Abstract
In this work, the most detrimental missense mutations of aspartoacylase that cause Canavan’s disease were identified computationally and the substrate binding efficiencies of those missense mutations were analyzed. Out of 30 missense mutations, I-Mutant 2.0, SIFT and PolyPhen programs identified 22 variants that were less stable, deleterious and damaging respectively. Subsequently, modeling of these 22 variants was performed to understand the change in their conformations with respect to the native aspartoacylase by computing their root mean squared deviation (RMSD). Furthermore, the native protein and the 22 mutants were docked with the substrate NAA (N-Acetyl-Aspartic acid) to explain the substrate binding efficiencies of those detrimental missense mutations. Among the 22 mutants, the docking studies identified that 15 mutants caused lower binding affinity for NAA than the native protein. Finally, normal mode analysis determined that the loss of binding affinity of these 15 mutants was caused by altered flexibility in the amino acids that bind to NAA compared with the native protein. Thus, the present study showed that the majority of the substrate-binding amino acids in those 15 mutants displayed loss of flexibility, which could be the theoretical explanation of decreased binding affinity between the mutant aspartoacylases and NAA.
Article PDF
Similar content being viewed by others
Avoid common mistakes on your manuscript.
References
Matalon R, Michals-Matalon K, Sebesta M, et al. Aspartoacylase deficiency and N-acetylaspartic aciduria in patient with Canavan disease. Am J Med Genet, 1988, 29: 463–471
Surendran S, Michals-Matalon K, Quast M J, et al. Canavan disease: a monogenic trait with complex genomic interaction. Mol Genet Metab, 2003, 80: 74–80
Zeng B J, Wang Z H, Ribeiro L A, et al. Identification and characterization of novel mutations of the aspartoacylase gene in non-Jewish patients with Canavan disease. J Inherit Metab Dis, 2002, 25: 557–570
Matalon R, Michals-Matalon K. Spongy degeneration of the brain, Canavan disease: biochemical and molecular findings. Front Biosci D, 2000, 5: 307–311
Shaag A, Anikster Y, Christensen E, et al. The molecular basis of Canavan (aspartoacylase deficiency) disease in European non-Jewish patients. Am J Hum Genet, 1995, 57: 572–580
Kaul R, Gao G P, Michals K, et al. Novel (cys 125 arg) missense mutation in an Arab patient with Canavan disease. Hum Mutat, 1995, 5: 269–271
Kaul R, Gao G P, Matalon R, et al. Identification and expression of eight novel mutations among non-Jewish patients with Canavan disease. Am J Hum Genet, 1996, 59: 95–102
Kobayashi K, Tsujino S, Ezoe T, et al. A missense mutation I143T in a Japanese patient with Canavan disease. Hum Mutat, 1998, 1: S308–S309
Adornato B T, O’Brien J S, Lampert P W. Cerebral spongy degeneration of infancy: a biochemical and ultrastructural study of affected twins. Neurology, 1972, 22: 202–210
Baslow M H. Molecular water pumps and the aetiology of Canavan disease: a case of the sorcerer’s apprentice. J Inherit Metab Dis, 1999, 22: 99–101
Adachi M, Torii J, Schneck L, et al. Electron microscopic and enzyme histochemical studies of the cerebellum in spongy degeneration (van Bogaert and Bertrand type). Acta Neuropathol, 1972, 20: 22–31
Luo Y, Huang K. Spongy degeneration of the CNS in infancy. Arch Neurol, 1984, 41: 164–170
Barash V, Flhor D, Morag B, et al. A radiometric assay for aspartoacylase activity in human fibroblasts: application for the diagnosis of Canavan’s disease. Clin Chim Acta, 1991, 201: 175–181
Bitto E, Bingman C A, Wesenberg G E, et al. Structure of aspartoacylase, the brain enzyme impaired in Canavan disease. Proc Natl Acad Sci USA, 2007, 104: 456–461
Hershfield J R, Pattabiraman N, Madhavarao C N, et al. Mutational analysis of aspartoacylase: implications for Canavan disease. Brain Res, 2008, 1148: 1–14
