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Analyzing the Sequences of Intrinsically Disordered Regions with CIDER and localCIDER

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Intrinsically Disordered Proteins

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2141))

Abstract

Intrinsically disordered proteins and protein regions are ubiquitous across eukaryotic proteomes where they play a range of functional roles. Unlike folded proteins, IDRs lack a well-defined native state but exist in heterogeneous ensembles of conformations. In the absence of a defined native state, structure-guided mutations to test specific mechanistic hypotheses are generally not possible. Despite this, the use of mutations to alter sequence properties has become a relatively common approach for teasing out the relationship between sequence, ensemble, and function. A key step in designing informative mutants is the ability to identify specific sequence features that may reveal an interpretable response if perturbed. Here, we provide guidance on using the CIDER and localCIDER tools for amino acid sequence analysis, with a focus on building intuition with respect to the most commonly described features.

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References

  1. Whisstock JC, Lesk AM (2003) Prediction of protein function from protein sequence and structure. Q Rev Biophys 36:307–340

    CAS  PubMed  Google Scholar 

  2. Sadowski MI, Jones DT (2009) The sequence–structure relationship and protein function prediction. Curr Opin Struct Biol 19:357–362

    CAS  PubMed  Google Scholar 

  3. Kühlbrandt W (2004) Biology, structure and mechanism of P-type ATPases. Nat Rev Mol Cell Biol 5:282–295

    PubMed  Google Scholar 

  4. Caruthers JM, McKay DB (2002) Helicase structure and mechanism. Curr Opin Struct Biol 12:123–133

    CAS  PubMed  Google Scholar 

  5. Hollenstein K, Dawson RJP, Locher KP (2007) Structure and mechanism of ABC transporter proteins. Curr Opin Struct Biol 17:412–418

    CAS  PubMed  Google Scholar 

  6. Reetz MT, Carballeira JD (2007) Iterative saturation mutagenesis (ISM) for rapid directed evolution of functional enzymes. Nat Protoc 2:891–903

    CAS  PubMed  Google Scholar 

  7. McLaughlin RN Jr, Poelwijk FJ, Raman A, Gosal WS, Ranganathan R (2012) The spatial architecture of protein function and adaptation. Nature 491:138–142

    CAS  PubMed  PubMed Central  Google Scholar 

  8. Fowler DM, Araya CL, Fleishman SJ, Kellogg EH, Stephany JJ, Baker D, Fields S (2010) High-resolution mapping of protein sequence-function relationships. Nat Methods 7:741–746

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Kitzman JO, Starita LM, Lo RS, Fields S, Shendure J (2015) Massively parallel single-amino-acid mutagenesis. Nat. Methods 12:203–206, 4 p following 206

    CAS  PubMed  PubMed Central  Google Scholar 

  10. Dorrity MW, Queitsch C, Fields S (2019) High-throughput identification of dominant negative polypeptides in yeast. Nat Methods 16:413–416

    CAS  PubMed  PubMed Central  Google Scholar 

  11. van der Lee R, Buljan M, Lang B, Weatheritt RJ, Daughdrill GW, Dunker AK, Fuxreiter M, Gough J, Gsponer J, Jones DT, Kim PM, Kriwacki RW, Oldfield CJ, Pappu RV, Tompa P, Uversky VN, Wright PE, Babu MM (2014) Classification of intrinsically disordered regions and proteins. Chem Rev 114:6589–6631

    PubMed  PubMed Central  Google Scholar 

  12. Wright PE, Dyson HJ (1999) Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. J Mol Biol 293:321–331

    CAS  PubMed  Google Scholar 

  13. Dyson HJ, Wright PE (2005) Intrinsically unstructured proteins and their functions. Nat Rev Mol Cell Biol 6:197–208

    CAS  PubMed  Google Scholar 

  14. Staller MV, Holehouse AS, Swain-Lenz D, Das RK, Pappu RV, Cohen BA (2018) A high-throughput mutational scan of an intrinsically disordered acidic transcriptional activation domain. Cell Syst 6:444–455.e6

