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Protlego: a Python package for the analysis and design of chimeric proteins.

Noelia Ferruz1, Jakob Noske1, Birte Höcker1

  • 1Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany.

Bioinformatics (Oxford, England)
|April 26, 2021
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Summary

This study introduces Protlego, a Python package for automated protein chimera design and structural analysis. Protlego streamlines the creation and evaluation of novel protein structures, accelerating protein engineering research.

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Area of Science:

  • * Protein Engineering
  • * Computational Biology
  • * Structural Bioinformatics

Background:

  • * Natural protein diversity arises from fragment duplication and recombination.
  • * Designing protein chimeras via fragment recombination is a successful strategy for creating customizable proteins.
  • * Current in silico modeling and analysis of chimeric proteins are manual, hindering high-throughput studies.

Purpose of the Study:

  • * To develop an automated, high-throughput pipeline for designing and analyzing protein chimeras.
  • * To provide a user-friendly tool that integrates fragment fetching, chimera construction, and structural analysis.
  • * To facilitate the exploration of protein superfamilies and the characterization of novel chimeric proteins.

Main Methods:

  • * Implementation of a Python package (Protlego) for automated chimera design.
  • * Utilization of a built-in database for fetching evolutionarily conserved protein fragments.
  • * Application of CHARMM and AMBER force fields for scoring and minimizing designed protein structures.
  • * Analysis of structural features and relationships between protein superfamilies (e.g., P-loop and Rossmann).

Main Results:

  • * Protlego enables automated, high-throughput design and structural analysis of protein chimeras.
  • * The package can fetch conserved fragments, represent evolutionary relationships, and construct chimeras via recombination.
  • * Designed chimeras and natural proteins are scored and minimized, with diverse structural features analyzed.
  • * A case study demonstrates Protlego's utility in exploring P-loop and Rossmann superfolds and their chimeric offspring.

Conclusions:

  • * Protlego offers a powerful new tool for the protein design community.
  • * The automated pipeline simplifies and accelerates the design and analysis of chimeric proteins.
  • * This approach supports high-throughput studies and the exploration of novel protein structures.