DispHred is a protein disorder predictor over pH for IDPs/IDRs.
Users can introduce or upload a fasta sequence for analysis or try the server provided example.
Intrinsically disordered proteins (IDPs) do not require a stable folded structure to develop their biological activities. The unfolded nature is encoded in their primary sequence, generally enriched in ionizable and polar residues and depleted of hydrophobic and aromatic residues. However, ligands, binding partners or solvent conditions such as ion concentration or pH, have been reported to induce conditional folding on different IDPs.
Past studies proposed that IDPs populate a defined region in the mean net-charge-hydropathy (C-H) phase space diagram (Uversky et al, 2000); and that an empirical boundary can successfuly discriminate between folded and unfolded proteins.
IDPs disordered nature makes them highly context dependent. While environmental pH's influence on protein net charge has been deeply studied, its influence on lipophylicity has been mostly neglected.
DipHred uses a recent pH-dependent hydrophobicity scale (Zamora et al., 2020) and protein net charge calculation to detect pH-dependent folding and unfolding of IDPs.
Under the "Submission" section, users may type or cut/paste the sequence in FASTA format or insert a valid Uniprot Accession Number. Next, select the range of pH for the analysis and the desired pH interval or step size (default is 0.5) and click Submit. Users may alternatively select to predict disorder at a specific pH by clicking the checkbox and choosing a pH for the analysis.
DispHred uses a sliding window to calculate hydrophobicity and net charge, this is set to 51 by default but can be manually changed. DispH score and global protein analysis remain largely unaffected by the window size; however, it influences local predictions along the sequence and the resulting profile. We strongly recommend adopting the window size for the intended purpose. The default window of 51 is suitable for full protein or large disorder analyses. For detailed region-specific sequence analysis, we suggest window sizes of 7, 11, or 21 residues, even if the performance of these size values are significantly dependent on the analyzed protein.
Users can also pre-populate the application form with Human Prothymosin alpha by clicking the Example button.
DispHred will display two clickable links with a json file containing all calculations or a zip folder with all generated files in the prediction.
The primary output is an interactive table with DispH score, lipophicility and net charge per residue (NCPR) for previously selected pHs, as well as a graph showing the average score along the pH range. By clicking on the table at each pH, a graph with DispH scores along the sequence for the selected pH will pop up.
Alternatively, predictions for a specific pH will show a table with DispHred score variation along the sequence and graph depicting it.
1.- Santos, J.; Iglesias, V.; Pintado, C.; Santos-Suárez, J.; Ventura, S. DispHred: A server for the prediction of pH-dependent order-disorder transitions of intrinsically disordered proteins from the primary sequence. IJMS 2020, 21, 5814. doi: 10.3390/ijms21165814
2.- Uversky, V.; Gillespie, J.; Flink, A. Why Are “Natively Unfolded” Proteins Unstructured Under Physiologic Conditions?. Proteins 2000, 41, 415-427, doi:10.1002/1097-0134(20001115)41:3<415::aid-prot130>3.0.co;2-7
3.- Santos, J.; Iglesias, V.; Santos-Suárez, J.; Mangiagalli, M.; Brocca, S.; Pallarès, I.; Ventura, S. pH-Dependent Aggregation in Intrinsically Disordered Proteins Is Determined by Charge and Lipophilicity. Cells 2020, 9, 145. doi:10.3390/cells9010145
4.- Zamora, W.J.; Campanera, J.M.; Luque, F.J. Development of a Structure-Based, pH-Dependent Lipophilicity Scale of Amino Acids from Continuum Solvation Calculations..J Phys Chem Lett 2019, 10, 883-889. doi:10.1021/acs.jpclett.9b00028