    CAS  PubMed  PubMed Central  Google Scholar 

  15. Boothby TC, Tapia H, Brozena AH, Piszkiewicz S, Smith AE, Giovannini I, Rebecchi L, Pielak GJ, Koshland D, Goldstein B (2017) Tardigrades use intrinsically disordered proteins to survive desiccation. Mol Cell 65:975–984.e5

    CAS  PubMed  PubMed Central  Google Scholar 

  16. Wright PE, Dyson HJ (2014) Intrinsically disordered proteins in cellular signalling and regulation. Nat Rev Mol Cell Biol 16:18–29

    Google Scholar 

  17. Powers SK, Holehouse AS, Korasick DA, Schreiber KH, Clark NM, Jing H, Emenecker R, Han S, Tycksen E, Hwang I, Sozzani R, Jez JM, Pappu RV, Strader LC (2019) Nucleo-cytoplasmic Partitioning of ARF Proteins Controls Auxin Responses in Arabidopsis thaliana. Mol. Cell 76(1):177–190. https://doi.org/10.1016/j.molcel.2019.06.044

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Uversky VN, Oldfield CJ, Dunker AK (2008) Intrinsically disordered proteins in human diseases: introducing the D2 concept. Annu Rev Biophys 37:215–246

    CAS  PubMed  Google Scholar 

  19. Brown CJ, Johnson AK, Dunker AK, Daughdrill GW (2011) Evolution and disorder. Curr Opin Struct Biol 21:441–446

    CAS  PubMed  PubMed Central  Google Scholar 

  20. Buske PJ, Levin PA (2013) A flexible C-terminal linker is required for proper FtsZ assembly in vitro and cytokinetic ring formation in vivo. Mol Microbiol 89:249–263

    CAS  PubMed  PubMed Central  Google Scholar 

  21. Sherry KP, Das RK, Pappu RV, Barrick D (2017) Control of transcriptional activity by design of charge patterning in the intrinsically disordered RAM region of the notch receptor. Proc Natl Acad Sci U S A 114:E9243–E9252

    CAS  PubMed  PubMed Central  Google Scholar 

  22. Keul ND, Oruganty K, Schaper Bergman ET, Beattie NR, McDonald WE, Kadirvelraj R, Gross ML, Phillips RS, Harvey SC, Wood ZA (2018) The entropic force generated by intrinsically disordered segments tunes protein function. Nature 563:584–588

    CAS  PubMed  PubMed Central  Google Scholar 

  23. Riback JA, Katanski CD, Kear-Scott JL, Pilipenko EV, Rojek AE, Sosnick TR, Drummond DA (2017) Stress-triggered phase separation is an adaptive, evolutionarily tuned response. Cell 168:1028–1040.e19

    CAS  PubMed  PubMed Central  Google Scholar 

  24. Ota H, Fukuchi S (2017) Sequence conservation of protein binding segments in intrinsically disordered regions. Biochem Biophys Res Commun 494:602–607

    CAS  PubMed  Google Scholar 

  25. Das RK, Huang Y, Phillips AH, Kriwacki RW, Pappu RV (2016) Cryptic sequence features within the disordered protein p27Kip1 regulate cell cycle signaling. Proc Natl Acad Sci U S A 113:5616–5621

    CAS  PubMed  PubMed Central  Google Scholar 

  26. Bouchard JJ, Otero JH, Scott DC, Szulc E, Martin EW, Sabri N, Granata D, Marzahn MR, Lindorff-Larsen K, Salvatella X, Schulman BA, Mittag T (2018) Cancer mutations of the tumor suppressor SPOP disrupt the formation of active, phase-separated compartments. Mol Cell 72:19–36.e8

    CAS  PubMed  PubMed Central  Google Scholar 

  27. Martin EW, Holehouse AS, Grace CR, Hughes A, Pappu RV, Mittag T (2016) Sequence determinants of the conformational properties of an intrinsically disordered protein prior to and upon multisite phosphorylation. J Am Chem Soc 138:15323–15335

    CAS  PubMed  PubMed Central  Google Scholar 

  28. Ortega E, Rengachari S, Ibrahim Z, Hoghoughi N, Gaucher J, Holehouse AS, Khochbin S, Panne D (2018) Transcription factor dimerization activates the p300 acetyltransferase. Nature 562:538–544

