DFT and ONIOM study on the alkylation of the lithium enolate in solution: microsolvation cluster models for CH2=CHOLi?+?CH3Cl?+?(THF)0�C6

DFT computational study on the alkylation of the lithium enolate derived from acetaldehyde with MeCl was performed. The reaction of the free enolate CH₂=CHO^? with MeCl has an early transition state with low barrier, and the reaction of its lithium enolate gave a cyclic transition structure with high activation energy; neither of them is a good model for reaction in solution. In the presence of 1?C6 THF molecule(s), a typical S_N2 transition structures were obtained with reasonable activation energies after the PCM correction. Especially, the reaction in the presence of three THF molecules completed the tetra-coordination of the lithium cation, and structurally and energetically, this is an optimal model for the reaction in the solution. The transition structures were also located at the ONIOM level (high?=?B3LYP/6?C31(+)G*: low?=?RHF/3?C21 G*). The results are favorably compared with the full DFT results.     

Radical polyaddition of bis(α-trifluoromethyl-β-difluorovinyl) terephthalate with 1,4-dioxane

To develop a radical polyaddition reaction of 2-benzoyloxypentafluoropropene [CF₂C(CF₃)-OCOC₆H₅] (BPFP) with tetrahydrofuran (THF), the reactions of bis(α-trifluoromethyl-β-difluorovinyl) terephthalate [CF₂C(CF₃)OCOC₆H₄COOC(CF₃)CF₂] (BFP) with THF and of BPFP with 1,4-dioxane were investigated as model reactions to form 1 : 1 and 1:2 addition products of BFP with THF. This evidenced that THF is monofunctional, and dioxane is bifunctional since the 1:1 and 2:1 addition products of BPFP with dioxane were formed. The polyaddition reaction of BFP with dioxane turned out to produce a white powdery substance which was found to possess a mole ratio of BFP units to dioxane units in the polymers of 1:1. The highest molecular weight obtained was M _n = 9.9 × 10³.     

Simultaneous biobehavior of trace elements, Sc, Mn, Fe, Co, Zn, Se, Rb and Zr in the brain and other organs of C57BL/6N mice

The radioactive multitracer technique was applied to a study on the uptake of trace elements in normal C57BL/6N mice. Comparative uptake behavior of⁴⁶Sc,⁵⁴Mn,⁵⁹Fe,⁵⁸Co,⁶⁵Se,⁸³Rb and⁸⁸Zr tracers was examined among 11 organs (brain, cardiac muscle, lung, liver, spleen, pancreas, kidneys, bone, muscle, eyeballs and testes) and blood, and evaluated in terms of the “tissue uptake rate (the radioactivity percentage of injected dose per gram of tissue, %dose/g)”. The multitracer technique revealed reliable data demonstrating characteristic uptake of the 8 trace elements, Sc, Mn, Fe, Co, Zn, Se, Rb and Zr by the brain and other organs, as well as the distinctive features of the accumulation and retention of each element in the brain.     

Line shape analyses on the CO stretching bands of acetone using a vibrational coupling model

The line shapes of the polarized and depolarized Raman bands of the CO stretching of acetone, as well as the infrared band, are analyzed on the basis of the vibrational coupling model. The analytical procedures are described in detail. Satisfactory agreement between the observed and simulated spectra is obtained using almost the same coupling scheme for the three types of spectra. The orientational correlation between the coupled oscillators is discussed. Copyright © 2006 John Wiley & Sons, Ltd.     

Oncogenic KRAS G12D mutation promotes dimerization through a second,phosphatidylserine–dependent interface: a model for KRAS oligomerization

