{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,5]],"date-time":"2026-07-05T04:10:25Z","timestamp":1783224625072,"version":"3.54.6"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1007390","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2019,10,30]],"date-time":"2019-10-30T00:00:00Z","timestamp":1572393600000}}],"reference-count":110,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2019,10,18]],"date-time":"2019-10-18T00:00:00Z","timestamp":1571356800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["MCB110149"],"award-info":[{"award-number":["MCB110149"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1007390","type":"journal-article","created":{"date-parts":[[2019,10,18]],"date-time":"2019-10-18T13:49:01Z","timestamp":1571406541000},"page":"e1007390","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":15,"title":["Sequence specificity despite intrinsic disorder: How a disease-associated Val\/Met polymorphism rearranges tertiary interactions in a long disordered protein"],"prefix":"10.1371","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3496-8197","authenticated-orcid":true,"given":"Ruchi","family":"Lohia","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Reza","family":"Salari","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8949-2694","authenticated-orcid":true,"given":"Grace","family":"Brannigan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2019,10,18]]},"reference":[{"issue":"5","key":"pcbi.1007390.ref001","doi-asserted-by":"crossref","first-page":"932","DOI":"10.1016\/j.bbapap.2012.12.008","article-title":"Unusual biophysics of intrinsically disordered proteins","volume":"1834","author":"VN Uversky","year":"2013","journal-title":"Biochim Biophys Acta"},{"key":"pcbi.1007390.ref002","doi-asserted-by":"crossref","first-page":"viii","DOI":"10.1016\/j.sbi.2015.06.005","article-title":"Editorial overview: Linking protein sequence and structural changes to function in the era of next-generation sequencing","volume":"32","author":"AR Panchenko","year":"2015","journal-title":"Curr Opin Struct Biol"},{"issue":"3","key":"pcbi.1007390.ref003","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1016\/j.jmb.2004.02.002","article-title":"Prediction and Functional Analysis of Native Disorder in Proteins from the Three Kingdoms of Life","volume":"337","author":"JJ Ward","year":"2004","journal-title":"J Mol Biol"},{"issue":"3","key":"pcbi.1007390.ref004","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1038\/nrm1589","article-title":"Intrinsically unstructured proteins and their functions","volume":"6","author":"HJ Dyson","year":"2005","journal-title":"Nat Rev Mol Cell Biol"},{"key":"pcbi.1007390.ref005","doi-asserted-by":"crossref","first-page":"10","DOI":"10.3389\/fphy.2019.00010","article-title":"Intrinsically Disordered Proteins and Their \u201cMysterious\u201d (Meta)Physics","volume":"7","author":"VN Uversky","year":"2019","journal-title":"Front Phys"},{"issue":"4","key":"pcbi.1007390.ref006","doi-asserted-by":"crossref","first-page":"1137","DOI":"10.1016\/j.jmb.2006.04.016","article-title":"Human Transcription Factors Contain a High Fraction of Intrinsically Disordered Regions Essential for Transcriptional Regulation","volume":"359","author":"Y Minezaki","year":"2006","journal-title":"J Mol Biol"},{"issue":"20","key":"pcbi.1007390.ref007","doi-asserted-by":"crossref","first-page":"5129","DOI":"10.1111\/j.1742-4658.2005.04948.x","article-title":"Flexible nets. The roles of intrinsic disorder in protein interaction networks","volume":"272","author":"AK Dunker","year":"2005","journal-title":"FEBS J"},{"issue":"1","key":"pcbi.1007390.ref008","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1038\/nrm3920","article-title":"Intrinsically disordered proteins in cellular signalling and regulation","volume":"16","author":"PE Wright","year":"2015","journal-title":"Nat Rev Mol Cell Biol"},{"issue":"5","key":"pcbi.1007390.ref009","doi-asserted-by":"crossref","first-page":"1899","DOI":"10.1021\/pr060393m","article-title":"Functional anthology of intrinsic disorder. 