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This raises the possibility that some IDPs may behave as marginal proteins, exhibiting properties of both disordered and folded states. HYPK is one such recently discovered marginal protein studied by fluorescence assays (with fluorescent proteins attached at the termini) and circular dichroism (CD) while modulating temperature, crowding, ionic strength and sequence (by altering charge composition and patterning). Here, we use all-atom molecular dynamics (MD) simulations to understand the sequence-specific and structural origin of this marginality by investigating the conformation landscape of both the wild-type and a charge-variant mutant of HYPK, with and without fluorescent proteins (FPs) attached at the N- and C- termini. We find the charge-variant mutant is more compact compared to the wild type both with and without FPs, showing the importance of charge patterning that is consistent with experimental observations and theoretical predictions used for experimental characterization. The wild-type HYPK fused to FPs reveals two distinct conformational populations differing in helix packing, which may account for the marginality observed experimentally. The charge-variant mutant protein with FPs also displays bimodal conformational populations, but through a different mechanism involving competitive electrostatic interactions between different protein segments and the FPs. Bimodality is observed in the mutant without FPs under different salt conditions due to competitive interactions between different segments of the chain or between the chain and counterions, while it becomes less evident in the wild-type HYPK without the crowding and surface interactions provided by the FPs. These findings offer broad insights into the origin of marginality, competing interactions, as well as the roles charge patterning and folded domains play on IDP conformation both in vitro and in-cell.<\/jats:p>","DOI":"10.1021\/acs.jpcb.6c03835","type":"journal-article","created":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T21:01:23Z","timestamp":1789765283000},"page":"10161-10174","source":"Crossref","is-referenced-by-count":0,"title":["Conformational\nLandscape of a Marginally Disordered\nProtein HYPK and its Charge-Variant Mutant in the Context of Folded\nDomains"],"prefix":"10.1021","volume":"130","author":[{"given":"Kari","family":"Gaalswyk","sequence":"first","affiliation":[{"name":"University of Denver , , , ,","place":["Denver, Colorado, United States, 80210"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9291-8123","authenticated-orcid":true,"given":"Martin","family":"Gruebele","sequence":"additional","affiliation":[{"name":"University of Illinois at Urbana-Champaign , , , ,","place":["Urbana, Illinois, United States, 61801"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4976-0986","authenticated-orcid":true,"given":"Kingshuk","family":"Ghosh","sequence":"additional","affiliation":[{"name":"University of Denver , , , ,","place":["Denver, Colorado, United States, 80210"]},{"name":"University of Denver , , , ,","place":["Denver, Colorado, United States, 80210"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,9,18]]},"reference":[{"key":"2026100109062565400_cit1","doi-asserted-by":"publisher","first-page":"739","DOI":"10.1110\/ps.4210102","article-title":"Natively\nunfolded proteins: A point where biology waits for physics","volume":"11","author":"Uversky","year":"2002","journal-title":"Protein Sci."},{"key":"2026100109062565400_cit2","doi-asserted-by":"publisher","first-page":"S33","DOI":"10.1134\/S0006297918140043","article-title":"The molten\nglobule concept: 45 years later","volume":"83","author":"Bychkova","year":"2018","journal-title":"Biochemistry\n(Moscow)"},{"key":"2026100109062565400_cit3","doi-asserted-by":"publisher","first-page":"1681","DOI":"10.1002\/bip.360281004","article-title":"Theory\nof cooperative transitions in protein molecules.\nII. Phase diagram for a protein molecule in solution","volume":"28","author":"Finkelstein","year":"1989","journal-title":"Biopolymers"},{"key":"2026100109062565400_cit4","doi-asserted-by":"publisher","first-page":"549","DOI":"10.1038\/415549a","article-title":"Mutual synergistic\nfolding in recruitment of CBP\/p300 by p160 nuclear receptor coactivators","volume":"415","author":"Demarest","year":"2002","journal-title":"Nature"},{"key":"2026100109062565400_cit5","doi-asserted-by":"publisher","first-page":"6714","DOI":"10.1074\/jbc.R115.692020","article-title":"Role of intrinsic\nprotein disorder in the function\nand interactions of the transcriptional coactivators CREB-binding\nprotein and p300","volume":"291","author":"Dyson","year":"2016","journal-title":"J. Biol. Chem."},{"key":"2026100109062565400_cit6","doi-asserted-by":"publisher","first-page":"12681","DOI":"10.1073\/pnas.202331299","article-title":"FlgM gains structure\nin living cells","volume":"99","author":"Dedmon","year":"2002","journal-title":"Proc. Natl. Acad. Sci. U. S.\nA."},{"key":"2026100109062565400_cit7","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2316408121","article-title":"HYPK: A marginally\ndisordered protein sensitive to\ncharge decoration","volume":"121","author":"Firouzbakht","year":"2024","journal-title":"Proc. Natl. Acad. Sci. U.\nS. A."