Scientific article

PDB-wide identification of biological assemblies from conserved quaternary structure geometry

Published inNature methods, vol. 15, no. 1, p. 67-72
Publication date2017-11-20
First online date2017-11-20

Protein structures are key to understanding biomolecular mechanisms and diseases, yet their interpretation is hampered by limited knowledge of their biologically relevant quaternary structure (QS). A critical challenge in inferring QS information from crystallographic data is distinguishing biological interfaces from fortuitous crystal-packing contacts. Here, we tackled this problem by developing strategies for aligning and comparing QS states across both homologs and data repositories. QS conservation across homologs proved remarkably strong at predicting biological relevance and is implemented in two methods, QSalign and anti-QSalign, for annotating homo-oligomers and monomers, respectively. QS conservation across repositories is implemented in QSbio (http://www.QSbio.org), which approaches the accuracy of manual curation and allowed us to predict >100,000 QS states across the Protein Data Bank. Based on this high-quality data set, we analyzed pairs of structurally conserved interfaces, and this analysis revealed a striking plasticity whereby evolutionary distant interfaces maintain similar interaction geometries through widely divergent chemical properties.

Affiliation Not a UNIGE publication
Citation (ISO format)
DEY, Sucharita, RITCHIE, David W., LEVY, Emmanuel. PDB-wide identification of biological assemblies from conserved quaternary structure geometry. In: Nature methods, 2017, vol. 15, n° 1, p. 67–72. doi: 10.1038/nmeth.4510
Main files (1)
Article (Published version)
ISSN of the journal1548-7091

Technical informations

Creation04/27/2024 10:07:35 AM
First validation05/07/2024 12:53:35 PM
Update time05/07/2024 12:53:35 PM
Status update05/07/2024 12:53:35 PM
Last indexation05/07/2024 12:53:56 PM
All rights reserved by Archive ouverte UNIGE and the University of GenevaunigeBlack