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Related Experiment Video

Updated: Apr 18, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Evolutionary patterns in coiled-coils.

Jaroslaw Surkont¹, Jose B Pereira-Leal²

¹Instituto Gulbenkian de Ciencia, Oeiras, Portugal jsurkont@igc.gulbenkian.pt.

Genome Biology and Evolution

|January 12, 2015

Summary

This summary is machine-generated.

A new coiled-coil specific (CC) model improves phylogenetic analysis and homology detection for coiled-coil proteins. This model accounts for unique evolutionary constraints in these structures, outperforming general models.

Keywords:

amino acid substitutions coiled-coil homology detection phylogenetic inference protein evolution protein structure

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Last Updated: Apr 18, 2026

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Published on: July 14, 2015

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Production, Crystallization, and Structure Determination of the IKK-binding Domain of NEMO

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Published on: December 28, 2019

Area of Science:

Protein evolution
Structural bioinformatics
Phylogenetics

Background:

General protein evolution models are biased towards globular domains.
Coiled-coil proteins, common structural motifs, have unique evolutionary constraints due to their heptad repeat structure.
Existing models lack resolution for non-globular protein types like coiled-coils.

Purpose of the Study:

To investigate evolutionary patterns in coiled-coil forming proteins.
To develop a specific model for coiled-coil protein evolution.
To enhance phylogenetic reconstruction and homology detection for coiled-coil proteins.

Main Methods:

Analysis of substitution patterns in coiled-coil regions.
Development of a coiled-coil specific (CC) substitution model.
Testing the CC model against general models in phylogenetic reconstruction and homology detection.
Evaluation of combined CC and general models for multidomain proteins.

Main Results:

Substitution patterns in coiled-coil regions differ significantly from globular regions.
The CC model outperforms general models in phylogenetic tree likelihood and can alter topologies.
A combination of CC and general models provides higher likelihoods for multidomain proteins.
The CC model increases search sensitivity for coiled-coil protein homology detection.

Conclusions:

Coiled-coil proteins exhibit distinct evolutionary constraints.
The developed CC model enhances the accuracy of phylogenetic analysis and homology detection for coiled-coil proteins.
The CC model represents a significant advancement for studying the evolution of coiled-coil proteins.