The deleterious variants of N-acetylgalactosamine-6-sulfatase (GalN6S) enzyme trigger Morquio a syndrome by disrupting protein foldings.

Lysosomal enzymes degrade cellular macromolecules, while their inactivation causes human hereditary metabolic disorders. Mucopolysaccharidosis IVA (MPS IVA; Moquio A syndrome) is one of the lysosomal storage disorders caused by a defective Galactosamine-6-sulfatase (GalN6S) enzyme. In several populations, disease incidence is elevated due to missense mutations brought on by non-synonymous allelic variation in the GalN6S enzyme. Here, we studied the effect of non-synonymous single nucleotide polymorphism (nsSNPs) on the structural dynamics of the GalN6S enzyme and its binding with N-acetylgalactosamine (GalNAc) using all-atom molecular dynamics simulation and an essential dynamics approach. Consequently, in this study, we have identified three functionally disruptive mutations in domain-I and domain-II, that is, S80L, R90W, and S162F, which presumably contribute to post-translational modifications. The study delineated that both domains work cooperatively, and alteration in domain II (S80L, R90W) leads to conformational changes in the catalytic site in domain-I, while mutation S162F mainly provokes higher residual flexibility of domain II. These results show that these mutations impair the hydrophobic core, implying that Morquio A syndrome is caused by misfolding of the GalN6S enzyme. The results also show the instability of the GalN6S-GalNAc complex upon substitution. Overall, the structural dynamics resulting from point mutations give the molecular rationale for Moquio A syndrome and, more importantly, the Mucopolysaccharidoses (MPS) family of diseases, re-establishing MPS IVA as a protein-folding disease.Communicated by Ramaswamy H. Sarma.

[1]  Ashfaq Ur Rehman,et al.  Fragment-Based Approaches Identified Tecovirimat-Competitive Novel Drug Candidate for Targeting the F13 Protein of the Monkeypox Virus , 2023, Viruses.

[2]  H. Ng,et al.  Computational approaches for the design of modulators targeting protein-protein interactions , 2023, Expert opinion on drug discovery.

[3]  N. Haq,et al.  Structural Evaluation and Conformational Dynamics of ZNF141T474I Mutation Provoking Postaxial Polydactyly Type A , 2022, Bioengineering.

[4]  A. Rehman,et al.  Identification of novel peptide inhibitors for the KRas-G12C variant to prevent oncogenic signaling , 2022, Journal of biomolecular structure & dynamics.

[5]  K. Xia,et al.  Molecular Insights into the Role of Pathogenic nsSNPs in GRIN2B Gene Provoking Neurodevelopmental Disorders , 2022, Genes.

[6]  M. Rather,et al.  A comprehensive genomic study, mutation screening, phylogenetic and statistical analysis of SARS-CoV-2 and its variant omicron among different countries , 2022, Journal of Infection and Public Health.

[7]  S. U. Rahman,et al.  In-silico Analysis of 2-cysteine peroxiredoxin Genes in Arabidopsis thaliana with Possible Role in Carbon Dioxide Fixation through Carbonic Anhydrase regulation , 2022, Pakistan Journal of Biochemistry and Biotechnology.

[8]  Dong-Dong Wu,et al.  Genome-Wide Analysis of Codon Usage Patterns of SARS-CoV-2 Virus Reveals Global Heterogeneity of COVID-19 , 2021, Biomolecules.

[9]  J. Shendure,et al.  CADD-Splice—improving genome-wide variant effect prediction using deep learning-derived splice scores , 2021, Genome Medicine.

[10]  A. Ballabio,et al.  The rapidly evolving view of lysosomal storage diseases , 2021, EMBO molecular medicine.

[11]  M. Couce,et al.  Mucopolysaccharidosis IVA: Diagnosis, Treatment, and Management , 2020, International journal of molecular sciences.

[12]  Marianne Rohrbach,et al.  Epidemiology of mucopolysaccharidoses. , 2017, Molecular genetics and metabolism.

[13]  Piero Fariselli,et al.  PhD-SNPg: a webserver and lightweight tool for scoring single nucleotide variants , 2017, Nucleic Acids Res..

[14]  Trevor Hastie,et al.  REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants. , 2016, American journal of human genetics.

