How a crosslinker agent interacts with the ß-glucosidase enzyme surface in an aqueous solution: Insight from quantum mechanics calculations and molecular dynamics simulations.

In this study, surficial interactions of glutaraldehyde (GA) as an important crosslinker agent with the ß-glucosidase (BGL) enzyme surface were investigated by theoretical methods. Since the inherent constraints of experimental methods limit their application to find the molecular perspective of these significant interactions in enzyme immobilization, theoretical methods were used as a complementary tool to understand this concept. The Minnesota density functional calculations showed that the chair conformations of the oxane-2,6-diol form of the GA were more stable than its free aldehyde form. MD simulations of propylamine-GA molecules, as a representative of attached-GA, in aqueous solutions of different concentrations were done to determine the molecular basis of surficial interactions with the BGL surface. The root mean square fluctuation (RMSF) demonstrated that the maximum flexibility of the BGL enzyme belonged to 460-480 residues in all solutions. Based on the spatial distribution function (SDF) analysis, the active site entrance was the most favored region to accumulate solute molecules. Radial distribution function (RDF) results showed that all forms of propylamine-GA molecules interacted from their head side with the lysine residues of BGL, which Lys247, Lys376, and Lys384 were found to be the most interactive lysine residues. Also, hydrogen bond (HB) analysis from two viewpoints confirmed HB formation possibility between propylamine-GA molecules and these lysine residues. These results explained which regions of the BGL have the maximum possibility to interact and link to GA and help us in understanding the process of enzyme immobilization.

Configurational study of amino-functionalized silica surfaces: A density functional theory modeling.

Despite extensive studies of the amino-functionalized silica surfaces, a comprehensive investigation of the effects of configuration and hydrolysis of 3-aminopropyltriethoxysilan (APTES) molecules attached on silica has not been studied yet. Therefore, the methods of quantum mechanics were used for the study of configuration and hydrolysis forms of APTES molecules attached on the surface. For this purpose, five different categories based on the number of hydrolyzed ethoxy groups including 16 configurations were designed and analyzed by the density functional theory (DFT) method. The steric hindrance as an effective factor on the stability order was extracted from structural analysis. Other impressive parameters such as the effects of hydrogen bond and electron delocalization energy were obtained by using the atoms in molecules (AIM) and natural bond orbitals (NBO) theories. Consequently, it was found that the stability of configurations was attributed to steric effects, hydrogen bond numbers and electron delocalization energy. The maximum stability was achieved when at least two of these parameters cooperate with each other.