User:Pedrobeltrao/Notebook/Structural analysis of phosphorylation sites/domain based analysis

From OpenWetWare

Jump to: navigation, search
(Domain based analysis)
Current revision (19:58, 23 November 2009) (view source)
(Domain based analysis)
 
Line 1: Line 1:
==Domain based analysis==
==Domain based analysis==
-
Phosphorylation sites from S. cerevisiae were collected from different sources . In addition phosphorylation sites from H. sapiens, D. melanogaster, C. albicans and S. pombe were transfered by homology to S. cerevisiae proteins by aligning S. cerevisiae proteins with orthologous proteins in these species. Up to date values for phospho-sites can be seen  [[http://openwetware.org/wiki/User:Pedrobeltrao/Notebook/Structural_analysis_of_phosphorylation_sites/data_collection_and_stats| here]]).
+
Phosphorylation sites from S. cerevisiae were collected from different sources . In addition phosphorylation sites from H. sapiens, D. melanogaster, C. albicans and S. pombe were transfered by homology to S. cerevisiae proteins by aligning S. cerevisiae proteins with orthologous proteins in these species. Up to date values for phospho-sites can be seen  [[http://openwetware.org/wiki/User:Pedrobeltrao/Notebook/Structural_analysis_of_phosphorylation_sites/data_collection_and_stats here]]).
One possible type of analysis that can be done with this information is to predict modes of regulation for protein domains that are commonly phosphorylated. For each PFAM domain we can we have picked an example structure to use as a structural model. We then  mapped all phosphorylation sites that occur in  instances of these domain in S. cerevisiae or orthologous proteins to this model structure and calculated phosphorylation propensity . As an example we show below the results obtained for the protein kinase domain.
One possible type of analysis that can be done with this information is to predict modes of regulation for protein domains that are commonly phosphorylated. For each PFAM domain we can we have picked an example structure to use as a structural model. We then  mapped all phosphorylation sites that occur in  instances of these domain in S. cerevisiae or orthologous proteins to this model structure and calculated phosphorylation propensity . As an example we show below the results obtained for the protein kinase domain.
[[Image:Pkinase_phos_prop.jpg|550px|alt=alt text|left]]
[[Image:Pkinase_phos_prop.jpg|550px|alt=alt text|left]]
In this example the phosphorylation propensity matches well with the known modes of regulation of protein kinases. The phosphorylation of the activation loop (in red) with the highest propensity as well as a moderate phosphorylation propensity of the glicine rich loop (light blue). We are currently analyzing other domains for to search for novel regulatory sites.
In this example the phosphorylation propensity matches well with the known modes of regulation of protein kinases. The phosphorylation of the activation loop (in red) with the highest propensity as well as a moderate phosphorylation propensity of the glicine rich loop (light blue). We are currently analyzing other domains for to search for novel regulatory sites.

Current revision

Domain based analysis

Phosphorylation sites from S. cerevisiae were collected from different sources . In addition phosphorylation sites from H. sapiens, D. melanogaster, C. albicans and S. pombe were transfered by homology to S. cerevisiae proteins by aligning S. cerevisiae proteins with orthologous proteins in these species. Up to date values for phospho-sites can be seen [here]).

One possible type of analysis that can be done with this information is to predict modes of regulation for protein domains that are commonly phosphorylated. For each PFAM domain we can we have picked an example structure to use as a structural model. We then mapped all phosphorylation sites that occur in instances of these domain in S. cerevisiae or orthologous proteins to this model structure and calculated phosphorylation propensity . As an example we show below the results obtained for the protein kinase domain.

alt=alt text

In this example the phosphorylation propensity matches well with the known modes of regulation of protein kinases. The phosphorylation of the activation loop (in red) with the highest propensity as well as a moderate phosphorylation propensity of the glicine rich loop (light blue). We are currently analyzing other domains for to search for novel regulatory sites.

Personal tools