Overview

Protein–protein interactions are one of the most important biological interaction and play crucial role in many biological events. The ability to design peptides that bind specifically and with high affinity to any given protein is a promising approach to either activate or inhibit a protein implicated in a disease.

Large conformational changes in both the targeted protein and the peptide may make these similarities difficult to recognize.

This service implements a method based on an approach previously developed and that aims to the recognition of small molecules binding sites. The core computation of PatchSearch[1, 2] allows for local nonsequential searching for similar regions on protein surfaces. Several changes have been made to adapt it to the specific features of peptide binding sites, in particular, their large interfacial surface (around 750 – 1500 Ų) which is often shallow and relatively featureless in comparison with small molecule binding pocket. It is based on the detection of cliques in product graphs followed by a fast maximal matching in bipartite graphs between atoms of a binding site and atoms of the compared structures.

The service is fully embedded in the Mobyle framework. It embeds simple yet powerful data management features that allow the user to reproduce analyses. It gives to the users the possibility to create registered accounts, which allows user data and jobs to be maintained and managed across multiple work sessions and therefore to reuse and share data and results.

When using this service, please cite the following references:

Rey J, Rasolohery I, Tufféry P, Guyon F, Moroy G.
PatchSearch: a web server for off-target protein identification.
Nucleic Acids Res. 2019 Jul 2;47(W1):W365-W372.
Rasolohery I, Moroy G, Guyon F.
PatchSearch: A Fast Computational Method for Off-Target Detection.
J Chem Inf Model. 2017 Apr 24;57(4):769-777.

PepiT Usage

Input

Depending on the input, the Web server proposes two different modes:

Mode 1: structural comparaisons between a peptide binding site and a protein surface.

1. Structure of a protein-peptide complex
   Enter the PDB identifier containing the protein-peptide complex. To define a binding site used for searching, enter one or more chains from the protein separated by a comma. Enter the chain corresponding to the peptide. All the atoms from the proteins located at given distance threshold are selected.
   
2. Collection of proteins to mine:
   • Paste a comma separated list of PDB identifiers into the text field.
   or
   • Select a preset list of PDB identifiers:
     • Human protein structures with sequence identity less than 30%
     • Human protein structures with sequence identity less than 50%
     • Human protein structures with sequence identity less than 70%

Mode 2: identification of peptide binding sites on a protein surface.

1. Enter the PDB identifier containing the protein of the interest and its chain. The "Peptide chain identifier" field MUST be empty
2. Select the preset list of peptide binding sites.

Results

• 

  Progress report

  This section will incrementally provide information about job progression and errors if any. A typical run should produce a report similar to the following :

  

  Errors related to the input data specified are also reported in this field.

• 

  Search results

  At the end, the service outputs a table of hits ranked in order of the binding affinity. Pep-it results is a table for each retrieved peptide binding site.

  Similar protein regions are output to a table with the PDB identifier, the coverage (number of retrieved atoms), the RMSD (between the query patch and the retrieved patch), the MD Score (Mean Deviation score) and the affinity computed by a scoring step using Smina program[3].

  
• 

  Visualization of the best hits

  An interactive page allowing to browse the retrieved peptide binding site. The residues forming the peptide binding site are in red. The peptide is in cyan cartoon representation. The user can visualize the each solutions ranking to the estimated affinity by Smina program.

  
• 

  Downloadable results

  The table of results is downloadable in csv or Excel format.

Example, sample test

In this example, we aim to detect proteins which may have structural homologies with a given peptide binding site. We use the structure of GroEL in interaction with a 12-mer peptide (PDB ID: 1DKD). Similar peptide binding sites will be searched in a list of 58 proteins structures.

As a simple test, you can:

1. Use Mobyle facilities: fetch a protein structure from the PDB databank using a PDB identifier.

   1. Click the db button.

   2. Select pdb in the menu.

   3. Enter a PDB identifier: 1DKD.

   4. Press select button.

   

2. Define the peptide binding site:

   1. Enter the protein chain identifier: A

   2. Enter the peptide chain identifier: E

   

3. Define the targeted proteins:

   Input a list of targeted proteins into the field:

   1KID, 2R7G, 1I27, 1LB4, 1GO5, 2Q0U, 1T0H, 2A31, 5GW6, 3RVQ, 2C5J, 2IV9, 2HPJ, 1S0E, 3GC7, 2PE8, 2YQL, 1M5Y, 4RJL, 2OVA, 2OEV, 3OD4, 2YB6, 3AU0, 5AZ9, 5AFY, 1QBH, 3LBJ, 1E9I, 3HB2, 2MHS, 1G9L, 3U69, 1QFZ, 4YAT, 1M94, 2YLF, 3FTO, 4U5U, 3BPP, 1RKE, 2Q91, 4HH5, 3W5O, 4JIZ, 3UTK, 2Y1Y, 3TX7, 4BW7, 3HVP, 3SO8, 2BNX, 4YKD, 5CK9, 2DJK, 3HU3, 5IC0, 1W24

   

4. Run:

   Launch PatchSearch by clicking Run either at the top or at the bottom of the page.

5. Results:

   The results of the search can be accessed here.

References

[1] Rasolohery I, Moroy G, Guyon F.
PatchSearch: A Fast Computational Method for Off-Target Detection.
J Chem Inf Model. 2017 Apr 24;57(4):769-777.

[2] Rey J, Rasolohery I, Tufféry P, Guyon F, Moroy G.
PatchSearch: a web server for off-target protein identification.
Nucleic Acids Res. 2019 Jul 2; 47(W1): W365–W372.

[3] Koes DR, Baumgartner MP, Camacho CJ.
Lessons learned in empirical scoring with smina from the CSAR 2011 benchmarking exercise.
J Chem Inf Model. 2013 Aug 15;53(8):1893-904.