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Protein Organization

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Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
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Related Experiment Video

Updated: Oct 5, 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

QSalignWeb: A Server to Predict and Analyze Protein Quaternary Structure.

Sucharita Dey¹, Jaime Prilusky², Emmanuel D Levy¹

¹Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel.

Frontiers in Molecular Biosciences

|January 24, 2022

Summary

Predicting protein quaternary structures (QSs) is difficult. The new QSalign webserver (www.QSalign.org) identifies physiologically relevant QSs by comparing user-submitted structures with homologous proteins, expanding upon previous methods.

Keywords:

crystal contact physiological interface protein evolution protein interactions protein quaternary structure protein structure alignment protein superposition web server

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Area of Science:

Structural biology
Bioinformatics
Computational biology

Background:

Identifying physiologically relevant quaternary structures (QSs) from crystal lattices is a significant challenge in structural biology.
Previous methods like QSalign were accurate but limited to existing Protein Data Bank (PDB) entries.

Purpose of the Study:

To develop a user-friendly webserver for predicting the physiological relevance of user-submitted homo-oligomeric protein structures.
To expand the applicability of the QSalign pipeline beyond the PDB.

Main Methods:

Users upload homo-oligomeric structures to the QSalign webserver (www.QSalign.org).
The pipeline extracts sequences, searches for homologous proteins using sequence similarity and PFAM domain architecture.
Structural conservation between the query and homologs infers physiological relevance; alternative QSs are generated using PISA.

Main Results:

The webserver successfully predicts physiological relevance by detecting structural conservation in homologous proteins.
It provides representative QSs for the protein family, aiding in cases of monomeric proteins or no detected QS conservation.
Generated representative QSs can be utilized as starting points for homology modeling.

Conclusions:

The QSalign webserver democratizes the prediction of physiologically relevant quaternary structures.
It offers a valuable tool for researchers studying protein assembly and function.
The server enhances structural biology research by providing insights into protein oligomerization states.