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Complexes++: Efficient and versatile coarse-grained simulations of protein complexes and their dense solutions

MPG-Autoren
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Linke,  Max       
Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max Planck Society;

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Quoika,  Patrick K.       
Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max Planck Society;
Center for Protein Assemblies (CPA), Physics Department, Chair of Theoretical Biophysics (T38), Technical University of Munich, Germany;

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Köfinger,  Jürgen       
Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max Planck Society;

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Hummer,  Gerhard       
Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max Planck Society;
Department of Physics, Goethe University Frankfurt, Frankfurt am Main, Germany;

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Zitation

Linke, M., Quoika, P. K., Bramas, B., Köfinger, J., & Hummer, G. (2022). Complexes++: Efficient and versatile coarse-grained simulations of protein complexes and their dense solutions. The Journal of Chemical Physics, 157(20): 204802. doi:10.1063/5.0117520.


Zitierlink: https://hdl.handle.net/21.11116/0000-000B-A844-B
Zusammenfassung
The interior of living cells is densely filled with proteins and their complexes, which perform multitudes of biological functions. We use coarse-grained simulations to reach the system sizes and time scales needed to study protein complexes and their dense solutions and to interpret experiments. To take full advantage of coarse-graining, the models have to be efficiently implemented in simulation engines that are easy to use, modify, and extend. Here, we introduce the Complexes++ simulation software to simulate a residue-level coarse-grained model for proteins and their complexes, applying a Markov chain Monte Carlo engine to sample configurations. We designed a parallelization scheme for the energy evaluation capable of simulating both dilute and dense systems efficiently. Additionally, we designed the software toolbox pycomplexes to easily set up complex topologies of multi-protein complexes and their solutions in different thermodynamic ensembles and in replica-exchange simulations, to grow flexible polypeptide structures connecting ordered protein domains, and to automatically visualize structural ensembles. Complexes++ simulations can easily be modified and they can be used for efficient explorations of different simulation systems and settings. Thus, the Complexes++ software is well suited for the integration of experimental data and for method development.