The role of the putative catalytic base in the phosphoryl transfer reaction in a protein kinase: first-principles calculations

Protein kinases are important enzymes controlling the majority of cellular signaling events via a transfer of the gamma-phosphate of ATP to a target protein. Even after many years of study, the mechanism of this reaction is still poorly understood. Among many factors that may be responsible for the 1011-fold rate enhancement due to this enzyme, the role of the conserved aspartate (Asp166) has been given special consideration. While the essential presence of Asp166 has been established by mutational studies, its function is still debated. The general base catalyst role assigned to Asp166 on the basis of its position in the active site has been brought into question by the pH dependence of the reaction rate, isotope measurements, and pre-steady-state kinetics. Recent semiempirical calculations have added to the controversy surrounding the role of Asp166 in the catalytic mechanism. No major role for Asp166 has been found in these calculations, which have predicted the reaction process consisting of an early transfer of a substrate proton onto the phosphate group. These conclusions were inconsistent with experimental observations. To address these differences between experimental results and theory with a more reliable computational approach and to provide a theoretical platform for understanding catalysis in this important enzyme family, we have carried out first-principles structural and dynamical calculations of the reaction process in cAPK kinase. To preserve the essential features of the reaction, representations of all of the key conserved residues (82 atoms) were included in the calculation. The structural calculations were performed using the local basis density functional (DFT) approach with both hybrid B3LYP and PBE96 generalized gradient approximations. This kind of calculation has been shown to yield highly accurate structural information for a large number of systems. The optimized reactant state structure is in good agreement with X-ray data. In contrast to semiempirical methods, the lowest energy product state places the substrate proton on Asp166. First-principles molecular dynamics simulations provide additional support for the stability of this product state. The latter also demonstrate that the proton transfer to Asp166 occurs at a point in the reaction where bond cleavage at the PO bridging position is already advanced. This mechanism is further supported by the calculated structure of the transition state in which the substrate hydroxyl group is largely intact. A metaphoshate-like structure is present in the transition state, which is consistent with the X-ray structures of transition state mimics. On the basis of the calculated structure of the transition state, it is estimated to be 85% dissociative. Our analysis also indicates an increase in the hydrogen bond strength between Asp166 and substrate hydroxyl and a small decrease in the bond strength of the latter in the transition state. In summary, our calculations demonstrate the importance of Asp166 in the enzymatic mechanism as a proton acceptor. However, the proton abstraction from the substrate occurs late in the reaction process. Thus, in the catalytic mechanism of cAPK protein kinase, Asp166 plays a role of a "proton trap" that locks the transferred phosphoryl group to the substrate. These results resolve prior inconsistencies between theory and experiment and bring new understanding of the role of Asp166 in the protein kinase catalytic mechanism.     

Synthesis of the common left-half part of pectenotoxins

The common left-half [C31-C33(OC1-C7)-C40] part of pectenotoxins has been synthesized convergently from the C31-C35, C36-C40, and C1-C7 parts. The C31-C35 part, prepared via a new route shorter than our previous route, was coupled with the C36-C40 part through reductive lithiation and addition reactions to give an adduct stereoselectively, which was converted to a cyclic acetal corresponding to the C31-C40 part. The left-half was synthesized by a three-step process including esterification of the C31-C40 part with the C1-C7 part.     

Chemical compositional separation of styrene-methyl methacrylate copolymers using high-performance liquid chromatography with liquefied carbon dioxide as eluent

Chromatographic separation of styrene-methyl methacrylate (MMA) copolymers depending on the chemical composition was studied using liquefied carbon dioxide as an adsorption promoting solvent, and tetrahydrofuran, chloroform containing ethanol as a desorption promoting solvent in the mobile phase and the column packed non-bonded silica gel by a solvent gradient method. With the increase of MMA content, the elution was retarded indicating that the typical normal-phase type of adsorption occurred. The effects of type of desorption solvents, molecular mass of sample, and column temperature on the elution were investigated.     

Physical and Chemical Properties of Four-Membered Bis(triphenylphosphane)platinum(II) Sulfenato Thiolato Complexes

The reaction of isolable dithiirane 1-oxides with (Ph 3 P) 2 Pt( m 2 -C 2 H 4 ) provided the title complexes in high yields. 31 P NMR spectroscopy of the phosphine ligands of the complexes and x-ray crystallographic analysis of a complex were reported.     

Synthesis of green organogelators with a sulfide linkage via solvent-free Michael addition: soft templates for the preparation of size-controlled gold nanoparticles

Green organogelators with a sulfide linkage and free amino groups were synthesized via phase transfer catalysis using a N-benzylcinchonidinium bromide catalyst. Their self-assemblies in various common solvents were examined. These compounds exhibit high gelation ability especially in aromatic and highly polar solvents with a low critical gelation of 0.1 wt %. The organogels were analyzed by ¹H nuclear magnetic resonance (¹H NMR) and Fourier transfer-infrared spectroscopies (FT-IR), and their phase transition temperatures were determined by differential scanning calorimetry. The homogeneity of the gel networks was examined by field emission scanning electron microscopy and transmission electron microscopy (TEM). A lamellar structure was also confirmed by X-ray diffraction analysis. The organogels were employed as soft-templates for the in situ generation of stable gold nanoparticles dispersed in the gel matrix, and the resulting GNP dispersions were studied by ¹H NMR and UV–vis absorption. Transmission electron microscopy showed that GNPs assemble into a thin membrane-like structure.     

Chiral Dinuclear EuIII,TbIII, and YIII Complexes Supported by P-Stereogenic Linear Tetraphosphine Tetraoxide

A P-stereogenic linear tetraphosphine tetraoxide, (R,R)- or (S,S)-dpmppm(=O)₄, was synthesized to prepare C₂ dinuclear M(hfa)₃ complexes (M=Eu, Tb, Y) as the first example of lanthanide(III) complexes with P-chiral multidentate phosphine oxides. The mononuclear M(hfa)₃ complexes (M=Eu, Y) with a P-chiral diphosphine dioxide, tpdpb(=O)₂, were also prepared, and comparison of their photophysical properties for the Eu^III complexes revealed that significant chiral induction from the P-chiral centers arises on the achiral M(hfa)₃ units through intramolecular π-π stacking constraint in the dinuclear system.     

Polymerization of Acrolein by Imidazole

Polymerization of acrolein(AL) in the presence of imidazole(Im) has been investigated in tetrahydrofuran or methanol below room temperature. The polymers obtained, white or pale yellow powders, were found to be composed of vinyl polymer with one Im group attached and having an aldehyde side chain, of which 70–80 mole % of the aldehyde revealed bridge structure. The number-average molecular weight (M _n) of these polymers was determined to be in the range of 317 to 691. The rate of polmerization R_p was expressed by the equation, R + k[Im] [AL]².

The addition of water or dimethyl sulfoxide accelerated the polymerization reaction, while the presence of benzaldehyde or N,N'-dimethylformamide decreased R_p. The structure of addition products in the initial polymerization step was confirmed by IR and NMR spectra, and the observations of polymerization system was carried out by UV and NMR spectra. The polymerization mechanisms were discussed on the basis of these results.