Acetylacetonato-based pincer-type nickel(ii) complexes: synthesis and catalysis in cross-couplings of aryl chlorides with aryl Grignard reagents.

In this work, three different types of acetylacetonato-based pincer-type nickel(ii) complexes (2) were prepared. Complex 2a possessed the tridentate ONN ligand, which was constructed by the condensation reaction of acetylacetone with N,N-diethylethylenediamine. Complex 2b contained the PPh2 donor group in contrast to the NEt2 group in 2a, i.

Several transition states from (4)C(1) to skew conformations of beta-D-glucopyranose.

The interconversion pathways in the ring distortion of beta-D-glucopyranose were investigated using density functional calculations. We examined the energies of several conformers of beta-D-glucopyranose and tried to obtain the transition-state conformation and determine the pathway between a (4)C(1) chair and some distorted ring conformers. The results showed that two E(3)/(2)H(3) conformations and one E(3)/(4)H(3) conformation were transition states in such ring puckering.

An investigation of the pyranose ring interconversion path of alpha-L-idose calculated using density functional theory.

The interconversion pathways of the pyranose ring conformation of alpha-L-idose from a (4)C1 chair to other conformations were investigated using density functional calculations. From these calculations, four different ring interconversion paths and their transition state structures from the (4)C1 chair to other conformations, such as B(3,O), and (1)S3, were obtained. These four transition-state conformations cover four possible combinations of the network patterns of the hydroxyl group hydrogen bonds (clockwise and counterclockwise) and the conformations of the primary alcohol group (tg and gg).

Interaction between the antigen and antibody is controlled by the constant domains: normal mode dynamics of the HEL-HyHEL-10 complex.

The antigen binding fragment (Fab) of a monoclonal antibody (HyHEL-10) consists of variable domains (Fv) and constant domains (CL-CH1). Normal modes have been calculated from the three-dimensional structures of hen egg lysozyme (HEL) with Fab, those of HEL with Fv, and so on. Only a small structural change was found between HEL-Fab and HEL-Fv complexes.

Dynamic flexibility of a peptide-binding groove of human HLA-DR1 class II MHC molecules: normal mode analysis of the antigen peptide-class II MHC complex.

Class II major histocompatibility complex (MHC) has tolerance for binding longer antigen peptides than those bound by class I MHC. In this paper, a normal mode analysis on HLA-DR1 class II MHC involving an antigen peptide indicated that the peptide-binding groove had some different dynamic characteristics from that of HLA-A2 class I MHC. The dynamic changes in the class I groove with removal of the bound peptide were limited primarily to the central region and the C-terminal side (corresponding to the C-terminal side of the bound peptide) of the groove, while the dynamic changes in the class II groove with removal of the bound peptide extended to the whole of the groove, and were especially remarkable around a strand located in the N-terminal side (corresponding to the N-terminal side of the bound peptide) of the groove.

Dynamic character of human growth hormone and its receptor: normal mode analysis.

Human growth hormone (hGH) induces dimerization of its binding protein (hGHbp). hGH binds to the first hGHbp (bp1) on site 1, and then the hGH-bp1 heterodimer complex binds to the second hGHbp (bp2) on site 2. Although the interactions of hGH and hGHbps have been studied from different viewpoints, few studies from a dynamic viewpoint have been reported.

Evaluation of the third solvent clusters fitting procedure for the prediction of protein-protein interactions based on the results at the CAPRI blind docking study.

To predict protein-protein interactions, rough or coarse handling for the induced fit problem is proposed. Our method involves the overlap of two hydrophobic interactions as "third solvent clusters fitting." Predictions for binding sites and geometric centers were acceptable, but those of the binding axes were poor.

Motion of an antiviral compound in a rhinovirus capsid under rotational symmetry boundary conditions.

A molecular dynamics (MD) simulation of a complex of a rhinovirus protein shell referred to as a "capsid" and an anti-rhinovirus drug, WIN52084s, was performed under the rotational symmetry boundary conditions. For the simulation, the energy parameters of WIN52084s in all-atom approximations were determined by ab initio calculations using a 6-31G* basis set and the two-conformational two-stage restricted electrostatic potential fit method. The motion of WIN52084s and the capsid was focused on in the analysis of the trajectory of the simulation.

Dynamic characteristics of a peptide-binding groove of human HLA-A2 class I MHC molecules: normal mode analysis of the antigen peptide-class I MHC complex.

Class I major histocompatibility complex (MHC) binds antigen peptides with various sequences. We performed a normal mode analysis of HLA-A2 MHC that binds three peptides with different affinity. HLA-A2 MHC has a peptide-binding groove composed of two alpha-helices (residue 49-84, residue 140-179).