Intrinsically disordered proteins (English Wikipedia)

Analysis of information sources in references of the Wikipedia article "Intrinsically disordered proteins" in English language version.

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Garaizar A, Espinosa JR (September 2021). "Salt dependent phase behavior of intrinsically disordered proteins from a coarse-grained model with explicit water and ions". The Journal of Chemical Physics. 155 (12): 125103. Bibcode:2021JChPh.155l5103G. doi:10.1063/5.0062687. PMID 34598583. S2CID 238249229.
Uversky VN (2013). "Digested disorder: Quarterly intrinsic disorder digest (January/February/March, 2013)". Intrinsically Disordered Proteins. 1 (1): e25496. doi:10.4161/idp.25496. PMC 5424799. PMID 28516015.
Costantini S, Sharma A, Raucci R, Costantini M, Autiero I, Colonna G (March 2013). "Genealogy of an ancient protein family: the Sirtuins, a family of disordered members". BMC Evolutionary Biology. 13 (1): 60. Bibcode:2013BMCEE..13...60C. doi:10.1186/1471-2148-13-60. PMC 3599600. PMID 23497088.

handle.net

hdl.handle.net

Apicella A, Marascio M, Colangelo V, Soncini M, Gautieri A, Plummer CJ (June 2017). "Molecular dynamics simulations of the intrinsically disordered protein amelogenin". Journal of Biomolecular Structure & Dynamics. 35 (8): 1813–1823. doi:10.1080/07391102.2016.1196151. hdl:11311/1004711. PMID 27366858. S2CID 205576649.

harvard.edu

ui.adsabs.harvard.edu

Anfinsen CB (July 1973). "Principles that govern the folding of protein chains". Science. 181 (4096): 223–230. Bibcode:1973Sci...181..223A. doi:10.1126/science.181.4096.223. PMID 4124164.
Wilson BA, Foy SG, Neme R, Masel J (June 2017). "Young Genes are Highly Disordered as Predicted by the Preadaptation Hypothesis of De Novo Gene Birth". Nature Ecology & Evolution. 1 (6): 0146–146. Bibcode:2017NatEE...1..146W. doi:10.1038/s41559-017-0146. PMC 5476217. PMID 28642936.
Atkinson SC, Audsley MD, Lieu KG, Marsh GA, Thomas DR, Heaton SM, Paxman JJ, Wagstaff KM, Buckle AM, Moseley GW, Jans DA, Borg NA (January 2018). "Recognition by host nuclear transport proteins drives disorder-to-order transition in Hendra virus V". Scientific Reports. 8 (1): 358. Bibcode:2018NatSR...8..358A. doi:10.1038/s41598-017-18742-8. PMC 5762688. PMID 29321677.
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 (March 2018). "Extreme disorder in an ultrahigh-affinity protein complex". Nature. 555 (7694): 61–66. Bibcode:2018Natur.555...61B. doi:10.1038/nature25762. PMC 6264893. PMID 29466338.
Theillet FX, Binolfi A, Bekei B, Martorana A, Rose HM, Stuiver M, Verzini S, Lorenz D, van Rossum M, Goldfarb D, Selenko P (2016). "Structural disorder of monomeric α-synuclein persists in mammalian cells". Nature. 530 (7588): 45–50. Bibcode:2016Natur.530...45T. doi:10.1038/nature16531. PMID 26808899. S2CID 4461465.
Minde DP, Maurice MM, Rüdiger SG (2012). Uversky VN (ed.). "Determining biophysical protein stability in lysates by a fast proteolysis assay, FASTpp". PLOS ONE. 7 (10): e46147. Bibcode:2012PLoSO...746147M. doi:10.1371/journal.pone.0046147. PMC 3463568. PMID 23056252.
Minde DP, Radli M, Forneris F, Maurice MM, Rüdiger SG (2013). Buckle AM (ed.). "Large extent of disorder in Adenomatous Polyposis Coli offers a strategy to guard Wnt signalling against point mutations". PLOS ONE. 8 (10): e77257. Bibcode:2013PLoSO...877257M. doi:10.1371/journal.pone.0077257. PMC 3793970. PMID 24130866.
Neupane K, Solanki A, Sosova I, Belov M, Woodside MT (2014). "Diverse metastable structures formed by small oligomers of α-synuclein probed by force spectroscopy". PLOS ONE. 9 (1): e86495. Bibcode:2014PLoSO...986495N. doi:10.1371/journal.pone.0086495. PMC 3901707. PMID 24475132.
Min D, Kim K, Hyeon C, Cho YH, Shin YK, Yoon TY (2013). "Mechanical unzipping and rezipping of a single SNARE complex reveals hysteresis as a force-generating mechanism". Nature Communications. 4 (4): 1705. Bibcode:2013NatCo...4.1705M. doi:10.1038/ncomms2692. PMC 3644077. PMID 23591872.
Dobson CM (December 2003). "Protein folding and misfolding". Nature. 426 (6968): 884–90. Bibcode:2003Natur.426..884D. doi:10.1038/nature02261. PMID 14685248. S2CID 1036192.
Chong SH, Chatterjee P, Ham S (May 2017). "Computer Simulations of Intrinsically Disordered Proteins". Annual Review of Physical Chemistry. 68: 117–134. Bibcode:2017ARPC...68..117C. doi:10.1146/annurev-physchem-052516-050843. PMID 28226222.
Terakawa T, Takada S (September 2011). "Multiscale ensemble modeling of intrinsically disordered proteins: p53 N-terminal domain". Biophysical Journal. 101 (6): 1450–1458. Bibcode:2011BpJ...101.1450T. doi:10.1016/j.bpj.2011.08.003. PMC 3177054. PMID 21943426.
Granata D, Baftizadeh F, Habchi J, Galvagnion C, De Simone A, Camilloni C, et al. (October 2015). "The inverted free energy landscape of an intrinsically disordered peptide by simulations and experiments". Scientific Reports. 5: 15449. Bibcode:2015NatSR...515449G. doi:10.1038/srep15449. PMC 4620491. PMID 26498066.
Garaizar A, Espinosa JR (September 2021). "Salt dependent phase behavior of intrinsically disordered proteins from a coarse-grained model with explicit water and ions". The Journal of Chemical Physics. 155 (12): 125103. Bibcode:2021JChPh.155l5103G. doi:10.1063/5.0062687. PMID 34598583. S2CID 238249229.
Costantini S, Sharma A, Raucci R, Costantini M, Autiero I, Colonna G (March 2013). "Genealogy of an ancient protein family: the Sirtuins, a family of disordered members". BMC Evolutionary Biology. 13 (1): 60. Bibcode:2013BMCEE..13...60C. doi:10.1186/1471-2148-13-60. PMC 3599600. PMID 23497088.

