Bioinformatic Tools in Crop Improvement - Crop Improvement: New Approaches and Modern Techniques - page 82

P3DB
The Plant Protein Phosphorylation Database (P3DB) is an information resource for
plant phosphoproteome research, andprovides a resource for protein phosphoryla-
tion data and detail information from multiple plant species (Gao et al. 2009 ).
Ubiquitination
Ubiquitination of protein is another one of the post-translational modifications oc-
curring in most eukaryotic cells, including plants. Protein ubiquitination is another
regulatory mechanism that controls protein localization and activity. Several large-
scale analyses of protein ubiquitination sites in plants have been reported (Maor
et al. 2007 ; Manzano et al. 2008 ; Igawa et al. 2009 ).
Anti-Ubiquitin Antibody
In Arabidopsis, affinity purification using an anti-ubiquitin antibody, and the subse-
quent use of MS/MS analyses has been performed to identify ubiquitinated proteins
(Igawa et al. 2009 ).
StructuralProteomics
Large data sets of protein 3D structures are also important as information resources
for elucidating relationships between protein function and structure, or for analys-
ing the active sites and their molecular identity in various protein complexes. To
deal with the technical aspects, methodology and interpretation of protein structure
in more detail is beyond the scope of this review, and I refer you to some recent
reviews on this topic (Yan and Chen 2005 ; Wlodawer et al. 2008 ). However listed
below in summary form are some of the most important features for structural pro-
teomics and web-based sites for protein structural projects, their purpose and URL
are detailed in Table 2.8 .
ISGO
The International Structural Genomics Organization (ISGO) site (Stevens et al.
2001 ) is designed to facilitate co-operation to determine protein structures using
existing instrumentation in a number of international laboratories for structural pro-
teomics, and have identified many DNA-binding domains (DBDs) of plant-specific
transcription factors (TF) (Yamasaki et al. 2004 ; Yamasaki et al. 2008b ).