A Novel Peptide Reagent for Investigating Disulfide-Coupled Folding Intermediates of Mid-Size Proteins.

Investigations of protein folding have largely involved the use of disulfide-containing proteins, since the disulfide-coupled folding of proteins allows folding intermediates to be trapped and their conformations determined. However, studies of the folding mechanisms of mid-size proteins face several problems, one of which is that detecting folding intermediates is difficult. Therefore, to solve this issue, a novel peptide reagent, maleimidohexanoyl-Arg5-Tyr-NH2, was designed and applied to the detection of folding intermediates of model proteins. BPTI was chosen as a model small protein to estimate the ability of the novel reagent to detect folding intermediates. In addition, a precursor protein (prococoonase) of Bombyx mori cocoonase was used as a model mid-size protein. Cocoonase is classified as a serine protease and has a high homology with trypsin. We recently found that the propeptide sequence of prococoonase (proCCN) is important for the folding of cocoonase. However, it was difficult to study the folding pathway of proCCN since the folding intermediates could not be separated on a reversed-phase HPLC (RP-HPLC). Therefore, to separate the folding intermediates by RP-HPLC, the novel labeling reagent was used to accomplish this for proCCN. The results indicated that the peptide reagent allowed the intermediates to be captured, separated on SDS-PAGE, and analyzed by RP-HPLC without the occurrence of undesirable disulfide-exchange reactions during the labeling reactions. The peptide reagent reported herein is a practical tool for investigating the mechanisms of disulfide-coupled folding of mid-size proteins.

Insights into the quality of recombinant proteins produced by two different Bombyx mori expression systems.

The silkworm, Bombyx mori, is an attractive host for recombinant protein production due to its high expression efficiency, quality, and quantity. Two expression systems have been widely used for recombinant protein production in B. mori: baculovirus/silkworm expression system and transgenic silkworm expression system. Both expression systems enable high protein production, but the qualities of the resulting recombinant proteins have not been well evaluated. In this study, we expressed bovine interferon γ (IFN-γ) using the two systems and examined the quality of the resulting proteins in terms of N-glycosylation and protein cleavage. Both expression systems successfully produced IFN-γ as an N-glycoprotein. Although the production in the baculovirus/silkworm expression system was much more efficient than that in the transgenic silkworm expression system, unexpected variants of IFN-γ were also produced in the former system due to the different N-glycosylation and C-terminal truncations. These results indicate that while high protein production could be achieved in the baculovirus/silkworm expression system, unintentional protein modification might occur, and therefore protein expression in the transgenic silkworm expression system is preferable from the point-of-view of N-glycosylation of the recombinant protein and evasion of unexpected attack by a protease in B. mori.

Degradation-Suppressed Cocoonase for Investigating the Propeptide-Mediated Activation Mechanism.

Cocoonase is folded in the form of a zymogen precursor protein (prococoonase) with the assistance of the propeptide region. To investigate the role of the propeptide sequence on the disulfide-coupled folding of cocoonase and prococoonase, the amino acid residues at the degradation sites during the refolding and auto-processing reactions were determined by mass spectrometric analyses and were mutated to suppress the numerous degradation reactions that occur during the reactions. In addition, the Lys8 residue at the propeptide region was also mutated to estimate whether the entire sequence is absolutely required for the activation of cocoonase. Finally, a degradation-suppressed [K8D,K63G,K131G,K133A]-proCCN protein was prepared and was found to refold readily without significant degradation. The results of an enzyme assay using casein or Bz-Arg-OEt suggested that the mutations had no significant effect on either the enzyme activity or the protein conformation. Thus, we, herein, provide the non-degradative cocoonase protein to investigate the propeptide-mediated protein folding of the molecule. We also examined the catalytic residues using the degradation-suppressed cocoonase. The point mutations at the putative catalytic residues in cocoonase resulted in the loss of catalytic activity without any secondary structural changes, indicating that the mutated residues play a role in the catalytic activity of this enzyme.

The propeptide sequence assists the correct folding required for the enzymatic activity of cocoonase.

