Factors that regulate the conformation of m-benziporphodimethene complexes: agostic metal-arene interaction, hydrogen bonding, and η2,π coordination.

Group 12 and silver(I) tetramethyl-m-benziporphodimethene (TMBPDM) complexes with phenyl, methylbenzoate, or nitrophenyl groups as meso substituents were synthesized and fully characterized. The dimeric silver(I) complex displays an unusual η(2),π coordination from the ß-pyrrolic C=C bond to the silver ion. All of the complexes displayed a close contact between the metal ion and the inner C(22)-H(22) on the m-phenylene ring. The downfield chemical shifts of H(22) and large coupling constants between Cd(II) and H(22) strongly support the presence of an agostic interaction between the metal ion and inner C(22)-H(22). Crystal structures revealed that the syn form is the predominant conformation for TMBPDM complexes. This is distinctively different from the exclusive anti conformation observed in m-benziporphyrin and tetraphenyl-m-benziporphodimethene (TPBPDM) complexes. Evidently, intramolecular hydrogen-bonding interactions between axial chloride and methyl groups stabilize syn conformations. Unlike the merely syn conformation observed in the solid-state structures of TMBPDM complexes that contain an axial chloride, in solution these complexes display highly solvent- and temperature-dependent syn/anti ratio changes. The observation of dynamic (1)H NMR spectroscopic scrambling between syn and anti conformations from the titration of chloride ion into the solution of the TMBPDM complex suggests that axial ligand exchange is a likely pathway for the conversion between syn and anti forms. Theoretical calculations revealed that intermolecular hydrogen-bonding interactions between the axial chloride and CHCl(3) stabilizes the anti conformation, which explains the increased ratio for the anti form when dichloromethane or chloroform was used as the solvent.

Toxicological and immunomodulatory assessments of botryosphaeran (ß-glucan) produced by Botryosphaeria rhodina RCYU 30101.

Toxicological and immunomodulatory activities of botryosphaeran (BR), a newly emerged ß-glucan that comprises a ß-(1 → 3) backbone and ß-(1 → 6) branched glucose residues were assessed. BR was 1.82 × 10(6) Da (M.W.) estimated by reversely-linear equation constructed by regression of logarithms of standard polysaccharides and their retention times of gel permeation chromatography. Sprague-Dawley rats were daily gavage-administered with BR at doses of 0, 1.25, 12.5, and 125 mg/kg body weight (BW) for 28 d. Serum hematological and biochemical analysis of all treatment were all within normal ranges. Mitogen-stimulated lymphoblastogenesis of spleno-lymphocytes was enhanced by BR at doses of 1.25 and 12.5 mg/kg BW. Through in vitro comparative assessments, RAW 264.7 macrophage (RAW) cells were treated with BR and two commercial ß-glucans, zymosan (ZY) and barley ß-glucan (GB), to characterize their relative immunomodulatory properties. All three ß-glucans stimulated phagocytosis on fluorescence-labeled Escherichia coli. At dose levels from 5 to 200 µg/mL for 24h, nitric oxide produced by BR- and ZY-treated cells were higher than those produced by GB-treated and control groups. BR, ZY but GB also stimulated RAW cells in producing TNF-α. The results demonstrate that BR is toxicologically accepted and features as a potent immunomodulator.

Crystallization and preliminary X-ray diffraction analysis of the N-terminal domain of human coronavirus OC43 nucleocapsid protein.

The N-terminal domain of nucleocapsid protein from human coronavirus OC43 (HCoV-OC43 N-NTD) mostly contains positively charged residues and has been identified as being responsible for RNA binding during ribonucleocapsid formation in the coronavirus. In this study, the crystallization and preliminary crystallographic analysis of HCoV-OC43 N-NTD (amino acids 58-195) with a molecular weight of 20 kDa are reported. HCoV-OC43 N-NTD was crystallized at 293 K using PEG 1500 as a precipitant and a 99.9% complete native data set was collected to 1.7 A resolution at 100 K with an overall R(merge) of 5.0%. The crystals belonged to the hexagonal space group P6(5), with unit-cell parameters a = 81.57, c = 42.87 A. Solvent-content calculations suggest that there is likely to be one subunit of N-NTD in the asymmetric unit.