    CAS  PubMed  PubMed Central  Google Scholar 

  29. Wang J, Choi J-M, Holehouse AS, Lee HO, Zhang X, Jahnel M, Maharana S, Lemaitre R, Pozniakovsky A, Drechsel D, Poser I, Pappu RV, Alberti S, Hyman AA (2018) A molecular grammar governing the driving forces for phase separation of prion-like RNA binding proteins. Cell 174:688–699.e16

    CAS  PubMed  PubMed Central  Google Scholar 

  30. Das RK, Ruff KM, Pappu RV (2015) Relating sequence encoded information to form and function of intrinsically disordered proteins. Curr Opin Struct Biol 32:102–112

    CAS  PubMed  PubMed Central  Google Scholar 

  31. Mao AH, Lyle N, Pappu RV (2013) Describing sequence-ensemble relationships for intrinsically disordered proteins. Biochem J 449:307–318

    CAS  PubMed  Google Scholar 

  32. Holehouse AS, Pappu RV (2018) Collapse transitions of proteins and the interplay among backbone, Sidechain, and solvent interactions. Annu Rev Biophys 47:19–39

    CAS  PubMed  Google Scholar 

  33. Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer ELL, Tate J, Punta M (2014) Pfam: the protein families database. Nucleic Acids Res 42:D222–D230

    CAS  PubMed  Google Scholar 

  34. Mao AH, Crick SL, Vitalis A, Chicoine CL, Pappu RV (2010) Net charge per residue modulates conformational ensembles of intrinsically disordered proteins. Proc Natl Acad Sci U S A 107:8183–8188

    CAS  PubMed  PubMed Central  Google Scholar 

  35. Müller-Späth S, Soranno A, Hirschfeld V, Hofmann H, Rüegger S, Reymond L, Nettels D, Schuler B (2010) Charge interactions can dominate the dimensions of intrinsically disordered proteins. Proc Natl Acad Sci U S A 107:14609–14614

    PubMed  PubMed Central  Google Scholar 

  36. Marsh JA, Forman-Kay JD (2010) Sequence determinants of compaction in intrinsically disordered proteins. Biophys J 98:2383–2390

    CAS  PubMed  PubMed Central  Google Scholar 

  37. Das RK, Pappu RV (2013) Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues. Proc Natl Acad Sci U S A 110:13392–13397

    CAS  PubMed  PubMed Central  Google Scholar 

  38. C.S. Sørensen, M. Kjaergaard, Effective concentrations enforced by intrinsically disordered linkers are governed by polymer physics, bioRxiv. (2019) 577536. https://doi.org/10.1101/577536

  39. Hofmann H, Soranno A, Borgia A, Gast K, Nettels D, Schuler B (2012) Polymer scaling laws of unfolded and intrinsically disordered proteins quantified with single-molecule spectroscopy. Proc Natl Acad Sci U S A 109:16155–16160

    CAS  PubMed  PubMed Central  Google Scholar 

  40. Holehouse AS, Das RK, Ahad JN, Richardson MOG, Pappu RV (2017) CIDER: resources to analyze sequence-ensemble relationships of intrinsically disordered proteins. Biophys J 112:16–21

    CAS  PubMed  PubMed Central  Google Scholar 

  41. Conda—Conda documentation, (n.d.). https://docs.conda.io/en/latest/. Accessed June 12, 2019

  42. Borgia A, Borgia MB, Bugge K, Kissling VM, Heidarsson PO, Fernandes CB, Sottini A, Soranno A, Buholzer KJ, Nettels D, Kragelund BB, Best RB, Schuler B (2018) Extreme disorder in an ultrahigh-affinity protein complex. Nature 555:61

    CAS  PubMed  PubMed Central  Google Scholar 

  43. M.C. Cohan, A.E. Posey, S.J. Grigsby, A. Mittal, A.S. Holehouse, P.J. Buske, P.A. Levin, R.V. Pappu, Evolved sequence features within the intrinsically disordered tail influence FtsZ assembly and bacterial cell division, bioRxiv. (2018) 301622. https://doi.org/10.1101/301622

  44. Campen A, Williams RM, Brown CJ, Meng J, Uversky VN, Dunker AK (2008) TOP-IDP-scale: a new amino acid scale measuring propensity for intrinsic disorder. Protein Pept Lett 15:956–963

