The single chain antibody scFv2F3 can be converted into selenium-containing Se-scFv2F3 by chemical mutation of the Ser residues. With antibody fragment 1NQB as a template, the catalytic domain of scFv2F3 was built by using homology modeling and molecular dynamics(MD) simulations. On the basis of the 3D model, we discussed the importance of Ser52 as the chemical modification site and redesigned the protein groups nearby Ser52 via introducing a catalytic triad. The following 10 ns MD results show that the designed Ser52-Trp29-Gln72 catalytic triad is stable enough and high close to the local structural features of native glutathione peroxidases(GPX). Our results may be useful for creating a new abzyme with higher catalytic efficiency and stability.
By means of molecular dynamics simulation, the transition of the conformations of polyvinyl chloride during a cooling process from 600 to 300 K was studied. The results show that the amorphous polyvinyl chloride chain experiences the melting state, elastic state and glass state and the conformations can be characterized by the increases of the trans-state of C—C—C—C and the near gauche-state of C—C—C—Cl with the decrease of temperature. It is found that the transition of the conformations is driven mainly by the Coulomb interaction between chain segments.
YANG Hua LI Ze-sheng YANG Yong-biao ZHANG Xiu-bin SUN Chia-chung
The density functional theory at the B3LYP/6-311G(d, p) level was applied to exploring the inhibition mechanism of cholinesterases by carbamate. The results indicate that the inhibition reactions with or without the catalytic effect of the catalytic triad in cholinesterases underwent a two-step addition-elimination mechanism, which is in good agreement with the proposed mechanism. The solvent has a strong effect on the inhibition reactions and the reaction with the catalytic triad in the solvent phase is close to the real reaction under biological condition.