[15]  Itay Mayrose,et al.  ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules , 2016, Nucleic Acids Res..

[16]  J. Kleijnen,et al.  A systematic review of the prevalence of Morquio A syndrome: challenges for study reporting in rare diseases , 2014, Orphanet Journal of Rare Diseases.

[17]  Tatiana A. Tatusova,et al.  Gene: a gene-centered information resource at NCBI , 2014, Nucleic Acids Res..

[18]  The Uniprot Consortium,et al.  UniProt: a hub for protein information , 2014, Nucleic Acids Res..

[19]  T. Oron,et al.  Morquio A Syndrome-Associated Mutations: A Review of Alterations in the GALNS Gene and a New Locus-Specific Database , 2014, Human mutation.

[20]  C. Hendriksz,et al.  Review of clinical presentation and diagnosis of mucopolysaccharidosis IVA. , 2013, Molecular genetics and metabolism.

[21]  Emily K. Schutsky,et al.  The structure of human GALNS reveals the molecular basis for mucopolysaccharidosis IV A. , 2012, Journal of molecular biology.

[22]  C. Sander,et al.  Predicting the functional impact of protein mutations: application to cancer genomics , 2011, Nucleic acids research.

[23]  Y. Suzuki,et al.  Mucopolysaccharidosis type IVA (Morquio A disease): clinical review and current treatment. , 2011, Current pharmaceutical biotechnology.

[24]  Ivet Bahar,et al.  ProDy: Protein Dynamics Inferred from Theory and Experiments , 2011, Bioinform..

[25]  P. Popelier,et al.  Properties of liquid water from a systematic refinement of a high-rank multipolar electrostatic potential. , 2010, The Journal of chemical physics.

[26]  P. Bork,et al.  A method and server for predicting damaging missense mutations , 2010, Nature Methods.

[27]  A. Liwo,et al.  Principal component analysis for protein folding dynamics. , 2009, Journal of molecular biology.

[28]  S. Tomatsu,et al.  International Morquio A Registry: Clinical manifestation and natural course of Morquio A disease , 2007, Journal of Inherited Metabolic Disease.

[29]  A. Komar.  SNPs, Silent But Not Invisible , 2007, Science.

[30]  J. Moult,et al.  Identification and analysis of deleterious human SNPs. , 2006, Journal of molecular biology.

[31]  Akihiko Noguchi,et al.  Mutation and polymorphism spectrum of the GALNS gene in mucopolysaccharidosis IVA (Morquio A) , 2005, Human Mutation.

[32]  Robert Henke,et al.  High-resolution identification of chromosomal abnormalities using oligonucleotide arrays containing 116,204 SNPs. , 2005, American journal of human genetics.

[33]  David E. Shaw,et al.  A fast, scalable method for the parallel evaluation of distance‐limited pairwise particle interactions , 2005, J. Comput. Chem..

[34]  J. Nelson,et al.  Incidence of the mucopolysaccharidoses in Western Australia , 2003, American journal of medical genetics. Part A.

[35]  Steven Henikoff,et al.  SIFT: predicting amino acid changes that affect protein function , 2003, Nucleic Acids Res..

[36]  T. Fukao,et al.  Biochemical and structural analysis of missense mutations in N-acetylgalactosamine-6-sulfate sulfatase causing mucopolysaccharidosis IVA phenotypes. , 2000, Human molecular genetics.

[37]  K. Sirotkin,et al.  dbSNP-database for single nucleotide polymorphisms and other classes of minor genetic variation. , 1999, Genome research.

[38]  W. L. Jorgensen,et al.  Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids , 1996 .

[39]  M. Klein,et al.  Constant pressure molecular dynamics algorithms , 1994 .

[40]  Y. Suzuki,et al.  Mucopolysaccharidosis IV A: molecular cloning of the human N-acetylgalactosamine-6-sulfatase gene (GALNS) and analysis of the 5'-flanking region. , 1994, Genomics.

[41]  T. Yeates,et al.  Verification of protein structures: Patterns of nonbonded atomic interactions , 1993, Protein science : a publication of the Protein Society.

[42]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[43]  J. McCammon.  Protein dynamics , 1984 .