{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,12]],"date-time":"2026-06-12T19:36:17Z","timestamp":1781292977629,"version":"3.54.1"},"reference-count":62,"publisher":"Wiley","issue":"6","license":[{"start":{"date-parts":[[2026,1,21]],"date-time":"2026-01-21T00:00:00Z","timestamp":1768953600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"},{"start":{"date-parts":[[2026,1,21]],"date-time":"2026-01-21T00:00:00Z","timestamp":1768953600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/100002108","name":"Friedreich's Ataxia Research Alliance","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100002108","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004410","name":"T\u00fcrkiye Bilimsel ve Teknolojik Ara\u015ft\u0131rma Kurumu","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004410","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100020410","name":"T\u00fcrkiye Sa\u011fl\u0131k Enstit\u00fcleri Ba\u015fkanl\u0131\u011f\u0131","doi-asserted-by":"publisher","award":["4733406.03.2025\u2010A3\u201001"],"award-info":[{"award-number":["4733406.03.2025\u2010A3\u201001"]}],"id":[{"id":"10.13039\/100020410","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Proteins"],"published-print":{"date-parts":[[2026,6]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>\n                    Friedreich's ataxia (FRDA) is a neurodegenerative disorder caused by frataxin (FXN) deficiency, where protein replacement therapy is hampered by the inherent instability and aggregation propensity of wild\u2010type (WT) FXN. The structural flexibility of Loop\u20101 (residues 115\u2013123), a critical region within the acidic ridge, represents a key determinant of protein stability. This study introduces a computational pipeline integrating evolutionary conservation analysis (ConSurf) with diffusion\u2010based de novo design (RFdiffusion) to redesign both the backbone and sequence of Loop\u20101. Through systematic filtration of 1000 ProteinMPNN\u2010generated variants using aggregation propensity screening (AGGRESCAN) and 450\u2009ns of molecular dynamics (MD) simulations, four lead candidates were identified. Design_188 (EERVGGREI) demonstrated optimal performance with 2.3\u2010fold improvement in aggregation resistance (Na4vSS: \u221253.8 vs. \u221223.5 for WT), superior structural stability (RMSD: 0.486\u2009nm), reduced conformational diversity (62.3% dominant cluster occupancy), and 93% retention of ISCU binding capacity (\u0394\u0394G: +6.4\u2009kcal\/mol). Experimental validation through\n                    <jats:sup>15<\/jats:sup>\n                    N NMR relaxation analysis confirmed computational predictions, with Design_188 exhibiting uniform backbone rigidification (S\n                    <jats:sup>2<\/jats:sup>\n                    \u2009=\u20090.81\u20130.95) and strong MD\u2010NMR correlation (Pearson\n                    <jats:italic>r<\/jats:italic>\n                    \u2009=\u20090.675,\n                    <jats:italic>p<\/jats:italic>\n                    \u2009=\u20090.003). SEC\u2010MALS analysis demonstrated near\u2010complete monomeric behavior (&gt;\u200998% monomer content) compared to WT's heterogeneous oligomerization (68% monomer, 32% oligomers), directly confirming the predicted anti\u2010aggregation properties. K\u2010means clustering analysis revealed an inverse relationship between conformational heterogeneity and stability, while correlation analysis identified a fundamental trade\u2010off between aggregation resistance and structural stability (\n                    <jats:italic>r<\/jats:italic>\n                    \u2009=\u2009\u22120.82,\n                    <jats:italic>p<\/jats:italic>\n                    \u2009&lt;\u20090.01). This work establishes a generalizable framework for therapeutic protein engineering where backbone redesign enables conformational ensemble modulation beyond the limitations of sequence optimization alone.\n                  <\/jats:p>","DOI":"10.1002\/prot.70114","type":"journal-article","created":{"date-parts":[[2026,1,21]],"date-time":"2026-01-21T15:30:39Z","timestamp":1769009439000},"page":"1225-1244","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Integration of Evolutionary Analysis With\n                    <scp>RFdiffusion<\/scp>\n                    for De Novo Design of Aggregation\u2010Resistant Frataxin"],"prefix":"10.1002","volume":"94","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2917-8860","authenticated-orcid":false,"given":"Kevser K\u00fcbra","family":"K\u0131rbo\u011fa","sequence":"first","affiliation":[{"name":"Faculty of Engineering, Department of Bioengineering Bilecik \u015eeyh Edebali University  Bilecik TR T\u00fcrkiye"},{"name":"Department of Bioengineering S\u00fcleyman Demirel University  Isparta TR T\u00fcrkiye"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3293-9878","authenticated-orcid":false,"given":"Ecir U\u011fur","family":"K\u00fc\u00e7\u00fcksille","sequence":"additional","affiliation":[{"name":"S\u00fcleyman Demirel University Engineering Faculty, Department of Computer Engineering  Isparta T\u00fcrkiye"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,1,21]]},"reference":[{"key":"e_1_2_11_2_1","doi-asserted-by":"publisher","DOI":"10.1155\/2013\/487534"},{"key":"e_1_2_11_3_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1742\u20104658.2008.06512.x"},{"key":"e_1_2_11_4_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.abb.2020.108491"},{"key":"e_1_2_11_5_1","doi-asserted-by":"publisher","DOI":"10.1093\/hmg\/ddr554"},{"key":"e_1_2_11_6_1","doi-asserted-by":"publisher","DOI":"10.1208\/s12248\u2010025\u201001054\u20105"},{"key":"e_1_2_11_7_1","doi-asserted-by":"publisher","DOI":"10.1208\/s12249\u2010025\u201003189\u20102"},{"key":"e_1_2_11_8_1","doi-asserted-by":"publisher","DOI":"10.1021\/bi00168a003"},{"key":"e_1_2_11_9_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.redox.2020.101483"},{"key":"e_1_2_11_10_1","doi-asserted-by":"publisher","DOI":"10.1038\/s44324\u2010024\u201000045\u2010y"},{"key":"e_1_2_11_11_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.277.5326.653"},{"key":"e_1_2_11_12_1","doi-asserted-by":"publisher","DOI":"10.3389\/fcell.2022.894591"},{"key":"e_1_2_11_13_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2023.12.016"},{"key":"e_1_2_11_14_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2012.03.042"},{"key":"e_1_2_11_15_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2019.03.045"},{"key":"e_1_2_11_16_1","doi-asserted-by":"publisher","DOI":"10.1016\/s0969\u20102126(00)00158\u20101"},{"key":"e_1_2_11_17_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jinorgbio.2018.03.007"},{"key":"e_1_2_11_18_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbapap.2019.07.007"},{"key":"e_1_2_11_19_1","doi-asserted-by":"publisher","DOI":"10.3390\/ijms21249619"},{"key":"e_1_2_11_20_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.abb.2017.10.022"},{"key":"e_1_2_11_21_1","doi-asserted-by":"publisher","DOI":"10.3390\/biomedicines10020425"},{"key":"e_1_2_11_22_1","doi-asserted-by":"publisher","DOI":"10.3390\/ijms25115796"},{"key":"e_1_2_11_23_1","doi-asserted-by":"crossref","unstructured":"R.N\u00fa\u00f1ez\u2010Franco A.Torres\u2010Mozas C. 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