An evolutionarily conserved glycine-tyrosine motif forms a folding core in outer membrane proteins

Marcin Michalik; Marcella Orwick-Rydmark; Michael Habeck; Vikram Alva; Thomas Arnold; Dirk Linke

doi:10.1371/journal.pone.0182016

An evolutionarily conserved glycine-tyrosine motif forms a folding core in outer membrane proteins

PLoS One. 2017 Aug 3;12(8):e0182016. doi: 10.1371/journal.pone.0182016. eCollection 2017.

Authors

Marcin Michalik^{1

2}, Marcella Orwick-Rydmark¹, Michael Habeck^{3

4}, Vikram Alva⁵, Thomas Arnold^{2

6}, Dirk Linke^{1

2}

Affiliations

¹ Department of Biosciences, University of Oslo, Oslo, Norway.
² Previous affiliation: Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany.
³ Statistical inverse problems in Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
⁴ Felix Bernstein Institute for Mathematical Statistics in the Biosciences, University of Göttingen, Göttingen, Germany.
⁵ Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany.
⁶ Boehringer Ingelheim Veterinary Research Center, Hannover, Germany.

Abstract

An intimate interaction between a pair of amino acids, a tyrosine and glycine on neighboring β-strands, has been previously reported to be important for the structural stability of autotransporters. Here, we show that the conservation of this interacting pair extends to nearly all major families of outer membrane β-barrel proteins, which are thought to have originated through duplication events involving an ancestral ββ hairpin. We analyzed the function of this motif using the prototypical outer membrane protein OmpX. Stopped-flow fluorescence shows that two folding processes occur in the millisecond time regime, the rates of which are reduced in the tyrosine mutant. Folding assays further demonstrate a reduction in the yield of folded protein for the mutant compared to the wild-type, as well as a reduction in thermal stability. Taken together, our data support the idea of an evolutionarily conserved 'folding core' that affects the folding, membrane insertion, and thermal stability of outer membrane protein β-barrels.

MeSH terms

Amino Acid Motifs
Amino Acid Sequence
Bacterial Outer Membrane Proteins / chemistry*
Bacterial Outer Membrane Proteins / genetics
Bacterial Outer Membrane Proteins / metabolism
Escherichia coli / metabolism*
Escherichia coli Proteins / chemistry*
Escherichia coli Proteins / genetics
Escherichia coli Proteins / metabolism
Evolution, Molecular*
Glycine / chemistry*
Glycine / genetics
Glycine / metabolism
Lipid Bilayers / chemistry
Models, Molecular
Protein Folding
Protein Structure, Secondary
Sequence Alignment
Tyrosine / chemistry*
Tyrosine / genetics
Tyrosine / metabolism

Substances

Bacterial Outer Membrane Proteins
Escherichia coli Proteins
Lipid Bilayers
Tyrosine
Glycine

Grants and funding

Funding to DL from the German Science Foundation (DFG Li 1673/4-1) and from the Department of Biosciences, University of Oslo, and funding to MOR from the Norwegian Research Council (NFR 240909), is gratefully acknowledged. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.