Cocoonase, a protein that is produced by the silkworm (Bombyx mori), is thought to specifically digest the sericin protein of the cocoon and has a high homology with trypsin. Similar to trypsin, cocoonase is folded as an inactive precursor protein which is activated by releasing the propeptide moiety. However, the mechanism responsible for the activation of its catalytic structure has not yet been determined in detail. Therefore, to investigate the activation and folding mechanism of cocoonase, recombinant cocoonase (CCN) and prococoonase (proCCN) were over-expressed in E. coli cells. Both recombinant proteins (proCCN and CCN) were expressed as inclusion bodies in E. coli cells and their folding was examined under several sets of conditions. After the refolding reactions, both of the recombinant proteins were present as the oxidized soluble forms. The proCCN protein was then auto-processed to release the propeptide region for activation. Interestingly, the CCN (CCN∗) derived from the refolded proCCN showed a much stronger protease activity than the refolded CCN from the reduced CCN in a protease assay using Bz-Arg-OEt as a substrate. In addition, the secondary structure of the refolded CCN protein was similar to that of the CCN∗ protein, as evidenced by CD measurements. These results suggest that the CCN protein becomes trapped in a molten globule-like state without the assistance of the propeptide region during the folding process. We therefore conclude that the propeptide region of CCN kinetically accelerates the folding of CCN to adopt the correct conformation of cocoonase at the final step of the folding pathway.

Molecular Structural Analysis of Spider's Capture Thread and Viscid Droplets Studied by Microscopic FT-IR Spectroscopy.

The molecular structural analysis of capture thread, including its viscid droplets of oriental golden orb-web spider Nephila clavata, has been performed by microscopic FT-IR spectroscopy. The obtained spectra of capture threads with and without viscid droplets indicate that the features in the region of 1400 - 1000 cm-1 will be useful as marker bands for the degree of the dissolving of viscid droplet; further, the bands at 1395 and 1335 cm-1 are attributable to the components of anchoring granules located at the inner side of viscid droplets. By recrystallization and its infrared measurements, the main chemical component of viscid droplets is assignable to glycosylated proline. It has also been demonstrated that the components of the anchoring granule of a viscid droplet are decomposed by UV irradiation, and that the molecular conformation of silk fiber protein of a capture thread is denatured at over 60°C, whereas the viscid droplets on a capture thread retain their structure.

Niemann-Pick type C2 protein mediating chemical communication in the worker ant.

Ants are eusocial insects that are found in most regions of the world. Within its caste, worker ants are responsible for various tasks that are required for colony maintenance. In their chemical communication, α-helical carrier proteins, odorant-binding proteins, and chemosensory proteins, which accumulate in the sensillum lymph in the antennae, play essential roles in transferring hydrophobic semiochemicals to chemosensory receptors. It has been hypothesized that semiochemicals are recognized by α-helical carrier proteins. The number of these proteins, however, is not sufficient to interact with a large number of semiochemicals estimated from chemosensory receptor genes. Here we shed light on this conundrum by identifying a Niemann-Pick type C2 (NPC2) protein from the antenna of the worker Japanese carpenter ant, Camponotus japonicus (CjapNPC2). CjapNPC2 accumulated in the sensillum cavity in the basiconic sensillum. The ligand-binding pocket of CjapNPC2 was composed of a flexible ß-structure that allowed it to bind to a wide range of potential semiochemicals. Some of the semiochemicals elicited electrophysiolgical responses in the worker antenna. In vertebrates, NPC2 acts as an essential carrier protein for cholesterol from late endosomes and lysosomes to other cellular organelles. However, the ants have evolved an NPC2 with a malleable ligand-binding pocket as a moderately selective carrier protein in the sensillum cavity of the basiconic sensillum. CjapNPC2 might be able to deliver various hydrophobic semiochemicals to chemosensory receptor neurons and plays crucial roles in chemical communication required to perform the worker ant tasks.

Overexpression of an antimicrobial peptide derived from C. elegans using an aggregation-prone protein coexpression system.

Antibacterial factor 2 (ABF-2) is a 67-residue antimicrobial peptide derived from the nematode Caenorhabditis elegans. Although it has been reported that ABF-2 exerts in vitro microbicidal activity against a range of bacteria and fungi, the structure of ABF-2 has not yet been solved. To enable structural studies of ABF-2 by NMR spectroscopy, a large amount of isotopically labeled ABF-2 is essential. However, the direct expression of ABF-2 in Escherichia coli is difficult to achieve due to its instability. Therefore, we applied a coexpression method to the production of ABF-2 in order to enhance the inclusion body formation of ABF-2. The inclusion body formation of ABF-2 was vastly enhanced by coexpression of aggregation-prone proteins (partner proteins). By using this method, we succeeded in obtaining milligram quantities of active, correctly folded ABF-2. In addition, 15 N-labeled ABF-2 and a well-dispersed heteronuclear single quantum coherence (HSQC) spectrum were also obtained successfully. Moreover, the effect of the charge of the partner protein on the inclusion body formation of ABF-2 in this method was investigated by using four structurally homologous proteins. We concluded that a partner protein of opposite charge enhanced the formation of an inclusion body of the target peptide efficiently.

