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Balasundaram A, Ramireddy S, S UK, D TK, Tayubi IA, Zayed H, C GPD. A new horizon in the phosphorylated sites of AGA: the structural impact of C163S mutation in aspartylglucosaminuria through molecular dynamics simulation. J Biomol Struct Dyn 2024; 42:4313-4324. [PMID: 37334725 DOI: 10.1080/07391102.2023.2220798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 05/28/2023] [Indexed: 06/20/2023]
Abstract
Aspartylglucosaminuria (AGU) is a lysosomal storage disorder caused by insufficient aspartylglucosaminidase (AGA) activity leading to chronic neurodegeneration. We utilized the PhosphoSitePlus tool to identify the AGA protein's phosphorylation sites. The phosphorylation was induced on the specific residue of the three-dimensional AGA protein, and the structural changes upon phosphorylation were studied via molecular dynamics simulation. Furthermore, the structural behaviour of C163S mutation and C163S mutation with adjacent phosphorylation was investigated. We have examined the structural impact of phosphorylated forms and C163S mutation in AGA. Molecular dynamics simulations (200 ns) exposed patterns of deviation, fluctuation, and change in compactness of Y178 phosphorylated AGA protein (Y178-p), T215 phosphorylated AGA protein (T215-p), T324 phosphorylated AGA protein (T324-p), C163S mutant AGA protein (C163S), and C163S mutation with Y178 phosphorylated AGA protein (C163S-Y178-p). Y178-p, T215-p, and C163S mutation demonstrated an increase in intramolecular hydrogen bonds, leading to greater compactness of the AGA forms. Principle component analysis (PCA) and Gibbs free energy of the phosphorylated/C163S mutation structures exhibit transition in motion/orientation than Wild type (WT). T215-p may be more dominant among these than the other studied phosphorylated forms. It might contribute to hydrolyzing L-asparagine functioning as an asparaginase, thereby regulating neurotransmitter activity. This study revealed structural insights into the phosphorylation of Y178, T215, and T324 in AGA protein. Additionally, it exposed the structural changes of the C163S mutation and C163S-Y178-p of AGA protein. This research will shed light on a better understanding of AGA's phosphorylated mechanism.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ambritha Balasundaram
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - Sriroopreddy Ramireddy
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - Udhaya Kumar S
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - Thirumal Kumar D
- Faculty of Allied Health Sciences, Meenakshi Academy of Higher Education and Research, Chennai, Tamil Nadu, India
| | - Iftikhar Aslam Tayubi
- Department of Computer Science, Faculty of Computing and Information Technology, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Hatem Zayed
- Department of Biomedical Sciences College of Health Sciences, QU Health, Qatar University, Doha, Qatar
| | - George Priya Doss C
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
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Zárybnický T, Heikkinen A, Kangas SM, Karikoski M, Martínez-Nieto GA, Salo MH, Uusimaa J, Vuolteenaho R, Hinttala R, Sipilä P, Kuure S. Modeling Rare Human Disorders in Mice: The Finnish Disease Heritage. Cells 2021; 10:cells10113158. [PMID: 34831381 PMCID: PMC8621025 DOI: 10.3390/cells10113158] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/04/2021] [Accepted: 11/06/2021] [Indexed: 12/31/2022] Open
Abstract
The modification of genes in animal models has evidently and comprehensively improved our knowledge on proteins and signaling pathways in human physiology and pathology. In this review, we discuss almost 40 monogenic rare diseases that are enriched in the Finnish population and defined as the Finnish disease heritage (FDH). We will highlight how gene-modified mouse models have greatly facilitated the understanding of the pathological manifestations of these diseases and how some of the diseases still lack proper models. We urge the establishment of subsequent international consortiums to cooperatively plan and carry out future human disease modeling strategies. Detailed information on disease mechanisms brings along broader understanding of the molecular pathways they act along both parallel and transverse to the proteins affected in rare diseases, therefore also aiding understanding of common disease pathologies.
