Determinants of trafficking, conduction, and disease within a K+ channel revealed through multiparametric deep mutational scanning

  1. Willow Coyote-Maestas
  2. David Nedrud
  3. Yungui He
  4. Daniel Schmidt  Is a corresponding author
  1. University of Minnesota, United States

Abstract

A longstanding goal in protein science and clinical genetics is to develop quantitative models of sequence, structure, and function relationships and delineate the mechanisms by which mutations cause disease. Deep Mutational Scanning (DMS) is a promising strategy to map how amino acids contribute to protein structure and function and to advance clinical variant interpretation. Here, we introduce 7,429 single residue missense mutations into the Inward Rectifier K+ channel Kir2.1 and determine how this affects folding, assembly, and trafficking, as well as regulation by allosteric ligands and ion conduction. Our data provide high-resolution information on a cotranslationally-folded biogenic unit, trafficking and quality control signals, and segregated roles of different structural elements in fold-stability and function. We show that Kir2.1 surface trafficking mutants are underrepresented in variant effect databases, which has implications for clinical practice. By comparing fitness scores with expert-reviewed variant effects, we can predict the pathogenicity of 'variants of unknown significance' and disease mechanisms of known pathogenic mutations. Our study in Kir2.1 provides a blueprint for how multiparametric DMS can help us understand the mechanistic basis of genetic disorders and the structure-function relationships of proteins.

Data availability

Sequencing data generated in this study have been deposited in the Sequence Raw Archive (https://www.ncbi.nlm.nih.gov/sra) under accession code PRJNA791691. All remaining source data (including processed data and R scripts to reproduce manuscript figures) are included as supplementary information (Source_Data.zip) and are also available at github.com/schmidt-lab/Kir21DMS.

The following data sets were generated

Article and author information

Author details

  1. Willow Coyote-Maestas

    Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9614-5340
  2. David Nedrud

    Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Yungui He

    Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Daniel Schmidt

    Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, United States
    For correspondence
    schmida@umn.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7609-4873

Funding

National Institute of General Medical Sciences (R01GM136851)

  • Daniel Schmidt

Howard Hughes Medical Institute

  • Willow Coyote-Maestas

Illumina

  • Daniel Schmidt

National Science Foundation

  • Willow Coyote-Maestas

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

Reviewing Editor

  1. Andrés Jara-Oseguera, The University of Texas at Austin, United States

Publication history

  1. Preprint posted: January 6, 2022 (view preprint)
  2. Received: January 8, 2022
  3. Accepted: May 27, 2022
  4. Accepted Manuscript published: May 31, 2022 (version 1)

Copyright

© 2022, Coyote-Maestas 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.

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  1. Willow Coyote-Maestas
  2. David Nedrud
  3. Yungui He
  4. Daniel Schmidt
(2022)
Determinants of trafficking, conduction, and disease within a K+ channel revealed through multiparametric deep mutational scanning
eLife 11:e76903.
https://doi.org/10.7554/eLife.76903

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