Bhattacharya Roshni, Rose Peter W, Burley Stephen K, Prlić Andreas
Bioinformatics and Medical Informatics, San Diego State University, San Diego, California, United States of America.
RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, California, United States of America.
PLoS One. 2017 Mar 15;12(3):e0171355. doi: 10.1371/journal.pone.0171355. eCollection 2017.
The Protein Data Bank (PDB; http://wwpdb.org) was established in 1971 as the first open access digital data resource in biology with seven protein structures as its initial holdings. The global PDB archive now contains more than 126,000 experimentally determined atomic level three-dimensional (3D) structures of biological macromolecules (proteins, DNA, RNA), all of which are freely accessible via the Internet. Knowledge of the 3D structure of the gene product can help in understanding its function and role in disease. Of particular interest in the PDB archive are proteins for which 3D structures of genetic variant proteins have been determined, thus revealing atomic-level structural differences caused by the variation at the DNA level. Herein, we present a systematic and qualitative analysis of such cases. We observe a wide range of structural and functional changes caused by single amino acid differences, including changes in enzyme activity, aggregation propensity, structural stability, binding, and dissociation, some in the context of large assemblies. Structural comparison of wild type and mutated proteins, when both are available, provide insights into atomic-level structural differences caused by the genetic variation.
