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

Julia Koehler Leman, Andrew R. D'Avino, Yash Bhatnagar, Jeffrey J. Gray

Research output: Contribution to journalArticlepeer-review

2 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)57-74
Number of pages18
JournalProteins: Structure, Function and Bioinformatics
Issue number1
StatePublished - Jan 2018


  • Rosetta software
  • membrane proteins
  • protein modeling
  • protein structure
  • structural quality
  • structure refinement

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology


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