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The TNG50 Simulation of the IllustrisTNG Project: Bridging the Gap Between Large Cosmological Volumes and Resolved Galaxies Read chapter Read first chapter

2019 | OriginalPaper | Chapter

A Multi-resolution Approach to the Simulation of Protein Complexes in a Membrane Bilayer

Authors : Goutam Mukherjee, Prajwal Nandekar, Ghulam Mustafa, Stefan Richter, Rebecca C. Wade

Published in: High Performance Computing in Science and Engineering ' 18

Publisher: Springer International Publishing

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Abstract

We describe a transferable multiresolution computational approach to build and simulate complexes of two proteins—cytochrome P450 (CYP) and CYP reductase (CPR)—in a membrane bilayer using Brownian dynamics (BD) and all-atom molecular dynamics (MD) simulations. Our benchmarks showed that MD simulations of these systems could be carried out efficiently with up to 180 nodes (4320 cores) using NAMD version 2.12. Our results provide a basis for defining the ensemble of electron transfer-competent arrangements of CYP-CPR-membrane complexes and for understanding differences in the interactions with CPR of different CYPs, which have implications for CYP-mediated drug metabolism and the exploitation of CYPs as drug targets. This work was carried out in the DYNATHOR (DYNAmics of THe complex of cytOchrome P450 and cytochrome P450 Reductase in a phospholipid bilayer) project at HLRS.

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Metadata
Title
A Multi-resolution Approach to the Simulation of Protein Complexes in a Membrane Bilayer
Authors
Goutam Mukherjee
Prajwal Nandekar
Ghulam Mustafa
Stefan Richter
Rebecca C. Wade
Copyright Year
2019
Book
High Performance Computing in Science and Engineering ' 18

Print ISBN: 978-3-030-13324-5

Electronic ISBN: 978-3-030-13325-2

Copyright Year: 2019

DOI
https://doi.org/10.1007/978-3-030-13325-2_32

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