Inward-facing glycine residues create sharp turns in β-barrel membrane proteins

Zijian Zhang, David Ryoo, Curtis Balusek, Atanu Acharya, Marcella Orwick Rydmark, Dirk Linke, James C. Gumbart

Research output: Contribution to journalArticlepeer-review

2 Scopus citations

Abstract

The transmembrane region of outer-membrane proteins (OMPs) of Gram-negative bacteria are almost exclusively β-barrels composed of between 8 and 26 β-strands. To explore the relationship between β-barrel size and shape, we modeled and simulated engineered variants of the Escherichia coli protein OmpX with 8, 10, 12, 14, and 16 β-strands. We found that while smaller barrels maintained a roughly circular shape, the 16-stranded variant developed a flattened cross section. This flat cross section impeded its ability to conduct ions, in agreement with previous experimental observations. Flattening was determined to arise from the presence of inward-facing glycines at sharp turns in the β-barrel. An analysis of all simulations revealed that glycines, on average, make significantly smaller angles with residues on neighboring strands than all other amino acids, including alanine, and create sharp turns in β-barrel cross sections. This observation was generalized to 119 unique structurally resolved OMPs. We also found that the fraction of glycines in β-barrels decreases as the strand number increases, suggesting an evolutionary role for the addition or removal of glycine in OMP sequences.

Original languageEnglish (US)
Article number183662
JournalBiochimica et Biophysica Acta - Biomembranes
Volume1863
Issue number10
DOIs
StatePublished - Oct 1 2021
Externally publishedYes

Keywords

  • Electrophysiology
  • OmpX
  • Outer membrane proteins (OMPs)
  • Protein evolution
  • β-Barrel shape

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Cell Biology

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