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Affiliation(s)
- Tomáš Zárybnický
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, P.O. Box 63, 00014 Helsinki, Finland;
| | - Anne Heikkinen
- Biocenter Oulu, University of Oulu, P.O. Box 5000, 90014 Oulu, Finland; (A.H.); (S.M.K.); (M.H.S.); (R.V.)
- Oulu Center for Cell-Matrix Research, Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. Box 8000, 90014 Oulu, Finland
| | - Salla M. Kangas
- Biocenter Oulu, University of Oulu, P.O. Box 5000, 90014 Oulu, Finland; (A.H.); (S.M.K.); (M.H.S.); (R.V.)
- PEDEGO Research Unit, University of Oulu, P.O. Box 8000, 90014 Oulu, Finland;
- Medical Research Center, Oulu University Hospital, University of Oulu, P.O. Box 5000, 90014 Oulu, Finland
| | - Marika Karikoski
- Research Centre for Integrative Physiology and Pharmacology, Institute of Biomedicine, University of Turku, 20520 Turku, Finland; (M.K.); (G.A.M.-N.)
| | - Guillermo Antonio Martínez-Nieto
- Research Centre for Integrative Physiology and Pharmacology, Institute of Biomedicine, University of Turku, 20520 Turku, Finland; (M.K.); (G.A.M.-N.)
- Turku Center for Disease Modelling (TCDM), Institute of Biomedicine, University of Turku, 20520 Turku, Finland
| | - Miia H. Salo
- Biocenter Oulu, University of Oulu, P.O. Box 5000, 90014 Oulu, Finland; (A.H.); (S.M.K.); (M.H.S.); (R.V.)
- PEDEGO Research Unit, University of Oulu, P.O. Box 8000, 90014 Oulu, Finland;
- Medical Research Center, Oulu University Hospital, University of Oulu, P.O. Box 5000, 90014 Oulu, Finland
| | - Johanna Uusimaa
- PEDEGO Research Unit, University of Oulu, P.O. Box 8000, 90014 Oulu, Finland;
- Medical Research Center, Oulu University Hospital, University of Oulu, P.O. Box 5000, 90014 Oulu, Finland
- Clinic for Children and Adolescents, Division of Pediatric Neurology, Oulu University Hospital, P.O. Box 20, 90029 Oulu, Finland
| | - Reetta Vuolteenaho
- Biocenter Oulu, University of Oulu, P.O. Box 5000, 90014 Oulu, Finland; (A.H.); (S.M.K.); (M.H.S.); (R.V.)
| | - Reetta Hinttala
- Biocenter Oulu, University of Oulu, P.O. Box 5000, 90014 Oulu, Finland; (A.H.); (S.M.K.); (M.H.S.); (R.V.)
- PEDEGO Research Unit, University of Oulu, P.O. Box 8000, 90014 Oulu, Finland;
- Medical Research Center, Oulu University Hospital, University of Oulu, P.O. Box 5000, 90014 Oulu, Finland
- Correspondence: (R.H.); (P.S.); (S.K.)
| | - Petra Sipilä
- Research Centre for Integrative Physiology and Pharmacology, Institute of Biomedicine, University of Turku, 20520 Turku, Finland; (M.K.); (G.A.M.-N.)
- Turku Center for Disease Modelling (TCDM), Institute of Biomedicine, University of Turku, 20520 Turku, Finland
- Correspondence: (R.H.); (P.S.); (S.K.)
| | - Satu Kuure
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, P.O. Box 63, 00014 Helsinki, Finland;
- GM-Unit, Laboratory Animal Center, Helsinki Institute of Life Science, University of Helsinki, 00790 Helsinki, Finland
- Correspondence: (R.H.); (P.S.); (S.K.)