},{"key":"2026100109062565400_cit8","doi-asserted-by":"publisher","first-page":"1942","DOI":"10.1073\/pnas.90.5.1942","article-title":"Cooperativity in\nprotein-folding\nkinetics","volume":"90","author":"Dill","year":"1993","journal-title":"Proc. Natl. Acad. Sci. U. S. 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Sci."},{"key":"2026100109062565400_cit19","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2200559119","article-title":"Competing interactions give rise\nto two-state behavior and switch-like transitions in charge-rich intrinsically\ndisordered proteins","volume":"119","author":"Zeng","year":"2022","journal-title":"Proc. Natl. Acad. Sci.\nU. S. A."},{"key":"2026100109062565400_cit20","doi-asserted-by":"publisher","first-page":"521","DOI":"10.1021\/jp015514e","article-title":"A view\nof the hydrophobic effect","volume":"106","author":"Southall","year":"2002","journal-title":"J. Phys. Chem. B"},{"key":"2026100109062565400_cit21","doi-asserted-by":"publisher","first-page":"6632","DOI":"10.1021\/cr400688u","article-title":"Exploring\nfree-energy landscapes of intrinsically disordered proteins at atomic\nresolution using NMR spectroscopy","volume":"114","author":"Jensen","year":"2014","journal-title":"Chem. 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Theory Comput."},{"key":"2026100109062565400_cit34","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1016\/0010-4655(95)00042-E","article-title":"GROMACS: A message-passing\nparallel molecular dynamics implementation","volume":"91","author":"Berendsen","year":"1995","journal-title":"Comput. Phys. Commun."},{"key":"2026100109062565400_cit35","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1109\/TSMC.1979.4310076","article-title":"A threshold\nselection method from gray-level histograms","volume":"9","author":"Otsu","year":"1979","journal-title":"IEEE Trans. Syst. Man Cybern."},{"key":"2026100109062565400_cit36","doi-asserted-by":"publisher","first-page":"267","DOI":"10.1146\/annurev-biophys-052118-115517","article-title":"The role of conformational\ndynamics and allostery in modulating protein evolution","volume":"49","author":"Campitelli","year":"2020","journal-title":"Annu. Rev. Biophys."},{"key":"2026100109062565400_cit37","doi-asserted-by":"publisher","first-page":"169175","DOI":"10.1016\/j.jmb.2025.169175","article-title":"Dynamic allostery:\nEvolution\u2019s double-edged sword in protein function and disease","volume":"437","author":"Campitelli","year":"2025","journal-title":"J. Mol. Biol."},{"key":"2026100109062565400_cit38","doi-asserted-by":"publisher","first-page":"1273","DOI":"10.1016\/j.bpj.2015.06.060","article-title":"The role\nof conformational dynamics\nand allostery in the disease development of human ferritin","volume":"109","author":"Kumar","year":"2015","journal-title":"Biophys. J."},{"key":"2026100109062565400_cit39","doi-asserted-by":"publisher","first-page":"1852","DOI":"10.1038\/s41467-021-22089-0","article-title":"Hinge-shift\nmechanism as a protein design principle for the evolution of \u03b2-lactamases\nfrom substrate promiscuity to specificity","volume":"12","author":"Modi","year":"2021","journal-title":"Nat.\nCommun."},{"key":"2026100109062565400_cit40","doi-asserted-by":"publisher","first-page":"20170184","DOI":"10.1098\/rstb.2017.0184","article-title":"Ancient thioredoxins\nevolved to modern-day stability-function requirement by altering native\nstate ensemble","volume":"373","author":"Modi","year":"2018","journal-title":"Phil. Trans. Biol. Sci."},{"key":"2026100109062565400_cit41","doi-asserted-by":"publisher","first-page":"3808","DOI":"10.3390\/ijms19123808","article-title":"Mutations utilize dynamic allostery to confer resistance\nin TEM-1 \u03b2-lactamase","volume":"19","author":"Modi","year":"2018","journal-title":"Int. J. Mol. Sci."},{"key":"2026100109062565400_cit42","doi-asserted-by":"publisher","first-page":"1483","DOI":"10.1016\/j.bpj.2022.03.012","article-title":"Dynamic allostery highlights the evolutionary differences\nbetween the CoV-1 and CoV-2 main proteases","volume":"121","author":"Campitelli","year":"2022","journal-title":"Biophys. J."},{"key":"2026100109062565400_cit43","doi-asserted-by":"publisher","first-page":"423","DOI":"10.1111\/eva.12052","article-title":"Structural\ndynamics flexibility informs function and evolution at a proteome\nscale","volume":"6","author":"Nevin Gerek","year":"2013","journal-title":"Evol. 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A."},{"key":"2026100109062565400_cit50","doi-asserted-by":"publisher","first-page":"123305","DOI":"10.1063\/1.5005821","article-title":"Sequence charge decoration dictates coil-globule transition in Intrinsically\nDisordered Proteins","volume":"148","author":"Firman","year":"2018","journal-title":"J. Chem. Phys."},{"key":"2026100109062565400_cit51","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1146\/annurev-biophys-120221-095357","article-title":"Rules of physical mathematics\ngovern intrinsically disordered proteins","volume":"51","author":"Ghosh","year":"2022","journal-title":"Annu.\nRev. Biophys."},{"key":"2026100109062565400_cit52","doi-asserted-by":"publisher","first-page":"13392","DOI":"10.1073\/pnas.1304749110","article-title":"Conformations of\nintrinsically disordered proteins\nare influenced by linear sequence distributions of oppositely charged\nresidues","volume":"110","author":"Das","year":"2013","journal-title":"Proc. Natl. Acad. Sci. U. S. 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