Post-Translational Modification site Prediction - User Interface

Introduction

By covalently attaching to individual amino acids various functional molecules such as phosphates, lipids, or proteins, post-translational modifications (PTMs) alter a protein’s biochemical nature significantly, and play essential roles in a wide variety of cellular processes. Although more than 350 types of PTMs have been discovered (see the database of protein translational modifications at http://abrf.org/index.cfm/dm.home), only a few of them have been well-characterized (please refer to the following list of PTM prediction servers). Experimental identification of proteins’ PTM sites is labor-intensive and usually limited by the availability of enzymatic reactions. In silico prediction could be a promising strategy to conduct preliminary analyses and greatly reduce the number of potential targets that need further in vivo or in vitro confirmation.

Since the diversity in the user interface of different prediction servers could greatly hinder experimental biologists in using these servers, we propose to develop a protocol of a unified user interface (UI) for in silico prediction servers for proteins’ PTMs, based on our own work and other groups’ work on PTM site prediction. Computational biologists may follow this protocol to provide a uniform user interface, regardless of the PTM types and the computation algorithms. And wet lab biologists would be able to use any PTM site prediction servers compliant to this protocol after getting familiar with one of them.

Reference

A general user interface for prediction servers of proteins' post-translational modification sites.
Fengfeng Zhou, Yu Xue, Xuebiao Yao, Ying Xu.
Nature Protocols 1 (3): 1318-1321.

Some tools for PTM site prediction servers which comply with this protocol

This protocol tries to propose a unified user interface which represents the common features of almost all the available PTM site prediction servers. We also collect here some tools adoptting the output data of those servers complying with this protocol. We take the server, CSS-Palm, as an example.

Please contact the authors of this protocol for adding to this list your tools facilitating the PTM site prediction servers that comply with this protocol.

1. Incorporate the prediction results with 3-d structure information

This tool, including two Perl script, get_pdb_pep_pl and gen_rasmol_script_pl, could generate an automatic script for the widely-used structure viewing software, RasMol, to highlight the predicted PTM sites in a given PDB data file.

The procedure to use this tool is illustrated as follows:

Notes:

  1. The PTM site prediction server should provide the final prediction results in a TAB deliminated text file, as suggested in this protocol. Two examples are:
    1) No ending line,
    >1a0b;;DefaultChain;;658;;774
    1 -------KSEALLDI 5 18 1
    99 GEWIEEMKEEWRHDV 1.812 18 1
    2) With ending line "//"
    >1a0b;;DefaultChain;;658;;774
    1 -------KSEALLDI 5 18 1
    99 GEWIEEMKEEWRHDV 1.812 18 1
    //
    The first column should be the position of prediction PTM sites, and the peptide names should be kept in the original form.



Step 1: Download a PDB file from http://www.pdb.org/. Take 1a0b as an example. The pdb file is downloaded from this URL: http://www.pdb.org/pdb/files/1a0b.pdb.gz , and the plain text PDB file is uncompressed with this command:

  $ gunzip 1a0b.pdb.gz  

Step 2: Run the script get_pdb_pep_pl

  $ perl ./get_pdb_pep_pl 1a0b  

Step 3: Predict the potential palmitoylation sites using CSS-Palm, and the prediction results are saved in file 1a0b.result

Step 4: Run the script gen_rasmol_script_pl

  $ perl gen_rasmol_script_pl 1a0b.result  
The color used to highlight the prediction PTM sites has a default value: green, and it can be reset through
  $ perl gen_rasmol_script_pl 1a0b.result 0,0,255  
The color is reset to blue in the format of R,G,B.

Step 5: Load the generated RasMol script 1a0b.rasmol.script

  $ rasmol -script 1a0b.rasmol.script  
or run this command within RasMol command line window:
  RasMol> script 1a0b.rasmol.script  

Results: There are two predicted palmitoylation sites, 1 and 99, and the figure of the structure plotted by RasMol is as follows:

The atoms belonging to the two prediction palmitoylation sites are highlighted as green.
 
 
 
 
 

Computational Systems Biology Laboratory,
Department of Biochemical and Molecular Biology and Institute of Bioinformatics,
University of Georgia, Athens, GA 30602, USA

Laboratory of Cellular Dynamics,
Hefei National Laboratory for Physical Sciences,
and the University of Science and Technology of China, Hefei, China 230027

Last update: 2007-04-06