c097ee5e30b1384dc6aeadf996aa2c3f pmc_32823616.pdf e956b0e7f5b296cd66d462db040429729125b837 pmc_32823616.pdf d0c932ec158cc2d0a7cc1a320d577039d12d0a82ff4cbd7924bd8b9d357d0ca1 pmc_32823616.pdf Title: DispHred: A Server to Predict pH-Dependent Order–Disorder Transitions in Intrinsically Disordered Proteins Subject: The natively unfolded nature of intrinsically disordered proteins (IDPs) relies on several physicochemical principles, of which the balance between a low sequence hydrophobicity and a high net charge appears to be critical. Under this premise, it is well-known that disordered proteins populate a defined region of the charge–hydropathy (C–H) space and that a linear boundary condition is sufficient to distinguish between folded and disordered proteins, an approach widely applied for the prediction of protein disorder. Nevertheless, it is evident that the C–H relation of a protein is not unalterable but can be modulated by factors extrinsic to its sequence. Here, we applied a C–H-based analysis to develop a computational approach that evaluates sequence disorder as a function of pH, assuming that both protein net charge and hydrophobicity are dependent on pH solution. On that basis, we developed DispHred, the first pH-dependent predictor of protein disorder. Despite its simplicity, DispHred displays very high accuracy in identifying pH-induced order/disorder protein transitions. DispHred might be useful for diverse applications, from the analysis of conditionally disordered segments to the synthetic design of disorder tags for biotechnological applications. Importantly, since many disorder predictors use hydrophobicity as an input, the here developed framework can be implemented in other state-of-the-art algorithms. Keywords: intrinsically disordered proteins; pH; bioinformatics; disorder prediction; conditional folding; machine learning Author: Jaime Santos, Valentín Iglesias, Carlos Pintado, Juan Santos-Suárez and Salvador Ventura Creator: LaTeX with hyperref package Producer: pdfTeX-1.40.18 CreationDate: Thu Aug 13 11:38:14 2020 CEST ModDate: Thu Aug 13 11:38:14 2020 CEST Custom Metadata: yes Metadata Stream: no Tagged: no UserProperties: no Suspects: no Form: none JavaScript: no Pages: 12 Encrypted: no Page size: 595.276 x 841.89 pts (A4) Page rot: 0 File size: 1475225 bytes Optimized: no PDF version: 1.5 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- RDUUBD+URWPalladioL-Ital Type 1 Custom yes yes no 92 0 FGVVGZ+URWPalladioL-Bold Type 1 Custom yes yes no 93 0 QTLELQ+Pxbsy Type 1 Builtin yes yes no 94 0 SSNIUI+VnURWPalladioL-Bold Type 1 Custom yes yes no 95 0 NSKGRW+URWPalladioL-Roma Type 1 Custom yes yes no 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