2. Cellular components, domains, technical terms, developmental processes, and coding sequence diversities correlated with long disordered regions","volume":"6","author":"S Vucetic","year":"2007","journal-title":"J Proteome Res"},{"issue":"3","key":"pcbi.1007390.ref010","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1016\/S0022-2836(02)00969-5","article-title":"Intrinsic Disorder in Cell-signaling and Cancer-associated Proteins","volume":"323","author":"LM Iakoucheva","year":"2002","journal-title":"J Mol Biol"},{"issue":"13","key":"pcbi.1007390.ref011","doi-asserted-by":"crossref","first-page":"6561","DOI":"10.1021\/cr400514h","article-title":"Introducing Protein Intrinsic Disorder","volume":"114","author":"J Habchi","year":"2014","journal-title":"Chem Rev"},{"issue":"1","key":"pcbi.1007390.ref012","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1016\/S0165-0173(00)00019-9","article-title":"Tau protein isoforms, phosphorylation and role in neurodegenerative disorders","volume":"33","author":"L Bu\u00e9e","year":"2000","journal-title":"Brain Res Rev"},{"issue":"1","key":"pcbi.1007390.ref013","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1002\/prot.21055","article-title":"Insights into protein structure and function from disorder-complexity space","volume":"66","author":"EA Weathers","year":"2006","journal-title":"Proteins Struct Funct Bioinforma"},{"issue":"1","key":"pcbi.1007390.ref014","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1002\/1097-0134(20010101)42:1<38::AID-PROT50>3.0.CO;2-3","article-title":"Sequence complexity of disordered protein","volume":"42","author":"P Romero","year":"2001","journal-title":"Proteins Struct Funct Genet"},{"issue":"12","key":"pcbi.1007390.ref015","doi-asserted-by":"crossref","first-page":"2673","DOI":"10.1111\/j.1742-4658.2010.07684.x","article-title":"Protein tandem repeats\u2014the more perfect, the less structured","volume":"277","author":"J Jorda","year":"2010","journal-title":"FEBS J"},{"issue":"7","key":"pcbi.1007390.ref016","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1038\/739","article-title":"Equilibrium NMR studies of unfolded and partially folded proteins","volume":"5","author":"HJ Dyson","year":"1998","journal-title":"Nat Struct Biol"},{"issue":"8","key":"pcbi.1007390.ref017","doi-asserted-by":"crossref","first-page":"2649","DOI":"10.1073\/pnas.0611503104","article-title":"A natively unfolded yeast prion monomer adopts an ensemble of collapsed and rapidly fluctuating structures","volume":"104","author":"S Mukhopadhyay","year":"2007","journal-title":"Proc Natl Acad Sci"},{"issue":"12","key":"pcbi.1007390.ref018","doi-asserted-by":"crossref","first-page":"e1000241","DOI":"10.1371\/journal.pcbi.1000241","article-title":"Disordered flanks prevent peptide aggregation","volume":"4","author":"S Abeln","year":"2008","journal-title":"PLoS Comput Biol"},{"issue":"Database issue","key":"pcbi.1007390.ref019","doi-asserted-by":"crossref","first-page":"D786","DOI":"10.1093\/nar\/gkl893","article-title":"DisProt: the Database of Disordered Proteins","volume":"35","author":"M Sickmeier","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1007390.ref020","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1016\/j.sbi.2015.03.008","article-title":"Relating sequence encoded information to form and function of intrinsically disordered proteins","volume":"32","author":"RK Das","year":"2015","journal-title":"Curr Opin Struct Biol"},{"issue":"33","key":"pcbi.1007390.ref021","doi-asserted-by":"crossref","first-page":"13392","DOI":"10.1073\/pnas.1304749110","article-title":"Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues","volume":"110","author":"RK Das","year":"2013","journal-title":"Proc Natl Acad Sci"},{"issue":"8","key":"pcbi.1007390.ref022","doi-asserted-by":"crossref","first-page":"085101","DOI":"10.1063\/1.4929391","article-title":"A theoretical method to compute sequence dependent configurational properties in charged polymers and proteins","volume":"143","author":"L Sawle","year":"2015","journal-title":"J Chem Phys"},{"issue":"12","key":"pcbi.1007390.ref023","doi-asserted-by":"crossref","first-page":"123305","DOI":"10.1063\/1.5005821","article-title":"Sequence charge decoration dictates coil-globule transition in intrinsically disordered proteins","volume":"148","author":"T Firman","year":"2018","journal-title":"J Chem Phys"},{"issue":"1","key":"pcbi.1007390.ref024","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1146\/annurev.biophys.37.032807.125924","article-title":"Intrinsically Disordered Proteins in Human Diseases: Introducing the D 2 Concept","volume":"37","author":"VN Uversky","year":"2008","journal-title":"Annu Rev Biophys"},{"issue":"10","key":"pcbi.1007390.ref025","doi-asserted-by":"crossref","first-page":"e1002709","DOI":"10.1371\/journal.pcbi.1002709","article-title":"Disease-associated mutations disrupt functionally important regions of intrinsic protein disorder","volume":"8","author":"V Vacic","year":"2012","journal-title":"PLoS Comput Biol"},{"issue":"23","key":"pcbi.1007390.ref026","doi-asserted-by":"crossref","first-page":"8916","DOI":"10.1039\/c3cp00063j","article-title":"Initiation