Mass-fractal clustering and power-law decay of cluster size in 1-propanol aqueous solution

Mesoscale structure of 1-propanol aqueous solutions with propanol mole fraction xp ranging from 0.1 to 0.33 has been studied by means of small angle neutron scattering (SANS) and large-scale reverse Monte Carlo (RMC) technique. Analysis of the SANS intensities in terms of a fractal model shows that the fractal dimension df of mesoscale structure of the solution is about 1.8-1.9 for water-rich solution and about 1.5 for propanol-rich solution. Percolation analysis on the RMC results reveals that the water molecules and the propanol molecules cluster, respectively, as a mass fractal, the dimension dM of which is about 2.3-2.5 for both clusters for water-rich solution. Furthermore, the distribution of the cluster size is expressed by a simple power law with an exponent tau of about 1.35-1.5 for the propanol clusters and 1.05-1.2 for the water clusters. These results imply that the current solution is characterized by polydisperse mass fractals. In fact, a theoretical relation for polydisperse system of mass fractals, df = dM(2-tau), holds well in the current solution. The characteristic change in df from 1.8-1.9 to 1.5 described above is attributed to the crossover between the water-rich regime and the propanol-rich regime. Most of the water molecules and the propanol molecules are located on the interface between clusters, and the water molecules form thin layers of about 10 A thick irrespective of 1-propanol content studied.

Synthesis and properties of a new type DNA dendrimer

We have designed a new type of a DNA dendrimer which has rigid branched structure. The branching molecule was prepared from 1,3,5-tribromobenzene. The dendrimer unit, in which three oligonucleotide-chains, two molecules of T15 and one molecule of A15, linked to the branching molecule, was synthesized by an automated DNA synthesizer. The properties of the dendrimer unit and dendrimer formation by inter-molecular association of T15 and A15 chains of the dendrimer unit will be presented.

EBV replicon vector system enhances transgene expression in vivo: applications to cancer gene therapy

BACKGROUND

A major limitation of current cancer gene therapies is low and transient expression of the therapeutic gene. For long-term expression of transgenes in vivo, an Epstein-Barr virus (EBV) replicon vector has been developed. The present study examines the effect of the EBV replicon vector system and its application to a suicide gene therapy for melanoma in mice.

METHODS

An EBV replicon vector system, pEBc, consisting of EBV nuclear antigen-1 (EBNA-1) and the origin of latent viral DNA replication, oriP, was used to express either the luciferase gene or the herpes simplex virus (HSV) thymidine kinase (TK) gene. The expression vector was introduced in vivo into melanoma tumor masses in mice by means of HVJ-cationic liposomes. The time-course of gene expression and the anticancer effect of the EBV replicon vector were investigated in comparison with pcLuc, which lacks the EBV components.

RESULTS

Luciferase expression was sustained in both cultured cells and melanoma masses by pEBc but not by pcLuc. The luciferase expression level in melanoma masses was higher by pEBcLuc than by pcLuc, although Southern blot analysis showed the number of copies of pEBcLuc retained in the melanoma masses to be fewer than that of pcLuc. The effectiveness of EBV replicon vector on suicide gene therapy of melanoma in mice was also demonstrated.

CONCLUSION

The EBV replicon vector appears useful for cancer gene therapy. Analysis of the transgene in tumors suggests that the EBV replicon system may be responsible for efficient transcription but not retention of the transgene.

Structure of the heterodimeric complex between CAD domains of CAD and ICAD

We present here the structure of the complex between the CAD domain of caspase activated deoxyribonuclease (CAD) and the CAD domain of its inhibitor (ICAD), determined by nuclear magnetic resonance spectroscopy. The two domains adopt a very similar fold, which consists of an alpha-helix and a beta-sheet, and are aligned side by side in the complex. Notably, the positive charges on the strand beta2 at one end of the beta-sheet of CAD and negative charges around the opposite end of the beta-sheet of ICAD are paired in the complex. Point mutations of the charged amino acids at this interface, on either CAD or ICAD, prevented formation of the functional CAD-ICAD complex. This implies that the interaction between the CAD domains of CAD and ICAD is an essential step in the correct folding of CAD in the complex.

Structural study of the N-terminal domain of the alpha subunit of Escherichia coli RNA polymerase solubilized with non-denaturing detergents

The amino-terminal domain of the alpha subunit (alphaNTD) of Escherichia coli RNA polymerase consisting of 235 amino acid residues functions in the assembly of the alpha, beta, and beta' subunits into the core-enzyme. It has a tendency to form aggregates by itself at higher concentrations. For NMR structural analysis of alphaNTD, the solution conditions, including the use of non-denaturing detergents, were optimized by monitoring the translational diffusion coefficients using the field gradient NMR technique. Under the optimal conditions with taurodeoxycholate and with the aid of deuteration of the sample, alphaNTD gave triple-resonance spectra of good quality, which allowed the assignment of a large part of the backbone resonances. Analysis of the pattern of NOEs observed between the backbone amide and alpha-protons demonstrated that alphaNTD has three alpha-helices and two beta-sheets. Although the secondary structure elements essentially coincide with those in the crystal structure, the larger of the two beta-sheets has two additional beta-strands. The irregular NOE patterns observed for the three positions in the beta-sheets suggest the presence of beta-bulge structures. The positions of the three helices coincide with the conserved sequence regions that are responsible for the subunit assembly.

