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Updated: May 30, 2025
07:08
Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
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Protein stability is determined by single-site bias rather than pairwise covariance
Matt Sternke1,2, Katherine W Tripp1, Doug Barrick1
1T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore MD 21219 USA.
Biorxiv : the Preprint Server for Biology
|January 27, 2025
Summary
Protein sequence biases offer insights into structure and stability. Surprisingly, eliminating pair correlations enhances protein stability, while maximizing them boosts enzyme activity, aiding protein design.
Area of Science:
- Biophysics
- Computational Biology
- Protein Engineering
Background:
- Protein sequence alignments reveal biases linked to structure, stability, and function.
- Single-site biases and residue-pair correlations inform protein design and prediction.
- Potts models integrate these biases for improved predictions of protein fitness.
Purpose of the Study:
- To investigate the impact of single-site biases and pair correlations on protein thermodynamic stability and function.
- To design protein sequences with varying levels of these biases using a Potts model.
- To determine how manipulating these evolutionary constraints affects protein stability and activity.
Main Methods:
- Utilized a Potts model to generate protein sequences with controlled single-site biases and pair correlations.
- Measured the thermodynamic stability of designed protein sequences.
- Assessed the enzyme activity of designed adenylate kinase proteins.
Main Results:
- Sequences maximizing thermodynamic stability were found to exclude pair correlations.
- Sequences maximizing pair correlations exhibited reduced stability but significantly increased adenylate kinase activity.
- Eliminating covariant residue pairs led to hyperstable homeodomain and adenylate kinase proteins with retained activity.
Conclusions:
- Protein stability and activity are distinct properties influenced differently by sequence biases.
- Maximizing stability involves minimizing (or eliminating) residue-pair correlations.
- Maximizing pair correlations enhances enzyme activity, offering a strategy for designing functional and stable proteins.
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