Abstract
Cytochrome P450 enzymes are found in all life forms. P450s play an important role in drug metabolism, and have potential uses as biocatalysts. Human P450s are membrane-bound proteins. However, the interactions between P450s and their membrane environment are not well-understood. To date, all P450 crystal structures have been obtained from engineered proteins, from which the transmembrane helix was absent. A significant number of computational studies have been performed on P450s, but the majority of these have been performed on the solubilised forms of P450s. Here we present a multiscale approach for modelling P450s, spanning from coarse-grained and atomistic molecular dynamics simulations to reaction modelling using hybrid quantum mechanics/molecular mechanics (QM/MM) methods. To our knowledge, this is the first application of such an integrated multiscale approach to modelling of a membrane-bound enzyme. We have applied this protocol to a key human P450 involved in drug metabolism: CYP3A4. A biologically realistic model of CYP3A4, complete with its transmembrane helix and a membrane, has been constructed and characterised. The dynamics of this complex have been studied, and the oxidation of the anticoagulant R-warfarin has been modelled in the active site. Calculations have also been performed on the soluble form of the enzyme in aqueous solution. Important differences are observed between the membrane and solution systems, most notably for the gating residues and channels that control access to the active site. The protocol that we describe here is applicable to other membrane-bound enzymes.
Highlights
Molecular simulation methods are widely used to study membrane proteins. [1] An advantage of these methods is that the protein of interest can be studied in an approximately native environment
[2] hybrid quantum mechanics/molecular mechanics (QM/molecular mechanical (MM)) methods enable the calculation of reaction mechanisms in enzymes to high accuracy, whilst explicitly including the effects of the surrounding enzyme and solvent environment
[3] In order to model the reactions of enzymes in large biological assemblies, multiscale methods, which span the range from CG through AT up to the QM/MM level, will allow us to answer these important questions in chemical biology
Summary
Molecular simulation methods are widely used to study membrane proteins. [1] An advantage of these methods is that the protein of interest can be studied in an approximately native environment. It may be useful or necessary to investigate levels of detail ranging from protein-lipid interactions on long timescales, to chemical reactions and electronic structure. This type of application is well exemplified by the cytochrome P450 enzymes, where the questions of adverse drug interactions and of substrate access are still not well-understood. [3] In order to model the reactions of enzymes in large biological assemblies, multiscale methods, which span the range from CG through AT up to the QM/MM level, will allow us to answer these important questions in chemical biology. The framework that we introduce here allows these questions to be answered
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