Novel DNA-peptide interaction networks.

Allostery in the binding of peptides to DNA has been studied by quantitative DNase I footprinting using four newly designed peptides containing the XP(Hyp)RK motif and N-methylpyrrole (Py) moieties. Apparent binding constants in the micromolar range as well as Hill coefficients were determined for each peptide. The results, together with previous studies on five other peptides support the proposal that interaction network cooperativity is highly preferred in DNA-peptide interactions that involve multiple recognition sites. It is envisaged that interstrand bidentate interactions participate in the relay of conformational changes between recognition sites on the complementary strands. Models for interpreting DNA allostery based upon interaction networks are outlined. Circular dichroism experiments involving the titration of peptides against a short oligonucleotide duplex indicate that some of these peptides bind in a dimeric manner to DNA via the minor groove, inducing characteristic conformational changes. These insights should prompt the design of new DNA-binding peptides for investigating allosteric interactions between peptides and DNA, as well as novel interaction networks, and ultimately may shed light upon the fundamental chemical rules that govern allostery in more complex biological process such as DNA-protein interaction networks.

Detection of cyanidin in different-colored peanut testae and identification of peanut cyanidin 3-sambubioside.

Peanut testae are potent sources of polyphenols. When the water extracts and acid hydrolysates of five different-colored testae were analyzed by HPLC, chromatograms monitored at 280 nm varied remarkably, whereas two major peaks in the chromatograms monitored at 530 nm were detected only in kernels having completely or partially black color. After acid hydrolysis of the extracts, cyanidin was detected in each of the hydrolysates. By respectively subjecting the black testae of raw and roasted (175 degrees C for 20 min) kernels of a black colored cultivar to water extraction and HPLC analysis, a prominent peak was detected in both extracts. The structure of the substance under those peaks was identified by mass and NMR spectrometry as cyanidin 3-sambubioside in peanut testae for the first time. Subjection of cyanidin 3-sambubioside to antioxidation and anti-inflammation assessments revealed that it was a potent antioxidant and inhibitor of nitric oxide production.

Characterization of the interactions of lysozyme with DNA by surface plasmon resonance and circular dichroism spectroscopy.

Association with nucleic acid has been recognized as a unique role of lysozyme and may explain why lysozyme was called a killer protein against HIV infection. In the present study, we characterized the interactions of lysozyme and its derived peptides with a biotin-labeled pUC19 plasmid DNA. Real-time detection of the macromolecular interaction was performed using the SPR (surface plasmon resonance) spectroscopy. The SPR sensorgrams were analyzed and the association and dissociation rate constants as well as the dissociation equilibrium constant KD were, thus, estimated. The results reveal that other than the electrostatic interactions between the basic protein and the nucleotide sequences carrying negative charges, the specific DNA-binding motifs at the N- and C-termini of lysozyme were also involved in the interactions. The nonapeptide RAWVAWRNR (aa 107-115 of lysozyme) reported previously to block HIV-1 viral entrance and replication was also able to bind DNA with its KD value comparable to that of histones. The possibilities of ligand-binding-induced conformational changes were investigated using the circular dichroism spectroscopy. The CD spectra (200-320 nm) reveal that the conformational changes indeed occur as the spectra of lysozyme-DNA interactions are much less at the major trough region than the sum of individual spectra. The interaction of lysozyme with DNA molecules may interfere with DNA replication, modulate gene expression, and block bacterial and viral infections. These all suggest that human lysozyme may represent part of the innate immune system with a very broad protective spectrum.

Direct observation of single molecule conformational change of tight-turn paperclip DNA triplex in solution.

DNA triplex modulates gene expression by forming stable conformation in physiological condition. However, it is not feasible to observe this unique molecular structure of large molecule with 54 oligodeoxynucleotides directly by conventional nuclear magnetic approach. In this study, we observed directly single molecular images of paperclip DNA triplexes formation in a buffer solution of pH 6.0 by atomic force microscopy (AFM). Meanwhile, a diffuse "tail" of unwound DNA was observed in pH 8.0 solution. This designable approach in visualizing the overall structures and shapes of oligo-DNAs at the single molecular level, by AFM, is applicable to other biopolymers as well.

