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Conservation of Protein Domains Over Different Proteins

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Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
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Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
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Updated: Jul 30, 2025

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Cross-phyla protein annotation by structural prediction and alignment.

Fabian Ruperti^1,2, Nikolaos Papadopoulos^1,3, Jacob M Musser¹

¹Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.

|May 12, 2023

Summary

This summary is machine-generated.

Protein annotation for non-model organisms is challenging. A new structural similarity workflow (MorphologFinder) enhances functional annotation beyond sequence-based methods, revealing novel sponge proteome functions.

Keywords:

Conservation Functional annotation Morpholog Protein homology Proteins Spongilla Structural similarity Structure scRNA-seq

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An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Area of Science:

Molecular Biology
Bioinformatics
Evolutionary Biology

Background:

Protein annotation is crucial but limited in non-model organisms.
Sequence-based orthology prediction loses accuracy over long evolutionary distances.
Structural similarity offers a more conserved alternative for homology detection.

Purpose of the Study:

To develop and apply a novel workflow for protein annotation using structural similarity.
To functionally annotate the sponge proteome, a key group for understanding early animal evolution.
To overcome limitations of sequence-based methods in non-model species.

Main Methods:

Developed MorphologFinder (MorF), a workflow of open-source tools for protein annotation via structural similarity.
Applied MorF to annotate the complete proteome of a sponge species.
Compared results with standard sequence-based annotation methods.

Main Results:

MorF accurately predicted functions for proteins with known homology.
Annotated a significant portion of the sponge proteome beyond sequence-based predictions.
Discovered new functions in sponge epithelia (FGF, TGF, Ephrin signaling) and myopeptidocytes (redox metabolism).
Annotated genes in sponge mesocytes, suggesting a role in cell wall digestion.

Conclusions:

Structural similarity is a powerful complement to sequence similarity for identifying homologous proteins across long evolutionary distances.
The MorF workflow significantly boosts discovery in -omics datasets, particularly for non-model organisms.
This approach enhances our understanding of proteomes in evolutionarily distant species.