Molecular mechanism of carbon nanotube to activate Subtilisin Carlsberg in polar and non-polar organic media

Abstract

In the work, we mainly used molecular dynamics (MD) simulation and protein structure network (PSN) to study subtilisin Carlsberg (SC) immobilized onto carbon nanotube (CNT) in water, acetonitrile and heptane solvents, in order to explore activation mechanism of enzymes in non-aqueous media. The result indicates that the affinity of SC with CNT follows the decreasing order of water > acetonitrile > heptane. The overall structure of SC and the catalytic triad display strong robustness to the change of environments, responsible for the activity retaining. However, the distances between two β-strands of substrate-binding pocket are significantly expanded by the immobilization in the increasing order of water < acetonitrile < heptane, contributing to the highest substrate-binding energy in heptane media. PSN analysis further reveals that the immobilization enhances structural communication paths to the substrate-binding pocket, leading to its larger change than the free-enzymes. Interestingly, the increase in the number of the pathways upon immobilization is not dependent on the absorbed extent but the desorbed one, indicating significant role of shifting process of experimental operations in influencing the functional region. In addition, some conserved and important hot-residues in the paths are identified, providing molecular information for functional modification.

Enzyme immobilization studied through molecular dynamic simulations

“…CNT surfaces were also used in order to understand the enzyme activation mechanism in non-aqueous media. The subtilisin carlsberg (SC) enzyme was immobilized onto CNT using water, acetonitrile and heptane as solvents ( Zhang et al, 2016 ). It was found that the affinity of SC on CNT decreases with acetonitrile and in more degree with heptane, in contrast to water.…”

Interactions between Endohedral Metallofullerenes and Proteins: The Gd@C60–Lysozyme Model

“…To estimate the binding energy between lysozyme and Gd@C 60 and their components, we carried out a MM-GBSA analysis of the trajectory. This methodology has provided valuable information to estimate the interaction between proteins and carbon nanomaterials. − …”

Recent Developments and Applications of the MMPBSA Method

“…The escape barrier from the binding site is ~21 kcal/mol as calculated via the umbrella sampling method, in good agreement with the MMPBSA result. MMPBSA was also used in the theoretical design of the cyclic lipopeptide nanotube as a molecular channel in the lipid bilayer (Izadyar et al, 2015 ; Khavani et al, 2015 , 2017 ), in the study of the enzyme immobilization mechanism of alpha-chymotrypsin onto carbon nanotubes in organic media (Zhang L. Y. et al, 2015 ), and the mechanism of carbon nanotube activation of subtilisin Carlsberg in polar and non-polar organic media (Zhang L. Y. et al, 2016 ).…”