All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution.

Small viruses that belong, for example, to the Picornaviridae, such as poliovirus and foot-and-mouth disease virus, consist simply of capsid proteins and a single-stranded RNA (ssRNA) genome. The capsids are quite stable in solution to protect the genome from the environment. Here, based on long-time and large-scale 6.5 × 10(6) all-atom molecular dynamics calculations for the Mahoney strain of poliovirus, we show microscopic properties of the viral capsids at a molecular level. First, we found equilibrium rapid exchange of water molecules across the capsid. The exchange rate is so high that all water molecules inside the capsid (about 200,000) can leave the capsid and be replaced by water molecules from the outside in about 25 µs. This explains the capsid's tolerance to high pressures and deactivation by exsiccation. In contrast, the capsid did not exchange ions, at least within the present simulation time of 200 ns. This implies that the capsid can function, in principle, as a semipermeable membrane. We also found that, similar to the xylem of trees, the pressure of the solution inside the capsid without the genome was negative. This is caused by coulombic interaction of the solution inside the capsid with the capsid excess charges. The negative pressure may be compensated by positive osmotic pressure by the solution-soluble ssRNA and the counter ions introduced into it.

Molecular dynamics study of free energy of transfer of alcohol and amine from water phase to the micelle by thermodynamic integration method.

Free energy of transfer of methylamine, octylamine, methanol, and octanol from water phase to sodium dodecyl sulfate (SDS) micelle has been calculated using thermodynamic integration method combined with molecular dynamics calculations. Together with the results for alkanes obtained in our previous study [K. Fujimoto, N. Yoshii, and S. Okazaki, J. Chem. Phys. 133, 074511 (2010)], the effect of polar group on the partition of hydrophilic solutes between water phase and the micelle has been investigated in detail at a molecular level. The calculations showed that the molecules with octyl group are more stable in the SDS micelle than in the water phase due to their hydrophobicity of long alkyl chain. In contrast, methanol and methylamine are stable in the water phase as well as in the micelle because of their high hydrophilicity. The spatial distribution of methylamine, octylamine, methanol, and octanol has also been evaluated as a function of the distance, R, from the center of mass of SDS micelle to the solutes. The distribution shows that the methylamine molecule is adsorbed on the SDS micelle surface, while the methanol molecule is delocalized among the whole system, i.e., in the water phase, on the surface of the micelle, and in the hydrophobic core of the micelle. The octylamine and octanol molecules are solubilized in the SDS micelle with palisade layer structure and are not found in the water phase.

Free energy profiles for penetration of methane and water molecules into spherical sodium dodecyl sulfate micelles obtained using the thermodynamic integration method combined with molecular dynamics calculations.

The free energy profiles, ΔG(r), for penetration of methane and water molecules into sodium dodecyl sulfate (SDS) micelles have been calculated as a function of distance r from the SDS micelle to the methane and water molecules, using the thermodynamic integration method combined with molecular dynamics calculations. The calculations showed that methane is about 6-12 kJ mol(-1) more stable in the SDS micelle than in the water phase, and no ΔG(r) barrier is observed in the vicinity of the sulfate ions of the SDS micelle, implying that methane is easily drawn into the SDS micelle. Based on analysis of the contributions from hydrophobic groups, sulfate ions, sodium ions, and solvent water to ΔG(r), it is clear that methane in the SDS micelle is about 25 kJ mol(-1) more stable than it is in the water phase because of the contribution from the solvent water itself. This can be understood by the hydrophobic effect. In contrast, methane is destabilized by 5-15 kJ mol(-1) by the contribution from the hydrophobic groups of the SDS micelle because of the repulsive interactions between the methane and the crowded hydrophobic groups of the SDS. The large stabilizing effect of the solvent water is higher than the repulsion by the hydrophobic groups, driving methane to become solubilized into the SDS micelle. A good correlation was found between the distribution of cavities and the distribution of methane molecules in the micelle. The methane may move about in the SDS micelle by diffusing between cavities. In contrast, with respect to the water, ΔG(r) has a large positive value of 24-35 kJ mol(-1), so water is not stabilized in the micelle. Analysis showed that the contributions change in complex ways as a function of r and cancel each other out. Reference calculations of the mean forces on a penetrating water molecule into a dodecane droplet clearly showed the same free energy behavior. The common feature is that water is less stable in the hydrophobic core than in the water phase because of the energetic disadvantage of breaking hydrogen bonds formed in the water phase. The difference between the behaviors of the SDS micelles and the dodecane droplets is found just at the interface; this is caused by the strong surface dipole moment formed by sulfate ions and sodium ions in the SDS micelles.