    CAS  PubMed  PubMed Central  Google Scholar 

  45. Dyson HJ, Wright PE (2002) Coupling of folding and binding for unstructured proteins. Curr Opin Struct Biol 12:54–60

    CAS  PubMed  Google Scholar 

  46. Sugase K, Dyson HJ, Wright PE (2007) Mechanism of coupled folding and binding of an intrinsically disordered protein. Nature 447:1021–1025

    CAS  PubMed  Google Scholar 

  47. Rogers JM, Oleinikovas V, Shammas SL, Wong CT, De Sancho D, Baker CM, Clarke J (2014) Interplay between partner and ligand facilitates the folding and binding of an intrinsically disordered protein. Proc Natl Acad Sci U S A 111:15420–15425

    CAS  PubMed  PubMed Central  Google Scholar 

  48. Kyte J, Doolittle RF (1982) A simple method for displaying the hydropathic character of a protein. J Mol Biol 157:105–132

    CAS  PubMed  Google Scholar 

  49. Ravarani CNJ, Erkina TY, De Baets G, Dudman DC, Erkine AM, Madan Babu M (2018) High-throughput discovery of functional disordered regions: investigation of transactivation domains. Mol Syst Biol 14:e8190

    PubMed  PubMed Central  Google Scholar 

  50. Davey NE, Van Roey K, Weatheritt RJ, Toedt G, Uyar B, Altenberg B, Budd A, Diella F, Dinkel H, Gibson TJ (2012) Attributes of short linear motifs. Mol BioSyst 8:268–281

    CAS  PubMed  Google Scholar 

  51. Gouw M, Michael S, Sámano-Sánchez H (2018) The eukaryotic linear motif resource–2018 update. Nucleic Acids 46(D1):D428–D434. https://academic.oup.com/nar/article-abstract/46/D1/D428/4612965

    CAS  Google Scholar 

  52. Van Roey K, Uyar B, Weatheritt RJ, Dinkel H, Seiler M, Budd A, Gibson TJ, Davey NE (2014) Short linear motifs: ubiquitous and functionally diverse protein interaction modules directing cell regulation. Chem Rev 114:6733–6778

    PubMed  Google Scholar 

  53. Mészáros B, Erdos G, Dosztányi Z (2018) IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding. Nucleic Acids Res 46:W329–W337

    PubMed  PubMed Central  Google Scholar 

  54. Fuertes G, Banterle N, Ruff KM, Chowdhury A, Mercadante D, Koehler C, Kachala M, Estrada Girona G, Milles S, Mishra A, Onck PR, Gräter F, Esteban-Martín S, Pappu RV, Svergun DI, Lemke EA (2017) Decoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS vs. FRET measurements. Proc Natl Acad Sci U S A 114:E6342–E6351

    CAS  PubMed  PubMed Central  Google Scholar 

  55. Mercadante D, Milles S, Fuertes G, Svergun DI, Lemke EA, Gräter F (2015) Kirkwood-buff approach rescues Overcollapse of a disordered protein in canonical protein force Fields. J Phys Chem B 119:7975–7984

    CAS  PubMed  Google Scholar 

  56. Gibbs EB, Lu F, Portz B, Fisher MJ, Medellin BP, Laremore TN, Zhang YJ, Gilmour DS, Showalter SA (2017) Phosphorylation induces sequence-specific conformational switches in the RNA polymerase II C-terminal domain. Nat Commun 8:15233

    CAS  PubMed  PubMed Central  Google Scholar 

  57. Portz B, Lu F, Gibbs EB, Mayfield JE, Rachel Mehaffey M, Zhang YJ, Brodbelt JS, Showalter SA, Gilmour DS (2017) Structural heterogeneity in the intrinsically disordered RNA polymerase II C-terminal domain. Nat Commun 8:15231

    CAS  PubMed  PubMed Central  Google Scholar 

  58. Riback JA, Bowman MA, Zmyslowski AM, Knoverek CR, Jumper JM, Hinshaw JR, Kaye EB, Freed KF, Clark PL, Sosnick TR (2017) Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water. Science 358:238–241

