{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,4]],"date-time":"2026-05-04T02:24:26Z","timestamp":1777861466371,"version":"3.51.4"},"reference-count":49,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2026,4,27]],"date-time":"2026-04-27T00:00:00Z","timestamp":1777248000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100019706","name":"Qatar Biomedical Research Institute","doi-asserted-by":"crossref","award":["IGP6"],"award-info":[{"award-number":["IGP6"]}],"id":[{"id":"10.13039\/100019706","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Biomolecules"],"abstract":"<jats:p>Sox9, a pivotal transcription factor belonging to the Sox family, orchestrates critical processes throughout embryonic development, maintenance and differentiation, and exerts a profound influence on organogenesis. Its regulatory versatility stems from precise binding to defined DNA regions, often in collaboration with tissue-specific partners. The dysregulation of Sox9 during chondrogenesis leads to a skeletal malformation termed campomelic dysplasia and has emerged as a significant factor in various other human diseases, including cancer. A point mutation at position 76 (alanine to glutamic acid, A76E) of Sox9 is recognized as one of the causes of campomelic dysplasia. We have used a combination of biophysical, structural and computational techniques to characterize the Sox9 A76E mutant and compare it with the wild-type (WT) Sox9. WT and A76E Sox9 assemble as homodimers, but form predominantly monomeric complexes in the presence of Sox-specific DNA. A CD analysis shows that the A76E mutant preserves the folding as well as the overall secondary structure of Sox9. Both A76E and WT Sox9 behave similarly in the presence of Sox-specific DNA. Perturbation, with increased temperature, displays a lower melting point for A76E, relative to WT Sox9, indicating decreased stability that may arise due to the long and charged side chain of glutamic acid compared to the small hydrophobic alanine, making unfavorable intra-molecular interactions. The destabilizing effect of the A76E mutant may disturb the formation of a stable higher-order complex that is a prerequisite for normal gene expression.<\/jats:p>","DOI":"10.3390\/biom16050646","type":"journal-article","created":{"date-parts":[[2026,4,29]],"date-time":"2026-04-29T10:34:42Z","timestamp":1777458882000},"page":"646","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["A Campomelic Dysplasia A76E Mutation in Sox9 Destabilizes Protein and DNA Binding Dynamics"],"prefix":"10.3390","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5444-3910","authenticated-orcid":false,"given":"Zeyaul","family":"Islam","sequence":"first","affiliation":[{"name":"Diabetes Research Center (DRC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha P.O. Box 34110, Qatar"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4970-5944","authenticated-orcid":false,"given":"Prasanna R.","family":"Kolatkar","sequence":"additional","affiliation":[{"name":"Diabetes Research Center (DRC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha P.O. Box 34110, Qatar"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2026,4,27]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1038\/nrm3951","article-title":"The Mediator Complex: A Central Integrator of Transcription","volume":"16","author":"Allen","year":"2015","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"650","DOI":"10.1016\/j.cell.2018.01.029","article-title":"The Human Transcription Factors","volume":"172","author":"Lambert","year":"2018","journal-title":"Cell"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"262","DOI":"10.1038\/nrm.2017.115","article-title":"Transcription Regulation by the Mediator Complex","volume":"19","author":"Soutourina","year":"2018","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1016\/j.ccr.2005.07.009","article-title":"The Transcriptional Repressor Snail Promotes Mammary Tumor Recurrence","volume":"8","author":"Moody","year":"2005","journal-title":"Cancer Cell"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"36435","DOI":"10.1074\/jbc.M112.397125","article-title":"Snail Represses the Splicing Regulator Epithelial Splicing Regulatory Protein 1 to Promote Epithelial-Mesenchymal Transition","volume":"287","author":"Reinke","year":"2012","journal-title":"J. Biol. Chem."