1. Biochemistry and Chemical Biology
  2. Structural Biology and Molecular Biophysics
Download icon

Single methyl groups can act as toggle switches to specify transmembrane protein-protein interactions

  1. Li He
  2. Helena Steinocher
  3. Ashish Shelar
  4. Emily B Cohen
  5. Erin N Heim
  6. Birthe B Kragelund
  7. Gevorg Grigoryan
  8. Daniel DiMaio  Is a corresponding author
  1. Yale School of Medicine, United States
  2. University of Copenhagen, Denmark
  3. Dartmouth College, United States
Research Article
  • Cited 7
  • Views 2,317
  • Annotations
Cite this article as: eLife 2017;6:e27701 doi: 10.7554/eLife.27701

Abstract

Transmembrane domains (TMDs) engage in protein-protein interactions that regulate many cellular processes, but the rules governing the specificity of these interactions are poorly understood. To discover these principles, we analyzed 26-residue model transmembrane proteins consisting exclusively of leucine and isoleucine (called LIL traptamers) that specifically activate the erythropoietin receptor (EPOR) in mouse cells to confer growth factor independence. We discovered that the placement of a single side chain methyl group at specific positions in a traptamer determined whether it associated productively with the TMD of the human EPOR, the mouse EPOR, or both receptors. Association of the traptamers with the EPOR induced EPOR oligomerization in an orientation that stimulated receptor activity. These results highlight the high intrinsic specificity of TMD interactions, demonstrate that a single methyl group can dictate specificity, and define the minimal chemical difference that can modulate the specificity of TMD interactions and the activity of transmembrane proteins.

Article and author information

Author details

  1. Li He

    Department of Genetics, Yale School of Medicine, New Haven, United States
    Competing interests
    The authors declare that no competing interests exist.

  2. Helena Steinocher

    Department of Biology, Structural Biology and NMR Laboratory, University of Copenhagen, Copenhagen, Denmark
    Competing interests
    The authors declare that no competing interests exist.

  3. Ashish Shelar

    Department of Genetics, Yale School of Medicine, New Haven, United States
    Competing interests
    The authors declare that no competing interests exist.

  4. Emily B Cohen

    Department of Genetics, Yale School of Medicine, New Haven, United States
    Competing interests
    The authors declare that no competing interests exist.

  5. Erin N Heim

    Department of Genetics, Yale School of Medicine, New Haven, United States
    Competing interests
    The authors declare that no competing interests exist.

  6. Birthe B Kragelund

    Department of Biology, University of Copenhagen, Copenhagen, Denmark
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7454-1761

  7. Gevorg Grigoryan

    Department of Computer Science, Dartmouth College, Hanover, United States
    Competing interests
    The authors declare that no competing interests exist.

  8. Daniel DiMaio

    Department of Genetics, Yale School of Medicine, New Haven, United States
    For correspondence
    daniel.dimaio@yale.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2060-5977

Funding

National Institutes of Health (R01 CA037157)

  • Daniel DiMaio

Lundbeckfonden (Lundbeck Foundation)

  • Birthe B Kragelund

Novo Nordisk Foundation (Novo Nordisk Foundation)

  • Birthe B Kragelund

National Institutes of Health (GM113132)

  • Gevorg Grigoryan

National Science Foundation (MCB151032)

  • Gevorg Grigoryan

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Nir Ben-Tal, Tel Aviv University, Israel

Publication history

  1. Received: April 11, 2017
  2. Accepted: September 1, 2017
  3. Accepted Manuscript published: September 4, 2017 (version 1)
  4. Version of Record published: September 13, 2017 (version 2)

Copyright

© 2017, He et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 2,317
    Page views
  • 340
    Downloads
  • 7
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, Scopus, PubMed Central.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Download citations (links to download the citations from this article in formats compatible with various reference manager tools)

Open citations (links to open the citations from this article in various online reference manager services)

Categories and tags

Further reading

    1. Biochemistry and Chemical Biology
    2. Chromosomes and Gene Expression

    Mutations in SKI in Shprintzen–Goldberg syndrome lead to attenuated TGF-β responses through SKI stabilization

    Ilaria Gori et al.
    Research Article Updated

    Shprintzen–Goldberg syndrome (SGS) is a multisystemic connective tissue disorder, with considerable clinical overlap with Marfan and Loeys–Dietz syndromes. These syndromes have commonly been associated with enhanced TGF-β signaling. In SGS patients, heterozygous point mutations have been mapped to the transcriptional co-repressor SKI, which is a negative regulator of TGF-β signaling that is rapidly degraded upon ligand stimulation. The molecular consequences of these mutations, however, are not understood. Here we use a combination of structural biology, genome editing, and biochemistry to show that SGS mutations in SKI abolish its binding to phosphorylated SMAD2 and SMAD3. This results in stabilization of SKI and consequently attenuation of TGF-β responses, both in knockin cells expressing an SGS mutation and in fibroblasts from SGS patients. Thus, we reveal that SGS is associated with an attenuation of TGF-β-induced transcriptional responses, and not enhancement, which has important implications for other Marfan-related syndromes.

    1. Biochemistry and Chemical Biology
    2. Chromosomes and Gene Expression

    A novel motif of Rad51 serves as an interaction hub for recombination auxiliary factors

    Negar Afshar et al.
    Research Article

    Homologous recombination (HR) is essential for maintaining genome stability. Although Rad51 is the key protein that drives HR, multiple auxiliary factors interact with Rad51 to potentiate its activity. Here, we present an interdisciplinary characterization of the interactions between Rad51 and these factors. Through structural analysis, we identified an evolutionarily conserved acidic patch of Rad51. The neutralization of this patch completely abolished recombinational DNA repair due to defects in the recruitment of Rad51 to DNA damage sites. This acidic patch was found to be important for the interaction with Rad55-Rad57 and essential for the interaction with Rad52. Furthermore, biochemical reconstitutions demonstrated that neutralization of this acidic patch also impaired the interaction with Rad54, indicating that a single motif is important for the interaction with multiple auxiliary factors. We propose that this patch is a fundamental motif that facilitates interactions with auxiliary factors and is therefore essential for recombinational DNA repair.

    1. Biochemistry and Chemical Biology
    2. Medicine

    The half-life of the bone-derived hormone osteocalcin is regulated through O-glycosylation in mice, but not in humans

    Omar Al Rifai et al.
    Research Article Updated

    Osteocalcin (OCN) is an osteoblast-derived hormone with pleiotropic physiological functions. Like many peptide hormones, OCN is subjected to post-translational modifications (PTMs) which control its activity. Here, we uncover O-glycosylation as a novel PTM present on mouse OCN and occurring on a single serine (S8) independently of its carboxylation and endoproteolysis, two other PTMs regulating this hormone. We also show that O-glycosylation increases OCN half-life in plasma ex vivo and in the circulation in vivo. Remarkably, in human OCN (hOCN), the residue corresponding to S8 is a tyrosine (Y12), which is not O-glycosylated. Yet, the Y12S mutation is sufficient to O-glycosylate hOCN and to increase its half-life in plasma compared to wildtype hOCN. These findings reveal an important species difference in OCN regulation, which may explain why serum concentrations of OCN are higher in mouse than in human.