    CAS  PubMed  PubMed Central  Google Scholar 

  59. Warner JB 4th, Ruff KM, Tan PS, Lemke EA, Pappu RV, Lashuel HA (2017) Monomeric Huntingtin exon 1 has similar overall structural features for wild-type and pathological Polyglutamine lengths. J Am Chem Soc 139:14456–14469

    CAS  PubMed  PubMed Central  Google Scholar 

  60. Mukhopadhyay S, Krishnan R, Lemke EA, Lindquist S, Deniz AA (2007) A natively unfolded yeast prion monomer adopts an ensemble of collapsed and rapidly fluctuating structures. Proc Natl Acad Sci U S A 104:2649–2654

    CAS  PubMed  PubMed Central  Google Scholar 

  61. Crick SL, Jayaraman M, Frieden C, Wetzel R, Pappu RV (2006) Fluorescence correlation spectroscopy shows that monomeric polyglutamine molecules form collapsed structures in aqueous solutions. Proc Natl Acad Sci U S A 103:16764–16769

    CAS  PubMed  PubMed Central  Google Scholar 

  62. Peran I, Holehouse AS, Carrico IS, Pappu RV, Bilsel O, Raleigh DP (2019) Unfolded states under folding conditions accommodate sequence-specific conformational preferences with random coil-like dimensions. Proc Natl Acad Sci U S A 116:12301–12310.

    Google Scholar 

  63. Martin EW, Holehouse AS, Peran I, Farag M, Incicco JJ, Bremer A, Grace CR, Soranno A, Pappu RV, Mittag T (2020) Valence and patterning of aromatic residues determine the phase behavior of prion-like domains. Science 367:694–699

    Google Scholar 

  64. Longhi S, Receveur-Bréchot V, Karlin D, Johansson K, Darbon H, Bhella D, Yeo R, Finet S, Canard B (2003) The C-terminal domain of the measles virus nucleoprotein is intrinsically disordered and folds upon binding to the C-terminal moiety of the phosphoprotein. J Biol Chem 278:18638–18648

    CAS  PubMed  Google Scholar 

  65. Fossat MJ, Pappu RV (2019) Q-canonical Monte Carlo sampling for Modeling the linkage between charge regulation and conformational Equilibria of peptides. J Phys Chem B 123:6952–6967

    CAS  PubMed  Google Scholar 

  66. Tanford C (1968) Protein denaturation. Adv Protein Chem 23:121–282

    CAS  PubMed  Google Scholar 

  67. Tanford C (1964) Isothermal unfolding of globular proteins in aqueous urea solutions. J Am Chem Soc 86:2050–2059

    CAS  Google Scholar 

  68. Nozaki Y, Tanford C (1963) The solubility of amino acids and related compounds in aqueous urea solutions. J Biol Chem 238:4074–4081

    CAS  PubMed  Google Scholar 

  69. Auton M, Holthauzen LMF, Bolen DW (2007) Anatomy of energetic changes accompanying urea-induced protein denaturation. Proc Natl Acad Sci U S A 104:15317–15322

    CAS  PubMed  PubMed Central  Google Scholar 

  70. Auton M, Bolen DW (2004) Additive transfer free energies of the peptide backbone unit that are independent of the model compound and the choice of concentration scale. Biochemistry 43:1329–1342

    CAS  PubMed  Google Scholar 

  71. Felitsky DJ, Record MT Jr (2003) Thermal and urea-induced unfolding of the marginally stable lac repressor DNA-binding domain: a model system for analysis of solute effects on protein processes. Biochemistry 42:2202–2217

    CAS  PubMed  Google Scholar 

  72. Cannon JG, Anderson CF, Record MT Jr (2007) Urea-amide preferential interactions in water: quantitative comparison of model compound data with biopolymer results using water accessible surface areas. J Phys Chem B 111:9675–9685

    CAS  PubMed  Google Scholar 

  73. Oates ME, Romero P, Ishida T, Ghalwash M, Mizianty MJ, Xue B, Dosztányi S, Uversky VN, Obradovic Z, Kurgan L, Dunker AK, Gough J (2013) D2P2: database of disordered protein predictions. Nucleic Acids Res 41:D508–D516