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Islam, Z., Ali, A.M., Naik, A., Eldaw, M., Decock, J., and Kolatkar, P.R. (2021). Transcription Factors: The Fulcrum Between Cell Development and Carcinogenesis. Front. Oncol., 11.","DOI":"10.3389\/fonc.2021.681377"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"448","DOI":"10.1038\/348448a0","article-title":"Genetic Evidence Equating SRY and the Testis-Determining Factor","volume":"348","author":"Berta","year":"1990","journal-title":"Nature"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1006\/dbio.2000.9883","article-title":"Phylogeny of the SOX Family of Developmental Transcription Factors Based on Sequence and Structural Indicators","volume":"227","author":"Bowles","year":"2000","journal-title":"Dev. Biol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"1409","DOI":"10.1093\/nar\/27.6.1409","article-title":"From Head to Toes: The Multiple Facets of Sox Proteins","volume":"27","author":"Wegner","year":"1999","journal-title":"Nucleic Acids Res."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"466","DOI":"10.1210\/er.2002-0025","article-title":"The Molecular Action and Regulation of the Testis-Determining Factors, SRY (Sex-Determining Region on the Y Chromosome) and SOX9 [SRY-Related High-Mobility Group (HMG) Box 9]","volume":"24","author":"Harley","year":"2003","journal-title":"Endocr. Rev."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1111","DOI":"10.1016\/0092-8674(94)90041-8","article-title":"Autosomal Sex Reversal and Campomelic Dysplasia Are Caused by Mutations in and around the SRY-Related Gene SOX9","volume":"79","author":"Wagner","year":"1994","journal-title":"Cell"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1038\/372525a0","article-title":"Campomelic Dysplasia and Autosomal Sex Reversal Caused by Mutations in an SRY-Related Gene","volume":"372","author":"Foster","year":"1994","journal-title":"Nature"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"5681","DOI":"10.1242\/dev.00808","article-title":"Neural Crest Development Is Regulated by the Transcription Factor Sox9","volume":"130","author":"Cheung","year":"2003","journal-title":"Development"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1016\/j.molmed.2010.12.001","article-title":"Understanding the Role of SOX9 in Acquired Diseases: Lessons from Development","volume":"17","author":"Pritchett","year":"2011","journal-title":"Trends Mol. Med."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1038\/ng0195-15","article-title":"The Sry-Related Gene Sox9 Is Expressed during Chondrogenesis in Mouse Embryos","volume":"9","author":"Wright","year":"1995","journal-title":"Nat. Genet."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"6698","DOI":"10.1073\/pnas.111092198","article-title":"Haploinsufficiency of Sox9 Results in Defective Cartilage Primordia and Premature Skeletal Mineralization","volume":"98","author":"Bi","year":"2001","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"2195","DOI":"10.1016\/j.biocel.2007.05.019","article-title":"Control of Cell Fate and Differentiation by Sry-Related High-Mobility-Group Box (Sox) Transcription Factors","volume":"39","author":"Lefebvre","year":"2007","journal-title":"Int. J. Biochem. Cell Biol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1016\/j.ydbio.2007.02.002","article-title":"Sox9 Is Required for Precursor Cell Expansion and Extracellular Matrix Organization during Mouse Heart Valve Development","volume":"305","author":"Lincoln","year":"2007","journal-title":"Dev. Biol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1865","DOI":"10.1073\/pnas.0609217104","article-title":"SOX9 Is Required for Maintenance of the Pancreatic Progenitor Cell Pool","volume":"104","author":"Seymour","year":"2007","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"111449","DOI":"10.1016\/j.yexcr.2019.05.030","article-title":"Sox9 Regulates the Luminal Stem\/Progenitor Cell Properties of Salivary Glands","volume":"382","author":"Tanaka","year":"2019","journal-title":"Exp. Cell Res."