Anticancer activity of botanical alkyl hydroquinones attributed to topoisomerase II poisoning.

Cytotoxic alkyl hydroquinone compounds have been isolated from many plants. We previously isolated 3 structurally similar cytotoxic alkyl hydroquinone compounds from the sap of the lacquer tree Rhus succedanea L. belonging to the sumac family, which have a long history of medicinal use in Asia. Each has an unsaturated alkyl chain attached to the 2-position of a hydroquinone ring. One of these isolates, 10'(Z),13'(E),15'(E)-heptadecatrienylhydroquinone [HQ17(3)], being the most cytotoxic, was chosen for studying the anticancer mechanism of these compounds. We found that HQ17(3) was a topoisomerase (Topo) II poison. It irreversibly inhibited Topo IIalpha activity through the accumulation of Topo II-DNA cleavable complexes. A cell-based assay showed that HQ17(3) inhibited the growth of leukemia HL-60 cells with an EC50 of 0.9 microM, inhibited the topoisomerase-II-deficient cells HL-60/MX2 with an EC50 of 9.6 microM, and exerted no effect on peripheral blood mononuclear cells at concentrations up to 50 microM. These results suggest that Topo II is the cellular drug target. In HL-60 cells, HQ17(3) promptly inhibited DNA synthesis, induced chromosomal breakage, and led to cell death with an EC50 about one-tenth that of hydroquinone. Pretreatment of the cells with N-acetylcysteine could not attenuate the cytotoxicity and DNA damage induced by HQ17(3). However, N-acetylcysteine did significantly reduce the cytotoxicity of hydroquinone. In F344 rats, intraperitoneal injection of HQ17(3) for 28 days induced no clinical signs of toxicity. These results indicated that HQ17(3) is a potential anticancer agent, and its structural features could be a model for anticancer drug design.

Self-assembled molecular magnets on patterned silicon substrates: bridging bio-molecules with nanoelectronics.

The paper reports the methods of preparing molecular magnets and patterning of the molecules on a semiconductor surface. A highly magnetically aligned metallothionein containing Mn and Cd (Mn,Cd-MT-2) is first synthesized, and the molecules are then placed into nanopores prepared on silicon (001) surfaces using electron beam lithography and reactive ion-etching techniques. We have observed the self-assemble growth of the MT molecules on the patterned Si surface such that the MT molecules have grown into rod or ring type three-dimensional nanostructures, depending on the patterned nanostructures on the surface. We also provide scanning electron microscopy, atomic force microscopy, and magnetic force microscope studies of the molecular nanostructures. This engineered molecule shows molecular magnetization and is biocompatible with conventional semiconductors. These features make Mn,Cd-MT-2 a good candidate for biological applications and sensing sources of new nanodevices. Using molecular self-assembly and topographical patterning of the semiconductor substrate, we can close the gap between bio-molecules and nanoelectronics built into the semiconductor chip.

The paperclip triplex: understanding the role of apex residues in tight turns.

In this study, we investigate the role of the apex nucleotides of the two turns found in the intramolecular "paperclip" type triplex DNA formed by 5'-TCTCTCCTCTCTAGAGAG-3'. Our previously published structure calculations show that residues C7-A18 form a hairpin turn via Watson-Crick basepairing and residues T1-C6 bind into the major groove of the hairpin via Hoogsteen basepairing resulting in a broad turn of the T1-T12 5'-pyrimidine section of the DNA. We find that only the C6C7/G18 apex triad (and not the T12A13/T1 apex triad) is required for intramolecular triplex formation, is base independent, and occurs whether the purine section is located at the 5' or 3' end of the sequence. NMR spectroscopy and molecular dynamics simulations are used to investigate a bimolecular complex (which retains only the C6C7/G18 apex) in which a pyrimidine strand 5'- TCTCTCCTCTCT-3' makes a broad fold stabilized by the purine strand 5'-AGAGAG-3' via Watson Crick pairing to the T8-T12 and Hoogsteen basepairing to T1-T5 of the pyrimidine strand. Interestingly, this investigation shows that this 5'-AGAGAG-3' oligo acts as a new kind of triplex forming oligonucleotide, and adds to the growing number of triplex forming oligonucleotides that may prove useful as therapeutic agents.

