Structural Studies of Autophagy-Related Proteins

Methods Mol Biol. 2019:1880:17-56. doi: 10.1007/978-1-4939-8873-0_2.

Abstract

Information about the structure and dynamics of proteins is crucial for understanding their physiological functions as well as for the development of strategies to modulate these activities. In this chapter we will describe the work packages required to determine the three-dimensional structures of proteins involved in autophagy by using X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. Further we will provide instructions how to perform a molecular dynamics (MD) simulation using GABARAP as example protein.

Keywords: MD simulation; NMR spectroscopy; X-ray crystallography.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Autophagy-Related Proteins / chemistry*
  • Cryopreservation / methods
  • Cryoprotective Agents / chemistry
  • Crystallization / methods
  • Crystallography, X-Ray / methods*
  • Humans
  • Molecular Dynamics Simulation
  • Nuclear Magnetic Resonance, Biomolecular / methods*
  • Protein Conformation
  • Software
  • Vesicular Transport Proteins / chemistry

Substances

  • ATG101 protein, human
  • Autophagy-Related Proteins
  • Cryoprotective Agents
  • Vesicular Transport Proteins