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"4149","DOI":"10.1128\/MCB.20.11.4149-4158.2000","article-title":"Phosphorylation of SOX9 by Cyclic AMP-Dependent Protein Kinase A Enhances SOX9\u2019s Ability to Transactivate a Col2a1 Chondrocyte-Specific Enhancer","volume":"20","author":"Huang","year":"2000","journal-title":"Mol. Cell. Biol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"799","DOI":"10.1083\/jcb.201204161","article-title":"SUMOylated SoxE Factors Recruit Grg4 and Function as Transcriptional Repressors in the Neural Crest","volume":"198","author":"Lee","year":"2012","journal-title":"J. Cell Biol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"2882","DOI":"10.1073\/pnas.1211747110","article-title":"Phosphorylation of Sox9 Is Required for Neural Crest Delamination and Is Regulated Downstream of BMP and Canonical Wnt Signaling","volume":"110","author":"Liu","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Islam, Z., Aldous, N., Choi, S., Schmidt, F., Mifsud, B., Abdelalim, E.M., and Kolatkar, P.R. (2022). Flavin Adenine Dinucleotide (FAD) and Pyridoxal 5\u2019-Phosphate (PLP) Bind to Sox9 and Alter the Expression of Key Pancreatic Progenitor Transcription Factors. Int. J. Mol. Sci., 23.","DOI":"10.3390\/ijms232214051"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"2048","DOI":"10.1101\/gad.269303","article-title":"Crystal Structure of a POU\/HMG\/DNA Ternary Complex Suggests Differential Assembly of Oct4 and Sox2 on Two Enhancers","volume":"17","author":"Remenyi","year":"2003","journal-title":"Genes Dev."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"705","DOI":"10.1016\/0092-8674(95)90532-4","article-title":"Molecular Basis of Human 46X,Y Sex Reversal Revealed from the Three-Dimensional Solution Structure of the Human SRY-DNA Complex","volume":"81","author":"Werner","year":"1995","journal-title":"Cell"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1449","DOI":"10.1074\/jbc.M309790200","article-title":"Molecular Basis for Synergistic Transcriptional Activation by Oct1 and Sox2 Revealed from the Solution Structure of the 42-KDa Oct1\u00b7Sox2\u00b7 Hoxb1-DNA Ternary Transcription Factor Complex","volume":"279","author":"Williams","year":"2004","journal-title":"J. Biol. Chem."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1500","DOI":"10.1093\/nar\/22.8.1500","article-title":"Definition of a Consensus DNA Binding Site for SRY","volume":"22","author":"Harley","year":"1994","journal-title":"Nucleic Acids Res."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"378","DOI":"10.1016\/j.biocel.2009.12.003","article-title":"The Early History of the Sox Genes","volume":"42","year":"2010","journal-title":"Int. J. Biochem. Cell Biol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1755","DOI":"10.1093\/hmg\/ddg182","article-title":"Dimerization of SOX9 Is Required for Chondrogenesis, but Not for Sex Determination","volume":"12","author":"Bernard","year":"2003","journal-title":"Hum. Mol. Genet."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"1439","DOI":"10.1093\/hmg\/ddg158","article-title":"Loss of DNA-Dependent Dimerization of the Transcription Factor SOX9 as a Cause for Campomelic Dysplasia","volume":"12","author":"Sock","year":"2003","journal-title":"Hum. Mol. Genet."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"E1436","DOI":"10.1002\/humu.21238","article-title":"Heterozygous SOX9 Mutations Allowing for Residual DNA-Binding and Transcriptional Activation Lead to the Acampomelic Variant of Campomelic Dysplasia","volume":"31","author":"Staffler","year":"2010","journal-title":"Hum. Mutat."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"3781","DOI":"10.1093\/hmg\/ddaa259","article-title":"Heterozygous Deletion of Sox9 in Mouse Mimics the Gonadal Sex Reversal Phenotype Associated with Campomelic Dysplasia in Humans","volume":"29","author":"Combes","year":"2021","journal-title":"Hum. Mol. Genet."