transition from alpha-helix to beta-sheet on a change in the solvent treatment from trifluoroacetic acid (TFA) to formic acid (FA). However, (A(6)SCS)(8) takes on the beta-sheet structure predominantly on TFA treatment and FA treatment. Structural analysis was performed on model peptides selected from spider dragline and S. c.ricini silks by means of (13)C CP/MAS NMR.     

Silk from crickets: a new twist on spinning

Raspy crickets (Orthoptera: Gryllacrididae) are unique among the orthopterans in producing silk, which is used to build shelters. This work studied the material composition and the fabrication of cricket silk for the first time. We examined silk-webs produced in captivity, which comprised cylindrical fibers and flat films. Spectra obtained from micro-Raman experiments indicated that the silk is composed of protein, primarily in a beta-sheet conformation, and that fibers and films are almost identical in terms of amino acid composition and secondary structure. The primary sequences of four silk proteins were identified through a mass spectrometry/cDNA library approach. The most abundant silk protein was large in size (300 and 220 kDa variants), rich in alanine, glycine and serine, and contained repetitive sequence motifs; these are features which are shared with several known beta-sheet forming silk proteins. Convergent evolution at the molecular level contrasts with development by crickets of a novel mechanism for silk fabrication. After secretion of cricket silk proteins by the labial glands they are fabricated into mature silk by the labium-hypopharynx, which is modified to allow the controlled formation of either fibers or films. Protein folding into beta-sheet structure during silk fabrication is not driven by shear forces, as is reported for other silks.     

The complete primary structure of ribosomal proteins L1, L14, L15, L23, L24 and L29 from Bacillus stearothermophilus

The amino acid sequences of ribosomal proteins L1, L14, L15, L23, L24 and L29 from Bacillus stearothermophilus have been completely determined. This has been achieved by sequence analyses of peptides derived from enzymatic digestions of the proteins with trypsin, chymotrypsin, pepsin, Staphylococcus aureus protease, and Armillaria mellea protease as well as by chemical cleavage with hydroxylamine and cyanogen bromide. Based on the primary structures of the six proteins, their secondary structures were predicted using four different computer prediction programs. A comparison of the amino acid sequences of the studied proteins from B. stearothermophilus with the homologous proteins from Escherichia coli revealed that in four proteins (L1, L15, L24 and L29) between 40-50% of the residue in the sequences are identical, whereas this value is significantly higher (69%) for L14 and lower (28%) for L23. The distribution of those amino acid residues which are identical in the corresponding proteins from the two bacteria is not random along the protein chain: some regions are highly conserved whereas others are not. This finding indicates that the regions which are conserved during evolution are important for the spatial structure and/or function of the protein.     

Synthesis and structural characterization of silk-like materials incorporated with an elastic motif

Genetic engineering strategies were applied to synthesize silk-like materials, [(GVPGV)(2)GG(GAGAGS)(3)AS](n). The primary structure of these materials represents the repetitive crystalline region of Bombyx mori silk fibroins incorporated with an elastic motif selected from animal elastin. The oligonucleotides were designed to encode the desired recombinant proteins and then expressed in the Escherichi coli system. The expression and purification conditions for the production of the recombinant proteins were optimized. (13)C CP/MAS NMR was used for structural characterization in the solid state, where the isotope labeling was performed using a modified M9 medium. The secondary structures of these materials are primarily governed by the designated amino acid sequence, where the B. mori silk fibroin block, (GAGAGS)(3), tends to form the crystalline region, which is interrupted by the flexible (GVPGV)(2) block. The CD data suggested that the structure of these materials was length-dependent in the solution state, i.e., a higher molecule weight leads to a higher ordered structure.     

Protein sequence and structure relationship ARMA spectral analysis: application to membrane proteins.

If it is assumed that the primary sequence determines the three-dimensional folded structure of a protein, then the regular folding patterns, such as alpha-helix, beta-sheet, and other ordered patterns in the three-dimensional structure must correspond to the periodic distribution of the physical properties of the amino acids along the primary sequence. An AutoRegressive Moving Average (ARMA) model method of spectral analysis is applied to analyze protein sequences represented by the hydrophobicity of their amino acids. The results for several membrane proteins of known structures indicate that the periodic distribution of hydrophobicity of the primary sequence is closely related to the regular folding patterns in a protein's three-dimensional structure. We also applied the method to the transmembrane regions of acetylcholine receptor alpha subunit and Shaker potassium channel for which no atomic resolution structure is available. This work is an extension of our analysis of globular proteins by a similar method.