Structure of the CAD domain of caspase-activated DNase and interaction with the CAD domain of its inhibitor

Caspase-activated DNase (CAD), which causes a genome fragmentation at the final stage of apoptosis, is a protein of about 40 kDa and exists as a complex form with the inhibitor ICAD in living cells. There is sequence homology of about 80 amino acid residues at the N termini of CAD and ICAD (called the CAD domain). Here, we report the three-dimensional structure of the CAD domain of CAD determined by multi-dimensional NMR spectroscopy and the property of CAD domains investigated by a surface plasmon resonance experiment. The CAD domain of CAD is an independently folded domain composed of one alpha-helix and five beta-strands forming a single sheet. The overall structure is categorized in the ubiquitin superfold. This domain can bind strongly to the isolated CAD domain of ICAD (dissociation constant: 5.48(+/-0.003)x10(-8) M). It suggests the function of the CAD domains in the CAD-ICAD system, that the protein-protein interaction through the CAD domains plays an important role in the inhibition of CAD DNase activity and in the correct folding of CAD. On the basis of structural comparison with other protein complexes containing the ubiquitin superfold, the interaction mode of the CAD domains is proposed.

NMR observation of selected segments in a larger protein: central-segment isotope labeling through intein-mediated ligation

Peptide segments in a protein, which can include an active site of interest or be a series of parts constituting the entire structure, are now selectively observed by nuclear magnetic resonance (NMR) spectroscopy using samples prepared by the intein-mediated ligation method. Two separate inteins were used to ligate NMR-transparent segments to both the ends of an NMR-visible segment, producing a partly visible intact protein molecule. The (15)N-(1)H correlation spectrum of a 370-residue maltose binding protein labeled with (15)N at a continuous segment comprising residues Gly(101)-Ser(238) showed the essential elimination of signal overlapping, the signals being at the same positions as for the uniformly labeled sample. This method will allow structural analysis by NMR of over 50-kDa proteins in combination with contemporary NMR techniques suppressing the signal decays of larger proteins.

Improved segmental isotope labeling of proteins and application to a larger protein

A new isotope labeling technique for peptide segments in a protein sample was recently established using the protein splicing element intein [Yamazaki et al. (1998) J. Am. Chem. Soc., 120, 5591-5592]. This method makes it possible to observe signals of a selected amino (N-) or carboxyl (C-) terminal region along a peptide chain. However, there is a problem with the yield of the segmentally labeled protein. In this paper, we report an increase in the yield of the protein that enables the production of sufficient amounts of segmentally 13C/15N-labeled protein samples. This was achieved by improvement of the expression level of the N-terminal fragment in cells and the efficiency of refolding into the active splicing conformation. The N-terminal fragment was expressed as a fused protein with the cellulose binding domain at its N-terminus, which was expressed as an insoluble peptide in cells and the expression level was increased. Incubation with 2.5 M urea and 50% glycerol increased the efficiency of the refolding greatly, thereby raising the final yields of the ligated proteins. The feasibility of application of the method to a high-molecular-weight protein was demonstrated by the results for a maltose binding protein consisting of 370 amino acids. All four examined joints in the maltose binding protein were successfully ligated to produce segmentally labeled protein samples.

Flexible linker in the RNA polymerase alpha subunit facilitates the independent motion of the C-terminal activator contact domain

The dynamic properties of the C-terminal one-third of the alpha subunit of RNA polymerase were investigated. The intact alpha subunit exhibited almost the same NMR spectral pattern as the isolated C-terminal fragment, indicating that the C-terminal domain retains the same conformation as the isolated fragment, and that its motion is independent of that of the associated N-terminal domain. Analysis of the NMR dynamics data for the intact alpha subunit indicated that at least 13 residues between the N and C-terminal domains show distinctly higher motional flexibility than the structured parts. This flexible linker may endow the C-terminal domain with locational freedom in different kinds of initiation complex. The dynamics data also revealed that the residues in the contact site for DNA and transcription factors exhibited higher mobility than other secondary structural elements.

Induction of resistance with heat-killed compact-type strains of Staphylococcus aureus against challenge with the diffuse variant of the Smith strain of Staphylococcus aureus

Active immunization of mice with high doses of heat-killed and autoclaved vaccine of unencapsulated strains of Staphylococcus aureus, which was grown in brain heart infusion media, protected against challenge with the Smith diffuse strain of Staphylococcus aureus. These organisms were capable of absorbing the protective antibody in rabbit hyperimmune sera prepared with the Smith diffuse strain. Also, mice treated with rabbit hyperimmune sera prepared with these strains (four out of six strains) protected against challenge with the Smith diffuse strain. Protective activities of these rabbit hyperimmune sera were assumed to be essentially identical to the protective antibody induced by the Smith diffuse strain.

Detection of capsular antigen production in unencapsulated strains of Staphylococcus aureus

Of 91 compact-type strains of Staphylococcus aureus in regular serum soft agar (SSA), 82 converted diffuse-type growth in serum soft agar (pH adjusted to 6.0). With the addition of four different rabbit anticapsular sera (anti-type A, B, C, and D sera) in low pH (6.0) SSA, 21 strains of S. aureus showed compact-type colonial morphologies. Eleven, one, and one strains of S. aureus reacted singly with rabbit anticapsular sera types A, B, and C, respectively, and no strain reacted with rabbit anticapsular type D. Eight of the e strains reacted with both rabbit anticapsular sera types A and B. When the ability to absorb the converting activities of the antisera (changes of colonial morphologies of anticapsular sera in SSA) was quantitatively tested, 7- to 27-fold of these organisms were capable of absorbing the activities compared with the Smith diffuse organisms. These results suggest that even unencapsulated S. aureus strains are capable of producing capsular substance, although the capability is quantitatively different from strain to strain.