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"W636","DOI":"10.1093\/nar\/gkz268","article-title":"The EMBL-EBI Search and Sequence Analysis Tools APIs in 2019","volume":"47","author":"Madeira","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"W529","DOI":"10.1093\/nar\/gkq399","article-title":"ConSurf 2010: Calculating Evolutionary Conservation in Sequence and Structure of Proteins and Nucleic Acids","volume":"38","author":"Ashkenazy","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1038\/nmeth0410-248","article-title":"A Method and Server for Predicting Damaging Missense Mutations","volume":"7","author":"Adzhubei","year":"2010","journal-title":"Nat. Methods"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"E7","DOI":"10.1038\/s41586-021-04207-6","article-title":"Publisher Correction: Disease Variant Prediction with Deep Generative Models of Evolutionary Data","volume":"601","author":"Frazer","year":"2022","journal-title":"Nature"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1002\/humu.22225","article-title":"Predicting the Functional, Molecular, and Phenotypic Consequences of Amino Acid Substitutions Using Hidden Markov Models","volume":"34","author":"Shihab","year":"2013","journal-title":"Hum. Mutat."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"W315","DOI":"10.1093\/nar\/gky497","article-title":"BeStSel: A Web Server for Accurate Protein Secondary Structure Prediction and Fold Recognition from the Circular Dichroism Spectra","volume":"46","author":"Micsonai","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1038\/s41586-024-07487-w","article-title":"Accurate Structure Prediction of Biomolecular Interactions with AlphaFold 3","volume":"630","author":"Abramson","year":"2024","journal-title":"Nature"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1093\/bioinformatics\/btt691","article-title":"MCSM: Predicting the Effects of Mutations in Proteins Using Graph-Based Signatures","volume":"30","author":"Pires","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"W229","DOI":"10.1093\/nar\/gkx439","article-title":"SDM: A Server for Predicting Effects of Mutations on Protein Stability","volume":"45","author":"Pandurangan","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"W239","DOI":"10.1093\/nar\/gkl190","article-title":"CUPSAT: Prediction of Protein Stability upon Point Mutations","volume":"34","author":"Parthiban","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1002\/pro.3943","article-title":"UCSF ChimeraX: Structure Visualization for Researchers, Educators, and Developers","volume":"30","author":"Pettersen","year":"2021","journal-title":"Protein Sci."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"6917","DOI":"10.1093\/nar\/gkz523","article-title":"The SOXE Transcription Factors-SOX8, SOX9 and SOX10-Share a Bi-Partite Transactivation Mechanism","volume":"47","author":"Haseeb","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"4999","DOI":"10.1128\/MCB.00695-08","article-title":"L-Sox5 and Sox6 Drive Expression of the Aggrecan Gene in Cartilage by Securing Binding of Sox9 to a Far-Upstream Enhancer","volume":"28","author":"Han","year":"2008","journal-title":"Mol. Cell. Biol."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"649","DOI":"10.1007\/s00109-011-0842-3","article-title":"Sox9\/Sox6 and Sp1 Are Involved in the Insulin-like Growth Factor-I-Mediated Upregulation of Human Type II Collagen Gene Expression in Articular Chondrocytes","volume":"90","author":"Renard","year":"2012","journal-title":"J. Mol. Med."},{"key":"ref_48","doi-asserted-by":"crossref","unstructured":"Leung, V.Y.L., Gao, B., Leung, K.K.H., Melhado, I.G., Wynn, S.L., Au, T.Y.K., Dung, N.W.F., Lau, J.Y.B., Mak, A.C.Y., and Chan, D. (2011). SOX9 Governs Differentiation Stage-Specific Gene Expression in Growth Plate Chondrocytes via Direct Concomitant Transactivation and Repression. PLoS Genet., 7.","DOI":"10.1371\/journal.pgen.1002356"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"7666","DOI":"10.1038\/s41598-019-43948-3","article-title":"Runx1 Contributes to Articular Cartilage Maintenance by Enhancement of Cartilage Matrix Production and Suppression of Hypertrophic Differentiation","volume":"9","author":"Yano","year":"2019","journal-title":"Sci. Rep."}],"container-title":["Biomolecules"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2218-273X\/16\/5\/646\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,30]],"date-time":"2026-04-30T04:13:41Z","timestamp":1777522421000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2218-273X\/16\/5\/646"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,4,27]]},"references-count":49,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2026,5]]}},"alternative-id":["biom16050646"],"URL":"https:\/\/doi.org\/10.3390\/biom16050646","relation":{},"ISSN":["2218-273X"],"issn-type":[{"value":"2218-273X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,4,27]]}}}