Aggregation of the amyloid b-peptide (A b) into insoluble fibrils is a key pathologi-cal event in Alzheimers disease. Zn(II) ion induces significant Ab aggregation at nearly physio-logical concentrations in vitro. In order to explore the induce mechanism, the possible binding modes of Zn(II) in Ab peptide are studied by molecular modeling method. First, the Ab species containing 1,2,4 and 12 peptides are established respectively. And next a Zn(II) ion is manually hold the different sits of the Ab species based on the experimental data and subsequently the coordinate atom and number are assigned. Finally, the optimum binding site is found by the system energy minimization. Modeling results show that in soluble Zn(II) complex, Nt of imidazole ring of His14, O of carbonyl of main-chain, and two O of water occupy the four ligand positions of the tetrahedral complex; in the aggregation of Ab, the His13(Nt)-Zn(II)-His14(Nt) bridges are formed by Zn(II) cross-linking action. Therefore, the possible Zn(II) binding mode obtained by the studies will be helpful to reveal the form mechanism of pathogenic aggregates in brain.
For the uracil-BX3 (X = F, Cl) systems, geometries and binding energies have been calculated by using the Lee-Young-Parr correlation functionals (B3LYP) method of density functional theory (DFT) and the second-order Moller-Plesset (MP2) method of ab initio at the 6- 311+G* or 6-311++G* basis set. Four isomers were found for each system, and then the single-point energy evaluations were performed using the larger basis sets of (6-311+G(2df,p) and aug-cc-pVDZ with DFT method. In the most stable isomer of uracil-BF3 or uracil-BCl3, the boron atom of BX3 (X = F, Cl) connects to the carbonyl oxygen O7 of uracil with a stabilization energy of –46.56 or –31.10 kJ/mol at the B3LYP/6-311+G* level (BSSE corrected). The analyses for combining interaction between BX3 and uracil with the atom-in-molecule theory (AIM) and natural bond orbital method (NBO) have been performed. The results indicate that all isomers were formed with σ-p type interactions between uracil and BX3, in which the carbonyl oxygen offers its lone pair electrons to the empty p orbital of boron atom and the concomitances of charge transfer from uracil to BX3 occur. Moreover, there exists one or two hydrogen bonds in most isomers of uracil-BX3 system and these hydrogen bonds contribute to the stability of the complex systems. Frequency analysis suggests that the stretching vibration of BX3 undergoes a red shift in complexes. Uracil-BF3 complex is more stable than uracil-BCl3 although the distance of B–O is shorter in the latter. Besides, the conversion mechanisms between different isomers of uracil-BF3 have been obtained.
We studied the binding of [Co(phen)2(HPIP)]Cl3 to mismatched d(GCGAGC)2 con- taining two sheared G:A mispairs by NMR. The result shows that the complex was intercalated into G:A region from the minor groove and extended to the major groove, and could selectively recognize the mispairs. 31P NMR indicates that the complex binding induced the change of the phosphate backbone in the mismatched base pairs region.
Cleavage of DNA pUC19 by [Cu(saldien)(NH3)]Cl2 (here, saldien=bis(salicylicdene)- diethylenetriamine) was investigated at different pHs, times, concentrations, and 37℃. It was found that the copper(Ⅱ) complex could cleave DNA without added coreactants.
