Folding/unfolding kinetics of lattice proteins studied using a simple statistical mechanical model for protein folding, I: Dependence on native structures and amino acid sequences

The folding/unfolding kinetics of a three-dimensional lattice protein was studied using a simple statistical mechanical model for protein folding that we developed earlier. We calculated a characteristic relaxation rate for the free energy profile starting from a completely unfolded structure (or native structure) that is assumed to be associated with a folding rate (or an unfolding rate). The chevron plot of these rates as a function of the inverse temperature was obtained for four lattice proteins, namely, proteins a1, a2, b1, and b2, in order to investigate the dependency of the folding and unfolding rates on their native structures and amino acid sequences. Proteins a1 and a2 fold to the same native conformation, but their amino acid sequences differ. The same is the case for proteins b1 and b2, but their native conformation is different from that of proteins a1 and a2. However, the chevron plots of proteins a1 and a2 are very similar to each other, and those of proteins b1 and b2 differ considerably. Since the contact orders of proteins b1 and b2 are identical, the differences in their kinetics should be attributed to the amino acid sequences and consequently to the interactions between the amino acid residues. A detailed analysis revealed that long-range interactions play an important role in causing the difference in the folding rates. The chevron plots for the four proteins exhibit a chevron rollover under both strongly folding and strongly unfolding conditions. The slower relaxation time on the broad and flat free energy surfaces of the unfolding conformations is considered to be the main origin of the chevron rollover, although the free energy surfaces have features that are rather complicated to be described in detail here. Finally, in order to concretely examine the relationship between changes in the free energy profiles and the chevron plots, we illustrate some examples of single amino acid substitutions that increase the folding rate.     

Detection and grading for esophageal varices in patients with chronic liver damage: comparison of gadolinium-enhanced and unenhanced steady-state coherent MR images

The purpose of this study was to compare observer interpreted steady-state coherent coronal images and gadolinium-enhanced axial images in terms of the detection and grading of esophageal varices. Magnetic resonance imaging (MRI) and gastrointestinal endoscopy were performed within 2 weeks in 90 patients with chronic liver damage, including 55 with untreated esophageal varices, for periodic screening purposes. Two blinded readers retrospectively reviewed T1- and T2-weighted images with gadolinium-enhanced (gadolinium image set) and steady-state coherent (coherent image set) images. Sensitivity for the detection of esophageal varices was higher (P<.001) in the gadolinium image set (76%) than in the coherent image set (35%); on the other hand, specificity was higher (P<.001) in the coherent image set (91%) than in the gadolinium image set (66%). Furthermore, area under the ROC curve was higher for the gadolinium image set (Az=0.823) than the coherent image set (Az=0.761) (P=.48). Moderate and weak positive correlations with endoscopic grades were found for the gadolinium image (r=0.48, P<.01) and coherent image sets (r=0.34, P=.018). The addition of steady-state coherent imaging to the current routine liver imaging protocol did not improve the detection or grading of esophageal varices, whereas gadolinium-enhanced imaging was found to be potentially valuable. Nevertheless, endoscopy was confirmed to be mandatory in patients with esophageal varices suspected by MRI of the liver.     

Preparation of Size Tunable Amphiphilic Poly(amino acid) Nanoparticles

Size tunable amphiphilic NPs composed of poly(γ‐PGA) and hydrophobic amino acids, such as Phe or Trp, were prepared. To prepare these size‐regulated NPs, γ‐PGA‐g‐Phe or γ‐PGA‐g‐Trp dissolved in DMSO was added to various concentrations of NaCl solution. The γ‐PGA‐Phe and γ‐PGA‐Trp formed monodispersed NPs, and the size of NPs can be easily controlled by NaCl concentration. The different‐sized NPs showed the same structure. The encapsulation of protein into the different‐sized NPs was successfully achieved and the size of protein‐encapsulated γ‐PGA‐Phe NPs was increased when protein was encapsulated.