mcponline.org

Collins MO, Yu L, Campuzano I, Grant SG, Choudhary JS (July 2008). "Phosphoproteomic analysis of the mouse brain cytosol reveals a predominance of protein phosphorylation in regions of intrinsic sequence disorder" (PDF). Molecular & Cellular Proteomics. 7 (7): 1331–48. doi:10.1074/mcp.M700564-MCP200. PMID 18388127. S2CID 22193414.

nih.gov

pubmed.ncbi.nlm.nih.gov

Dunker AK, Lawson JD, Brown CJ, Williams RM, Romero P, Oh JS, Oldfield CJ, Campen AM, Ratliff CM, Hipps KW, Ausio J, Nissen MS, Reeves R, Kang C, Kissinger CR, Bailey RW, Griswold MD, Chiu W, Garner EC, Obradovic Z (2001). "Intrinsically disordered protein". Journal of Molecular Graphics & Modelling. 19 (1): 26–59. CiteSeerX 10.1.1.113.556. doi:10.1016/s1093-3263(00)00138-8. PMID 11381529.
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ncbi.nlm.nih.gov

Andreeva A, Howorth D, Chothia C, Kulesha E, Murzin AG (January 2014). "SCOP2 prototype: a new approach to protein structure mining". Nucleic Acids Research. 42 (Database issue): D310–4. doi:10.1093/nar/gkt1242. PMC 3964979. PMID 24293656.
Mir M, Stadler MR, Ortiz SA, Hannon CE, Harrison MM, Darzacq X, Eisen MB (December 2018). Singer RH, Struhl K, Crocker J (eds.). "Dynamic multifactor hubs interact transiently with sites of active transcription in Drosophila embryos". eLife. 7: e40497. doi:10.7554/eLife.40497. PMC 6307861. PMID 30589412.
Wright PE, Dyson HJ (January 2015). "Intrinsically disordered proteins in cellular signalling and regulation". Nature Reviews. Molecular Cell Biology. 16 (1): 18–29. doi:10.1038/nrm3920. PMC 4405151. PMID 25531225.
van der Lee R, Buljan M, Lang B, Weatheritt RJ, Daughdrill GW, Dunker AK, et al. (July 2014). "Classification of intrinsically disordered regions and proteins". Chemical Reviews. 114 (13): 6589–6631. doi:10.1021/cr400525m. PMC 4095912. PMID 24773235.
Song J, Lee MS, Carlberg I, Vener AV, Markley JL (December 2006). "Micelle-induced folding of spinach thylakoid soluble phosphoprotein of 9 kDa and its functional implications". Biochemistry. 45 (51): 15633–43. doi:10.1021/bi062148m. PMC 2533273. PMID 17176085.
Kamerlin SC, Warshel A (May 2010). "At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?". Proteins. 78 (6): 1339–75. doi:10.1002/prot.22654. PMC 2841229. PMID 20099310.
Cermakova K, Hodges HC (May 2023). "Interaction modules that impart specificity to disordered protein". Trends in Biochemical Sciences. 48 (5): 477–490. doi:10.1016/j.tibs.2023.01.004. PMC 10106370. PMID 36754681.
Wilson BA, Foy SG, Neme R, Masel J (June 2017). "Young Genes are Highly Disordered as Predicted by the Preadaptation Hypothesis of De Novo Gene Birth". Nature Ecology & Evolution. 1 (6): 0146–146. Bibcode:2017NatEE...1..146W. doi:10.1038/s41559-017-0146. PMC 5476217. PMID 28642936.
Willis S, Masel J (September 2018). "Gene Birth Contributes to Structural Disorder Encoded by Overlapping Genes". Genetics. 210 (1): 303–313. doi:10.1534/genetics.118.301249. PMC 6116962. PMID 30026186.
James, Jennifer E; Nelson, Paul G; Masel, Joanna (4 April 2023). "Differential Retention of Pfam Domains Contributes to Long-term Evolutionary Trends". Molecular Biology and Evolution. 40 (4). doi:10.1093/molbev/msad073. PMC 10089649. PMID 36947137.
Prakash A, Shin J, Rajan S, Yoon HS (April 2016). "Structural basis of nucleic acid recognition by FK506-binding protein 25 (FKBP25), a nuclear immunophilin". Nucleic Acids Research. 44 (6): 2909–2925. doi:10.1093/nar/gkw001. PMC 4824100. PMID 26762975.
