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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.
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.
Keywords:
crystal contactphysiological interfaceprotein evolutionprotein interactionsprotein quaternary structureprotein structure alignmentprotein superpositionweb serverMore Related Videos
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