Protein calculations on parallel processors. II. Parallel algorithm for the forces and molecular dynamics

We describe two algorithms for the parallel calculation of a CHARMm-like force field in macromolecules. For a molecule with a given number of atoms, we show that there is an optimal number of processors leading to a minimum computation time. At the optimum, both the number of processors and the computation time are proportional to the number of atoms. © 1992 by John Wiley & Sons, Inc.     

Molecular dynamics simulation of a hydrated diphytanol phosphatidylcholine lipid bilayer containing an alpha-helical bundle of four transmembrane domains of the influenza A virus M2 protein

An alpha-helical bundle composed of four transmembrane portions of the M2 protein from the Influenza A virus has been studied in a hydrated diphytanol phosphatidylcholine bilayer using molecular dynamics (MD) calculations. Experimentally, the sequence utilized is known to aggregate as a four-helix bundle and act as a pH-gated proton-selective ion channel, which is blocked by the drug amantadine hydrochloride. In the presented simulation, the ion channel was initially set up as a parallel four-helix bundle. The all-atom simulation consisted of almost 16,000 atoms, described classically, using a forcefield from the CHARMM22 database. Bilayers with and without the bundle were shown to be stable throughout the nanosecond timescale of the MD simulation. Structural and dynamical properties of the bilayer both with and without the transmembrane protein are reported.     

Reduction of an aldehyde by a NADH/Zn2+ -dependent redox active ribozyme

We report here the ability of an alcohol dehydrogenase (ADH) ribozyme to reduce a benzaldehyde. While the ribozyme was initially evolved in vitro based on the activity for the NAD+-dependent oxidation of the benzyl alcohol, we found that this ADH ribozyme is also capable of reducing the aldehyde in the presence of NADH and Zn2+. The rate acceleration gained by ribozyme catalysis was more than 6 orders of magnitude larger than the spontaneous reaction. Although the reversibility of phosphordiester and acyl transfer reactions catalyzed by ribozymes was known, that of other chemical reactions has not been well established. This study has demonstrated the reversibility of a hydride transfer chemistry catalyzed by the ADH ribozyme. Most interestingly, the ribozyme shares many features with the protein ADHs, e.g., reversibility and NADH/Zn2+ dependence.     

A rapid,mild, and efficient method for C-5 iodination/thiocyanation of 2-aminothiazoles

An efficient, green, rapid multitasking protocol for the selective C-5 substitution of 2-aminothiazole using iodic acid and aqueous PEG-400 was developed. The method found suitable for C-5 substitution i.e. iodination and thiocyanation of 2-amino thiazole using iodine and ammonium thiocyanate respectively. Iodic acid was found to be a good oxidant and aqueous PEG-400 as green reaction solvent.     

Influence of crystallite shape on particle size broadening of Debye-Scherrer reflections

Formulae for the Scherrer constant K _β , the variance Scherrer constant K _ω and the taper parameter L _ω for crystals having the external shapes of a triangular prism, a square prism, a hexagonal prism and a cylinder have been obtained in terms of the reflection indices and proportionality factors,viz., the ratio of the height of the crystal to the square root of its basal area and the ratio of the two lattice constants of the unit cell. The numerical values of K _β , K _ω and L _ω have also been computed for direct application in particular cases.