Fiber formation of a synthetic spider peptide derived from Nephila clavata.

Dragline silk is a high-performance biopolymer with exceptional mechanical properties. Artificial spider dragline silk is currently prepared by a recombinant technique or chemical synthesis. However, the recombinant process is costly and large-sized synthetic peptides are needed for fiber formation. In addition, the silk fibers that are produced are much weaker than a fiber derived from a native spider. In this study, a small peptide was chemically synthesized and examined for its ability to participate in fiber formation. A short synthetic peptide derived from Nephila clavata was prepared by a solid-phase peptide method, based on a prediction using the hydrophobic parameter of each individual amino acid residue. After purification of the spider peptide, fiber formation was examined under several conditions. Fiber formation proceeded in the acidic pH range, and larger fibers were produced when organic solvents such as trifluoroethanol and acetonitrile were used at an acidic pH. Circular dichroism measurements of the spider peptide indicate that the peptide has a beta-sheet structure and that the formation of a beta-sheet structure is required for the spider peptide to undergo fiber formation.

Structural mechanism of JH delivery in hemolymph by JHBP of silkworm, Bombyx mori.

Juvenile hormone (JH) plays crucial roles in many aspects of the insect life. All the JH actions are initiated by transport of JH in the hemolymph as a complex with JH-binding protein (JHBP) to target tissues. Here, we report structural mechanism of JH delivery by JHBP based upon the crystal and solution structures of apo and JH-bound JHBP. In solution, apo-JHBP exists in equilibrium of multiple conformations with different orientations of the gate helix for the hormone-binding pocket ranging from closed to open forms. JH-binding to the gate-open form results in the fully closed JHBP-JH complex structure where the bound JH is completely buried inside the protein. JH-bound JHBP opens the gate helix to release the bound hormone likely by sensing the less polar environment at the membrane surface of target cells. This is the first report that provides structural insight into JH signaling.

Near-infrared spectroscopic assessment of contamination level of sewage.

We examined the use of near infrared (NIR) spectroscopy as a rapid technique for the evaluation of sewage quality. Influent water samples, primary sedimentation tank water samples, and final effluent water samples were collected from sewage treatment facilities in Nagoya, Japan and their NIR spectra obtained. Partial least squares (PLS) models for total phosphate (TP), total nitrogen (TN), biochemical oxygen demand (BOD), total organic carbon (TOC), and turbidity of sewage water were constructed from the NIR data. The models provided good correlation between measurements obtained conventionally and those predicted from spectroscopy. Spectral variation induced by background interference in samples affected accuracy. Loading plots and score plots derived from PLS regression analysis resolved the background interference and allowed highly accurate predictions. Spectral variation induced by contamination in the sewage was a main predictor of sewage quality. These results show that NIR spectroscopy shows potential for in-line, non-destructive measurement of sewage quality.

Random exchanges of non-conserved amino acid residues among four parental termite cellulases by family shuffling improved thermostability.

There have been two major problems preventing applications of termite cellulases; one was difficulty for their hetelologous overexpression, and another is their low thermostability. We previously achieved adaptation of termite cellulase genes to an overexpression system of Escherichia coli by family shuffling of four orthologous cDNAs (Biosci. Biotechnol. Biochem., 2005; 69: 1711-1720). Using the adapted mutant cDNAs as parental genes combined with native-form cDNAs, we performed further family shuffling and obtained mutant cDNAs, which gave enzymes with improved thermostability. The best-evolved clone (PA68) was improved by 10 degrees C in maximum stability (retaining 90% original activity for 30 min incubation) from the parental enzymes, and kept 54% of its original activity for 150 min at 50 degrees C, whereas the most thermostable enzyme amongst the parents (A18) retained 30% of its original activity. PA68 showed 889 (micromoles of reducing sugars/min/mg of protein) in V(max) and 560 (micromoles of reducing sugars/min/mg of protein) in the specific activity against carboxymethylcellulose, which corresponds to 9.8 and 13.1 times of those of one of the ancestral enzymes rRsEG. In summary, we improved thermostability of the termite cellulase and increased the V(max) value and specific activity by combining only cDNAs encoding enzymes adapted for normal temperatures.

Molecular orientation behavior of silk sericin film as revealed by ATR infrared spectroscopy.