of assembly of tau(273-284) and its \u0394K280 mutant: an experimental and computational study","volume":"15","author":"L Larini","year":"2013","journal-title":"Phys Chem Chem Phys"},{"issue":"4","key":"pcbi.1007390.ref027","doi-asserted-by":"crossref","first-page":"e1004247","DOI":"10.1371\/journal.pcbi.1004247","article-title":"Modulation of the Disordered Conformational Ensembles of the p53 Transactivation Domain by Cancer-Associated Mutations","volume":"11","author":"D Ganguly","year":"2015","journal-title":"PLOS Comput Biol"},{"issue":"8","key":"pcbi.1007390.ref028","doi-asserted-by":"crossref","first-page":"646","DOI":"10.1021\/cn500007j","article-title":"Effect of the English Familial Disease Mutation (H6R) on the Monomers and Dimers of A\u03b240 and A\u03b242","volume":"5","author":"MH Viet","year":"2014","journal-title":"ACS Chem Neurosci"},{"issue":"11","key":"pcbi.1007390.ref029","doi-asserted-by":"crossref","first-page":"1446","DOI":"10.1021\/cn400110d","article-title":"Effect of the Tottori Familial Disease Mutation (D7N) on the Monomers and Dimers of A\u03b2 40 and A\u03b2 42","volume":"4","author":"MH Viet","year":"2013","journal-title":"ACS Chem Neurosci"},{"issue":"30","key":"pcbi.1007390.ref030","doi-asserted-by":"crossref","first-page":"8972","DOI":"10.1021\/jp503652s","article-title":"Effect of Taiwan Mutation (D7H) on Structures of Amyloid-\u03b2 Peptides: Replica Exchange Molecular Dynamics Study","volume":"118","author":"PM Truong","year":"2014","journal-title":"J Phys Chem B"},{"issue":"10","key":"pcbi.1007390.ref031","doi-asserted-by":"crossref","first-page":"1738","DOI":"10.1002\/prot.24310","article-title":"Impact of the K24N mutation on the transactivation domain of p53 and its binding to murine double-minute clone 2","volume":"81","author":"YA Zhan","year":"2013","journal-title":"Proteins Struct Funct Bioinforma"},{"issue":"20","key":"pcbi.1007390.ref032","doi-asserted-by":"crossref","first-page":"6206","DOI":"10.1021\/jp403288b","article-title":"Single Point Mutation Alters the Microstate Dynamics of Amyloid \u03b2-Protein A\u03b242 as Revealed by Dihedral Dynamics Analyses","volume":"117","author":"L Xu","year":"2013","journal-title":"J Phys Chem B"},{"issue":"13","key":"pcbi.1007390.ref033","doi-asserted-by":"crossref","first-page":"6696","DOI":"10.1074\/jbc.R115.695056","article-title":"Modulation of Intrinsically Disordered Protein Function by Post-translational Modifications","volume":"291","author":"A Bah","year":"2016","journal-title":"J Biol Chem"},{"issue":"41","key":"pcbi.1007390.ref034","doi-asserted-by":"crossref","first-page":"25090","DOI":"10.1074\/jbc.M115.658583","article-title":"Phosphorylation-induced Conformational Ensemble Switching in an Intrinsically Disordered Cancer\/Testis Antigen","volume":"290","author":"Y He","year":"2015","journal-title":"J Biol Chem"},{"issue":"9","key":"pcbi.1007390.ref035","doi-asserted-by":"crossref","first-page":"1537","DOI":"10.1016\/j.str.2016.07.007","article-title":"ALS Mutations Disrupt Phase Separation Mediated by \u03b1-Helical Structure in the TDP-43 Low-Complexity C-Terminal Domain","volume":"24","author":"AE Conicella","year":"2016","journal-title":"Structure"},{"issue":"3","key":"pcbi.1007390.ref036","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1002\/humu.20671","article-title":"Annotating single amino acid polymorphisms in the UniProt\/Swiss-Prot knowledgebase","volume":"29","author":"YL Yip","year":"2008","journal-title":"Hum Mutat"},{"issue":"27","key":"pcbi.1007390.ref037","doi-asserted-by":"crossref","first-page":"10155","DOI":"10.1021\/ja4045532","article-title":"Modulation of the Intrinsic Helix Propensity of an Intrinsically Disordered Protein Reveals Long-Range Helix\u2013Helix Interactions","volume":"135","author":"V Ie\u0161mantavi\u010dius","year":"2013","journal-title":"J Am Chem Soc"},{"issue":"4-5","key":"pcbi.1007390.ref038","doi-asserted-by":"crossref","first-page":"310","DOI":"10.1016\/j.jmb.2012.04.023","article-title":"Transient Structure and SH3 Interaction Sites in an Intrinsically Disordered Fragment of the Hepatitis C Virus Protein NS5A","volume":"420","author":"S Feuerstein","year":"2012","journal-title":"J Mol Biol"},{"issue":"1","key":"pcbi.1007390.ref039","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/j.sbi.2007.01.009","article-title":"Atomic-level characterization of disordered protein ensembles","volume":"17","author":"T Mittag","year":"2007","journal-title":"Curr Opin Struct