    CAS  PubMed  Google Scholar 

  74. Ward JJ, Sodhi JS, McGuffin LJ, Buxton BF, Jones DT (2004) Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J Mol Biol 337:635–645

    CAS  PubMed  Google Scholar 

  75. Ward JJ, McGuffin LJ, Bryson K, Buxton BF, Jones DT (2004) The DISOPRED server for the prediction of protein disorder. Bioinformatics 20:2138–2139

    CAS  PubMed  Google Scholar 

  76. He B, Wang K, Liu Y, Xue B, Uversky VN, Dunker AK (2009) Predicting intrinsic disorder in proteins: an overview. Cell Res 19:929–949

    CAS  PubMed  Google Scholar 

  77. Dosztányi Z, Csizmok V, Tompa P, Simon I (2005) IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics 21:3433–3434

    PubMed  Google Scholar 

  78. Piovesan D, Tabaro F, Paladin L, Necci M, Micetic I, Camilloni C, Davey N, Dosztányi Z, Mészáros B, Monzon AM, Parisi G, Schad E, Sormanni P, Tompa P, Vendruscolo M, Vranken WF, Tosatto SCE (2018) MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins. Nucleic Acids Res 46:D471–D476

    CAS  PubMed  Google Scholar 

  79. Necci M, Piovesan D, Dosztányi Z, Tosatto SCE (2017) MobiDB-lite: fast and highly specific consensus prediction of intrinsic disorder in proteins. Bioinformatics 33:1402–1404

    CAS  PubMed  Google Scholar 

  80. Piovesan D, Tabaro F, Mičetić I, Necci M, Quaglia F, Oldfield CJ, Aspromonte MC, Davey NE, Davidović R, Dosztányi Z, Elofsson A, Gasparini A, Hatos A, Kajava AV, Kalmar L, Leonardi E, Lazar T, Macedo-Ribeiro S, Macossay-Castillo M, Meszaros A, Minervini G, Murvai N, Pujols J, Roche DB, Salladini E, Schad E, Schramm A, Szabo B, Tantos A, Tonello F, Tsirigos KD, Veljković N, Ventura S, Vranken W, Warholm P, Uversky VN, Dunker AK, Longhi S, Tompa P, Tosatto SCE (2017) DisProt 7.0: a major update of the database of disordered proteins. Nucleic Acids Res 45:D1123–D1124

    CAS  PubMed  Google Scholar 

  81. Monahan Z, Ryan VH, Janke AM, Burke KA, Rhoads SN, Zerze GH, O’Meally R, Dignon GL, Conicella AE, Zheng W, Best RB, Cole RN, Mittal J, Shewmaker F, Fawzi NL (2017) Phosphorylation of the FUS low-complexity domain disrupts phase separation, aggregation, and toxicity. EMBO J 36:2951–2967

    CAS  PubMed  PubMed Central  Google Scholar 

  82. Qamar S, Wang G, Randle SJ, Ruggeri FS, Varela JA, Lin JQ, Phillips EC, Miyashita A, Williams D, Ströhl F, Meadows W, Ferry R, Dardov VJ, Tartaglia GG, Farrer LA, Kaminski Schierle GS, Kaminski CF, Holt CE, Fraser PE, Schmitt-Ulms G, Klenerman D, Knowles T, Vendruscolo M, St George-Hyslop P (2018) FUS phase separation is modulated by a molecular chaperone and methylation of arginine Cation-π interactions. Cell 173:720–734.e15

    CAS  PubMed  PubMed Central  Google Scholar 

  83. Hofweber M, Hutten S, Bourgeois B, Spreitzer E, Niedner-Boblenz A, Schifferer M, Ruepp M-D, Simons M, Niessing D, Madl T, Dormann D (2018) Phase separation of FUS is suppressed by its nuclear import receptor and arginine methylation. Cell 173:706–719.e13

    CAS  PubMed  Google Scholar 

  84. Woodsmith J, Kamburov A, Stelzl U (2013) Dual coordination of post translational modifications in human protein networks. PLoS Comput Biol 9:e1002933

    CAS  PubMed  PubMed Central  Google Scholar 

  85. Tompa P, Davey NE, Gibson TJ, Babu MM (2014) A million peptide motifs for the molecular biologist. Mol Cell 55:161–169

