metadata

task_categories:
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  - tabular-classification
  - text-generation
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.

There are two datasets:

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 Protein Sequence	Mutation	ΔΔG_ML	Classification
FDIYVVTADYLPLGAEQDAITLREGQYVEVLDAAHPLRWLVRTKPTKSSPSRQGWVSPAYLDRRL	R63W	-0.2010871345320799	neutral
FDIYVVTADYLPLGAEQDAITLREGQYVEVLDAAHPLRWLVRTKPTKSSPSRQGWVSPAYLDRRL	R63Y	0.0194756159891467	neutral
FDIYVVTADYLPLGAEQDAITLREGQYVEVLDAAHPLRWLVRTKPTKSSPSRQGWVSPAYLDRRL	R63F	0.7231614929744659	stabilising
FDIYVVTADYLPLGAEQDAITLREGQYVEVLDAAHPLRWLVRTKPTKSSPSRQGWVSPAYLDRRL	R63P	-0.3668887752897785	neutral
FDIYVVTADYLPLGAEQDAITLREGQYVEVLDAAHPLRWLVRTKPTKSSPSRQGWVSPAYLDRRL	R63C	-0.5317304030261774	destabilising

Dataset Structure

The dataset focuses on the differential deltaG of unfolding (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 (free energy of unfolding) measured by two proteases, trypsin and chymotrypsin.
Classification: Classification is done purely on the basis of ddG. -- Rows below -0.5 standard deviations are classified as 'destabilising' -- Rows above +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 unfolding, it implies the protein is more stable in its unfolded form.
Positive ΔG: Indicates the process is not energetically favorable. In protein unfolding, it means the protein requires energy to maintain its unfolded state, i.e. it is stable in folded form.

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

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

Data Cleanup and Validation:

Filtering: The dataset has been curated to only include examples of single mutations.
Sequence mutations were extracted from the row names. Base mutations are labelled as 'base'.
Consistency Check: Only rows with a consistent 'mutation', aligned with both the base and mutated sequences from the raw data, have been retained.