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Artículo

On the dynamical incompleteness of the Protein Data Bank

Monzón, AlexanderIcon ; Marino Buslje, Cristina; Zea, Diego JavierIcon ; Fornasari, Maria SilvinaIcon ; Parisi, Gustavo DanielIcon
Fecha de publicación: 07/2017
Editorial: Oxford University Press
Revista: Briefings In Bioinformatics
ISSN: 1467-5463
Idioma: Inglés
Tipo de recurso: Artículo publicado
Clasificación temática:
Otras Ciencias Biológicas

Resumen

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.
Palabras clave: Protein Dynamic , Protein Function , Protein Data Bank , Protein Structure
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info:eu-repo/semantics/openAccess Excepto donde se diga explícitamente, este item se publica bajo la siguiente descripción: Creative Commons Attribution-NonCommercial-ShareAlike 2.5 Unported (CC BY-NC-SA 2.5)
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URI: http://hdl.handle.net/11336/41093
DOI: http://dx.doi.org/10.1093/bib/bbx084
URL: https://academic.oup.com/bib/advance-article-abstract/doi/10.1093/bib/bbx084/406
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Citación
Monzón, Alexander; Marino Buslje, Cristina; Zea, Diego Javier; Fornasari, Maria Silvina; Parisi, Gustavo Daniel; On the dynamical incompleteness of the Protein Data Bank; Oxford University Press; Briefings In Bioinformatics; 7-2017; 1-4
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