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The analytic derivative of the electrostatic interaction between far separated fragments is developed and a number of restricted Hartree-Fock (RHF) geometry optimizations are performed by using the fragment molecular orbital method (FMO) and ab initio methods. The [alpha]-helix, [beta]-turn and extended conformers of a 10-residue polyanaline are analyzed and the good FMO accuracy is established.

Molecular dynamics simulations were performed to simulate Ca2+-dependent conformational change of calmodulin (CaM). Simulations of the fully Ca2+-bound form of CaM (Holo-CaM) and the Ca2+-free form (Apo-CaM) were performed in solution for 4 ns starting from the X-ray crystal structure of Holo-CaM. A striking difference was observed between the trajectories of Holo-CaM and Apo-CaM: the central helix remained straight in the former but became largely bent in the latter. Also, the flexibility of Apo-CaM was higher than that of Holo-CaM. The results indicated that the bound Ca2+ ions harden the structure of CaM. [Copyright &y& Elsevier]

The article presents information about a study conducted on enantiotopic differentiation in horse-liver. Some of the chemicals used in the study are, crystalline HLADH, NAD, NADH and beef liver glutamate dehydrogenase, N,N-dimethylaminomethylferrocene and silica gel for column chromatography. Each compound showed the M peak for the expected molecular formula in the MS spectrum. Active MnO2 as the oxidant was prepared according to the literature and stored as a powder after lyophilization. Melting points were measured on a hot stage and are uncorrected. Optical rotations were measured with a Jasco DIP-360 digital polarimeter.

4-Hydroxycyclohexanecarboxylate dehydrogenase, which requires NAD as a cofactor, was detected in crude soluble extracts of Corynebacterium cyclohexanicum grown on cyclohexanecarboxylic acid as the sole carbon source. The dehydrogenase was purified from extracts to an electrophoretically homogenous state by ammonium sulfate precipitation and chromatography on DEAE-650s, agarose-NAD and hydroxyapatite. The enzyme consisted of two identical subunits and had a native relative molecular mass of 53600. There were two residues each of cysteine and tryptophan in the enzyme molecule. Oxo acid rather than hydroxy acid was routinely used as substrate for assay of the enzyme. The enzyme is highly specific for 4-oxocyclohexanecarboxylic acid: the carboxyl group is essential and the position of carbonyl group is important; neither the 2-oxo nor the 3-oxo homologue was used as substrate. A methyl substitution on the ring of 4-oxocyclohexanecarboxylate resulted in an almost complete loss of its activity. The reduction product was identified as trans-4-hydroxycyclohexanecarboxylic acid by gasliquid chromatography and mass spectrometry. It was used as a substrate for the reverse reaction in the presence of NAD but not its cis-isomer. The enzyme was specific for the B-side (pro-S) hydrogen of NADH in the hydrogen transfer from NADH to 4-oxocyclohexanecarboxylate. The Km values for 4-oxocyclohexanecarboxylate and NADH in the reduction reaction at pH 6.8 were 0.50 mM and 0.28 mM, respectively, whereas those for trans-4hydroxycyclohexanecarboxylate and NAD in the oxidation reaction at pH 8.8 were 0.51 mM and 0.23 mM, respectively. The equilibrium constant of the reaction was 1.79 × 10-10 M. The enzyme was strongly inhibited by N-bromosuccinimide. [ABSTRACT FROM AUTHOR]

Presents the results of a study which examine the roles of metal ions in the enzymatic cleavage of RNA. Results of study.

Examines the stabilities of oxyphosphoranes with various ionic valences. Preferred location for protonation of the monoanionic intermediate; Kinetic stability of the dianionic phosphorane; Neutral complex between the dianionic phosphorane and the divalent magnesium.

We have theoretically examined the relative binding affinities (RBA) of typical ligands, 17beta-estradiol (EST), 17alpha-estradiol (ESTA), genistein (GEN), raloxifene (RAL), 4-hydroxytamoxifen (OHT), tamoxifen (TAM), clomifene (CLO), 4-hydroxyclomifene (OHC), diethylstilbestrol (DES), bisphenol A (BISA), and bisphenol F (BISF), to the alpha-subtype of the human estrogen receptor ligand-binding domain (hERalpha LBD), by calculating their binding energies. The ab initio fragment molecular orbital (FMO) method, which we have recently proposed for the calculations of macromolecules such as proteins, was applied at the HF/STO-3G level. The receptor protein was primarily modeled by 50 amino acid residues surrounding the ligand. The number of atoms in these model complexes is about 850, including hydrogen atoms. For the complexes with EST, RAL, OHT, and DES, the binding energies were calculated again with the entire ERalphaLBD consisting of 241 residues or about 4000 atoms. No significant difference was found in the calculated binding energies between the model and the real protein complexes. This indicates that the binding between the protein and its ligands is well characterized by the model protein with the 50 residues. The calculated binding energies relative to EST were very well correlated with the experimental RBA (the correlation coefficient r=0.837) for the ligands studied in this work. We also found that the charge transfer between ER and ligands is significant on ER-ligand binding. To our knowledge, this is the first achievement of ab initio quantum mechanical calculations of large molecules such as the entire ERalphaLBD protein.