Enzyme immobilization studied through molecular dynamic simulations

Abstract

In recent years, simulations have been used to great advantage to understand the structural and dynamic aspects of distinct enzyme immobilization strategies, as experimental techniques have limitations in establishing their impact at the molecular level. In this review, we discuss how molecular dynamic simulations have been employed to characterize the surface phenomenon in the enzyme immobilization procedure, in an attempt to decipher its impact on the enzyme features, such as activity and stability. In particular, computational studies on the immobilization of enzymes using i) nanoparticles, ii) self-assembled monolayers, iii) graphene and carbon nanotubes, and iv) other surfaces are covered. Importantly, this thorough literature survey reveals that, while simulations have been primarily performed to rationalize the molecular aspects of the immobilization event, their use to predict adequate protocols that can control its impact on the enzyme properties is, up to date, mostly missing.

Keywords: carbon nanotube; enzyme immobilization; graphene; molecular dynamics simulations; nanoparticles; self assembled monolayers.

FIGURE 1

An illustration for different types of enzyme immobilization methods.

FIGURE 2

Schematic view of most (bottom) and least (top) attractive orientations of chymotrypsin (left) and lysozyme (right) placed over the SiO₂ surface. The scheme is based upon Figure 4 from Hildebrand et al., 2015.

FIGURE 3

Diagrammatic representation of cytochrome c heme group orientation with respect to different SAM surfaces. The scheme is based upon Figure 2 from Zhou et al., 2004, Figure 12 from Xie et al., 2015, Figure 3 from Rivas et al., 2005 and Figure 6 from Peng et al., 2016.

FIGURE 4

Scheme showing orientation of the RNase A active site with respect to different types of SAM surfaces. The scheme is based upon Figure 3 from Liu et al., 2015b.