Contributors |
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ix | |
Preface: The Patchwork Quilt of Intrinsic Disorder |
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xiii | |
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1 Intrinsic disorder and phase transitions: Pieces in the puzzling role of the prion protein in health and disease |
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1 | (44) |
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2 | (6) |
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2 Considerations on intrinsic disorder and phase separation ability of the prion protein family |
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8 | (6) |
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3 The manifold interactions of PrP with nucleic acid targets: Can phase separation explain it? |
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14 | (10) |
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4 Phase transitions of PrP in health and disease |
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24 | (21) |
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32 | (1) |
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32 | (13) |
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2 Functions of intrinsically disordered proteins through evolutionary lenses |
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45 | (30) |
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46 | (1) |
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2 Functional categories of IDPs |
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47 | (8) |
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3 Distinct evolutionary scenarios of IDRs |
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55 | (8) |
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4 Evolutionary conservation of SLIMs |
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63 | (3) |
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5 Evolutionary origin IDRs mutated in cancer |
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66 | (2) |
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68 | (7) |
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69 | (6) |
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3 Non-specific porins of Gram-negative bacteria as proteins containing intrinsically disordered regions with amyloidogenic potential |
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75 | (26) |
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96 | (1) |
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96 | (1) |
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96 | (5) |
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4 Intrinsic disorder in integral membrane proteins |
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101 | (34) |
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1 Distinction between intrinsically disordered and structured proteins |
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102 | (4) |
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2 Intrinsic disorder in IMPs: Potential functional advantages |
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106 | (12) |
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3 Mutations in IMP: Consideration of IDR |
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118 | (4) |
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4 IMP intrinsic disorder: Investigational approaches |
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122 | (5) |
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127 | (8) |
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128 | (7) |
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5 Molecular simulations of IDPs: From ensemble generation to IDP interactions leading to disorder-to-order transitions |
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135 | (52) |
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136 | (13) |
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149 | (8) |
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3 Simulation-based IDP ensemble generation and characterization |
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157 | (9) |
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4 Modeling the disorder-to-order transition of IDPs |
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166 | (7) |
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173 | (14) |
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174 | (1) |
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174 | (13) |
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6 Target-binding behavior of IDPs via pre-structured motifs |
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187 | (62) |
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189 | (1) |
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190 | (6) |
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3 The pre-structured motif (PreSMo) |
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196 | (10) |
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4 PreSMos in transcriptional and translational factors |
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206 | (16) |
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5 PreSMos in neurodegenerative IDPs |
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222 | (6) |
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228 | (5) |
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7 Summary and perspective |
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233 | (16) |
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235 | (1) |
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235 | (14) |
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7 The role of dancing duplexes in biology and disease |
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249 | (22) |
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250 | (1) |
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2 LC8-facilitated dimerization in IDP duplexes |
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250 | (5) |
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3 Multivalent binding of LC8 along IDP duplexes |
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255 | (5) |
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4 Nupl 59: A multivalent LC8 binder with a self-association domain |
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260 | (1) |
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5 VSV-P: The role of disorder in a non-LC8 binding IDP duplex |
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261 | (1) |
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6 The role of disorder and dimerization of the SARS-CoV-2 nucleocapsid phosphoprotein IDP duplex |
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262 | (3) |
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265 | (2) |
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267 | (4) |
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267 | (1) |
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267 | (4) |
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8 Intrinsic disorder in protein kinase A anchoring proteins signaling complexes |
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271 | (24) |
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1 Tethered phosphorylation |
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273 | (2) |
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2 Intrinsic disorder in PKA-AKAP signaling complexes |
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275 | (2) |
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3 The prevalence of intrinsic disorder in AKAPs |
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277 | (7) |
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4 Modeling the reach and effective concentration of PKA-AKAP signaling complexes |
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284 | (4) |
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5 Allosteric regulation of tethered reactions by AKAP structure |
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288 | (3) |
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291 | (4) |
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291 | (4) |
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9 Protein intrinsic disorder on a dynamic nucleosomal landscape |
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295 | (60) |
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296 | (1) |
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2 Protein intrinsic disorder on a nucleosomal landscape |
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297 | (10) |
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3 Disordered interactions with nucleosomes |
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307 | (29) |
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4 Common sequence features of disordered nucleosome-binding proteins |
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336 | (3) |
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339 | (16) |
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340 | (1) |
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340 | (15) |
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10 Flexible spandrels of the global plant virome: Proteomic-wide evolutionary patterns of structural intrinsic protein disorder elucidate modulation at the functional virus-host interplay |
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355 | (56) |
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1 The highly modular plant virus proteome |
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357 | (6) |
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2 Protein disorder composition in plant viruses: Terra incognita |
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363 | (3) |
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3 The global plant virus proteome reveals overhauling IDP abundance and variability |
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366 | (4) |
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4 General affinity of phylogenomically unrelated small plant virus proteomes with increased IDP |
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370 | (1) |
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5 Emerging patterns in amino acid composition as a potential predictor of IDP and virus functional biology |
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371 | (7) |
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6 The global plant virus MoRFome: Gaining functional insights in viral IDP-mediated binding contextual landscape via harnessing interface molecular recognition features |
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378 | (3) |
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7 Evolutionary proteomic comparative analysis of conserved viral modules make up reveals IDP landscape of viral-host interacting disordomes |
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381 | (5) |
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8 Functional IDP and evolutionary conserved structures expand evidence for modulation of transmission mode of plant viruses by insect vectors |
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386 | (4) |
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9 Outlook and new challenging prospects for plant virology |
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390 | (10) |
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400 | (11) |
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400 | (8) |
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408 | (3) |
Index |
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411 | |