Computational design of a lipase for catalysis of the Diels-Alder reaction.
Combined molecular docking, molecular dynamics (MD) and density functional theory (DFT) studies have been employed to study catalysis of the Diels-Alder reaction by a modified lipase. Six variants of the versatile enzyme Candida Antarctica lipase B (CALB) have been rationally engineered in silico based on the specific characteristics of the pericyclic addition. A kinetic analysis reveals that hydrogen bond stabilization of the transition state and substrate binding are key components of the catalytic process. In the case of substrate binding, which has the greater potential for optimization, both binding strength and positioning of the substrates are important for catalytic efficiency. The binding strength is determined by hydrophobic interactions and can be tuned by careful selection of solvent and substrates. The MD simulations show that substrate positioning is sensitive to cavity shape and size, and can be controlled by a few rational mutations. The well-documented S105A mutation is essential to enable sufficient space in the vicinity of the oxyanion hole. Moreover, bulky residues on the edge of the active site hinders the formation of a sandwich-like nearattack conformer (NAC), and the I189A mutation is needed to obtain enough space above the face of the α,β-double bond on the dienophile. The double mutant S105A/I189A performs quite well for two of three dienophiles. Based on binding constants and NAC energies obtained from MD simulations combined with activation energies from DFT computations, relative catalytic rates (v(cat)/v(uncat)) of up to 103 are predicted.
Linder
Mats
M
Physical Chemistry, Royal Institute of Technology (KTH), Stockholm, Sweden. linder@physchem.kth.se
Hermansson
Anders
A
Liebeschuetz
John
J
Brinck
Tore
T
D019943:Amino Acid Substitution; D001665:Binding Sites; D002384:Catalysis; D017076:Computer-Aided Design; D006860:Hydrogen Bonding; D007700:Kinetics; D008049:Lipase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D009154:Mutation / Q000235:genetics; D011485:Protein Binding; D015202:Protein Engineering; D013379:Substrate Specificity
D008049:Lipase