Login / Signup

Comparison of NMR and crystal structures of membrane proteins and computational refinement to improve model quality.

Julia Koehler LemanAndrew R D'AvinoYash BhatnagarJeffrey J Gray
Published in: Proteins (2017)
Membrane proteins are challenging to study and restraints for structure determination are typically sparse or of low resolution because the membrane environment that surrounds them leads to a variety of experimental challenges. When membrane protein structures are determined by different techniques in different environments, a natural question is "which structure is most biologically relevant?" Towards answering this question, we compiled a dataset of membrane proteins with known structures determined by both solution NMR and X-ray crystallography. By investigating differences between the structures, we found that RMSDs between crystal and NMR structures are below 5 Å in the membrane region, NMR ensembles have a higher convergence in the membrane region, crystal structures typically have a straighter transmembrane region, have higher stereo-chemical correctness, and are more tightly packed. After quantifying these differences, we used high-resolution refinement of the NMR structures to mitigate them, which paves the way for identifying and improving the structural quality of membrane proteins.
Keyphrases
  • high resolution
  • magnetic resonance
  • solid state
  • mass spectrometry
  • computed tomography
  • tandem mass spectrometry
  • quality improvement