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Atak E, Karaoğlu D, Serttürk S, Koyuncu Irmak D, Yenenler-Kutlu A. Performing the comparative analysis to understand the functional roles of genes in different pathways of cardiomyopathy disease. Meta Gene 2021. [DOI: 10.1016/j.mgene.2021.100975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Aslan T, Yenenler-Kutlu A, Gerlevik U, Aktuğlu Zeybek AÇ, Kıykım E, Sezerman OU, Birgul Iyison N. Identifying and elucidating the roles of Y198N and Y204F mutations in the PAH enzyme through molecular dynamic simulations. J Biomol Struct Dyn 2021; 40:9018-9029. [PMID: 33970801 DOI: 10.1080/07391102.2021.1921619] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Phenylketonuria is an autosomal recessive disorder caused by mutations in the phenylalanine hydroxylase gene. In phenylketonuria causes various symptoms including severe mental retardation. PAH gene of a classical Phenylketonuria patient was sequenced, and two novel heterozygous mutations, p.Y198N and p.Y204F, were found. This study aimed to reveal the impacts of these variants on the structural stability of the PAH enzyme. In-silico analyses using prediction tools and molecular dynamics simulations were performed. Mutations were introduced to the wild type catalytic monomer and full length tetramer crystal structures. Variant pathogenicity analyses predicted p.Y198N to be damaging, and p.Y204F to be benign by some prediction tools and damaging by others. Simulations suggested p.Y198N mutation cause significant fluctuations in the spatial organization of two catalytic residues in the temperature accelerated MD simulations with the monomer and increased root-mean-square deviations in the tetramer structure. p.Y204F causes noticeable changes in the spatial positioning of T278 suggesting a possible segregation from the catalytic site in temperature accelerated MD simulations with the monomer. This mutation also leads to increased root-mean-square fluctuations in the regulatory domain which may lead to conformational change resulting in inhibition of dimerization and enzyme activation. Our study reports two novel mutations in the PAH gene and gives insight to their effects on the PAH activity. MD simulations did not yield conclusive results that explains the phenotype but gave plausible insight to possible effects which should be investigated further with in-silico and in-vitro studies to assess the roles of these mutations in etiology of PKU. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Tolga Aslan
- Faculty of Arts and Sciences, Department of Molecular Biology and Genetics, Bogazici University, Istanbul, Turkey
| | - Aslı Yenenler-Kutlu
- Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey.,Faculty of Science and Literature, Department of Molecular Biology & Genetics, Istinye University, Istanbul, Turkey
| | - Umut Gerlevik
- Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Ayşe Çiğdem Aktuğlu Zeybek
- Cerrahpasa Faculty of Medicine, Divisions of Nutrition and Metabolism, Department of Pediatrics, Istanbul University, İstanbul, Turkey
| | - Ertuğrul Kıykım
- Cerrahpasa Faculty of Medicine, Divisions of Nutrition and Metabolism, Department of Pediatrics, Istanbul University, İstanbul, Turkey
| | - Osman Uğur Sezerman
- Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Necla Birgul Iyison
- Faculty of Arts and Sciences, Department of Molecular Biology and Genetics, Bogazici University, Istanbul, Turkey
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