title: Lessons from molecular modeling human α-L-iduronidase.
abstract: Human α-L-iduronidase (IDUA) is a member of glycoside hydrolase family and is involved in the catabolism of glycosaminoglycans (GAGs), heparan sulfate (HS) and dermatan sulfate (DS). Mutations in this enzyme are responsible for mucopolysaccharidosis I (MPS I), an inherited lysosomal storage disorder. Despite great interest in determining and studying this enzyme structure, the lack of a high identity to templates and other technical issues have challenged both bioinformaticians and crystallographers, until the recent publication of an IDUA crystal structure (PDB: 4JXP). In the present work, four alternative IDUA models, generated and evaluated prior to crystallographic determination, were compared to the 4JXP structure. A combined analysis using several viability assessment tools and molecular dynamics simulations highlights the strengths and limitations of different comparative modeling protocols, all of which are based on the same low identity template (only 22%). Incorrect alignment between the target and template was confirmed to be a major bottleneck in homology modeling, regardless of the modeling software used. Moreover, secondary structure analysis during a 50ns simulation seems to be useful for indicating alignment errors and structural instabilities. The best model was achieved through the combined use of Phyre 2 and Modeller, suggesting the use of this protocol for the modeling of other proteins that still lack high identity templates.
authors.affiliation: NBLI - Núcleo de Bioinformática do Laboratório de Imunogenética, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil; Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil.
authors.forename: Danieli Forgiarini
authors.initials: DF
authors.lastname: Figueiredo
authors.affiliation: NBLI - Núcleo de Bioinformática do Laboratório de Imunogenética, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil; Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil.
authors.forename: Dinler A
authors.initials: DA
authors.lastname: Antunes
authors.affiliation: NBLI - Núcleo de Bioinformática do Laboratório de Imunogenética, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil; Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil.
authors.forename: Maurício M
authors.initials: MM
authors.lastname: Rigo
authors.affiliation: NBLI - Núcleo de Bioinformática do Laboratório de Imunogenética, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil; Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil.
authors.forename: Marcus F A
authors.initials: MF
authors.lastname: Mendes
authors.affiliation: NBLI - Núcleo de Bioinformática do Laboratório de Imunogenética, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil.
authors.forename: Jader P
authors.initials: JP
authors.lastname: Silva
authors.affiliation: Molecular Biology Laboratory, Instituto de Pesquisas Veterinárias Desidério Finamor, Fundação Estadual de Pesquisa Agropecuária Porto Alegre, Rio Grande do Sul, Brazil.
authors.forename: Fabiana Q
authors.initials: FQ
authors.lastname: Mayer
authors.affiliation: Gene Therapy Center, Experimental Research Center, Hospital de Clínicas de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil; Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil.
authors.forename: Ursula
authors.initials: U
authors.lastname: Matte
authors.affiliation: Gene Therapy Center, Experimental Research Center, Hospital de Clínicas de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil; Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil.
authors.forename: Roberto
authors.initials: R
authors.lastname: Giugliani
authors.affiliation: NBLI - Núcleo de Bioinformática do Laboratório de Imunogenética, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil; Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil.
authors.forename: Gustavo F
authors.initials: GF
authors.lastname: Vieira
authors.affiliation: NBLI - Núcleo de Bioinformática do Laboratório de Imunogenética, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil; Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil. Electronic address: msinigaglia@gmail.com.
authors.forename: Marialva
authors.initials: M
authors.lastname: Sinigaglia
mesh_terms: D006801:Humans; D007068:Iduronidase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D008958:Models, Molecular; D008059:Mucopolysaccharidosis I / Q000201:enzymology; D009154:Mutation; D017433:Protein Structure, Secondary
chemical_list: D007068:Iduronidase
keywords: Homology modeling; Low identity template; Model evaluation tools; Molecular dynamics; Secondary structure assessment; α-l-Iduronidase (IDUA)