A multi-resolution model to capture both global fluctuations of an enzyme and molecular recognition in the ligand-binding site

Abstract

In multi-resolution simulations, different system components are simultaneously modelled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is needed in the active site to capture the chemistry of substrate binding. Global properties of the rest of the protein also play an essential role, determining the structure and fluctuations of the binding site; however, these can be modelled on a coarser level. Similarly, in the most computationally efficient scheme only the solvent hydrating the active site requires atomistic detail. We present a methodology to couple atomistic and coarse-grained protein models, while solvating the atomistic part of the protein in atomistic water. This allows a free choice of which protein and solvent degrees of freedom to include atomistically, without loss of accuracy in the atomistic description. This multi-resolution methodology can successfully model stable ligand binding, and we further confirm its validity via an exploration of system properties relevant to enzymatic function. In addition to a computational speedup, such an approach can allow the identification of the essential degrees of freedom playing a role in a given process, potentially yielding new insights into biomolecular function.

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Cited by in corpus (4)

• ESPResSo++ 2.0: Advanced methods for multiscale molecular simulation
• Open Boundary Simulations of Proteins and Their Hydration Shells by Hamiltonian Adaptive Resolution Scheme
• Towards Open Boundary Molecular Dynamics Simulation of Ionic Liquids
• Extending Hamiltonian-Adaptive Resolution Simulation to Interfaces: An Updated LAMMPS Implementation and Application to Porous Solids