article · CONICET Digital (CONICET) · 2017
On the dynamical incompleteness of the Protein Data Bank
Monzón, Alexander, Marino Buslje, Cristina, Zea, Diego Javier, Fornasari, Maria Silvina, Parisi, Gustavo Daniel
Cited by 0Open access
Abstract
Major scientific challenges that are beyond the capability of individuals need to be addressed by multi-disciplinary and multi-institutional consortia. Examples of these endeavours include the Human Genome Project, and more recently, the Structural Genomics (SG) initiative.The SG initiative pursues the expansion of structural coverage to include at least one structural representative for each protein family to derive the remaining structures using homology modelling. However, biological function is inherently connected with protein dynamics that can be studied by knowing different structures of the same protein. This ensemble of structures provides snapshots of protein conformational diversity under native conditions. Thus, sequence redundancy in the Protein Data Bank (PDB) (i.e. crystallization of the same protein under different conditions) is therefore an essential input contributing to experimentally based studies of protein dynamics and providing insights into protein function.In this work, we show that sequence redundancy, a key concept for exploring protein dynamics, is highly biased and fundamentally incomplete in the PDB. Additionally, our results show that dynamical behaviour of proteins cannot be inferred using homologous proteins. Minor to moderate changes in sequence can produce great differences in dynamical behaviour.Nonetheless, the structural and dynamical incompleteness of the PDB is apparently unrelated concepts in SG. While the first could be reversed by promoting the extension of the structural coverage, we would like to emphasize that furtherfocused efforts will be needed to amend the incompleteness of the PDB in terms of dynamical information content, essential to fully understand protein function.
Cite this paper
Monzón, A., Marino Buslje, C., Zea, D. J., Fornasari, M. S., & Parisi, G. D. (2017). On the dynamical incompleteness of the Protein Data Bank. CONICET Digital (CONICET).
Monzón, Alexander, et al. “On the dynamical incompleteness of the Protein Data Bank.” CONICET Digital (CONICET), 2017.
Monzón, Alexander, Cristina Marino Buslje, Diego Javier Zea, Maria Silvina Fornasari, and Gustavo Daniel Parisi. 2017. “On the dynamical incompleteness of the Protein Data Bank.” CONICET Digital (CONICET).
Monzón, A. et al. (2017) ‘On the dynamical incompleteness of the Protein Data Bank’, CONICET Digital (CONICET).
@article{monzon2017dynamical,
title = {{On the dynamical incompleteness of the Protein Data Bank}},
author = {Monzón, Alexander and Marino Buslje, Cristina and Zea, Diego Javier and Fornasari, Maria Silvina and Parisi, Gustavo Daniel},
journal = {CONICET Digital (CONICET)},
year = {2017}
}Made from the index record. Check names, capitalisation and page numbers against the paper. Need another style? AI for Research has over 10,000.