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To evaluate the enthalpic and entropic contributions of polar residues in alanine-based peptides to α-helical propensities of peptides, we applied a Brownian dynamics simulation, together with the umbrella sampling, to two alanine-based 21-residue peptides: one composed of alanine only (AAA), the other composed of 18 alanines and 3 arginines (ARA). Higher α-helical propensity of ARA than that of AAA was obtained. However, they showed similar conformational stability in enthalpy, considering the contribution of the solvation energy and the potential energy. As an evaluation of entropic effects, the fluctuation of a dihedral angle, ψ, was investigated. Arginine residue showed smaller fluctuation than alanine in elongated states. Higher α-helical propensity might originate from entropic effects. Furthermore, arginine seems to affect the α-helical propensity of alanines interacting with arginine.

To evaluate the relationship between the amount of available Silicon (Si) in paddy soils and their mineral properties on the Shounai Plain in Japan, which is formed from several parent materials, we evaluated the amount of available Si, the particle size distribution, the oxide composition of crystalline minerals and the amount of oxalate-extractable Si (Sio), iron (Feo) and aluminum (Alo) in the soil. The amount of available Si in the soil and the oxide content of the crystalline minerals differed among four soil groups that were distinguished by their clay mineral composition. There was no difference in the particle size distribution among the soil groups. The amount of available Si was positively related to the SiO2/Al2O3 ratio of clay, the CaO concentration of silt and fine sand, and the amounts of Sio, Feo and Alo in the soil. The amount of available Si in the soils was negative correlated with the Na2O and K2O concentrations of silt, the K2O concentration of fine sand, and the coarse sand c...

We applied an atomistic Brownian dynamics (BD) simulation with multiple time step method for the folding simulation of a 13-mer α-helical peptide and a 12-mer β-hairpin peptide, giving successful folding simulations. In this model, the driving energy contribution towards folding came from both electrostatic and van der Waals interactions for the α-helical peptide and from van der Waals interactions for the β-hairpin peptide. Although, many non-native structures having the same or lower energy than that of native structure were observed, the folded states formed the most populated cluster when the structures obtained by the BD simulations were subjected to the cluster analysis based on distance-based root mean square deviation of side-chains between different structures. This result indicates that we can predict the native structures from conformations sampled by BD simulation.

We report a multiple time step algorithm applied to an atomistic Brownian dynamics simulation for simulating the long time scale dynamics of biomolecules. The algorithm was based on the original multiple time step method; a short time step was used to keep faster motions in local equilibrium. When applied to a 28-mer # # ! folded peptide, the simulation gave stable trajectories and the computation time was reduced by a factor of 160 compared to a conventional molecular dynamics simulation using explicit water molecules. We applied it for the folding simulation of a 13-mer ! -helical peptide, giving a successful folding simulation. These results indicate that the Brownian dynamics with the multiple time step algorithm is useful for studies of biomolecular motions by long time simulation.

A new tripodal ligand with an asymmetric carbon atom, Ph2PCH2CH(Me)N(CH2CH2PPh2)2 (S-mnp3) was prepared using L-alanine as an optically active starting material; a series of its complexes, [M(X)(S-mnp3)]BPh4(M = Ni(II) and Co(II); X = NCS−, Cl−, Br− and I−) was prepared. Electronic spectra of these complexes indicated that their coordination geometries are essentially the same as those of corresponding complexes containing the tripodal ligand tris (diphenylphosphinoethyl) amine. Thus, all the present nickel complexes in solution exhibit electronic spectra typical of trigonal-bipyramidal complexes of diamagnetic configuration. CD spectra of these nickel complexes have been discussed on the basis of the selection rules for magnetic dipole transitions under C 3v symmetry. Cobalt(II) complexes are either high-spin or low-spin, depending on the nature of the unidentate ligand. The high-spin cobalt(II) complexes did not show CD spectra typical of trigonal-bipyramidal geometry.