Current Proteomics

Bernd Rehm  
Institute of Molecular BioSciences Massey University
Private Bag 11222
Palmerston North
New Zealand

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Interactome Analysis and Docking Sites Prediction of Radiation Sensitive 23 (RAD 23) Proteins in Arabidopsis thaliana

Author(s): Secic Ena, Jasmin  Sutkovic, Mohamed Ragab Abdel Gawwad.

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Abstract:

Exposure to UV radiation is a major cause of DNA damage in plants. One of the proteins involved in nucleotide excision repair, as part of a complex that recognizes DNA damage with AtXPC, is RAD23, also involved in Ub/proteasomal degradation pathway. Arabidopsis thaliana has 4 homologues of RAD23, whose 3D structure has been predicted and validated in this study by different bioinformatics tools. Phylogenetic analysis showed that AtRAD23A/B and AtRAD23C/D homologues have significant similarity among themselves. All four homologues have conserved domains identified: UBL, STI1 and 2 UBA domains, with PFAM domain search identifying XPC-binding domains too. Subcellular localization indicated differences among AtRAD23 homologues, with AtRAD23A localized to the nucleus and AtRAD23D to the cytoplasm. The predicted interactome for the homologues indicates a complex role of AtRAD23 in DNA repair mechanisms, beyond simple recognition of DNA damage and supports extensive interactions with various proteasomal subunits, as well as proteins that are to be degraded in order to maintain cellular integrity. Additionally, an interaction with PNG1 enzyme, a link with the ERAD pathway, was predicted. Docking sites prediction and visualization is shown for the AtRAD23D homologue with AtXPC and AtPNG1.

Keywords: Arabidopsis thaliana, docking sites, DNA repair, 3-D structure, interactome, RAD 23 protein.

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Article Details

VOLUME: 12
ISSUE: 1
Year: 2015
Page: [28 - 44]
Pages: 17
DOI: 10.2174/1570164612666150225234240