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A Protocol for Computer-Based Protein Structure and Function Prediction
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CONSTRUCT: an algorithmic tool for identifying functional or structurally important regions in protein tertiary

Lucas Chivot1, Noé Mathieux1, Anna Cosson1

  • 1Université de Rouen Normandie, Laboratoire de Parasitologie-Mycologie, ESCAPE, F-76000 Rouen, France.

Bioinformatics (Oxford, England)
|April 12, 2025
PubMed
Summary

CONSTRUCT identifies functional protein regions by analyzing evolutionary rates and spatial correlations of amino acid sites. This method improves upon standard approaches by considering the 3D clustering of important residues, aiding in protein function studies.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Protein evolution exhibits variable rates due to functional and structural constraints.
  • Essential or highly expressed proteins evolve slowly, with distinct selective pressures at different amino acid sites.
  • Standard methods often overlook the 3D spatial clustering of functionally important amino acid sites.

Purpose of the Study:

  • To develop an improved strategy, CONSTRUCT, for detecting functional and structurally important regions in protein tertiary structures.
  • To address the biological unrealism of standard methods that assume independent substitution rates across sites.

Main Methods:

  • CONSTRUCT estimates site-specific substitution rates using the Rate4site model.
  • Rates are weighted by neighboring sites within an optimally defined window based on spatial correlation.
  • Clustering detection is refined by analyzing Cα atoms or center of mass, accounting for side chain orientation.

Main Results:

  • CONSTRUCT demonstrated robustness through extensive simulations and validation on 14 diverse proteins.
  • The method effectively identifies functional and structurally important regions by considering spatial correlations.
  • CONSTRUCT accurately models the non-independent nature of selective pressures across amino acid sites.

Conclusions:

  • CONSTRUCT is a powerful tool for identifying functionally and structurally important protein regions.
  • The method enhances the understanding of protein evolution and constraints.
  • CONSTRUCT can guide site-directed mutagenesis experiments to elucidate protein function.