HomePh.D. Study at IOCBArchive - 2018Physical and Computational Chemistry

Physical and Computational Chemistry

Tutor RNDr. Luboš Rulíšek D.Sc.
Team Luboš Rulíšek
Topic Computer Design of Catalytic Metallopeptides
Faculty PřF UK

For many decades, metalloenzymes have inspired and fascinated chemists as some of the most efficient catalysts in nature.1 Many fundamental and difficult reactions, such as C‑H activations, O=O and N≡N bond cleavages, are carried out under mild (often physiological) conditions at the metal centres in metalloenzyme active sites.2 Therefore, understanding their reaction mechanisms (or catalytic action) is of key importance for the progress in catalysis in general. On the one hand, coordination chemists have used small molecular models to understand these systems better; on the other hand, numerous recent contributions from theoretical and computational chemistry have greatly assisted in elucidating the metalloenzyme catalysis at the atomic or even electronic level.3 In parallel, there are ongoing efforts to design small metalloproteins or even metallopeptides that might approach the catalytic efficiency of the parent metalloenzyme. The first reports of successfully implemented structural or catalytic metal sites into non-native environments date back to the 1990s, whereas the recent progress made in the field places us into the position where we ‘begin to meet the challenge of building a metalloenzyme systematically from the bottom up by engineering and analyzing interactions directly around the metal site and beyond.’. Therefore, computer-assisted design of novel minimalistic functional metallopeptides does not look as the science-fiction today and it may open new horizons in the environment-friendly catalysis.4,5

(1) Ragsdale, S. W. Chem. Rev. 2006, 106, 3317.
(2) (a) Balcells, D.; Clot, E.; Eisenstein, O. Chem. Rev. 2010, 110, 749; (b) Seefeldt, L. C.; Hoffman, B. M.; Dean, D. R. Annu. Rev. Biochem. 2009, 78, 701. (c) Dance, I. Dalton Trans. 2010, 2972.
(3) Siegbahn, P. E. M.; Borowski, T. Acc. Chem. Res. 2006, 39, 729.
(4) Bím, D.; Svobodová, E.; Eigner, V.; Rulíšek, L.; Hodačová, J.: Copper(II) and Zinc(II) Complexes of Conformationally Constrained Polyazamacrocycles as Efficient Catalysts for RNA Model Substrate Cleavage in Aqueous Solution at Physiological pH. Chem. Eur. J. 2016, 22, 10426‑10437.
(5) Kožíšek, M.; Svatoš, A.; Buděšínský, M.; Muck, A.; Bauer, M. C.; Kotrba, P.; Ruml, T.; Havlas, Z.; Linse, S.; Rulíšek, L.: Molecular Design of Specific Metal-Binding Peptide Sequences from Protein Fragments. Theory and Experiment. Chem. Eur. J. 2008, 14, 7836‑7846.