Biol"},{"key":"pcbi.1007390.ref040","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1016\/j.pbiomolbio.2015.03.003","article-title":"Progress in studying intrinsically disordered proteins with atomistic simulations","volume":"119","author":"N Stanley","year":"2015","journal-title":"Prog Biophys Mol Biol"},{"issue":"28","key":"pcbi.1007390.ref041","doi-asserted-by":"crossref","first-page":"8742","DOI":"10.1021\/jacs.6b02016","article-title":"Structured and Unstructured Binding of an Intrinsically Disordered Protein as Revealed by Atomistic Simulations","volume":"138","author":"RE Ithuralde","year":"2016","journal-title":"J Am Chem Soc"},{"issue":"7","key":"pcbi.1007390.ref042","doi-asserted-by":"crossref","first-page":"e1002605","DOI":"10.1371\/journal.pcbi.1002605","article-title":"A Preformed Binding Interface in the Unbound Ensemble of an Intrinsically Disordered Protein: Evidence from Molecular Simulations","volume":"8","author":"M Knott","year":"2012","journal-title":"PLoS Comput Biol"},{"issue":"11","key":"pcbi.1007390.ref043","doi-asserted-by":"crossref","first-page":"5236","DOI":"10.1016\/j.bbagen.2013.07.007","article-title":"The conformational ensemble of the disordered and aggregation-protective 182-291 region of ataxin-3","volume":"1830","author":"G Invernizzi","year":"2013","journal-title":"Biochim Biophys Acta"},{"issue":"3","key":"pcbi.1007390.ref044","doi-asserted-by":"crossref","first-page":"896","DOI":"10.1021\/jp505902m","article-title":"Disordered Structural Ensembles of Vasopressin and Oxytocin and Their Mutants","volume":"119","author":"E Yedvabny","year":"2015","journal-title":"J Phys Chem B"},{"key":"pcbi.1007390.ref045","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1016\/j.sbi.2016.11.006","article-title":"Simulations of disordered proteins and systems with conformational heterogeneity","volume":"43","author":"ZA Levine","year":"2017","journal-title":"Curr Opin Struct Biol"},{"issue":"9","key":"pcbi.1007390.ref046","doi-asserted-by":"crossref","first-page":"2758","DOI":"10.1073\/pnas.1418155112","article-title":"Regulation and aggregation of intrinsically disordered peptides","volume":"112","author":"ZA Levine","year":"2015","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"1","key":"pcbi.1007390.ref047","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1016\/j.abb.2007.08.033","article-title":"A polymer physics perspective on driving forces and mechanisms for protein aggregation","volume":"469","author":"RV Pappu","year":"2008","journal-title":"Arch Biochem Biophys"},{"issue":"19","key":"pcbi.1007390.ref048","doi-asserted-by":"crossref","first-page":"8856","DOI":"10.1073\/pnas.92.19.8856","article-title":"Hippocampal long-term potentiation is impaired in mice lacking brain-derived neurotrophic factor","volume":"92","author":"M Korte","year":"1995","journal-title":"Proc Natl Acad Sci"},{"issue":"11","key":"pcbi.1007390.ref049","doi-asserted-by":"crossref","first-page":"2537","DOI":"10.1093\/emboj\/cdg254","article-title":"Regulation of neuronal survival and death by extracellular signals during development","volume":"22","author":"AM Davies","year":"2003","journal-title":"EMBO J"},{"issue":"45","key":"pcbi.1007390.ref050","doi-asserted-by":"crossref","first-page":"10099","DOI":"10.1523\/JNEUROSCI.2680-04.2004","article-title":"The brain-derived neurotrophic factor val66met polymorphism and variation in human cortical morphology","volume":"24","author":"L Pezawas","year":"2004","journal-title":"J Neurosci"},{"issue":"4","key":"pcbi.1007390.ref051","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1097\/JGP.0b013e3181cabd2b","article-title":"The Brain-Derived Neurotrophic Factor Val66Met Polymorphism, Hippocampal Volume, and Cognitive Function in Geriatric Depression","volume":"18","author":"S Benjamin","year":"2010","journal-title":"Am J Geriatr Psychiatry"},{"issue":"6","key":"pcbi.1007390.ref052","doi-asserted-by":"crossref","first-page":"739","DOI":"10.1016\/S0092-8674(00)81509-3","article-title":"BDNF Regulates the Maturation of Inhibition and the Critical Period of Plasticity in Mouse Visual Cortex","volume":"98","author":"ZJ Huang","year":"1999","journal-title":"Cell"},{"issue":"3","key":"pcbi.1007390.ref053","doi-asserted-by":"crossref","first-page":"542","DOI":"10.1016\/j.neuron.2011.06.017","article-title":"Broad Inhibition Sharpens Orientation Selectivity by Expanding Input Dynamic Range in Mouse Simple Cells","volume":"71","author":"Bh Liu","year":"2011","journal-title":"Neuron"},{"issue":"32","key":"pcbi.1007390.ref054","doi-asserted-by":"crossref","first-page":"10770","DOI":"10.1523\/JNEUROSCI.5454-13.2014","article-title":"Rebound