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Dynathor: Dynamics of the Complex of Cytochrome P450 and Cytochrome P450 Reductase in a Phospholipid Bilayer

  • Xiaofeng Yu
  • Daria B. Kokh
  • Prajwal Nandekar
  • Ghulam Mustafa
  • Stefan Richter
  • Rebecca C. Wade
Conference paper

Abstract

The Dynathor project aims at understanding the interaction of cytochrome P450 (CYP, P450) enzymes and their redox partner, cytochrome P450 reductase (CPR), in a phospholipid bilayer. Through simulation studies on the HLRS CRAY systems (initially XE6, later on XC40), we investigated the interactions of models of membrane-bound P450s (CYP51 and CYP1A1) and CPR. A model of membrane-bound T. brucei CYP51 and the human CPR was successfully built and simulated for 217.5 ns. A model of human CYP1A1 and the human CPR in a phospholipid bilayer was also built and is being simulated. These models can be used as starting points to understand the selectivity of the interactions of CYPs with CPR in the native membrane-bound forms, and thus may aid drug discovery projects.

Furthermore, we evaluated the method of Random Acceleration Molecular Dynamics (RAMD) for use in calculating relative residence times of proteins with small molecules. This would allow the computation of relative off rates for drug molecules. As a small model system for this evaluation, we use the N-terminal domain of human heat shock protein 90 (HSP90) and a set of different ligands. The obtained RAMD simulated residence times show a clear correlation with experimental values.

Keywords

Nicotinamide Adenine Dinucleotide Phosphate Flavin Adenine Dinucleotide Nicotinamide Adenine Dinucleotide Phosphate Cytochrome P450 Reductase Redox Partner 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgements

We gratefully acknowledge the support of the Klaus Tschira Foundation, the German Academic Exchange Service (DAAD) for scholarships to Prajwal Nandekar and Ghulam Mustafa as well as the EU/EFPIA Innovative Medicines Initiative (IMI) Joint Undertaking, “Kinetics for Drug Discovery”, K4DD (grant no. 115366). Finally, we would like to thank the HLRS for providing CPU time for this project.

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Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  • Xiaofeng Yu
    • 1
  • Daria B. Kokh
    • 1
  • Prajwal Nandekar
    • 1
  • Ghulam Mustafa
    • 1
  • Stefan Richter
    • 1
  • Rebecca C. Wade
    • 1
    • 2
    • 3
  1. 1.HITS gGmbHHeidelbergGermany
  2. 2.Center for Molecular Biology (ZMBH), DKFZ-ZMBH AllianceHeidelberg UniversityHeidelbergGermany
  3. 3.Interdisciplinary Center for Scientific Computing (IWR)Heidelberg UniversityHeidelbergGermany

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