The Cold Shock Domain of YB-1 Segregates RNA from DNA by Non-Bonded Interactions.

Vladislav Kljashtorny, Stanislav Nikonov, Lev Ovchinnikov, Dmitry Lyabin, Nicolas Vodovar, Patrick Curmi, Philippe Manivet

Journal: PloS one 2016;10(7):e0130318

PMID: 26147853

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Abstract

The human YB-1 protein plays multiple cellular roles, of which many are dictated by its binding to RNA and DNA through its Cold Shock Domain (CSD). Using molecular dynamics simulation approaches validated by experimental assays, the YB1 CSD was found to interact with nucleic acids in a sequence-dependent manner and with a higher affinity for RNA than DNA. The binding properties of the YB1 CSD were close to those observed for the related bacterial Cold Shock Proteins (CSP), albeit some differences in sequence specificity. The results provide insights in the molecular mechanisms whereby YB-1 interacts with nucleic acids.

Address: Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia; Institut National de la Santé et de la Recherche Médicale (INSERM), UMR 829, Laboratoire Structure-Activité des Biomolécules Normales et Pathologiques, Bd François Mitterrand, 91025 Evry Cedex, France; Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS 942, Hôpital Lariboisière, 41 boulevard de la Chapelle, 75475 Paris cedex 10, France; Assistance Publique-Hôpitaux de paris (APHP), Hôpital Lariboisière, Service de Biochimie et de Biologie Moléculaire, Paris, France.; Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.; Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS 942, Hôpital Lariboisière, 41 boulevard de la Chapelle, 75475 Paris cedex 10, France.; Institut National de la Santé et de la Recherche Médicale (INSERM), UMR 829, Laboratoire Structure-Activité des Biomolécules Normales et Pathologiques, Bd François Mitterrand, 91025 Evry Cedex, France.; Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS 942, Hôpital Lariboisière, 41 boulevard de la Chapelle, 75475 Paris cedex 10, France; Assistance Publique-Hôpitaux de paris (APHP), Hôpital Lariboisière, Service de Biochimie et de Biologie Moléculaire, Paris, France; UBCS (Unité de Biologie Clinique Structurale)-Centre de Ressources Biologiques BB-0033-00064, 2 rue Ambroise Paré, 75475 Paris cedex 10, France.

DOI: 10.1371/journal.pone.0130318

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MeSH Terms: Amino Acid Sequence, Bacterial Proteins, Binding Sites, Cold Shock Proteins and Peptides, DNA, DNA-Binding Proteins, Humans, Molecular Dynamics Simulation, Molecular Sequence Data, Nucleic Acids, Protein Structure, Tertiary, RNA, RNA-Binding Proteins, Sequence Alignment, Y-Box-Binding Protein 1