Molecular dynamics study of solubilization of immiscible solutes by a micelle: Free energy of transfer of alkanes from water to the micelle core by thermodynamic integration method.

Free energy of transfer, DeltaG(w-->m), from water phase to a sodium dodecyl sulfate (SDS) micelle core has been calculated for a series of hydrophobic solutes originally immiscible with water by thermodynamic integration method combined with molecular dynamics calculations. The calculated free energy of transfer is in good correspondence to the experiment as well as the theoretical free energy of transfer. The calculated DeltaG(w-->m)'s are all negative, implying that the alkane molecules are more stable in the micelle than in the water phase. It decreases almost linearly as a function of the number of carbon atoms of the alkanes longer than methane with a decrement of 3.3 kJ mol(-1) per one methylene group. The calculated free energy of transfer indicates that, for example, at the micelle concentration of 50 CMC (critical micelle concentration), about only 1 of 6 micelles or 1 of 32 000 micelles does not contain a solute methane or n-octane molecule, respectively.

[Surgical treatment for Pancoast tumors--significance of surgical approach and induction chemoradiotherapy].

We analyzed 46 patients with Pancoast tumor who underwent surgical resection. Anterior approach was employed for 16 patients and hook approach for 30 patients. Twenty-one patients received preoperative treatment; chemotherapy for 1 patient, radiotherapy for 11 patients, and chemoradiotherapy for 9 patients. Complete resection was achieved in 59% (27/46) of patients. The overall 5-year survival rate was 10.9%. Five-year survival was significantly higher in the patients received complete resection than the patients received incomplete resection (18.5 vs 0%, p=0.0016). The complete resection rate has improved in recent cases, and one of the reasons seems to be the adoption of preoperative chemoradiotherapy. But postoperative complications occurred more frequently in patients who received induction therapy than the others. Optimal selection of surgical approach and induction chemoradiotherapy for Pancoast tumors appear to provide improved complete resection rate and long term survival.

Multiple intravascular papillary endothelial hyperplasia affecting skin and bone.

We report a 75-year-old man with multiple recurrent black papules involving his entire body. In the course of 3 years, 20 lesions were resected, which were histologically confirmed as intravascular papillary endothelial hyperplasia (IPEH). A similar vascular lesion was found on his tibia. The occurrence of multiple IPEH affecting skin and bone is extremely rare. The patient's medical history included hepatitis C, hepatoma and associated coagulopathy. We suggest that this patient's multiple lesions were induced by microthrombus formation due to liver dysfunction.

[Evaluation of tracheobronchoplasty for lung cancer].

Tracheobronchoplasty has become one of the standard procedures for lung cancer. In this study, we examined the incidence of complications and survival of tracheobronchoplasty and compared with these of pneumonectomy. In 119 patients underwent tracheobronchoplasty, bronchopleural fistula occurred in 6 (5.0%) and anastomotic stenosis occurred in 5 (4.2%). Five-year survival rate of 119 patients underwent tracheobronchoplasty was 47.3%, and the median survival time was 49.3 months. We compared the sleeve or wedge lobectomy and pneumonectomy, the incidence of complications and 30-days death were similar, but the rate of in-hospital death and the prognosis of the sleeve or wedge lobectomy were better than these of pneumonectomy. So to preserve a respiratory function, we should use a bronchoplastic procedures to avoid pneumonectomy.

Transcripts of the human herpesvirus 8 genome in skin lesions and peripheral blood mononuclear cells of a patient with classic Kaposi's sarcoma.

We report a 75-year-old Japanese woman with classic Kaposi's sarcoma. PCR amplified human herpesvirus 8 (HHV-8) DNA sequences from her skin lesions and peripheral blood mononuclear cells (PBMC), but not her plasma, saliva or urine. An antibody test against HHV-8 lytic antigens was positive. Immunohistochemical staining detected latent antigen. There was no evidence of HHV-8 infection in her husband, sister or daughter. Genes coding for HHV-8-encoded viral interleukin-6, viral macrophage inflammatory protein I, viral G protein-coupled receptor, viral cyclin D and viral Bcl-2 were expressed to the same degree in both her skin lesion and PBMC. Latency-associated T0.7 mRNA and HHV-8-encoded viral tegument protein genes were expressed in her PBMC at levels lower than in the skin lesions. Based on the gene expression profile, we concluded that lytic HHV-8 infection was present in her skin lesions and PBMC.

Improvement of adult Still's disease with granulocyte and monocyte adsorption apheresis.

