Computational strategies for the design of new enzymatic functions

Abstract

In this contribution, recent developments in the design of biocatalysts are reviewed with particular emphasis in the de novo strategy. Studies based on three different reactions, Kemp elimination, Diels-Alder and Retro-Aldolase, are used to illustrate different success achieved during the last years. Finally, a section is devoted to the particular case of designed metalloenzymes. As a general conclusion, the interplay between new and more sophisticated engineering protocols and computational methods, based on molecular dynamics simulations with Quantum Mechanics/Molecular Mechanics potentials and fully flexible models, seems to constitute the bed rock for present and future successful design strategies.

Keywords: De novo design; Diels–Alder; Kemp elimination; Molecular dynamics; Protein design; QM/MM; Retro-Aldolase.

Figure 1

Schematic representation of the de novo design of new enzymes

Figure 2

Schematic representation of an artificial metalloenzyme, where a metal ligand complex is posed in the cavity of an enzyme by means of different possible anchoring strategies.

Figure 3

Schematic representation of of proposed artificial metalloenzymes based on Cu(II) complexes grafted on the dimer interface of a protein.

Figure 4

Schematic representation of of proposed artificial metalloenzymes based on modular assembly of a copper complex of a non-chiral ligand to a DNA scaffold.

Figure 5

Crystal structure of the binuclear center of cytochrome ba3 oxidase (PDB code 1XME).

Figure 6

Schematic representation of artificial metalloenzymes based on the biotinavidin technology.

Scheme 1

Representation of the base-catalyzed Kemp elimination

Scheme 2

Representation of the Diels Alder cycloaddition reaction

Scheme 3

Representation of the Retro-Aldol reaction mechanism

Scheme 4

Representation of the Diels-Alder cycloadition between azachalcone and cyclopentadiene