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

Goutam Mukherjee, Prajwal Nandekar, Ghulam Mustafa, Stefan Richter and Rebecca C. Wade ()
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Goutam Mukherjee: Heidelberg Institute for Theoretical Studies (HITS), Molecular and Cellular Modeling Group
Prajwal Nandekar: Heidelberg Institute for Theoretical Studies (HITS), Molecular and Cellular Modeling Group
Ghulam Mustafa: Heidelberg Institute for Theoretical Studies (HITS), Molecular and Cellular Modeling Group
Stefan Richter: Heidelberg Institute for Theoretical Studies (HITS), Molecular and Cellular Modeling Group
Rebecca C. Wade: Heidelberg Institute for Theoretical Studies (HITS), Molecular and Cellular Modeling Group

A chapter in High Performance Computing in Science and Engineering ' 18, 2019, pp 505-514 from Springer

Abstract: 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.

Date: 2019
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Persistent link: https://EconPapers.repec.org/RePEc:spr:sprchp:978-3-030-13325-2_32

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DOI: 10.1007/978-3-030-13325-2_32

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