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 journalArticle

Abstract

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
Volume86
Issue number1
DOIs
StatePublished - Jan 1 2018

Keywords

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

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology

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