engleski

Molecular modelling-help in an experiment on protein design

Understanding of protein behaviour and functioning in a living organism is crucial for understanding life. To achieve this, the structural and dynamical information about protein complexes is valuable and could be further exploit for protein engineering or drug design purposes. We studied two sets of protein-protein complexes: a) between extracellular ribonuclease barnase and its intracellular inhibitor barstar, and b) between the small GTP binding Ras proteins and their effectors, protein kinase Raf and RalDGS. Using the COMBINE (COMparative BINding Energy) approach1, 2 we derived 3D QSAR models of predictive value3 and developed a procedure that might be useful for planning experiments on protein complexes. This approach is based upon the assumption that the binding free energy ( G) can be correlated with a subset of suitably weighted energy components (ui) determined from the structures of the two proteins in bound and unbound forms, . Similar study we performed for the complexes between BCL (Burkholderia cepacea lipase) and secondary alcohol esters.4, 5 Since the binding mode for the slow reaction secondary alcohol enantiomer, predicted by molecular modelling differ from the one determined experimentally, we accomplished a series of quantum mechanical6 and QM/MM studies in order to elucidate possible reaction pathways. For each enantiomer of 1-phenoxy-2-butanol ester we considered two different binding modes (theoretical and experimental7), and modelled chemical transformation of the covalent to the non-covalent protein-substrate (either alcohol or ester) complexes.

molecular modelling; proteins

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