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Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation
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Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation

Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation

DOI:
10.3791/61125-v

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15:05 min

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May 20, 2020

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, , ,
1Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering,Åbo Akademi University, 2Medicity Research Laboratories and Institute of Biomedicine,University of Turku, 3Turku Bioscience Centre,University of Turku and Åbo Akademi University, 4Department of Oncology and Radiotherapy,University of Turku and Turku University Hospital

Chapters

  • 00:04Introduction
  • 00:47Structure Preparation
  • 04:12System Setup
  • 05:17Molecular Dynamics Simulation
  • 07:15Visual Inspection Analysis
  • 08:29Root-Mean Square Deviation (RMSD) and Root-Mean Square Fluctuation (RMSF) Analysis
  • 09:58Hydrogen Bond Analysis
  • 10:57Free Energy Calculations
  • 12:25Representative Results: Molecular Dynamics Simulation of EGFR Somatic Mutations
  • 14:23Conclusion

Summary

자동 번역

자동 번역

The objective of this protocol is to use molecular dynamics simulations to examine the dynamic structural changes that occur due to activating mutations of the EGFR kinase protein.

Tags

Molecular Dynamics SimulationEGFRSomatic MutationsProtein StructureKinaseConformational ChangesLigand BindingCancerWild-typeDeletion MutantActiveInactiveAsymmetric DimerKymeraProtein Data BankModeling

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