Ganoderiol F, a ganoderma triterpene, induces senescence in hepatoma HepG2 cells.

Ganoderiol F (GolF), a tetracyclic triterpene, was isolated from Ganoderma amboinense and found to induce senescence of cancer cell lines. GolF induced growth arrest of cancer cell lines HepG2, Huh7 and K562, but exerted much less effect in hepatoma Hep3B cells and normal lung fibroblast MRC5 cells, and no effect on peripheral blood mononuclear cells. GolF treatment of the cancer cells, with the exception of Hep3B, resulted in prompt inhibition of DNA synthesis and arrest of cell progression cycle in G1 phase. Short-term exposure of HepG2 cells to GolF temporarily arrested progression of the cell cycle; cell growth was recovered if the drug was withdrawn from the medium after a 24-h exposure. After 18 days of continuous treatment of HepG2 cells with 30 muM GolF, over 50% of cells were found to be enlarged and flattened, and were beta-galactosidase positive phenotypes of senescent cells. GolF was found to inhibit activity of topoisomerases in vitro, which may contribute to the inhibition of cellular DNA synthesis. Activation of the mitogen-activated protein kinase EKR and up-regulation of cyclin-dependent kinase inhibitor p16 were found in early stages of GolF treatment and were presumed to cause cell-cycle arrest and trigger premature senescence of HepG2 cells. The growth-arrest and senescence induction capability on cancer cells suggest anticancer potential of GolF.

Mn,Cd-metallothionein-2: a room temperature magnetic protein.

Naturally occurring metallothionein (MT) is a metal binding protein, which binds to seven Zn2+ through 20 conserved cysteines and forms two metal binding clusters with a Zinc-Blende structure. We demonstrate that the MT, when substituting the Zn2+ ions by Mn2+ and Cd2+, exhibits magnetic hysteresis loop observable by SQUID from 10 to 330 K. The magnetic moment may have originated from the bridging effect of the sulfur atoms between the metal ions that leads to the alignment of the electron spins of the Mn2+ ions inside the clusters. The protein backbone may restrain the net spin moment of Mn2+ ions from thermal fluctuation. The modified magnetic-metallothionein is a novel approach to creating molecular magnets with operating temperatures up to 330 K.

Ganoderic acid X, a lanostanoid triterpene, inhibits topoisomerases and induces apoptosis of cancer cells.

Lanostanoid triterpenes isolated from Ganoderma amboinense were found to inhibit the growth of numerous cancer cell lines, and some of them inhibited the activities of topoisomerases I and IIalpha in vitro. Among the bioactive isolates, one of the most potent triterpene was identified to be 3 alpha-hydroxy-15 alpha-acetoxy-lanosta-7,9(11),24-trien-26-oic acid, ganoderic acid X (GAX). Treatment of human hepatoma HuH-7 cells with GAX caused immediate inhibition of DNA synthesis as well as activation of ERK and JNK mitogen-activated protein kinases, and cell apoptosis. Molecular events of apoptosis including degradation of chromosomal DNA, decrease in the level of Bcl-xL, the disruption of mitochondrial membrane, cytosolic release of cytochrome c and activation of caspase-3 were elucidated. The ability of GAX to inhibit topoisomerases and to sensitize the cancer cells toward apoptosis fulfills the feature of a potential anticancer drug.

Protein folding stabilizing time measurement: a direct folding process and three-dimensional random walk simulation.

Protein particles undergo Brownian motion and collisions in solution. The diffusive collisions may lead to aggregation. For proteins to fold successfully the process has to occur quickly and before significant collision takes place. The speed of protein folding was deduced by studying the correlation time of a lysozyme refolding process from autocorrelation function analysis of the mean collision time and aggregation/soluble ratio of protein. It is a measure of time before which an aggregate can be formed and also is the time measure for a protein to fold into a stable state. We report on the protein folding stabilizing time of a lysozyme system to be 25.5-27.5 micros (<+/-4%) between 295 and 279K via direct folding experimental studies, supported by a three-dimensional random walk simulation of diffusion-limited aggregation model. Aggregation is suppressed when the protein is folded to a stable form. Spontaneous folding and diffusion-limited aggregation are antagonistic in nature. Meanwhile, the resultant aggresome, suggested by Raman and mass spectroscopy, may be formed by cross-linkages of disulfide bonds and hydrophobic interactions.