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Goodspeed K, Feng C, Laine M, Lund TC. Aspartylglucosaminuria: Clinical Presentation and Potential Therapies. J Child Neurol 2021; 36:403-414. [PMID: 33439067 DOI: 10.1177/0883073820980904] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Aspartylglucosaminuria (AGU) is a recessively inherited neurodegenerative lysosomal storage disease characterized by progressive intellectual disability, skeletal abnormalities, connective tissue overgrowth, gait disturbance, and seizures followed by premature death. AGU is caused by pathogenic variants in the aspartylglucosaminidase (AGA) gene, leading to glycoasparagine accumulation and cellular dysfunction. Although more prevalent in the Finnish population, more than 30 AGA variants have been identified worldwide. Owing to its rarity, AGU may be largely underdiagnosed. Recognition of the following early clinical features may aid in AGU diagnosis: developmental delays, hyperactivity, early growth spurt, inguinal and abdominal hernias, clumsiness, characteristic facial features, recurring upper respiratory and ear infections, tonsillectomy, multiple sets of tympanostomy tube placement, and sleep problems. Although no curative therapies currently exist, early diagnosis may provide benefit through the provision of anticipatory guidance, management of expectations, early interventions, and prophylaxis; it will also be crucial for increased clinical benefits of future AGU disease-modifying therapies.
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Affiliation(s)
- Kimberly Goodspeed
- 7067University of Texas Southwestern Medical Center, Department of Pediatrics, Dallas, TX, USA
| | | | - Minna Laine
- Division of Child Neurology, Helsinki University Hospital, Helsinki, Finland
| | - Troy C Lund
- 5635University of Minnesota, Department of Pediatrics, Minneapolis, MN, USA
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Dunn PJ, Maher BH, Albury CL, Stuart S, Sutherland HG, Maksemous N, Benton MC, Smith RA, Haupt LM, Griffiths LR. Tiered analysis of whole-exome sequencing for epilepsy diagnosis. Mol Genet Genomics 2020; 295:751-763. [DOI: 10.1007/s00438-020-01657-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 02/19/2020] [Indexed: 12/11/2022]
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Pande S, Guo HC. The T99K variant of glycosylasparaginase shows a new structural mechanism of the genetic disease aspartylglucosaminuria. Protein Sci 2019; 28:1013-1023. [PMID: 30901125 DOI: 10.1002/pro.3607] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 03/21/2019] [Indexed: 12/16/2022]
Abstract
Aspartylglucosaminuria (AGU) is an inherited disease caused by mutations in a lysosomal amidase called aspartylglucosaminidase (AGA) or glycosylasparaginase (GA). This disorder results in an accumulation of glycoasparagines in the lysosomes of virtually all cell types, with severe clinical symptoms affecting the central nervous system, skeletal abnormalities, and connective tissue lesions. GA is synthesized as a single-chain precursor that requires an intramolecular autoprocessing to form a mature amidase. Previously, we showed that a Canadian AGU mutation disrupts this obligatory intramolecular autoprocessing with the enzyme trapped as an inactive precursor. Here, we report biochemical and structural characterization of a model enzyme corresponding to a new American AGU allele, the T99K variant. Unlike other variants with known 3D structures, this T99K model enzyme still has autoprocessing capacity to generate a mature form. However, its amidase activity to digest glycoasparagines remains low, consistent with its association with AGU. We have determined a 1.5-Å-resolution structure of this new AGU model enzyme and built an enzyme-substrate complex to provide a structural basis to analyze the negative effects of the T99K point mutation on KM and kcat of the amidase. It appears that a "molecular clamp" capable of fixing local disorders at the dimer interface might be able to rescue the deficiency of this new AGU variant.
