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Contiguously hydrophobic sequences are functionally significant throughout the human exome.

Ruchi Lohia1,2, Matthew E B Hansen3, Grace Brannigan1,4

  • 1Center for Computational and Integrative Biology, Rutgers University, Camden, NJ 08102.

Proceedings of the National Academy of Sciences of the United States of America
|March 16, 2022
PubMed
Summary

Functional impact of genetic variants is strongly linked to contiguous hydrophobic sequences, not just individual amino acid hydrophobicity. This finding aids in identifying disease-causing genetic variations.

Keywords:
computational methodspopulation geneticsprotein hydrophobicitysequence–function relationshipsingle-nucleotide polymorphism

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Area of Science:

  • Genomics
  • Protein Science
  • Bioinformatics

Background:

  • Hydrophobic interactions stabilize proteins and drive aggregation.
  • The role of hydrophobicity in functional significance of sequence variants is understudied genome-wide.

Purpose of the Study:

  • To investigate the impact of hydrophobicity on the functional significance of single-nucleotide polymorphisms (SNPs) across the genome.
  • To determine if hydrophobicity parameters of contiguous hydrophobic sequences (blobs) correlate with disease association.

Main Methods:

  • Analyzed 70,000 disease- and non-disease-associated SNPs.
  • Assessed correlation between SNP functional impact (disease association) and hydrophobicity parameters (size, minimum hydrophobicity) of contiguous hydrophobic sequences (blobs).
  • Examined selective constraint on hydrophobic blobs and disease association with SNPs affecting blob structure.

Main Results:

  • Functional impact is uncorrelated with SNP hydrophobicity but strongly correlated with the size and minimum hydrophobicity of the containing hydrophobic blob.
  • Disease association varied significantly (sixfold) based on contiguous hydrophobicity parameters.
  • SNPs splitting long or joining short hydrophobic blobs showed higher disease association.
  • Trends held for both aggregating and non-aggregating proteins.

Conclusions:

  • Contiguous hydrophobicity of protein sequences, particularly hydrophobic blobs, is a critical factor in the functional impact of genetic variants.
  • Hydrophobicity parameters of these blobs can serve as a predictive prior for identifying disease-associated causal variations.
  • The influence of contiguous hydrophobicity extends beyond protein aggregation risk, impacting broader protein function and disease association.