Refolding of lysozyme by quasistatic and direct dilution reaction paths: a first-order-like state transition.

A first-order-like state transition model is considered to be a global reaction mechanism to directly folded proteins from an unfolded state to its native form. In order to verify the general applicability of this mechanism, we used lysozyme as a model protein. It was fully unfolded by 4.5 M urea, 0.1 M dithiothreitol (DTT) in pH 3 and refolded to its native form by way of an overcritical reaction path (a quasistatic process) or directly crossing transition boundary path (a directly dilution process). In addition to the two states coexisting in the direct folding path, lysozyme might be trapped in a glassy state. However, it can escape from the glassy state by concentration twice. This indicates the existence of a state transition line or boundary in the direct folding reaction. However, lysozyme can continuously fold from unfolded to native by an overcritical reaction path. During the overcritical path, four stable folding intermediates and native lysozyme were obtained. The secondary structures, particle size distributions, thermal stabilities, and oxidation state of disulfide bonds of folding intermediates were analyzed by circular dichroism spectra, dynamic light scattering, differential scanning calorimetry, and Raman spectra, respectively. According to the data, the intermediates of both the overcritical reaction and the direct crossing transition boundary paths can be described by a common concept pertaining to a model that undergoes collapse, sequential, and first-order-like state transition. This indicated that protein folding by way of different reaction paths might follow a similar folding mechanism-i.e., a mechanism of overcritical folding of intermediates. A protein folding reaction diagram is postulated and discussed. In spite of a global interaction mechanism the alpha -helix is formed prior to the beta -sheet, which may indicate that protein folding is initiated by local interactions.

A first-order-like state transition for recombinant protein folding.

Normally, proteins will aggregate and precipitate by direct folding processes. In this study, we report that quasi-static processes can restore both the structure and bio-function of two kinds of fish recombinant growth hormones (Plecoglossus altivelis and Epinephelus awoara). The conformational changes and the particle-size-distribution (PSD) of each refolding intermediate can be monitored by circular dichroism spectroscopy (CD) and dynamic light scattering (DLS), respectively. Conformation analysis of the CD spectra of the refolding intermediates indicated that the secondary structures were restored in the initial refolding intermediate. However, the tertiary interactions of the proteins were restored during the last two refolding stages, as elucidated by thermal stability tests. This is consistent with a sequential model. DLS analysis suggested that the average hydrodynamic radii of the refolding intermediates shrank to their native-like sizes after the first refolding stage. This is consistent with a collapse model. After comparison with the data on the direct folding process, it is concluded that the denaturant-containing protein folding reaction is a first-order-like state transition process.

Production and characterization of bioactive recombinant resistin in Escherichia coli.

Type 2 diabetes, characterized by peripheral target tissue resistance to insulin, is epidemic in industrialized countries and is strongly associated with obesity. The protein hormone, resistin, secreted specifically by the adipose tissues, is found to antagonize insulin action upon glucose uptake and may serve as an important role between human obesity and insulin resistance. Here, we report the production of bioactive recombinant resistin in Escherichia coli. cDNA of resistin was obtained by RT-PCR from mRNA of mouse differentiated NIH/3T3-L1 cells. The cDNA of mature resistin was inserted in the pQE-31 vector and the recombinant plasmid was transferred into E. coli JM109. After IPTG induction, the rec. resistin found in the inclusion body was dissolved in 6 M guanidine-HCl in the presence of 10 mM beta-mercaptoethanol. The His-tag containing protein was purified by Ni-NTA column to 95% homogeneity. After a quasi-static-like refolding process, the secondary structure of the rec. resistin was elucidated by circular dichroism which indicated that the protein was composed of 34.3% alpha-helix, 8.9% beta-sheet, 23.4% beta-turn, and 31.2% unordered structure. No disulfide-linked homodimers were formed in SDS-PAGE analysis under non-reducing conditions. The rec. resistin showed a dose-dependent antagonizing action against insulin in [3H]-2-deoxy-glucose transport in a broad range from 1 ng ml(-1) to 10 microg ml(-1) of resistin. A suppression of 85% of transport was achieved at the dosage of 10 microg ml(-1). This result may indicate that the rec. resistin does not need to form homodimers to establish its bioactivity. The rec. resistin will be useful for exploring the biological functions of this newly discovered hormone.

