Protein structure predictions by parallel simulated annealing molecular dynamics using genetic crossover

We propose a conformational search method to find a global minimum energy structure for protein systems. The simulated annealing is a powerful method for local conformational search. On the other hand, the genetic crossover can search the global conformational space. Our method incorporates these attractive features of the simulated annealing and genetic crossover. In the previous works, we have been using the Monte Carlo algorithm for simulated annealing. In the present work, we use the molecular dynamics algorithm instead. To examine the effectiveness of our method, we compared our results with those of the normal simulated annealing molecular dynamics simulations by using an α-helical miniprotein. We used genetic two-point crossover here. The conformations, which have lower energy than those obtained from the conventional simulated annealing, were obtained.     

Reversible photocontrol of surface wettability between hydrophilic and superhydrophobic surfaces on an asymmetric diarylethene solid surface

By alternate UV and visible light irradiation, reversible topographical changes were observed on a newly synthesized diarylethene microcrystalline surface between the rough crystalline surface of an open-ring isomer and flat eutectic surfaces. The contact angle changes of a water droplet between 80° and 150° and peak intensities changes of the open-ring isomer in XRD patterns within 2 h of repeating cycle were observed. The results indicated that reversibly photogenerated rod-shaped crystals on the surface were produced based on the lattice of the open-ring isomer crystals in the subphase.     

Transformation of actoHMM assembly confined in cell-sized liposome

To construct a simple model of a cellular system equipped with motor proteins, cell-sized giant liposomes encapsulating various amounts of actoHMM, the complexes of actin filaments (F-actin) and heavy meromyosin (HMM, an actin-related molecular motor), with a depletion reagent to mimic the crowding effect of inside of living cell, were prepared. We adapted the methodology of the spontaneous transfer of water-in-oil (W/O) droplets through a phospholipid monolayer into the bulk aqueous phase and successfully prepared stable giant liposomes encapsulating the solution with a physiological salt concentration containing the desired concentrations of actoHMM, which had been almost impossible to obtain using currently adapted methodologies such as natural swelling and electro-formation on an electrode. We then examined the effect of ATP on the cytoskeleton components confined in those cell-sized liposomes, because ATP is known to drive the sliding motion for actoHMM. We added α-hemolysin, a bacterial membrane pore-forming toxin, to the bathing solution and obtained liposomes with the protein pores embedded on the bilayer membrane to allow the transfer of ATP inside the liposomes. We show that, by the ATP supply, the actoHMM bundles inside the liposomes exhibit specific changes in spatial distribution, caused by the active sliding between F-actin and HMM. Interestingly, all F-actins localized around the inner periphery of liposomes smaller than a critical size, whereas in the bulk solution and also in larger liposomes, the actin bundles formed aster-like structures under the same conditions.     

Sc2C2@C80 rather than Sc2@C82: templated formation of unexpected C2v(5)-C80 and temperature-dependent dynamic motion of internal Sc2C2 cluster

Unambiguous X-ray crystallographic results of the carbene adduct of Sc(2)C(82) reveal a new carbide cluster metallofullerene with the unexpected C(2v)(5)-C(80) cage, that is, Sc(2)C(2)@C(2v)(5)-C(80). More interestingly, DFT calculations and NMR results disclose that the dynamic motion of the internal Sc(2)C(2) cluster depends strongly on temperature. At 293 K, the cluster is fixed inside the cage with two nonequivalent Sc atoms on the mirror plane, thereby leading to C(s) symmetry of the whole molecule. However, when the temperature increases to 413 K, the (13)C and (45)Sc NMR spectra show that the cluster rotates rapidly inside the C(2v)(5)-C(80) cage, featuring two equivalent Sc atoms and weaker metal-cage interactions.     

Structural elucidation and regioselective functionalization of an unexplored carbide cluster metallofullerene Sc2C2@C(s)(6)-C82

A Sc(2)C(84) isomer, previously assumed to be Sc(2)@C(84), is unambiguously identified as a new carbide cluster metallofullerene Sc(2)C(2)@C(s)(6)-C(82) using both NMR spectroscopy and X-ray crystallography. The (13)C-nuclei signal of the internal C(2)-unit was observed at 244.4 ppm with a 15% (13)C-enriched sample. Temperature-dependent dynamic motion of the internal Sc(2)C(2) cluster is also revealed with NMR spectrometry. Moreover, the chemical property of Sc(2)C(2)@C(s)(6)-C(82) is investigated for the first time using 3-triphenylmethyl-5-oxazolidinone (1) which provides a 1,3-dipolar reagent under heating. Regarding the low cage symmetry of this endohedral which contains 44 types of nonequivalent cage carbons, it is surprising to find that only one monoadduct isomer is formed in the reaction. Single-crystal X-ray results of the isolated pyrrolidino derivative Sc(2)C(2)@C(s)(6)-C(82)N(CH(2))(2)Trt (2) reveal that the addition takes place at a [6,6]-bond junction, which is far from either of the two Sc atoms. Such a highly regioselective addition pattern can be reasonably interpreted by analyzing the frontier molecular orbitals of the endohedral. Electronic and electrochemical investigations reveal that adduct 2 has a larger highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) gap than pristine Sc(2)C(2)@C(s)(6)-C(82); accordingly, it is more stable.     

Synthesis and structural revision of phomopsin B, a novel polyketide carrying a 10-membered cyclic-ether ring

Total synthesis of the proposed structure 2 for phomopsin B was achieved by using an intramolecular olefin metathesis as a key step. The spectral data, however, did not match with those of the natural product reported. Re-examination of the reported NMR data led to the structural revision of phomopsin B to known dothiorelone A 18. The R configuration of dothiorelone A was determined by total synthesis through a cross-metathesis with a chiral olefin 19.     

Weighted Composition Operators on the Space of Bounded Harmonic Functions

We determine the norm and the essential norm of the difference of weighted composition operators on the space of bounded harmonic functions on the open unit disk. The argument is done on the boundary.     

Monitoring the aggregation processes of amyloid-β using a spin-labeled, fluorescent nitroxyl radical

Amyloid nitroxyl radical (nitroxide) ligands were used to detect amyloid-β fibrils, the main constituents of senile plaques in Alzheimer's disease, using anisotropic ESR spectra, and were found to affect the aggregation process due to the radical functionality. These compounds have great potential as novel and multifunctional probes, combining spin labels, spin probes, and fluorescence probes.     

Low-melting zwitterion: effect of oxyethylene units on thermal properties and conductivity

An imidazolium-based zwitterion containing two oxyethylene units was obtained as a colorless liquid at room temperature. The equimolar mixture of the liquid zwitterion and lithium bis(trifluoromethylsulfonyl)amide showed an ionic conductivity of over 10(-4) S cm(-1) at 80 °C, which was higher than those of mixtures composed of analogous solid zwitterions.