     

On the necessary and sufficient condition for the extended Wedderburn–Guttman theorem

Let A be a u by v matrix, and let M and N be u by p and v by q matrices, where p may not be equal to q or rank(M^′AN)<min(p,q). Recently, Galantai [A. Galantai, A note on the generalized rank reduction, Acta Math. Hungarica 116 (2007) 239–246] presented what he claimed to be the necessary and sufficient condition for rank(A-AN(M^′AN)^-M^′A)=rank(A)-rank(AN(M^′AN)^-M^′A) to hold. This rank subtractivity formula along with the condition under which it holds is called the extended Wedderburn–Guttman theorem. In this paper, we show that some of Galantai’s assertions are incorrect.     

Light-harvesting energy transfer and subsequent electron transfer of cationic porphyrin complexes on clay surfaces

A novel energy-transfer system involving nonaggregated cationic porphyrins adsorbed on an anionic-type clay surface and the electron-transfer reaction that occurs after light harvesting are described. In the clay-porphyrin complexes, photochemical energy transfer from excited singlet zinc porphyrins to free-base porphyrins proceeds. The photochemical electron-transfer reaction from an electron donor in solution (hydroquinone) to the adsorbed porphyrin in the excited singlet state was also examined. Because the electron-transfer rate from the hydroquinone to the excited singlet free-base porphyrin is larger than that to the excited singlet zinc porphyrin, we conclude that the energy transfer accelerates the overall electron-transfer reaction.     

Syntheses and characterization of oxygen/sulfur-bridged incomplete cubane-type clusters, [Mo3S4Tp3]+ and [Mo3OS3Tp3]+, and a mixed-metal cubane-type cluster, [Mo3FeS4ClTp3]. X-ray structures of [Mo3S4Tp3]Cl, [Mo3OS3Tp3]PF6, and [Mo3FeS4ClTp3

The reaction of [Mo3S4(H2O)9]4+ (1) with hydrotris(pyrazolyl)borate (Tp) ligands produced [Mo3S4Tp3]Cl x 4 H2O ([3]Cl x 4 H2O) in an excellent yield. An X-ray structure analysis of [3]Cl x 4 H2O revealed that each molybdenum atom bonded to the Tp ligand. We report four salts of 3, [3]Cl x 4 H2O, [3]tof x 2 H2O, [3]PF6 x H2O, and [3]BF4 x 2 H2O in this paper. The solubility and stability of the chloride salt in organic solvents differ completely from those of the other salts. We have also prepared a new compound, [Mo3OS3Tp3]PF6 x H2O ([4]PF6 x H2O), via the reaction of [Mo3OS3(H2O)9]4+ (2) with KTp in the presence of NH4PF6. All the molybdenum atoms bonded to Tp ligand. 1H NMR signals corresponding to nine protons bonded to three pyrazole rings in one Tp were observed in a spectrum (at 253 K) of [3]BF4 x 2 H2O. It shows that cluster 3 has a 3-fold rotation axis in CD2Cl2 solution. Twenty-one 1H NMR signals corresponding to twenty-seven protons bonded to nine pyrazole rings in three Tp ligands were observed in a spectrum (at 233 K) of [4]PF6 x H2O; obviously, 4 has no 3-fold rotation axis, in contrast to 3. The short CH...mu3S distance caused large upfield chemical shifts in the 1H NMR spectra of 3 and 4. The reaction of 3 with metallic iron in CH2Cl2 produced [Mo3FeS4XTp3] (X = Cl (5), Br (6)). X-ray structure analysis of 5 has revealed the existence of a cubane-type core Mo3FeS4. Complex 3 functions as a metal-complex ligand for preparing a novel mixed-metal complex even in nonaqueous solvents. The cyclic voltammogram of 5 shows two reversible one-electron couples (E(1/2) = -1.40 and 0.52 V vs SCE) and two irreversible one-electron oxidation processes (E(pc) = 1.54 and 1.66 V vs SCE).     