Potentiation of Inhibition in Juvenile Visual Cortex Requires Vision-Induced BDNF Expression","volume":"34","author":"M Gao","year":"2014","journal-title":"J Neurosci"},{"issue":"2","key":"pcbi.1007390.ref055","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1124\/pr.111.005108","article-title":"Brain-Derived Neurotrophic Factor and Neuropsychiatric Disorders","volume":"64","author":"AE Autry","year":"2012","journal-title":"Pharmacol Rev"},{"key":"pcbi.1007390.ref056","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1016\/j.neuropharm.2015.10.034","article-title":"BDNF\u2014a key transducer of antidepressant effects","volume":"102","author":"C Bj\u00f6rkholm","year":"2016","journal-title":"Neuropharmacology"},{"issue":"7354","key":"pcbi.1007390.ref057","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1038\/nature10130","article-title":"NMDA receptor blockade at rest triggers rapid behavioural antidepressant responses","volume":"475","author":"AE Autry","year":"2011","journal-title":"Nature"},{"issue":"5967","key":"pcbi.1007390.ref058","doi-asserted-by":"crossref","first-page":"863","DOI":"10.1126\/science.1181886","article-title":"A genetic variant BDNF polymorphism alters extinction learning in both mouse and human","volume":"327","author":"F Soliman","year":"2010","journal-title":"Science"},{"key":"pcbi.1007390.ref059","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1002\/9780470751251.ch14","article-title":"Impact of genetic variant BDNF (Val66Met) on brain structure and function","volume":"289","author":"ZY Chen","year":"2008","journal-title":"Novartis Found Symp"},{"issue":"3","key":"pcbi.1007390.ref060","doi-asserted-by":"crossref","first-page":"260","DOI":"10.1038\/mp.2008.109","article-title":"Meta-analysis of the BDNF Val66Met polymorphism in major depressive disorder: effects of gender and ethnicity","volume":"15","author":"M Verhagen","year":"2010","journal-title":"Mol Psychiatry"},{"issue":"8","key":"pcbi.1007390.ref061","doi-asserted-by":"crossref","first-page":"916","DOI":"10.1038\/mp.2015.27","article-title":"The BDNF gene Val66Met polymorphism as a modifier of psychiatric disorder susceptibility: progress and controversy","volume":"20","author":"M Notaras","year":"2015","journal-title":"Mol Psychiatry"},{"issue":"4","key":"pcbi.1007390.ref062","doi-asserted-by":"crossref","first-page":"967","DOI":"10.1016\/j.jmb.2009.12.030","article-title":"Molecular and Structural Insight into proNGF Engagement of p75NTR and Sortilin","volume":"396","author":"D Feng","year":"2010","journal-title":"J Mol Biol"},{"key":"pcbi.1007390.ref063","doi-asserted-by":"crossref","first-page":"2490","DOI":"10.1038\/ncomms3490","article-title":"Val66Met polymorphism of BDNF alters prodomain structure to induce neuronal growth cone retraction","volume":"4","author":"A Anastasia","year":"2013","journal-title":"Nat Commun"},{"issue":"1","key":"pcbi.1007390.ref064","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1016\/j.neuron.2018.05.024","article-title":"The BDNF Val66Met Prodomain Disassembles Dendritic Spines Altering Fear Extinction Circuitry and Behavior","volume":"99","author":"JI Giza","year":"2018","journal-title":"Neuron"},{"issue":"1","key":"pcbi.1007390.ref065","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1016\/0022-2836(82)90515-0","article-title":"A simple method for displaying the hydropathic character of a protein","volume":"157","author":"J Kyte","year":"1982","journal-title":"J Mol Biol"},{"issue":"3","key":"pcbi.1007390.ref066","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1002\/1097-0134(20001115)41:3<415::AID-PROT130>3.0.CO;2-7","article-title":"Why are \u201cnatively unfolded\u201d proteins unstructured under physiologic conditions?","volume":"41","author":"VN Uversky","year":"2000","journal-title":"Proteins"},{"issue":"1","key":"pcbi.1007390.ref067","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1016\/j.bpj.2016.11.3200","article-title":"CIDER: Resources to Analyze Sequence-Ensemble Relationships of Intrinsically Disordered Proteins","volume":"112","author":"AS Holehouse","year":"2017","journal-title":"Biophys J"},{"issue":"6","key":"pcbi.1007390.ref068","doi-asserted-by":"crossref","first-page":"942","DOI":"10.1016\/j.molcel.2011.11.008","article-title":"The Acidic Transcription Activator Gcn4 Binds the Mediator Subunit Gal11\/Med15 Using a Simple Protein Interface Forming a Fuzzy Complex","volume":"44","author":"PS Brzovic","year":"2011","journal-title":"Mol