Összes szerző

Letif Mones

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Hoffka Gyula
The role of conformational heterogeneity in the evolution of enzymes

Aug 29 - csütörtök

08:45 – 09:05

Elméleti biofizika

E35

The role of conformational heterogeneity in the evolution of enzymes

Mónika Fuxreiter1, Gyula Hoffka1, Letif Mones2

1MTA-DE Laboratory of Protein Dynamics, Department of Biochemistry and Molecular Biology, University of Debrecen

2Department of Engineering, University of Cambridge

Designing artificial enzymes to catalyse reactions, which do not occur in Nature is a challenge for computational biology. The traditional procedure largely ignores protein motions, and exploits an interaction between a fixed quantum zone (QM) corresponding to the active site and a protein structure framework. The efficiency of such designs however, lags much behind that of natural enzymes. The only exception is the Kemp eliminase HG-3.17 [1], which has a catalytic activity comparable to the parent xylanase enzyme. We have employed multiscale QM/MM calculations to elucidate the molecular driving forces of the directed evolution process. Applying the Empirical Valence Bond [2] framework and the Free Energy Perturbation/Umbrella Sampling (FEP/US) method, we found that the reorganization energy is optimized throughout the development of HG-3.17 and enabled to suppress the promiscuous activities. Surprisingly, two conformers mutually play a role in optimization of the activity, and only the heterogeneous ensemble is capable to reproduce the experimental catalytic barriers. Determination of individual residue contributions highlighted the interplay between the different conformers and the optimization of the specific reaction. To our knowledge, this is the first example, where a conformationally heterogeneous system was involved in shaping enzymatic activity.

References

[1] R. Blomberg, H. Kries, D. M. Pinkas, P. R. Mittl, H. K. Privett, S. L. Mayo, D. Hilvert (2013) Nature, 503:418-421

[2] A. Warshel, R.M. Weiss, An empirical valence bond approach for comparing reactions in solutions and in enzymes, J. Am. Chem. Soc. (1980) 102: 6218–6226