Adult Still's disease is characterized by a high spiking fever, transient skin rash, and polyarthralgia. Joint pain is one of the major complaints and is often intractable. We assessed the efficacy of granulocyte and monocyte adsorption apheresis (GCAP) therapy for treating arthralgia in adult Still's disease. A 33-year-old woman with adult Still's disease who suffered from recalcitrant arthralgia resistant to systemic corticosteroids was treated with GCAP therapy. She underwent five GCAP treatments at 5-day intervals. Her joint pain responded dramatically to the GCAP therapy, suggesting that GCAP may be useful for treating adult Still's disease. We present a detailed description of the patient and this novel therapy.

Efficacy of topical tacrolimus for treating the malar rash of systemic lupus erythematosus.

The rash of systemic lupus erythematosus (SLE) is usually treated with topical corticosteroids, but prolonged use causes adverse cutaneous side-effects. We assessed the efficacy of topical tacrolimus for treating the skin lesions of SLE. Three patients with SLE affecting their facial skin applied 0.1% tacrolimus ointment on one side of their face twice daily for 3 weeks, in conjunction with a sunscreen cream. After 3 weeks, erythema on the treated side was ameliorated in all three patients compared with the untreated side. Although the study is preliminary, the results demonstrate that topical tacrolimus may be useful for treating the malar rash of SLE.

A new case of alpha-N-acetylgalactosaminidase deficiency with angiokeratoma corporis diffusum, with Ménière's syndrome and without mental retardation.

alpha-N-acetylgalactosaminidase (alpha-NAGA) deficiency is a rare hereditary lysosomal storage disease, and only three alpha-NAGA-deficient patients with angiokeratoma corporis diffusum (Kanzaki) have been described. We report a further case in a 47-year-old Japanese woman, the product of a consanguineous marriage. The remarkable findings in this patient were her normal intelligence, Ménière's syndrome, disturbance of peripheral sensory nerves, hearing loss and cardiac hypertrophy. alpha-NAGA enzyme activity in her plasma was 0.77% of the normal value. Other enzyme activities, such as alpha-galactosidase, beta-galactosidase, alpha-L-fucosidase, beta-mannosidase and aspartylglucosaminidase, were within normal limits. A large quantity of amino acid O-glycans was detected in her urine. Gene analysis revealed a novel point mutation (G-->A transition) at nucleotide 11018 (986 in the cDNA) resulting in an Arg-329-Gln substitution. Kanzaki disease has the same enzyme defect as Schindler disease, but the manifestations are quite different.

A case of symptomatic heterozygous female Fabry's disease without detectable mutation in the alpha-galactosidase gene.

We report a case of symptomatic heterozygous female Fabry's disease with low alpha-galactosidase blood activity. We could not find any mutations in the coding regions of either the signal peptide or the enzyme subunit in our case.

Cyclopropenone-containing cysteine proteinase inhibitors. Synthesis and enzyme inhibitory activities.

By focusing on the amphiphilic properties of cyclopropenone (e.g. a good electrophile and a precursor for a stable 2pi-aromatic hydroxycyclopropenium cation), a new class of cysteine proteinase inhibitors containing a cyclopropenone moiety was designed. For the purpose of the present research, we needed to devise a new method to introduce a peptide-related moiety as a substituent on the cyclopropenone residue. We investigated the reaction of metalated cyclopropenone acetal derivatives (2, R2 = metal) with N-protected alpha-aminoaldehydes 4 to obtain the adduct 5, and succeeded in the preparation of highly potentiated cysteine proteinase inhibitors 8 after several steps transformations. They showed strong inhibitory activities only to cysteine proteinases such as calpain, papain, cathepsin B, and cathepsin L and not to serine (e.g. thrombin and cathepsin G) and aspartic proteinases (e.g. cathepsin D). Kinetic studies indicated that they are competitive inhibitors, and by the examinations of their inhibitory mechanism it became clear that they are reversible inhibitors.

The discrepancy in hardness between clinical and histopathological findings in localized scleroderma treated with PUVA.

Topical PUVA therapy was applied to a patient with localized scleroderma. Her localized scleroderma responded very well to the topical PUVA therapy, i.e., her sclerotic skin softened to normal skin texture. However, despite this dramatic clinical change the histopathological findings did not change at all and were still "hard".

Demonstration of focal brain ischemia induced by hyperventilation using Tc-99m HMPAO SPECT.

