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Protein Complex Assembly

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types. Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...

Protein Complex Assembly

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types. Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...

Protein Organization

Protein Organization

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Related Experiment Video

Updated: Jul 9, 2026

Mapping Dysfunctional Protein-Protein Interactions in Disease

Mapping Dysfunctional Protein-Protein Interactions in Disease

Published on: October 24, 2025

PUFFIN: protein unit discovery with functional supervision.

Gökçe Uludoğan¹, Buse Giledereli¹, Elif Ozkirimli²

¹Department of Computer Engineering, Boğaziçi University, Bebek, Istanbul, 34342, Turkey.

Bioinformatics (Oxford, England)

|July 7, 2026

Summary

This summary is machine-generated.

We developed PUFFIN, a novel framework that identifies functional protein units by analyzing structure and function. This method reveals how these units contribute to molecular function, enhancing our understanding of protein structure-function relationships.

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Last Updated: Jul 9, 2026

Mapping Dysfunctional Protein-Protein Interactions in Disease

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Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells

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Published on: August 2, 2015

Area of Science:

Structural Biology
Computational Biology
Bioinformatics

Background:

Proteins perform biological functions via coordinated residue actions within structural arrangements called protein units.
Understanding protein units and their functional associations is key to deciphering protein function.
Current methods lack interpretability by focusing on residue-level data or ignoring functional context.

Purpose of the Study:

To introduce PUFFIN, a data-driven framework for discovering protein units.
To jointly learn structural partitioning and functional supervision for protein unit identification.
To provide an interpretable method for analyzing protein structure-function relationships.

Main Methods:

PUFFIN represents proteins as residue-level structure graphs.
A graph neural network with structure-aware pooling partitions proteins into multiresidue units.
Functional supervision guides the partitioning process to reflect molecular function.

Main Results:

Learned protein units are structurally coherent.
These units show organized associations with molecular function.
The identified units correspond meaningfully with curated InterPro annotations.

Conclusions:

PUFFIN offers an interpretable framework for analyzing structure-function relationships.
The framework effectively identifies functional protein units using a data-driven approach.
PUFFIN enhances the understanding of how protein units contribute to biological functions.