Cell"},{"issue":"5330","key":"pcbi.1007390.ref069","doi-asserted-by":"crossref","first-page":"1310","DOI":"10.1126\/science.277.5330.1310","article-title":"Induced alpha helix in the VP16 activation domain upon binding to a human TAF","volume":"277","author":"M Uesugi","year":"1997","journal-title":"Science"},{"issue":"6","key":"pcbi.1007390.ref070","doi-asserted-by":"crossref","first-page":"741","DOI":"10.1016\/S0092-8674(00)80463-8","article-title":"Solution Structure of the KIX Domain of CBP Bound to the Transactivation Domain of CREB: A Model for Activator:Coactivator Interactions","volume":"91","author":"I Radhakrishnan","year":"1997","journal-title":"Cell"},{"issue":"12","key":"pcbi.1007390.ref071","doi-asserted-by":"crossref","first-page":"e0189171","DOI":"10.1371\/journal.pone.0189171","article-title":"Hidden \u03b1-helical propensity segments within disordered regions of the transcriptional activator CHOP","volume":"12","author":"\u00c1 Canales","year":"2017","journal-title":"PLoS One"},{"issue":"4","key":"pcbi.1007390.ref072","doi-asserted-by":"crossref","first-page":"444","DOI":"10.1016\/j.cels.2018.01.015","article-title":"A High-Throughput Mutational Scan of an Intrinsically Disordered Acidic Transcriptional Activation Domain","volume":"6","author":"MV Staller","year":"2018","journal-title":"Cell Syst"},{"issue":"25","key":"pcbi.1007390.ref073","doi-asserted-by":"crossref","first-page":"7975","DOI":"10.1021\/acs.jpcb.5b03440","article-title":"Kirkwood\u2013Buff Approach Rescues Overcollapse of a Disordered Protein in Canonical Protein Force Fields","volume":"119","author":"D Mercadante","year":"2015","journal-title":"J Phys Chem B"},{"issue":"16","key":"pcbi.1007390.ref074","doi-asserted-by":"crossref","first-page":"5113","DOI":"10.1021\/jp508971m","article-title":"Water Dispersion Interactions Strongly Influence Simulated Structural Properties of Disordered Protein States","volume":"119","author":"S Piana","year":"2015","journal-title":"J Phys Chem B"},{"issue":"26","key":"pcbi.1007390.ref075","doi-asserted-by":"crossref","first-page":"9004","DOI":"10.1021\/jp901540t","article-title":"Optimized Molecular Dynamics Force Fields Applied to the Helix\u2212Coil Transition of Polypeptides","volume":"113","author":"RB Best","year":"2009","journal-title":"J Phys Chem B"},{"issue":"11","key":"pcbi.1007390.ref076","doi-asserted-by":"crossref","first-page":"5113","DOI":"10.1021\/ct500569b","article-title":"Balanced Protein\u2013Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association","volume":"10","author":"RB Best","year":"2014","journal-title":"J Chem Theory Comput"},{"issue":"23","key":"pcbi.1007390.ref077","doi-asserted-by":"crossref","first-page":"234505","DOI":"10.1063\/1.2121687","article-title":"A general purpose model for the condensed phases of water: TIP4P\/2005","volume":"123","author":"JLF Abascal","year":"2005","journal-title":"J Chem Phys"},{"issue":"8","key":"pcbi.1007390.ref078","doi-asserted-by":"crossref","first-page":"1950","DOI":"10.1002\/prot.22711","article-title":"Improved side-chain torsion potentials for the Amber ff99SB protein force field","volume":"78","author":"K Lindorff-Larsen","year":"2010","journal-title":"Proteins"},{"issue":"3","key":"pcbi.1007390.ref079","doi-asserted-by":"crossref","first-page":"712","DOI":"10.1002\/prot.21123","article-title":"Comparison of multiple Amber force fields and development of improved protein backbone parameters","volume":"65","author":"V Hornak","year":"2006","journal-title":"Proteins Struct Funct Bioinforma"},{"issue":"1","key":"pcbi.1007390.ref080","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1038\/nmeth.4067","article-title":"CHARMM36m: an improved force field for folded and intrinsically disordered proteins","volume":"14","author":"J Huang","year":"2017","journal-title":"Nat Methods"},{"issue":"2","key":"pcbi.1007390.ref081","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1021\/ja00392a016","article-title":"Quantum and statistical mechanical studies of liquids. 