A case with vasospasm of the right anterior cerebral artery induced by hyperventilation is presented. Consecutive Tc-99m HMPAO brain SPECT studies at rest and during hyperventilation greatly contributed to the quantitative evaluation of focal perfusion decrease in conjunction with contrast angiography. This technique seems to be useful for the detection of alterations in regional brain perfusion during short duration intervention.

Inhibitory effect of MY-1250 on histamine release from rat peritoneal mast cells and guinea pig lung fragments: the elucidation of the mechanism.

When the effect of MY-1250 (5,6-dihydro-7,8-dimethyl-4,5-dioxo-4 H-pyrano [3,2-c] quinoline-2-carboxylic acid) on histamine release from rat peritoneal mast cells induced by compound 48/80 was studied, MY-1250 caused a significant inhibition of histamine release at concentrations higher than 3 microM. Furthermore, the compound inhibited not only 45C a uptake into the mast cells but also Ca2+ release from the intracellular Ca store at a concentration of 10 microM in both cases. By contrast, MY-1250 did not affect either histamine release from permeabilized mast cells induced by TPA, IP3 and GTP gamma S or Ca2+ release from the endoplasmic reticulum induced by IP3. In the chopped lung preparations, MY-1250 at doses of 10 and 100 microM caused a significant inhibition in histamine release from the pieces of actively sensitized guinea pigs exposed to antigen and simultaneously prevented a decrease in intracellular cAMP contents taking place in association with antigen-antibody reaction. No significant changes were effected by MY-1250 in alpha-chymotrypsin activity and phospholipase A2 activity. Also, no antagonistic effects on LTD4 and PAF were observed.

Role of endoplasmic reticulum, an intracellular Ca2+ store, in histamine release from rat peritoneal mast cell.

By means of the Ca-antimonate precipitation technique, it was revealed that Ca2+ accumulates in the endoplasmic reticulum (ER) of rat peritoneal mast cells. The ER of rat mast cells was isolated using Percoll density gradient centrifugation, and its characteristics were studied. Although the uptake of 45Ca into the ER was enhanced by adenosine 5'-triphosphate (ATP) at concentrations lower than 2 mM, at higher concentrations ATP induced 45Ca release from the ER, suggesting that bidirectional translocation of Ca2+ takes place in the ER membrane. When apyrase was added to the reaction mixture to decompose all ATP molecules, the amount of 45Ca in the ER was decreased, indicating that ATP is necessary to retain Ca2+ in the ER. Not only inositol 1,4,5-trisphosphate (IP3) but also guanosine 5'-triphosphate (GTP) was effective in releasing Ca2+ from the ER at concentrations higher than 2 microM, while guanosine 5'-[gamma-thio]-triphosphate (GTP-gamma S), a non-hydrolysable analogue of GTP, was not effective. This may indicate that a hydrolysis of GTP is necessary for Ca2+ release from the ER. Intracellular Ca2+ blockers such as 8-(N,N-diethylamino)octyl-3,4,5-trimethoxybenzoate (TMB-8) and dantrolene sodium were effective in inhibiting Ca2+ release from ER induced by IP3. The Ca2+ release due to IP3 was also inhibited by flunarizine, a Ca2+ channel blocker, and by oxatomide, an antiallergic drug. Since these two compounds are diphenylpiperazine derivatives, it is suggested that a diphenylpiperazine moiety may be effective in inhibiting Ca2+ release from the ER.

Ca uptake and Ca releasing properties of the endoplasmic reticulum in rat peritoneal mast cells.

In order to study the characteristics of the intracellular Ca store of mast cells, organelles of rat peritoneal mast cells were fractionated. The binding of 45Ca was at its peak in the fractions where the highest activity of glucose-6-phosphatase, the marker enzyme for the endoplasmic reticulum (ER), was measured. The ER-rich fraction exhibited an ATP-dependent uptake of 45Ca and this uptake was inhibited by pretreatment with ATPase inhibitors such as LaCl3 or Na3VO4. When inositol 1,4,5-trisphosphate (IP3) was added to a medium containing the 45Ca-loaded ER fraction, it caused a dose-dependent release of 45Ca at concentrations higher than 0.5 microM, while inositol 1-monophosphate and inositol 1,4-bisphosphate were not effective even at higher concentrations. The results of a binding assay using 3H-labeled IP3 indicated that there exist two kinds of IP3 binding site in the ER: one is of high affinity but low capacity while the other is of low affinity and high capacity. IP3-induced 45Ca release was dose-dependently inhibited by pretreatment with c-AMP. The present study supports the assumption that the intracellular Ca store associated with histamine release from the mast cell is the ER.