Tarakhovsky A, Prinjha RK (July 2018). "Drawing on disorder: How viruses use histone mimicry to their advantage". The Journal of Experimental Medicine. 215 (7): 1777–1787. doi:10.1084/jem.20180099. PMC 6028506. PMID 29934321.
Atkinson SC, Audsley MD, Lieu KG, Marsh GA, Thomas DR, Heaton SM, Paxman JJ, Wagstaff KM, Buckle AM, Moseley GW, Jans DA, Borg NA (January 2018). "Recognition by host nuclear transport proteins drives disorder-to-order transition in Hendra virus V". Scientific Reports. 8 (1): 358. Bibcode:2018NatSR...8..358A. doi:10.1038/s41598-017-18742-8. PMC 5762688. PMID 29321677.
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 (March 2018). "Extreme disorder in an ultrahigh-affinity protein complex". Nature. 555 (7694): 61–66. Bibcode:2018Natur.555...61B. doi:10.1038/nature25762. PMC 6264893. PMID 29466338.
Feng H, Zhou BR, Bai Y (November 2018). "Binding Affinity and Function of the Extremely Disordered Protein Complex Containing Human Linker Histone H1.0 and Its Chaperone ProTα". Biochemistry. 57 (48): 6645–6648. doi:10.1021/acs.biochem.8b01075. PMC 7984725. PMID 30430826.
Minde DP, Ramakrishna M, Lilley KS (2020). "Biotin proximity tagging favours unfolded proteins and enables the study of intrinsically disordered regions". Communications Biology. 3 (1): 38. doi:10.1038/s42003-020-0758-y. PMC 6976632. PMID 31969649.
Minde DP, Maurice MM, Rüdiger SG (2012). Uversky VN (ed.). "Determining biophysical protein stability in lysates by a fast proteolysis assay, FASTpp". PLOS ONE. 7 (10): e46147. Bibcode:2012PLoSO...746147M. doi:10.1371/journal.pone.0046147. PMC 3463568. PMID 23056252.
Minde DP, Radli M, Forneris F, Maurice MM, Rüdiger SG (2013). Buckle AM (ed.). "Large extent of disorder in Adenomatous Polyposis Coli offers a strategy to guard Wnt signalling against point mutations". PLOS ONE. 8 (10): e77257. Bibcode:2013PLoSO...877257M. doi:10.1371/journal.pone.0077257. PMC 3793970. PMID 24130866.
Neupane K, Solanki A, Sosova I, Belov M, Woodside MT (2014). "Diverse metastable structures formed by small oligomers of α-synuclein probed by force spectroscopy". PLOS ONE. 9 (1): e86495. Bibcode:2014PLoSO...986495N. doi:10.1371/journal.pone.0086495. PMC 3901707. PMID 24475132.
Min D, Kim K, Hyeon C, Cho YH, Shin YK, Yoon TY (2013). "Mechanical unzipping and rezipping of a single SNARE complex reveals hysteresis as a force-generating mechanism". Nature Communications. 4 (4): 1705. Bibcode:2013NatCo...4.1705M. doi:10.1038/ncomms2692. PMC 3644077. PMID 23591872.
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 and Peptide Letters. 15 (9): 956–963. doi:10.2174/092986608785849164. PMC 2676888. PMID 18991772.
Wise-Scira O, Dunn A, Aloglu AK, Sakallioglu IT, Coskuner O (March 2013). "Structures of the E46K mutant-type α-synuclein protein and impact of E46K mutation on the structures of the wild-type α-synuclein protein". ACS Chemical Neuroscience. 4 (3): 498–508. doi:10.1021/cn3002027. PMC 3605821. PMID 23374074.
Best RB, Zhu X, Shim J, Lopes PE, Mittal J, Feig M, Mackerell AD (September 2012). "Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles". Journal of Chemical Theory and Computation. 8 (9): 3257–3273. doi:10.1021/ct300400x. PMC 3549273. PMID 23341755.
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