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Membranome 3.0: Database of single-pass membrane proteins with AlphaFold models
Andrei L Lomize1, Kevin A Schnitzer2, Spencer C Todd2
1Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA.
Protein Science : a Publication of the Protein Society
|April 28, 2022
Summary
Membranome 3.0 enhances structural insights into single-pass membrane proteins, integrating 5,758 bitopic proteins and AlphaFold 2 models for improved analysis of protein interactions and complexes.
Area of Science:
- Structural Biology
- Bioinformatics
- Membrane Protein Research
Background:
- The Membranome database offers structural data for single-pass (bitopic) membrane proteins across diverse organisms.
- It includes protein-protein interactions, complexes, mutations, and experimental structures.
Purpose of the Study:
- To introduce Membranome 3.0, an updated version of the database.
- To incorporate and refine structural models of bitopic membrane proteins, including those generated by AlphaFold 2.
Main Methods:
- Revised the dataset of 5,758 bitopic proteins.
- Integrated and processed AlphaFold 2 models, validating them against experimental structures and orienting them within membrane boundaries.
- Re-developed the database for enhanced visualization and comparative analysis.
Main Results:
- Membranome 3.0 provides updated structural information for 5,758 bitopic membrane proteins.
- Incorporated validated AlphaFold 2 models, offering new insights into transmembrane α-helical dimers.
- Introduced advanced search and analysis tools for proteins, interactions, complexes, and mutations.
Conclusions:
- Membranome 3.0 is a significantly enhanced resource for studying bitopic membrane proteins.
- The database facilitates deeper understanding of membrane protein structure, function, and interactions.
- It serves as a valuable, freely accessible tool for researchers in structural biology and bioinformatics.
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