10. Transferable intermolecular potential functions for water, alcohols, and ethers. Application to liquid water","volume":"103","author":"WL Jorgensen","year":"1981","journal-title":"J Am Chem Soc"},{"issue":"21","key":"pcbi.1007390.ref082","doi-asserted-by":"crossref","first-page":"E4758","DOI":"10.1073\/pnas.1800690115","article-title":"Developing a molecular dynamics force field for both folded and disordered protein states","volume":"115","author":"P Robustelli","year":"2018","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"1","key":"pcbi.1007390.ref083","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1007\/s10858-010-9433-9","article-title":"SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network","volume":"48","author":"Y Shen","year":"2010","journal-title":"J Biomol NMR"},{"issue":"11","key":"pcbi.1007390.ref084","doi-asserted-by":"crossref","first-page":"5513","DOI":"10.1021\/acs.jctc.5b00736","article-title":"Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field: A Comparison to Experiment","volume":"11","author":"S Rauscher","year":"2015","journal-title":"J Chem Theory Comput"},{"issue":"4","key":"pcbi.1007390.ref085","doi-asserted-by":"crossref","first-page":"870","DOI":"10.1016\/j.bpj.2017.12.025","article-title":"Highly Disordered Amyloid-\u03b2 Monomer Probed by Single-Molecule FRET and MD Simulation","volume":"114","author":"F Meng","year":"2018","journal-title":"Biophys J"},{"issue":"4","key":"pcbi.1007390.ref086","doi-asserted-by":"crossref","first-page":"892","DOI":"10.1016\/j.bpj.2011.06.046","article-title":"Prediction of hydrodynamic and other solution properties of rigid proteins from atomic- and residue-level models","volume":"101","author":"A Ortega","year":"2011","journal-title":"Biophys J"},{"issue":"13","key":"pcbi.1007390.ref087","doi-asserted-by":"crossref","first-page":"5937","DOI":"10.1073\/pnas.89.13.5937","article-title":"Side-chain entropy opposes alpha-helix formation but rationalizes experimentally determined helix-forming propensities","volume":"89","author":"TP Creamer","year":"1992","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"27","key":"pcbi.1007390.ref088","doi-asserted-by":"crossref","first-page":"8771","DOI":"10.1021\/bi00027a028","article-title":"Side-chain interactions between sulfur-containing amino acids and phenylalanine in alpha-helices","volume":"34","author":"AR Viguera","year":"1995","journal-title":"Biochemistry"},{"issue":"4","key":"pcbi.1007390.ref089","doi-asserted-by":"crossref","first-page":"626","DOI":"10.1016\/j.biochi.2007.11.007","article-title":"Protein contacts, inter-residue interactions and side-chain modelling","volume":"90","author":"G Faure","year":"2008","journal-title":"Biochimie"},{"issue":"42","key":"pcbi.1007390.ref090","doi-asserted-by":"crossref","first-page":"34979","DOI":"10.1074\/jbc.M112.374504","article-title":"The methionine-aromatic motif plays a unique role in stabilizing protein structure","volume":"287","author":"CC Valley","year":"2012","journal-title":"J Biol Chem"},{"issue":"8","key":"pcbi.1007390.ref091","doi-asserted-by":"crossref","first-page":"1517","DOI":"10.1002\/pro.2955","article-title":"Analysis of the interactions of sulfur-containing amino acids in membrane proteins","volume":"25","author":"JC G\u00f3mez-Tamayo","year":"2016","journal-title":"Protein Sci"},{"key":"pcbi.1007390.ref092","doi-asserted-by":"crossref","DOI":"10.1093\/oso\/9780198520597.001.0001","volume-title":"Polymer physics","author":"M Rubinstein","year":"2003"},{"issue":"26","key":"pcbi.1007390.ref093","doi-asserted-by":"crossref","first-page":"6156","DOI":"10.1523\/JNEUROSCI.1017-05.2005","article-title":"Sortilin controls intracellular sorting of brain-derived neurotrophic factor to the regulated secretory pathway","volume":"25","author":"ZY Chen","year":"2005","journal-title":"J Neurosci"},{"issue":"1","key":"pcbi.1007390.ref094","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1007\/s11064-017-2460-0","article-title":"Methionine in Proteins: It\u2019s Not Just for Protein Initiation Anymore","volume":"44","author":"JM Lim","year":"2019","journal-title":"Neurochem Res"},{"issue":"1","key":"pcbi.1007390.ref095","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1038\/nmeth.3213","article-title":"The I-TASSER Suite: protein structure and function prediction","volume":"12","author":"J Yang","year":"2014","journal-title":"Nat Methods"},{"issue":"4","key":"pcbi.1007390.ref096","doi-asserted-by":"crossref","first-page":"725","DOI":"10.1038\/nprot.2010.5","article-title":"I-TASSER: a unified platform for automated protein structure and function prediction","volume":"5","author":"A Roy","year":"2010","journal-title":"Nat Protoc"},{"issue":"1","key":"pcbi.1007390.ref097","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1186\/1471-2105-9-40","article-title":"I-TASSER server for protein 3D structure prediction","volume":"9","author":"Y Zhang","year":"2008","journal-title":"BMC Bioinformatics"},{"issue":"Web Server issue","key":"pcbi.1007390.ref098","doi-asserted-by":"crossref","first-page":"W526","DOI":"10.1093\/nar\/gkh468","article-title":"Protein structure prediction and analysis using the Robetta