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Inferring and Using Protein Quaternary Structure Information from Crystallographic Data

  • Sucharita Dey
  • Emmanuel D. Levy
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1764)

Abstract

A precise knowledge of the quaternary structure of proteins is essential to illuminate both their function and their evolution. The major part of our knowledge on quaternary structure is inferred from X-ray crystallography data, but this inference process is hard and error-prone. The difficulty lies in discriminating fortuitous protein contacts, which make up the lattice of protein crystals, from biological protein contacts that exist in the native cellular environment. Here, we review methods devised to discriminate between both types of contacts and describe resources for downloading protein quaternary structure information and identifying high-confidence quaternary structures. The use of high-confidence datasets of quaternary structures will be critical for the analysis of structural, functional, and evolutionary properties of proteins.

Key words

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

Notes

Acknowledgments

We thank Ohad Medalia for providing the lamina meshwork image in Fig. 1 and William Cramer for providing the crystal photography in Fig. 2. We thank the PDBe team and in particular Sameer Velankar for the integration of QSbio into PDBe assembly pages. This work was supported by a VATAT fellowship to S. Dey, by the Israel Science Foundation and the I-CORE Program of the Planning and Budgeting Committee (grant nos. 1775/12 and 2179/14), by the Marie Curie CIG Program (project no. 711715), by the HFSP Career Development Award to E. D. Levy (award no. CDA00077/2015), and by a research grant from AM. Boucher. E.D. Levy is incumbent of the Recanati Career Development Chair of Cancer Research.

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© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Structural BiologyWeizmann Institute of ScienceRehovotIsrael

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