Dual mineralization of dicalcium phosphate and hydroxyapatite formation on both sides of porous membrane: Alternating current induces pH-modulated crystal deposition

Dual mineralization on a porous membrane was carried out using an electrochemical approach. The porous membrane was interposed between a pair of glass cells, and calcium chloride (CaCl₂) and sodium hydrogenphosphate (Na₂HPO₄) solutions were separately injected into the cells. After inserting platinum electrodes into the cells, an alternating current with a sine waveform was applied for a given period of time. The resulting membrane was removed from the glass cells and rinsed with ultrapure water. The minerals formed on the membrane were analyzed by using spectroscopic methods such as scanning electron microscopy (SEM), infrared (IR) spectroscopy, and X-ray diffraction (XRD) and identified to be dicalcium phosphate and hydroxyapatite. It was noted that dicalcium phosphate formed on one side of the membrane, while hydroxyapatite was formed on the other side. Thus, dual mineralization could be successfully achieved on both sides of the porous membrane under an alternating current. This process of dual mineralization is very useful for the formation of versatile organic–inorganic hybrids and also for the regulation of the polymorphs on either side of a membrane.     

Fabrication of freestanding m-plane GaN wafer by using the HVPE technique on an aluminum carbide buffer layer on an m-plane sapphire substrate

A freestanding m-plane GaN wafer is fabricated by using the hydride vapor-phase epitaxy (HVPE) technique on an aluminum carbide buffer layer on an m-plane sapphire substrate. X-ray pole-figure measurements show a clear m-plane orientation of the GaN surface. The full-width at half-maximum (FWHM) of GaN (1 1¯ 0 0) X-ray rocking curve (XRC) with the scattering vector along the [1 1 2¯ 0] direction is approximately 800 arcsec; this indicates good crystallinity. On the other hand, the FWHM for the case in which the scattering vector is oriented along the [0 0 0 1] direction is broad; this suggests the influence of structural defects along this direction. In fact, basal plane stacking faults (BSF) with a density of approximately 3×10⁵ cm⁻¹ is observed by transmission electron microscopy (TEM). The preparation of a 45-mm-diameter m-plane GaN wafer due to spontaneous separation of the GaN layer from the sapphire substrate is demonstrated.     

Formation of various polymorphs of calcium carbonate on porous membrane by electrochemical approach

Calcium carbonate (CaCO₃) formation was observed without surface modification of the organic template and in the absence of chemical additives such as macromolecules and divalent cations. Our innovative electrochemical approach that involves the use of an alternating current facilitated the crystallization of CaCO₃ polymorphs on a porous polymer membrane. A solution of calcium chloride (CaCl₂) and sodium carbonate (Na₂CO₃) was filled in a glass cell, and the porous membrane was interposed in the cell. A sine waveform of 10 Hz was applied to the platinum electrodes using a high-speed bipolar power supply. An alternating current was generated for 60 min. The crystal morphology and crystal structure of the resulting hybrid membrane were studied. In this electrochemical approach, versatile polymorphs of vaterite, aragonite, and calcite were formed on the membrane, thereby showing that the alternating current induced the formation of various polymorphs of CaCO₃ on the porous membrane even in the absence of any additives.     

Two distinct pathways for essential metabolic precursors for isoprenoid biosynthesis

Isoprenoids are a diverse group of molecules found in all organisms, where they perform such important biological functions as hormone signaling (e.g., steroids) in mammals, antioxidation (e.g., carotenoids) in plants, electron transport (e.g., ubiquinone), and cell wall biosynthesis intermediates in bacteria. All isoprenoids are synthesized by the consecutive condensation of the five-carbon monomer isopentenyl diphosphate (IPP) to its isomer, dimethylallyl diphosphate (DMAPP). The biosynthetic pathway for the formation of IPP from acetyl-CoA (i.e., the mevalonate pathway) had been established mainly in mice and the budding yeast Saccharomyces cerevisiae. Curiously, most prokaryotic microorganisms lack homologs of the genes in the mevalonate pathway, even though IPP and DMAPP are essential for isoprenoid biosynthesis in bacteria. This observation provided an impetus to search for an alternative pathway to synthesize IPP and DMAPP, ultimately leading to the discovery of the mevalonate-independent 2-C-methyl-D-erythritol 4-phosphate pathway. This review article focuses on our significant contributions to a comprehensive understanding of the biosynthesis of IPP and DMAPP.