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task_categories:
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  - tabular-classification
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language:
  - en
tags:
  - biology
  - proteins
  - amino-acids
size_categories:
  - 100K<1M
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Protein Data Stability - Single Mutation

This repository contains data on the change in protein stability with a single mutation.

Attribution of Data Sources

  • Primary Source: Tsuboyama, K., Dauparas, J., Chen, J. et al. Mega-scale experimental analysis of protein folding stability in biology and design. Nature 620, 434–444 (2023). Link to the paper
  • Dataset Link: Zenodo Record

As to where the dataset comes from in this broader work, the relevant dataset (#3) is shown in dataset_table.jpeg of this repository's files.

Sample Protein Stability Data

Base Amino Acid Sequence Mutation ddG_ML Classification
DEIHIHFNGVTIEFRGLTEEAKKALEEAIKRGASEEELKELARRLIK base -0.0675543480388345 neutral
DEIHIHFNGVTIEFRGLTEEAKKALEEAIKRGASEEELKELARRLIK D1Q -0.0162349479755414 neutral
DEIHIHFNGVTIEFRGLTEEAKKALEEAIKRGASEEELKELARRLIK D1E -0.1402534094665108 neutral
DEIHIHFNGVTIEFRGLTEEAKKALEEAIKRGASEEELKELARRLIK D1N 0.0126650189159422 neutral
DEIHIHFNGVTIEFRGLTEEAKKALEEAIKRGASEEELKELARRLIK D1H 0.1970434798619962 neutral

Dataset Structure

The dataset focuses on the differential deltaG (mutation minus base) of various protein mutations.

  • Base Protein Sequence (aa_seq): A (sometimes shortened) amino acid sequence.
  • Mutation: Represented as a combination of amino acid and its position (e.g., F10N indicates changing the 10th amino acid (F) in a sequence for N).
  • delta deltaG (ddG_ML): Derived from a model that makes use of stability measurements measured by two proteases, trypsin and chymotrypsin.
  • Classification: Classification is done purely on the basis of ddG. The standard deviation of ddG in the dataset is measured and: -- Rows above 0.5 standard deviations are classified as 'destabilising' -- Rows below -0.5 standard deviations are classified as 'stabilising' -- Rows between -0.5 and 0.5 standard deviations are classified as 'neutral'

Understanding ΔG (delta G)

ΔG is the Gibbs free energy change of a process, dictating whether a process is thermodynamically favorable:

  • Negative ΔG: Indicates the process is energetically favorable. For protein folding, it implies the protein is stable in its folded form.
  • Positive ΔG: Indicates the process is not energetically favorable. In protein folding, it means the protein requires energy to maintain its folded state.

The delta delta G (ΔΔG) represents the deltaG of the mutation compared to the base protein:

  • Positive ΔΔG: Suggests the mutation decreases protein stability.
  • Negative ΔΔG: Suggests the mutation enhances protein stability.

Data Cleanup and Validation:

  1. Filtering: The dataset has been curated to only include examples of single mutations.
  2. Consistency Check: Only rows with consistent mutation indication, aligned with both the base and mutated sequences, have been retained.