KRAS forms transient dimers and higher-order multimers (nanoclusters) on the plasma membrane, which drive MAPK signaling and cell proliferation. KRAS is a frequently mutated oncogene, and while it is well known that the most prevalent mutation, G12D, impairs GTP hydrolysis, thereby increasing KRAS activation, G12D has also been shown to enhance nanoclustering. Elucidating structures of dynamic KRAS assemblies on a membrane has been challenging, thus we have refined our NMR approach that uses nanodiscs to study KRAS associated with membranes. We incorporated paramagnetic relaxation enhancement (PRE) titrations and interface mutagenesis, which revealed that, in addition to the symmetric ‘α–α’ dimerization interface shared with wild-type KRAS, the G12D mutant also self-associates through an asymmetric ‘α–β’ interface. The ‘α–β’ association is dependent on the presence of phosphatidylserine lipids, consistent with previous reports that this lipid promotes KRAS self-assembly on the plasma membrane in cells. Experiments using engineered mutants to spoil each interface, together with PRE probes attached to the membrane or free in solvent, suggest that dimerization through the primary ‘α–α’ interface releases β interfaces from the membrane promoting formation of the secondary ‘α–β’ interaction, potentially initiating nanoclustering. In addition, the small molecule BI-2852 binds at a β–β interface, stabilizing a new dimer configuration that outcompetes native dimerization and blocks the effector-binding site. Our data indicate that KRAS self-association involves a delicately balanced conformational equilibrium between transient states, which is sensitive to disease-associated mutation and small molecule inhibitors. The methods developed here are applicable to biologically important transient interactions involving other membrane-associated proteins.

Studies of membrane-dependent dimerization of KRAS on nanodiscs using paramagnetic NMR titrations and mutagenesis revealed a novel asymmetric ‘α–β’ interface that provides a potential mechanism for the enhanced assembly of KRAS–G12D nanoclusters.     

Synthesis of PEO/4Hb-TaS2 layered nanocomposite

Single-phase layered nanocomposite containing 4Hb-TaS₂ and poly(ethylene oxide) [PEO] has been first synthesized by using the exfoliation-adsorption technique. It has been characterized by powder X-ray diffraction (XRD) and electrical dc resistivity measurements. As the product exhibited lattice expansions along the stacking direction, PEO was intercalated into 4Hb-TaS₂ galleries.     

Relationship between human IgG structure and retention time in hydroxyapatite chromatography with sodium chloride gradient elution

Accurate prediction of the elution tendency of monoclonal antibodies in column chromatography would be beneficial for the efficient setup of purification procedures. Hydroxyapatite chromatography experiments using 37 recombinant human monoclonal antibodies were performed by sodium chloride gradient elution with 5 mM sodium phosphate to correlate the retention times with antibody structures (subclass and light‐chain isotypes). The contribution of metal affinity interactions in the interaction of antibodies with hydroxyapatite was investigated by (i) eliminating 5 mM sodium phosphate in buffers, (ii) comparing sodium chloride versus sodium phosphate gradient elutions, and (iii) using IgG₄ antibodies with a leucine→glutamate mutation. By using antibodies of different subclasses but with identical Fab regions, the elution behavior in sodium chloride elution could be classified by subclass and type of light chain. It is considered that the retention of monoclonal antibodies to hydroxyapatite is affected by the cooperation of phosphoryl cation exchange and metal affinity interactions. The contribution of the metal affinity interactions is greater in the sodium chloride gradient elution method than in the sodium phosphate gradient elution method.     

Genetic and expression analysis of all non‐synonymous single nucleotide polymorphisms in the human deoxyribonuclease I‐like 1 and 2 genes

Members of the human DNase I family, DNase I‐like 1 and 2 (DNases 1L1 and 1L2), with physiological role(s) other than those of DNase I, possess three and one non‐synonymous SNPs in the genes, respectively. However, only limited population data are available, and the effect of these SNPs on the catalytic activity of the enzyme remains unknown. Genotyping of all the non‐synonymous SNPs was performed in three ethnic groups including six different populations using the PCR‐RFLP method newly developed. Asian and African groups including Japanese, Koreans, Ghanaians and Ovambos were typed as a single genotype at each SNP, but polymorphism at only SNP V122I in DNase 1L1 was found in Caucasian groups including Germans and Turks; thus a Caucasian‐specific allele was identified. The DNase 1L1 and 1L2 genes show relatively low genetic diversity with regard to these non‐synonymous SNPs. The level of activity derived from the V122I, Q170H and D227A substituted DNase 1L1 corresponding to SNPs was similar to that of the wild‐type, whereas replacement of the Asp residue at position 197 in the DNase 1L2 protein with Ala, corresponding to SNP D197A, reduced its activity greatly. Thus, SNP V122I in DNase 1L1 exhibiting polymorphism exerts no effect on the catalytic activity, and furthermore SNP D197A in DNase 1L2, affecting its catalytic activity, shows no polymorphism. These findings permit us to postulate that the non‐synonymous SNPs identified in the DNase 1L1 and 1L2 genes may exert no influence on the activity levels of DNases 1L1 and 1L2 in human populations.