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Inferring and Using Protein Quaternary Structure Information from Crystallographic Data.

Sucharita Dey¹, Emmanuel D Levy²

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

Methods in Molecular Biology (Clifton, N.J.)

|April 2, 2018

Summary

Determining protein quaternary structure is vital for understanding protein function and evolution. This review covers methods and resources to accurately identify biological protein contacts from crystallographic data, improving structural analysis.

Keywords:

Biological assembly Crystal contact Crystallography Homo-oligomers Homomers Promiscuous interactions Protein Data Bank Protein interactions Protein quaternary structure

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Area of Science:

Structural Biology
Bioinformatics
Protein Science

Background:

Precise knowledge of protein quaternary structure is crucial for understanding protein function and evolution.
Inferring quaternary structure from X-ray crystallography data is challenging due to difficulties in distinguishing biological contacts from crystal lattice contacts.
Accurate determination of protein quaternary structure is essential for various biological analyses.

Purpose of the Study:

To review methods for discriminating between biological and fortuitous protein contacts in crystallographic data.
To describe resources for accessing protein quaternary structure information.
To highlight the importance of high-confidence quaternary structure datasets for biological analysis.

Main Methods:

Review of existing computational and experimental methods for quaternary structure determination.
Identification and description of databases and resources for protein structure data.
Discussion of criteria for assessing the confidence of identified quaternary structures.

Main Results:

Several methods exist to differentiate biological from non-biological protein contacts.
Publicly available resources offer access to protein quaternary structure information.
High-confidence datasets are key for reliable structural, functional, and evolutionary studies.

Conclusions:

Accurate identification of protein quaternary structure is achievable through refined methods and reliable data.
Utilizing high-confidence quaternary structure datasets is critical for advancing our understanding of protein properties.
Improved methods and resources will facilitate more accurate functional and evolutionary analyses of proteins.