This paper reports the structure-dependent molecular orientation behavior of sericin, an adhesive silk protein secreted by silkworm, Bombyx mori. Although application of sericin as a biomaterial is anticipated because of its unique characteristics, sericin's physicochemical properties remain unclear, mainly because of its vulnerability to heat or alkaline treatment during separation from fibroin threads. This study employed intact sericin obtained from fibroin-deficient mutant silkworm to investigate the relationship between molecular orientation and the secondary structure of sericin. Sericin films were artificially stretched after moistening with aqueous ethanol of various concentrations. The resulting molecular orientation was analyzed using polarized infrared spectroscopy. These analyses indicated that formation of aggregated strands among extended sericin chains induced by ethanol treatment is the key to generating molecular orientation. Strong intermolecular hydrogen bonds are inferred to allow aggregated strands' stretching-force transmission, thereby causing molecular orientation.

Hydrogen bonding structure and stability of alpha-chitin studied by 13C solid-state NMR.

The structure and stability of hydrogen bonds in alpha-chitin were investigated by (13)C solid-state NMR measurements at different temperatures. Splitting of the carbonyl carbon signal for alpha-chitin was interpreted as two types of hydrogen bonding; the peaks at 173.5 and 175.8 ppm were assigned, respectively, to a carbonyl carbon hydrogen bonded exclusively to the NH group and a carbonyl carbon hydrogen-bonded to both NH and C(6)-OH groups. Approximately 60% of carbonyl groups exclusively contributed to the intermolecular hydrogen bonding and ca. 40% of them to the combination of intermolecular and intramolecular hydrogen bonding. Internal rotation around the C(5)-C(6) bond was detected at 55 degrees 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.

Conformation of drawn poly(trimethylene terephthalate) studied by solid-state 13C NMR.

The change in the conformation of the flexible O-CH2-CH2-CH2-O segment of poly(trimethylene terephthalate) (PTT) monofilament caused by drawing was investigated by means of the gamma-gauche effect on the 13C solid-state NMR chemical shift of the internal methylene carbon, combined with the NMR relaxations. The conformation around the O-CH2 and CH2-O bonds for as-spun fiber was trans/trans. On drawing, followed by heat treatment, the conformation changed to gauche/gauche. The ratio of gauche/gauche to trans/trans for the drawn PTT fiber was determined quantitatively.

Structural analysis of an insect lysozyme exhibiting catalytic efficiency at low temperatures.

Bombyx mori lysozyme (BmLZ), from the silkworm, is an insect lysozyme. BmLZ has considerable activity at low temperatures and low activation energies compared with those of hen egg white lysozyme (HEWLZ), according to measurements of the temperature dependencies of relative activity (lytic and glycol chitin) and the estimation of activation energies using the Arrhenius equation. Being so active at low temperatures and low activation energies is characteristic of psychrophilic (cold-adapted) enzymes. The three-dimensional structure of BmLZ has been determined by X-ray crystallography at 2.5 A resolution. The core structure of BmLZ is similar to that of c-type lysozymes. However, BmLZ shows some distinct differences in the two exposed loops and the C-terminal region. A detailed comparison of BmLZ and HEWLZ suggests structural rationalizations for the differences in the catalytic efficiency, stability, and mode of activity between these two lysozymes.

Flufenoxuron, an insect growth regulator, promotes peroral infection by nucleopolyhedrovirus (BmNPV) budded particles in the silkworm, Bombyx mori L.

A novel method was developed to infect perorally the silkworm Bombyx mori L. with budded particles of nucleopolyhedrovirus (BmNPV) using flufenoxuron, an insect growth regulator. NPV vectors are used to obtain proteins that occur naturally in minute amounts. NPV vectors are constructed conventionally by replacing the polyhedrin gene with the foreign gene of interest. These vectors thus do not produce polyhedra. The budded virus particle suspension of these vectors is produced in a cell culture and used as the stock inoculum. Budded NPV particles do not infect their host perorally. The inoculum is injected manually into the individual host using a syringe. It was found that B. mori L. fed on the insect growth regulator flufenoxuron were sensitive to BmNPV budded particles given perorally. Over 90% of B. mori L. ingesting BmNPV budded particles (1.3 x 10(6) TCID(50) units per larva) after consuming an artificial diet for 24 h, containing 0.1% (w/w) flufenoxuron died of the viral infection. The peroral inoculation of BmNPV budded particles by flufenoxuron may thus lead to industrial pharmaceutical production using a baculovirus vector for large numbers of insect hosts.