title: Mutations in the KDM5C ARID Domain and Their Plausible Association with Syndromic Claes-Jensen-Type Disease.
abstract: Mutations in KDM5C gene are linked to X-linked mental retardation, the syndromic Claes-Jensen-type disease. This study focuses on non-synonymous mutations in the KDM5C ARID domain and evaluates the effects of two disease-associated missense mutations (A77T and D87G) and three not-yet-classified missense mutations (R108W, N142S, and R179H). We predict the ARID domain's folding and binding free energy changes due to mutations, and also study the effects of mutations on protein dynamics. Our computational results indicate that A77T and D87G mutants have minimal effect on the KDM5C ARID domain stability and DNA binding. In parallel, the change in the free energy unfolding caused by the mutants A77T and D87G were experimentally measured by urea-induced unfolding experiments and were shown to be similar to the in silico predictions. The evolutionary conservation analysis shows that the disease-associated mutations are located in a highly-conserved part of the ARID structure (N-terminal domain), indicating their importance for the KDM5C function. N-terminal residues' high conservation suggests that either the ARID domain utilizes the N-terminal to interact with other KDM5C domains or the N-terminal is involved in some yet unknown function. The analysis indicates that, among the non-classified mutations, R108W is possibly a disease-associated mutation, while N142S and R179H are probably harmless.
authors.affiliation: Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, SC 29634, USA. yunhuip@clemson.edu.
authors.forename: Yunhui
authors.initials: Y
authors.lastname: Peng
authors.affiliation: Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA. jsuryad@clemson.edu.
authors.forename: Jimmy
authors.initials: J
authors.lastname: Suryadi
authors.affiliation: Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA. yyang9@clemson.edu.
authors.forename: Ye
authors.initials: Y
authors.lastname: Yang
authors.affiliation: Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, SC 29634, USA. tugbak@g.clemson.edu.
authors.forename: Tugba G
authors.initials: TG
authors.lastname: Kucukkal
authors.affiliation: Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA. wgc@clemson.edu.
authors.forename: Weiguo
authors.initials: W
authors.lastname: Cao
authors.affiliation: Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, SC 29634, USA. ealexov@clemson.edu.
authors.forename: Emil
authors.initials: E
authors.lastname: Alexov
mesh_terms: D000595:Amino Acid Sequence; D017124:Conserved Sequence; D019143:Evolution, Molecular; D056726:Genetic Association Studies; D056466:Histone Demethylases / Q000737:chemistry* / Q000235:genetics*; D006801:Humans; D038901:X-Linked Intellectual Disability / Q000235:genetics*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009154:Mutation; D020125:Mutation, Missense; D011485:Protein Binding; D011487:Protein Conformation; D011489:Protein Denaturation; D017510:Protein Folding; D054730:Protein Interaction Domains and Motifs / Q000235:genetics*; D016415:Sequence Alignment; D013329:Structure-Activity Relationship
chemical_list: D056466:Histone Demethylases; C086877:KDM5C protein, human
keywords: X-linked syndromic Claes-Jensen type disease; binding free energy changes; folding free energy changes; free energy perturbation; molecular dynamics; sequence variants