Reversible folding of cysteine-rich metallothionein by an overcritical reaction path.

A first-order-like state transition is considered to be involved in the restoration of the activities of a few proteins by correctly folding the protein [Phys. Rev. E 66 (2002) 021903]. In order to understand the general applicability of this mechanism, we studied a metallothionein (MT) protein with an unconventional structure, i.e., without any alpha-helix or beta-sheet. MT is a 61 amino-acid peptide. There are 6-7 Zn(2+) ions, which bind avidly to 20 conserved cysteines (Cys) of MT. These properties indicate that the structure of MT is quite different from those of the other proteins. Similar to our previous findings, the denatured MT can be folded without any aggregation via a designated stepwise quasi-static process (an over-critical reaction path). The particle size of folded MT intermediates, determined by dynamic light scattering, shrank right after the first folding stage. It is consistent with a collapse-model. In addition, results from both atomic absorption and circular dichroism (CD) indicate that the stable intermediates may fold to the native conformation but with only partial Zn(2+) binding, which in turn implies that those folding intermediates are in a molten globular state. These reversible unfolding and folding processes indicate that Cys-rich protein, MT, may also be folded by way of a first-order-like state transition mechanism. We suspect that this process may likely be involved in the reaction of the metal substitution process in metal containing enzymes.

Triterpene-enriched extracts from Ganoderma lucidum inhibit growth of hepatoma cells via suppressing protein kinase C, activating mitogen-activated protein kinases and G2-phase cell cycle arrest.

The medicinal mushroom Ganoderma lucidum (G. lucidum) has been used in the Orient for the prevention and treatment of various diseases including cancer. Except for the immune enhancing properties of its polysaccharide constituent, very little is known about the anticancer activity of another major constituent, triterpenes. In this report, we studied the anticancer mechanism of triterpene-enriched extracts from G. lucidum. The triterpene-enriched fraction, WEES-G6, was prepared from mycelia of G. lucidum by sequential hot water extraction, removal of ethanol-insoluble polysaccharides and then gel-filtration chromatography. We found that WEES-G6 inhibited growth of human hepatoma Huh-7 cells, but not Chang liver cells, a normal human liver cell line. Treatment with WEES-G6 caused a rapid decrease in the activity of cell growth regulative protein, PKC, and the activation of JNK and p38 MAP kinases. The changes in these molecules resulted in a prolonged G2 cell cycle phase and strong growth inhibition. None of these effects were seen in the normal liver cells. Our findings suggest that the triterpenes contained in G. lucidum are potential anticancer agents.

Protein folding by a quasi-static-like process: a first-order state transition.

In this paper we report that quasi-static-like processes, in which stable intermediates were introduced carefully and deliberately, may be used to reversibly unfold and refold purified native porcine growth hormone. Through circular dichroism (CD) and dynamic light scattering (DLS), we were able to study the secondary structure conformational changes, tertiary structure thermal stabilities, and the particle size distributions of both the intermediates and the final folded product. The CD data showed that the secondary structure was restored in the initial folding stage, whereas the tertiary structure within the protein was restored one step before the last folding stage, as elucidated by thermal stability experiments. DLS analysis suggested that the average hydrodynamic radii of the folding intermediates shrunk to nativelike size immediately after the first folding stage. Our data suggested that the denaturant-containing protein folding reaction is a first-order-like state transition process. This quasi-static-like process may be useful in the prevention of aggregate formation in protein purification and thus can be used in protein engineering to improve the overall yield from harvesting proteins.