server","volume":"32","author":"DE Kim","year":"2004","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"pcbi.1007390.ref099","doi-asserted-by":"crossref","first-page":"779","DOI":"10.1006\/jmbi.1993.1626","article-title":"Comparative Protein Modelling by Satisfaction of Spatial Restraints","volume":"234","author":"A \u0160ali","year":"1993","journal-title":"J Mol Biol"},{"issue":"1-3","key":"pcbi.1007390.ref100","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1016\/0010-4655(95)00042-E","article-title":"GROMACS: A message-passing parallel molecular dynamics implementation","volume":"91","author":"HJC Berendsen","year":"1995","journal-title":"Comput Phys Commun"},{"key":"pcbi.1007390.ref101","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/j.softx.2015.06.001","article-title":"GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers","volume":"1-2","author":"MJ Abraham","year":"2015","journal-title":"SoftwareX"},{"issue":"19","key":"pcbi.1007390.ref102","doi-asserted-by":"crossref","first-page":"8577","DOI":"10.1063\/1.470117","article-title":"A smooth particle mesh Ewald method","volume":"103","author":"U Essmann","year":"1995","journal-title":"J Chem Phys"},{"issue":"1-2","key":"pcbi.1007390.ref103","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1016\/S0009-2614(99)01123-9","article-title":"Replica-exchange molecular dynamics method for protein folding","volume":"314","author":"Y Sugita","year":"1999","journal-title":"Chem Phys Lett"},{"issue":"4","key":"pcbi.1007390.ref104","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1007\/s10858-009-9333-z","article-title":"TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts","volume":"44","author":"Y Shen","year":"2009","journal-title":"J Biomol NMR"},{"issue":"12","key":"pcbi.1007390.ref105","doi-asserted-by":"crossref","first-page":"2795","DOI":"10.1110\/ps.062465306","article-title":"Sensitivity of secondary structure propensities to sequence differences between \u03b1- and \u03b3-synuclein: Implications for fibrillation","volume":"15","author":"JA Marsh","year":"2006","journal-title":"Protein Sci"},{"issue":"3","key":"pcbi.1007390.ref106","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1007\/s10858-018-0166-5","article-title":"POTENCI: prediction of temperature, neighbor and pH-corrected chemical shifts for intrinsically disordered proteins","volume":"70","author":"JT Nielsen","year":"2018","journal-title":"J Biomol NMR"},{"issue":"49","key":"pcbi.1007390.ref107","doi-asserted-by":"crossref","first-page":"17908","DOI":"10.1021\/ja9069024","article-title":"Quantitative Description of Backbone Conformational Sampling of Unfolded Proteins at Amino Acid Resolution from NMR Residual Dipolar Couplings","volume":"131","author":"G Nodet","year":"2009","journal-title":"J Am Chem Soc"},{"issue":"5","key":"pcbi.1007390.ref108","doi-asserted-by":"crossref","first-page":"2782","DOI":"10.1073\/pnas.042496899","article-title":"Alpha-helical stabilization by side chain shielding of backbone hydrogen bonds","volume":"99","author":"AE Garc\u00eda","year":"2002","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"1","key":"pcbi.1007390.ref109","doi-asserted-by":"crossref","first-page":"e25323","DOI":"10.4161\/idp.25323","article-title":"SS-map","volume":"1","author":"J Iglesias","year":"2013","journal-title":"Intrinsically Disord Proteins"},{"key":"pcbi.1007390.ref110","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1016\/j.jmgm.2013.10.003","article-title":"Network visualization of conformational sampling during molecular dynamics simulation","volume":"46","author":"LS Ahlstrom","year":"2013","journal-title":"J Mol Graph Model"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1007390","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2019,10,30]],"date-time":"2019-10-30T00:00:00Z","timestamp":1572393600000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007390","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,25]],"date-time":"2024-07-25T02:57:46Z","timestamp":1721876266000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007390"}},"subtitle":[],"editor":[{"given":"Bert L.","family":"de Groot","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2019,10,18]]},"references-count":110,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2019,10,18]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1007390","relation":{"has-preprint":[{"id-type":"doi","id":"10.26434\/chemrxiv.8135777.v2","asserted-by":"object"},{"id-type":"doi","id":"10.26434\/chemrxiv.8135777.v3","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,10,18]]}}}