Cation-Specific Effects on Enzymatic Catalysis Driven by Interactions at the Tunnel Mouth

Authors

Stepankova, V., Paterova, J., Damborsky, J., Jungwirth, P., Chaloupkova, R., Heyda, J.

Source

JOURNAL OF PHYSICAL CHEMISTRY B 117: 6394-6402 (2013)

Abstract

Cationic specificity which follows the Hofmeister series has been established for the catalytic efficiency of haloalkane dehalogenase LinB by a combination of molecular dynamics simulations and enzyme kinetic experiments. Simulations provided a detailed molecular picture of cation interactions with negatively charged residues on the protein surface, particularly at the tunnel mouth leading to the enzyme active site. On the basis of the binding affinities, cations were ordered as Na+ > K+ > Rb+ > Cs+. In agreement with this result, a steady-state kinetic analysis disclosed that the smaller alkali cations influence formation and productivity of enzyme–substrate complexes more efficiently than the larger ones. A subsequent systematic investigation of two LinB mutants with engineered charge in the cation-binding site revealed that the observed cation affinities are enhanced by increasing the number of negatively charged residues at the tunnel mouth, and vice versa, reduced by decreasing this number. However, the cation-specific effects are overwhelmed by strong electrostatic interactions in the former case. Interestingly, the substrate inhibition of the mutant LinB L177D in the presence of chloride salts was 7 times lower than that of LinB wild type in glycine buffer. Our work provides new insight into the mechanisms of specific cation effects on enzyme activity and suggests a potential strategy for suppression of substrate inhibition by the combination of protein and medium engineering.

Full text

Citation

Stepankova, V., Paterova, J., Damborsky, J., Jungwirth, P., Chaloupkova, R., Heyda, J., 2013: Cation-Specific Effects on Enzymatic Catalysis Driven by Interactions at the Tunnel Mouth. Journal of Physical Chemistry B 117: 6394-6402.

Ondrej Vavra celebrating success with his presentation on CaverDock
Lecture by Dr. Stavrakis from ETH Zurich
High evaluation of the team’s research performance
Klaudia Chmelova and Veronika Liskova passed doctoral state exam
ELIXIR CZ annual conference 15 – 16 Nov, 2017
New video explaining the goals of Rafts4Biotech EU project
Invitation to a presentation by Synthetic Genomics