Open Access Research article

In vivo and in silico analysis of PCNA ubiquitylation in the activation of the Post Replication Repair pathway in S. cerevisiae

Flavio Amara1, Riccardo Colombo2, Paolo Cazzaniga3, Dario Pescini4, Attila Csikász-Nagy5, Marco Muzi Falconi1, Daniela Besozzi6* and Paolo Plevani1*

Author Affiliations

1 Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy

2 Dipartimento di Informatica, Sistemistica e Comunicazione, Università degli Studi di Milano-Bicocca, Milano, Italy

3 Dipartimento di Scienze Umane e Sociali, Università degli Studi di Bergamo, Bergamo, Italy

4 Dipartimento di Statistica e Metodi Quantitativi, Università degli Studi di Milano-Bicocca, Milano, Italy

5 , The Microsoft Research - Università degli Studi di Trento, Centre for Computational and Systems Biology, Rovereto (Trento), Italy

6 Dipartimento di Informatica, Università degli Studi di Milano, Milano, Italy

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BMC Systems Biology 2013, 7:24  doi:10.1186/1752-0509-7-24

Published: 20 March 2013

Additional files

Additional file 1:

Histogram and density plots of CHX effect on protein synthesis and cell cycle progression of UV irradiated cells.

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Additional file 2:

Determination of mono- and poly-ubiquitylated PCNA ratio using western blots elaboration and representation of densitometry quantification.

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Additional file 3:

Global sensitivity analysis of the PRR model.

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Additional file 4:

Graphical representation of reactions ranking obtained by sensitivity analysis.

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Additional file 5:

Methods for the representation of simulation outcomes and comparison with experimental data.

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Additional file 6:

PDB accession codes for protein complexes analyzed through 3D structural modeling.

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Additional file 7:

Structural modeling of Uba1-Rad6 and Rad6-Rad18 complexes involved in PCNA mono-ubiquitylation.

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Additional file 8:

Hypothetical yeast E1-E2 and E2-E3 complexes involved in PCNA mono- and poly-ubiquitylation obtained through structural modeling of PRR complexes.

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Additional file 9:

Structural modeling of Uba1-Ubc13 and Ubc13-Rad5 complexes involved in PCNA poly-ubiquitylation.

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Additional file 10:

List of reactions involved in the formation of Ubc13 : Mms2 complex and simulation results.

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Additional file 11:

Early time-course of PCNA ubiquitylation after low acute UV irradiation.

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Additional file 12:

Effects of the variation of the initial amount of PCNA.

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Additional file 13:

Effects of the modulation of the binding between Rad6 and ubiquitin (reaction constant c4) and of PCNA mono-ubiquitylation (reaction constant c9).

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Additional file 14:

Effects of the modulation of the dissociation of mono-ubiquitylated PCNA from Rad18 dimer (reaction constant c10) and of the association of Rad5 with mono-ubiquitylated PCNA (reaction constant c12).

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Additional file 15:

Effects of the modulation of the formation of di-ubiquitylated (reaction constant c16) and of tri-ubiquitylated (reaction constant c22) PCNA isoforms.

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Additional file 16:

FACS analysis of wild type andrad14δ background cells irradiated at 10 J/m2 UV dose.

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Additional file 17:

Deletion ofUBP10 andUBP15 do not prevent PCNA deubiquitylation at later time-points after low acute UV irradiation.

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