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

Kljashtorny V, Nikonov S, Ovchinnikov L, Lyabin D, Vodovar N, Curmi P, Manivet P - PLoS ONE (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: 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.

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.

No MeSH data available.


Related in: MedlinePlus

Number of intermolecular H-bonds in the complexes of CSD with different ribooligonucleotides.
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pone.0130318.g005: Number of intermolecular H-bonds in the complexes of CSD with different ribooligonucleotides.

Mentions: The relative affinity of the CSDYB-1 for DNA and RNA was next examined. To this end MD simulations were extended to CSDYB-1:oligo(N) complexes. Comparing the RMSD plots for DNA and RNA show clearly that DNA complexes are fluctuating within a larger range of RMSD value pointing a higher flexibility for DNA than RNA (S5 and S6 Figs). As observed for the CSDYB-1:DNA interactions, a more stable binding of the CSDYB-1 was found for the oligo(G) with perfect stacking parameters especially at binding sites 2 and 3 (Table 1) and statistically significant (P-value < 0.001) higher average number of H-bonds between the protein and oligo(G) (Fig 5). Thus, the average number of H-bonds between CSD and oligoG was 6.7 which 0.8 to 1.2 standard deviations higher compared with other CSDYB-1:RNA complexes with absolute difference of above 2 H-bonds. Again such a difference could correspond to two folds of higher affinity of CSD for oligoG. The complex CSDYB-1:oligoG was used as a reference for ΔΔGbind calculation.


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

Kljashtorny V, Nikonov S, Ovchinnikov L, Lyabin D, Vodovar N, Curmi P, Manivet P - PLoS ONE (2015)

Number of intermolecular H-bonds in the complexes of CSD with different ribooligonucleotides.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4493011&req=5

pone.0130318.g005: Number of intermolecular H-bonds in the complexes of CSD with different ribooligonucleotides.
Mentions: The relative affinity of the CSDYB-1 for DNA and RNA was next examined. To this end MD simulations were extended to CSDYB-1:oligo(N) complexes. Comparing the RMSD plots for DNA and RNA show clearly that DNA complexes are fluctuating within a larger range of RMSD value pointing a higher flexibility for DNA than RNA (S5 and S6 Figs). As observed for the CSDYB-1:DNA interactions, a more stable binding of the CSDYB-1 was found for the oligo(G) with perfect stacking parameters especially at binding sites 2 and 3 (Table 1) and statistically significant (P-value < 0.001) higher average number of H-bonds between the protein and oligo(G) (Fig 5). Thus, the average number of H-bonds between CSD and oligoG was 6.7 which 0.8 to 1.2 standard deviations higher compared with other CSDYB-1:RNA complexes with absolute difference of above 2 H-bonds. Again such a difference could correspond to two folds of higher affinity of CSD for oligoG. The complex CSDYB-1:oligoG was used as a reference for ΔΔGbind calculation.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: 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.

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.

No MeSH data available.


Related in: MedlinePlus