Structural analysis of missense mutations in galactokinase 1 (GALK1) leading to galactosemia type‐2

Abstract

Galactosemia type 2 is an autosomal recessive disorder characterized by the deficiency of galactokinase (GALK) enzyme due to missense mutations in GALK1 gene, which is associated with various manifestations such as hyper galactosemia and formation of cataracts. GALK enzyme catalyzes the adenosine triphosphate (ATP)-dependent phosphorylation of α-d-galactose to galactose-1-phosphate. We searched 4 different literature databases (Google Scholar, PubMed, PubMed Central, and Science Direct) and 3 gene-variant databases (Online Mendelian Inheritance in Man, Human Gene Mutation Database, and UniProt) to collect all the reported missense mutations associated with GALK deficiency. Our search strategy yielded 32 missense mutations. We used several computational tools (pathogenicity and stability, biophysical characterization, and physiochemical analyses) to prioritize the most significant mutations for further analyses. On the basis of the pathogenicity and stability predictions, 3 mutations (P28T, A198V, and L139P) were chosen to be tested further for physicochemical characterization, molecular docking, and simulation analyses. Molecular docking analysis revealed a decrease in interaction between the protein and ATP in all the 3 mutations, and molecular dynamic simulations of 50 ns showed a loss of stability and compactness in the mutant proteins. As the next step, comparative physicochemical changes of the native and the mutant proteins were carried out using essential dynamics. Overall, P28T and A198V were predicted to alter the structure and function of GALK protein when compared to the mutant L139P. This study demonstrates the power of computational analysis in variant classification and interpretation and provides a platform for developing targeted therapeutics.

Galactosemia: Towards Pharmacological Chaperones

“…Some variants, including the one associated with the mildest known form of type II galactosemia (p.A198V), are expressed in reduced amounts by cells in comparison to the wild type [40,88]. Computational studies support the hypothesis that protein instability is a key factor in causing type II galactosemia [89,90]. Disease associated variants of UDP-galactose 4 epimerase are typically less stable then the wild type and, in some cases, have reduced affinity for the NAD + cofactor or aggregate in vivo [91][92][93][94][95][96].…”

“…The definition of orphan drug differs depending on the jurisdiction, but it is largely dependent on the disease being rare and therefore a drug having little profitability, but which would meet a public health need. Orphan drug status can have benefits such as tax incentives, direct government subsidiary, increased patent time or a streamlined approval process [89].…”

Bioinformatics classification of mutations in patients with Mucopolysaccharidosis IIIA

“…7). The mutational positions in the secondary structure of the proteins play an essential role in identifying structural alterations in the protein (Mosaeilhy et al 2017a; Mosaeilhy et al 2017b; Sneha et al 2018a; Sneha et al 2018b; Thirumal Kumar et al 2016; Yagawa et al 2010; Zaki et al 2017a). Alpha helices and beta strands are stabilized by hydrogen bonds (Schneider and Kelly 1995).…”

“…To increase in prediction accuracy of disease causing variants, we used Meta-SNP server (Capriotti et al 2013) that integrates four existing methods: PANTHER, SIFT, PhD-SNP, and SNAP to predict a mutation either disease (affecting the protein function) or neutral (having no impact). Further, a combination of these in silico tools and molecular dynamics studies in mutational analysis has been confirmed to be a dominant approach in understanding macromolecule behaviors and their microscopic interactions, allowing insights into the impact of mutations (Agrahari et al 2019; Ali et al 2017a; Ali et al 2017b; Nagarajan et al 2015; Sneha et al 2018a; Sneha and George Priya Doss 2016; Sneha et al 2018b; Thirumal Kumar et al 2019). Molecular dynamics (MD) aid in understanding the significant changes in the macromolecular structures of proteins due to mutations at an atomic level.…”

The Genetic Basis of Galactosemia in Iranian Patients: Identification of Twenty Novel Mutations in GALT, GALK1 and GALE Gene

“…The GALK1 gene has 8 exons of 7.3 kb on chromosome 17q25.1.15 (2). GALK1 de ciency occurs worldwide but has a high frequency rate among the Roma (5). The important mutations of GALK1 gene which have pathogenic effect including P28T, A198V, V32M, G36R, R68C, R239Q, T288M, G346S, G349S, and A384P (18).…”