MMEP · Understanding the molecular mechanism of enzymatic processes by a combination of NMR spectroscopy and molecular dynamics simulations
FP7 — People (Marie Curie Actions)
- Duration
- 2012-02-01 → 2014-01-31
- EU contribution
- €200,050
- Participants
- 1
- Scheme
- MC-IEF
Lines connect the coordinator with its partners.
Results in brief
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.
Data: CORDIS, © European Union
Project objective
Essentially all the biochemical processes taking place in living organisms require the intervention of enzymes, which are proteins capable of increasing the rates of chemical reactions by up to 15 orders of magnitude. A detailed definition of the molecular basis of the action of enzymes will not only represent a key advance in our understanding of the fundamental principles of macromolecular behavior, but also provide new opportunities for the rational development of effective treatments for human disease, and for the control of chemical processes in biotechnology. In this application, we propose to characterize in detail the enzymatic processes of two important proteins, cyclophilin A and PagP, by using an interdisciplinary approach in which experimental measurements are incorporated as structural restraints in molecular dynamics simulations. The innovative aspect of this project is the use of chemical shifts, which are the parameters that can be measured most readily and accurately in nuclear magnetic resonance spectroscopy, for protein structure determination. This approach, which has been pioneered in the host lab, enables to determine with high accuracy the structures of proteins in states that are not easily accessible through other types of measurements. We will therefore have the opportunity to gain access to conformations that are invisible by standard methods of structural biology, and in this way to clarify the mechanism of action of two important enzymes.""
Original text from CORDIS.
Participants
- THE CHANCELLOR MASTERS AND SCHOLARS OF THE UNIVERSITY OF CAMBRIDGE · CAMBRIDGECoordinatorUnited Kingdom
Links
Data: CORDIS, © European Union