    CAS  PubMed  Google Scholar 

  86. Davey NE, Morgan DO (2016) Building a regulatory network with short linear sequence motifs: lessons from the Degrons of the anaphase-promoting complex. Mol Cell 64:12–23

    CAS  PubMed  PubMed Central  Google Scholar 

  87. Davey NE, Seo M, Yadav VK, Jeon J, Nim S, Krystkowiak I, Blikstad C, Dong D, Markova N, Kim PM, Ivarsson Y (2017) Discovery of short linear motif-mediated interactions through phage display of intrinsically disordered regions of the human proteome. FEBS J 284:485–498

    CAS  PubMed  Google Scholar 

  88. Richardson MOG, Holehouse AS, Langstein I, Korber P, Pappu RV (2018) Large-Scale Analysis of the Evolution of Functions Mediated by Intrinsically Disordered Regions. Biophys J 114:79a

    Google Scholar 

  89. Davey NE, Haslam NJ, Shields DC, Edwards RJ (2011) SLiMSearch 2.0: biological context for short linear motifs in proteins. Nucleic Acids Res 39:W56–W60

    CAS  PubMed  PubMed Central  Google Scholar 

  90. Zarin T, Tsai CN, Nguyen Ba AN, Moses AM (2017) Selection maintains signaling function of a highly diverged intrinsically disordered region. Proc Natl Acad Sci U S A 114:E1450–E1459

    CAS  PubMed  PubMed Central  Google Scholar 

  91. Franzmann TM, Jahnel M, Pozniakovsky A, Mahamid J, Holehouse AS, Nüske E, Richter D, Baumeister W, Grill SW, Pappu RV, Hyman AA, Alberti S (2018) Phase separation of a yeast prion protein promotes cellular fitness. Science 359:eaao5654

    PubMed  Google Scholar 

  92. Oliveberg M, Arcus VL, Fersht AR (1995) pKA values of carboxyl groups in the native and denatured states of Barnase: the pKA values of the denatured state are on average 0.4 units lower than those of model compounds. Biochemistry 34:9424–9433

    CAS  PubMed  Google Scholar 

  93. Meng W, Raleigh DP (2011) Analysis of electrostatic interactions in the denatured state ensemble of the N-terminal domain of L9 under native conditions. Proteins 79:3500–3510

    CAS  PubMed  Google Scholar 

  94. Lin Y-H, Chan HS (2017) Phase separation and single-chain compactness of charged disordered proteins are strongly correlated. Biophys J 112:2043–2046

    CAS  PubMed  PubMed Central  Google Scholar 

  95. Nott TJ, Petsalaki E, Farber P, Jervis D, Fussner E, Plochowietz A, Craggs TD, Bazett-Jones DP, Pawson T, Forman-Kay JD, Baldwin AJ (2015) Phase transition of a disordered nuage protein generates environmentally responsive membraneless organelles. Mol Cell 57:936–947

    CAS  PubMed  PubMed Central  Google Scholar 

  96. Romero P, Obradovic Z, Li X, Garner EC, Brown CJ, Dunker AK (2001) Sequence complexity of disordered protein. Proteins 42:38–48

    CAS  PubMed  Google Scholar 

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Authors and Affiliations

  1. Graduate Program in Biochemistry, Biophysics, and Structural Biology, Division of Biological and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO, USA

    Garrett M. Ginell

  2. Center for the Science and Engineering of Living Systems, Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA

    Garrett M. Ginell & Alex S. Holehouse

  3. Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA

    Alex S. Holehouse

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  1. Garrett M. Ginell
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Correspondence to Alex S. Holehouse .

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Editors and Affiliations

  1. Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, København N, Denmark

    Birthe B. Kragelund

  2. Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark

    Karen Skriver

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Ginell, G.M., Holehouse, A.S. (2020). Analyzing the Sequences of Intrinsically Disordered Regions with CIDER and localCIDER. In: Kragelund, B.B., Skriver, K. (eds) Intrinsically Disordered Proteins. Methods in Molecular Biology, vol 2141. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0524-0_5

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  • DOI: https://doi.org/10.1007/978-1-0716-0524-0_5

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0523-3

  • Online ISBN: 978-1-0716-0524-0

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