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Content archived on 2024-06-18

Understanding the molecular mechanism of enzymatic processes by a combination of NMR spectroscopy and molecular dynamics simulations

Final Report Summary - MMEP (Understanding the molecular mechanism of enzymatic processes by a combination of NMR spectroscopy and molecular dynamics simulations)

FINAL PUBLISHABLE SUMMARY REPORT

This project aimed at providing an accurate characterization of the enzymatic processes carried out by CypA and by PagP, by studying the relationship between structure, dynamics and reaction pathways. We addressed this goal through a multidisciplinary approach that combined measurements obtained by NMR spectroscopy with advanced molecular dynamics simulations. We have developed at first a robust theoretical and computational framework to combine the use of NMR experimental data and molecular dynamics simulations.
The Maximum Entropy Principle has been employed to show that it is possible to integrate experimental data in standard molecular dynamics simulations by means of replica-averaged restraints. In this approach experimental data are used to restrained multiple copies of a simulation and this result in an effective correction of the force-field so that the simulation is in better agreement with the employed experimental data. Furthermore we have integrated this approach with advanced sampling methods in order to alleviate the problem of conformational sampling. In particular we have employed metadynamics.
This framework has been successfully applied to a number of cases and in particular has given us the possibility of unveiling the details underlying the catalysis of an important enzyme, Cyclophilin A. This involves the use of an electrostatic field that exert a force on a dipole of its substrate. The dipole is then used as a handle to make the isomerization reaction happen. We have designed a striking test for this model that resulted in a single atom substitution on the substrate that, we have shown, is enough to regulate the turnover.
All the development have been made public using open source software platforms.