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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
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Rosetta design with co-evolutionary information retains protein function.

Samuel Schmitz1, Moritz Ertelt2,3, Rainer Merkl3

  • 1Department of Chemistry, Vanderbilt University, Nashville, Tennessee, United States of America.

Plos Computational Biology
|January 19, 2021
PubMed
Summary
This summary is machine-generated.

We developed ResCue, a computational protein design method that uses co-evolutionary data to improve sequence recovery. ResCue successfully designs novel proteins by recapitulating natural correlated mutations, outperforming existing Rosetta approaches.

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Area of Science:

  • Computational biology
  • Protein engineering
  • Bioinformatics

Background:

  • Computational protein design aims to create novel proteins for biological and medical applications.
  • The Rosetta software suite is widely used for protein design tasks.
  • Identifying co-evolutionary couplings between residues is crucial for understanding protein function.

Purpose of the Study:

  • To develop a computational protein design method that incorporates co-evolutionary information.
  • To improve the accuracy of designing protein sequences that reflect natural evolutionary patterns.
  • To overcome limitations of existing Rosetta design methods in capturing residue interdependencies.

Main Methods:

  • Developed the Rosetta method ResCue (residue-coupling enhanced).
  • Leveraged co-evolutionary information from multiple sequence alignments.
  • Assessed protocol performance using recapitulation designs on a benchmark of ten proteins with two states each.

Main Results:

  • ResCue achieved an average sequence recovery rate of 70%, significantly higher than existing protocols (≤50%).
  • The method demonstrated improved recovery rates for functionally important residues.
  • The enhancement in sequence recovery had a minimal negative impact on the designed sequences' Rosetta energy (fitness).

Conclusions:

  • Informing computational protein design protocols with co-evolutionary signals enhances the design of stable, native-like proteins.
  • ResCue successfully recapitulates correlated mutations, leading to more accurate protein sequence design.
  • This approach facilitates the design of proteins compatible with multiple conformational states essential for complex functions.