f3b9a9b01916a2379cd354ec65764932 265131.pdf 30b6d05170144e62b77c9d74748a8db9f019bb21 265131.pdf 603b74d5a2e8dc5134973c9f47d1739bbd6b488ac9315f6f6db3f9fd7d01ae45 265131.pdf Title: In-Silico Analysis of pH-Dependent Liquid-Liquid Phase Separation in Intrinsically Disordered Proteins Subject: Intrinsically disordered proteins (IDPs) are essential players in the assembly of biomolecular condensates during liquid–liquid phase separation (LLPS). Disordered regions (IDRs) are significantly exposed to the solvent and, therefore, highly influenced by fluctuations in the microenvironment. Extrinsic factors, such as pH, modify the solubility and disorder state of IDPs, which in turn may impact the formation of liquid condensates. However, little attention has been paid to how the solution pH influences LLPS, despite knowing that this process is context-dependent. Here, we have conducted a large-scale in-silico analysis of pH-dependent solubility and disorder in IDRs known to be involved in LLPS (LLPS-DRs). We found that LLPS-DRs present maximum solubility around physiological pH, where LLPS often occurs, and identified significant differences in solubility and disorder between proteins that can phase-separate by themselves or those that require a partner. We also analyzed the effect of mutations in the resulting solubility profiles of LLPS-DRs and discussed how, as a general trend, LLPS-DRs display physicochemical properties that permit their LLPS at physiologically relevant pHs. Keywords: pH; liquid-liquid phase separation; intrinsically disordered proteins; protein solubility; protein disorder; mutations; bioinformatics Author: Carlos Pintado-Grima, Oriol Bárcenas and Salvador Ventura Creator: LaTeX with hyperref Producer: pdfTeX-1.40.21 CreationDate: Tue Jul 12 11:36:29 2022 CEST ModDate: Tue Jul 12 11:41:52 2022 CEST 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: 2679542 bytes Optimized: no PDF version: 1.7 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- AIQCCL+VnURWPalladioL-Bold Type 1 Custom yes yes no 10 0 PNJMNO+VnURWPalladioL Type 1 Custom yes yes no 15 0 OEIVFF+URWPalladioL-Bold Type 1 Custom yes yes no 19 0 RCSWOS+URWPalladioL-Roma Type 1 Custom yes yes no 24 0 WCXRZK+URWPalladioL-Ital Type 1 Custom yes yes no 28 0 IVVSWS+TimesNewRomanPS-BoldItalicMT Type 1C 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251 0 EMJPGF+PalatinoLinotype TrueType WinAnsi yes yes no 254 0 EMJPGH+PalatinoLinotype,Italic TrueType WinAnsi yes yes no 257 0 Jhove (Rel. 1.22.1, 2019-04-17) Date: 2023-06-17 02:31:56 CEST RepresentationInformation: 265131.pdf ReportingModule: PDF-hul, Rel. 1.12.1 (2019-04-17) LastModified: 2023-06-16 12:49:36 CEST Size: 2679542 Format: PDF Version: 1.7 Status: Well-Formed and valid SignatureMatches: PDF-hul MIMEtype: application/pdf PDFMetadata: Objects: 424 FreeObjects: 1 IncrementalUpdates: 0 DocumentCatalog: PageLayout: SinglePage PageMode: UseNone Outlines: Item: Title: Introduction Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@44c8afef Item: Title: Materials and Methods Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@7b69c6ba Children: Item: Title: Dataset Generation Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@46daef40 Item: Title: pH-Dependent Solubility and Disorder Analyses Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@12f41634 Item: Title: Results Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@13c27452 Children: Item: Title: LLPS-DRs Present Maximum Solubility around Neutral pH Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@262b2c86 Item: Title: A Link between pH-Dependent Solubility and pH-Dependent Disorder in LLPS-DRs Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@371a67ec Item: Title: Different Datasets in LLPS-DRs Present Distinct Property Distributions Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@5ed828d Item: Title: Psself Regions Present Lower Dispersion in Solubility and Disorder in the Physiological pH Range Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@50d0686 Item: Title: Case Study of Independent LLPS Happening at Physiological pH Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@7a3d45bd Item: Title: Mutations in LLPS Formation and Disease Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1e7c7811 Item: Title: pH-Dependent LLPS: Optimal Condition Evaluation Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@77ec78b9 Item: Title: Discussion Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1a3869f4 Item: Title: References Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@a38d7a3 Info: Title: In-Silico Analysis of pH-Dependent Liquid-Liquid Phase Separation in Intrinsically Disordered Proteins Author: Carlos Pintado-Grima, Oriol Bárcenas and Salvador Ventura Subject: Intrinsically disordered proteins (IDPs) are essential players in the assembly of biomolecular condensates during liquid liquid phase separation (LLPS). Disordered regions (IDRs) are significantly exposed to the solvent and, therefore, highly influenced by fluctuations in the microenvironment. Extrinsic factors, such as pH, modify the solubility and disorder state of IDPs, which in turn may impact the formation of liquid condensates. However, little attention has been paid to how the solution pH influences LLPS, despite knowing that this process is context-dependent. Here, we have conducted a large-scale in-silico analysis of pH-dependent solubility and disorder in IDRs known to be involved in LLPS (LLPS-DRs). We found that LLPS-DRs present maximum solubility around physiological pH, where LLPS often occurs, and identified significant differences in solubility and disorder between proteins that can phase-separate by themselves or those that require a partner. We also analyzed the effect of mutations in the resulting solubility profiles of LLPS-DRs and discussed how, as a general trend, LLPS-DRs display physicochemical properties that permit their LLPS at physiologically relevant pHs. 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