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Affiliation(s)
- Suchita Pande
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, Massachusetts, 01854
| | - Hwai-Chen Guo
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, Massachusetts, 01854
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Pande S, Bizilj W, Guo HC. Biochemical and structural insights into an allelic variant causing the lysosomal storage disorder - aspartylglucosaminuria. FEBS Lett 2018; 592:2550-2561. [PMID: 29993127 DOI: 10.1002/1873-3468.13190] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 06/29/2018] [Accepted: 07/03/2018] [Indexed: 01/03/2023]
Abstract
Aspartylglucosaminuria (AGU) is a lysosomal storage disorder caused by defects of the hydrolase glycosylasparaginase (GA). Previously, we showed that a Canadian AGU mutation disrupts an obligatory intramolecular autoprocessing with the enzyme trapped as an inactive precursor. Here, we report biochemical and structural characterizations of a model enzyme corresponding to a Finnish AGU allele, the T234I variant. Unlike the Canadian counterpart, the Finnish variant is capable of a slow autoprocessing to generate detectible hydrolyzation activity of the natural substrate of GA. We have determined a 1.6 Å-resolution structure of the Finnish AGU model and built an enzyme-substrate complex to provide a structural basis for analyzing the negative effects of the point mutation on KM and kcat of the mature enzyme. ENZYME Glycosylasparaginase or aspartylglucosaminidase, EC3.5.1.26.
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Affiliation(s)
- Suchita Pande
- Department of Biological Sciences, University of Massachusetts Lowell, MA, USA
| | - William Bizilj
- Department of Biological Sciences, University of Massachusetts Lowell, MA, USA
| | - Hwai-Chen Guo
- Department of Biological Sciences, University of Massachusetts Lowell, MA, USA
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Pande S, Lakshminarasimhan D, Guo HC. Crystal structure of a mutant glycosylasparaginase shedding light on aspartylglycosaminuria-causing mechanism as well as on hydrolysis of non-chitobiose substrate. Mol Genet Metab 2017; 121:150-156. [PMID: 28457719 PMCID: PMC5504686 DOI: 10.1016/j.ymgme.2017.04.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 04/18/2017] [Accepted: 04/18/2017] [Indexed: 10/19/2022]
Abstract
Glycosylasparaginase (GA) is an amidase that cleaves Asn-linked glycoproteins in lysosomes. Deficiency of this enzyme causes accumulation of glycoasparagines in lysosomes of cells, resulting in a genetic condition called aspartylglycosaminuria (AGU). To better understand the mechanism of a disease-causing mutation with a single residue change from a glycine to an aspartic acid, we generated a model mutant enzyme at the corresponding position (named G172D mutant). Here we report a 1.8Å resolution crystal structure of mature G172D mutant and analyzed the reason behind its low hydrolase activity. Comparison of mature G172D and wildtype GA models reveals that the presence of Asp 172 near the catalytic site affects substrate catabolism in mature G172D, making it less efficient in substrate processing. Also recent studies suggest that GA is capable of processing substrates that lack a chitobiose (Glycan, N-acetylchiobios, NAcGlc) moiety, by its exo-hydrolase activity. The mechanism for this type of catalysis is not yet clear. l-Aspartic acid β-hydroxamate (β-AHA) is a non-chitobiose substrate that is known to interact with GA. To study the underlying mechanism of non-chitobiose substrate processing, we built a GA-β-AHA complex structure by comparing to a previously published G172D mutant precursor in complex with a β-AHA molecule. A hydrolysis mechanism of β-AHA by GA is proposed based on this complex model.
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Affiliation(s)
- Suchita Pande
- Department of Biological Sciences, University of Massachusetts Lowell, 1 University Avenue, Lowell, MA 01854, USA
| | - Damodharan Lakshminarasimhan
- Department of Biological Sciences, University of Massachusetts Lowell, 1 University Avenue, Lowell, MA 01854, USA
| | - Hwai-Chen Guo
- Department of Biological Sciences, University of Massachusetts Lowell, 1 University Avenue, Lowell, MA 01854, USA.
