Importance of the single amino acid potential in water for secondary and tertiary structures of proteins

The structure of a protein molecule is considered to be primarily determined by the inter-amino-acid nonbonded interactions, such as hydrogen bonds. However, the conformational space of the polypeptide chain should be simultaneously restricted by the intrinsic conformational preferences of the individual amino acids. We present here precise single amino acid potential (SAAP) surfaces for glycine (For-Gly-NH(2)) and alanine (For-Ala-NH(2)) in water (epsilon = 78.39) and ether (epsilon = 4.335), which were calculated at the HF/6-31+G(d,p) level applying the self-consistent isodensity polarizable continuum model (SCIPCM) reaction field with geometry optimization in the corresponding solvents. The obtained Ramachandran potential surfaces in water showed distinct potential wells in the alpha- and beta-regions. The profiles were in almost perfect agreement with the Ramachandran plots of glycine and alanine residues in folded proteins, suggesting the Boltzmann distributions on the SAAP surfaces. Molecular simulations of polyalanines (For-Ala(n)-NH(2); n = 3-5) by using the SAAP force field equipped with the SCIPCM potentials revealed that the polyalanines readily form 3(10)-helical structures in water but not in vacuo. In ether (hydrophobic environments), the helical structures were relatively stable, but the most stable structure was assigned to a different one. These results indicated that the intrinsic conformational preferences of the individual amino acids (i.e., the SAAPs) in water are of significant importance not only for describing conformations of a polypeptide chain in the random coil state but also for understanding the folding to the secondary and tertiary structures.     

Scattering of tight-binding electrons off screw dislocations

The Schrödinger equation in the tight-binding approximation is solved numerically with the method of conjugate gradients to study the phase mismatching effect on the scattering of electrons off a screw dislocation. When an electron beam strikes on a screw dislocation, there appears in the down stream a semi-infinite plane on which the amplitude of electronic wave is reduced appreciably.Work partially performed within the research program of the Sonderforschungsbereich 125 Aachen-Jülich-Köln.     

Hyperfine interaction in a quantum spin chain

From an electron spin resonance measurement on a single crystal sample of theS=1 linear chain Heisenberg antiferromagnet Ni(C₃H₁₀N₂)₂NO₂ClO₄ (NINO) containing a small amount of Cu impurity atoms, we have observed two sets of four hyperfine lines, one of which has almost three times larger field splitting than the other. The hyperfine lines are well explained as arising from the hyperfine interaction between the Cu nuclear spin andthe Cu electron spin which interact with theS=1/2 degrees of freedom induced at the Ni sites by the quantum effect. A large anisotropy in the hyperfine constant is observed andanalyzed using a ligand field theory with covalency effects.     

Magnetic relaxation near a fishtail peak of isothermal magnetization in B1 NbCy encapsulated in multiwall carbon nanocages

Isothermal magnetization near a fishtail peak in nanocrystalline B1 NbC_y encapsulated in multiwall carbon nanocages is studied within the time window of 100 < t < 4000 s. The current density J exhibits a linear logarithmic time decay. The effective activation energy U_eff increases linearly with temperature T and is independent of applied magnetic field H. The results of J(t) and U_eff (T, H) are consistent with the Anderson–Kim flux–creep model for thermally activated motion of uncorrelated vortices or vortex bundles over a net potential barrier U_eff. U_eff at a fishtail peak field H_fp evolves quickly above a fishtail peak temperature T_fp, but slowly below that temperature. The result suggests that a decrease of flux viscosity coefficient above T_fp at H_fp is the origin of the fishtail peak in nanocrystalline B1 NbC_y encapsulated in multiwall carbon nanocages.     

Arsenic Compounds Accumulated in Sedimentary Microorganisms Cultivated in Media Containing Several Arsenicals

Sediments, as sources of microorganisms, were added to two kinds of media, 1/5 ZoBell 2216E and a solution of inorganic salts, which contained inorganic arsenic(III), inorganic arsenic(V), methanearsonic acid, dimethyl- arsinic acid, trimethylarsine oxide, tetramethylarsonium salt or arsenocholine. After 17 days of incubation at 20 °C, the arsenicals that had accumulated in the microorganisms were analysed by high-performance liquid chromatography (HPLC). While the more toxic arsenicals [inorganic arsenic(III), inorganic arsenic(V), methanearsonic acid, dimethylarsinic acid] were not converted in the microorganisms, trimethylarsine oxide and tetramethylarsonium salt were considerably degraded to inorganic arsenic(V), and arsenocholine to arsenobetaine. Arsenobetaine that had accumulated in the microorganisms was extracted and confirmed by thin-layer chromatography (TLC) and fast atom bombardment (FAB) mass spectrometry.