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Abstract
Aspartylglucosaminuria (AGU), a recessively inherited lysosomal storage disease, is the most common disorder of glycoprotein degradation with a high prevalence in the Finnish population. It is a lifelong condition affecting on the patient's appearance, cognition, adaptive skills, physical growth, personality, body structure, and health. An infantile growth spurt and development of macrocephalia associated to hernias and respiratory infections are the key signs to an early identification of AGU. Progressive intellectual and physical disability is the main symptom leading to death usually before the age of 50 years.The disease is caused by the deficient activity of the lysosomal enzyme glycosylasparaginase (aspartylglucosaminidase, AGA), which leads to a disorder in the degradation of glycoasparagines - aspartylglucosamine or other glycoconjugates with an aspartylglucosamine moiety at their reducing end - and accumulation of these undegraded glycoasparagines in tissues and body fluids. A single nucleotide change in the AGA gene resulting in a cysteine to serine substitution (C163S) in the AGA enzyme protein causes the deficiency of the glycosylasparaginase activity in the Finnish population. Homozygosity for the single nucleotide change causing the C163S mutation is responsible for 98% of the AGU cases in Finland simplifying the carrier detection and prenatal diagnosis of the disorder in the Finnish population. A mouse strain, which completely lacks the Aga activity has been generated through targeted disruption of the Aga gene in embryonic stem cells. These Aga-deficient mice share most of the clinical, histopathologic and biochemical characteristics of human AGU disease. Treatment of AGU mice with recombinant AGA resulted in rapid correction of the pathophysiologic characteristics of AGU in non-neuronal tissues of the animals. The accumulation of aspartylglucosamine was reduced by up to 40% in the brain tissue of the animals depending on the age of the animals and the therapeutic protocol. Enzyme replacement trials on human AGU patients have not been reported so far. Allogenic stem cell transplantation has not proved effective in curing AGU.
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Affiliation(s)
- Maria Arvio
- Päijät-Häme Social Welfare & Healthcare Joint Municipal Board, Lahti, Finland. .,KTO, The Special Welfare District of Southwestern Finland, Paimio, Finland. .,PEDEGO Research Unit, Oulu University Hospital, Finland, Oulu, Finland.
| | - Ilkka Mononen
- Newborn Screening Center Finland, Saske, Turku University Central Hospital, Turku, Finland.,The Joint Clinical Chemistry Laboratory at Turku University Hospital, Turku, Finland.,Department of Clinical Chemistry, University of Turku, PO Box 52, FIN-20521, Turku, Finland
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Identification of Small Molecule Compounds for Pharmacological Chaperone Therapy of Aspartylglucosaminuria. Sci Rep 2016; 6:37583. [PMID: 27876883 PMCID: PMC5120323 DOI: 10.1038/srep37583] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 11/02/2016] [Indexed: 12/16/2022] Open
Abstract
Aspartylglucosaminuria (AGU) is a lysosomal storage disorder that is caused by genetic deficiency of the enzyme aspartylglucosaminidase (AGA) which is involved in glycoprotein degradation. AGU is a progressive disorder that results in severe mental retardation in early adulthood. No curative therapy is currently available for AGU. We have here characterized the consequences of a novel AGU mutation that results in Thr122Lys exchange in AGA, and compared this mutant form to one carrying the worldwide most common AGU mutation, AGU-Fin. We show that T122K mutated AGA is expressed in normal amounts and localized in lysosomes, but exhibits low AGA activity due to impaired processing of the precursor molecule into subunits. Coexpression of T122K with wildtype AGA results in processing of the precursor into subunits, implicating that the mutation causes a local misfolding that prevents the precursor from becoming processed. Similar data were obtained for the AGU-Fin mutant polypeptide. We have here also identified small chemical compounds that function as chemical or pharmacological chaperones for the mutant AGA. Treatment of patient fibroblasts with these compounds results in increased AGA activity and processing, implicating that these substances may be suitable for chaperone mediated therapy for AGU.
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