Matalon R. Canavan disease: diagnosis and molecular analysis. Genet Test, 1997, 1: 21–25
Rajasekaran R, Sudandiradoss C, Doss C G, et al. Identification and in silico analysis of functional SNPs of the BRCA1 gene. Genomics, 2007, 90: 447–452
Rajasekaran R, Priya Doss C G, Sudandiradoss C, et al. In silico analysis of structural and functional consequences in p16INK4A by deleterious nsSNPs associated CDKN2A gene in malignant melanoma. Biochimie, 2008, 90: 1523–1529
Rajasekaran R, Sethumadhavan R. Application of molecular mechanics and molecular dynamic for investigating the detrimental missense mutations in tumour suppressor protein SMAD4. J Bionanosci, 2009, 3: 80–87
Yip Y L, Scheib H, Diemand A V, et al. The Swiss-Prot variant page and the ModSNP database: a resource for sequence and structure information on human protein variants. Hum Mutat, 2004, 23: 464–470
Yip Y L, Famiglietti M, Gos A, et al. Annotating single amino acid polymorphisms in the UniProt/Swiss-Prot knowledgebase. Hum Mutat, 2008, 29: 361–366
Boeckmann B, Bairoch A, Apweiler R, et al The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res, 2003, 31: 365–370
Berman H M, Westbrook J, Feng Z, et al. The Protein Data Bank. Nucleic Acids Res, 2000, 28: 235–242
Capriotti E, Fariselli P, Casadio R. I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure. Nucleic Acids Res, 2005, 33: 306–310
Bava K A, Gromiha M M, Uedaira H, et al. ProTherm, version 4.0: thermodynamic database for proteins and mutants. Nucleic Acids Res, 2004, 32: 120–121
Ng P C, Henikoff S. SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Res, 2003, 31: 3812–3814
Ng P C, Henikoff S. Predicting deleterious amino acid substitutions. Genome Res, 2001, 11: 863–874
Ramensky V, Bork P, Sunyaev S. Human non-synonymous SNPs: server and survey. Nucleic Acids Res, 2002, 30: 3894–3900
Cavallo A, Martin A C. Mapping SNPs to protein sequence and structure data. Bioinformatics, 2005, 21: 1443–1450
Lindahl E, Azuara C, Koehl P, et al. NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis. Nucleic acids Res, 2006, 34: 52–56
Delarue M, Dumas P. On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models. Proc Natl Acad Sci USA, 2004, 101: 6957–6962
Sharma S, Ding F, Nie H, et al. iFold: a platform for interactive folding simulation of proteins. Bioinformatics, 2006, 22: 2693–2694
Han J H, Kerrison N, Chothia C, et al. Divergence of interdomain geometry in two-domain proteins. Structure, 2006, 14: 935–945
Varfolomeev S D, Uporov I V, Fedorov E V. Bioinformatics and molecular modeling in chemical enzymology. Active sites of hydrolases. Biochemistry (Mosc), 2002, 67: 1099–1108
Leach A R. Molecular Modeling: Principles and Applications. 2nd ed. Sussex: Pearson Education EMA, 2001
Chou K C, Carlacci L. Simulated annealing approach to the study of protein structures. Protein Eng, 1991, 4: 661–667
Magyar C, Gromiha M M, Pujadas G, et al. SRide: a server for identifying stabilizing residues in proteins, Nucleic Acids Res, 2005, 33: W303–W305
Lo’pez G, Valencia A, Tress M L. Firestar-prediction of functionally important residues using structural templates and alignment reliability. Nucleic Acids Res, 2007, 35: 573–577
Feldman H J, Synder K A, Ticoll A, et al. A complete small molecule dataset from the protein data bank. FEBS Lett, 2006, 580: 1649–1653
Duhovny D, Nussinov R, Wolfson H J. Efficient unbound docking of rigid molecules. In: Proceedings of the 2nd Workshop on Algorithms in Bioinformatics (WABI) Lecture Notes in Computer Science, Rome, Italy, 2002. 2452: 185–200
Connolly M L. Solvent-accessible surfaces of proteins and nucleic acids. Science, 1983, 221: 709–713
Schneidman-Duhovny D, Inbar Y, Nussinov R, et al. PatchDock and SymmDock: servers for rigid and symmetric docking. Nucleic Acids Res, 2005, 33: 363–367
Zhang C, Vasmatzis G, Cornette J L, et al. Determination of atomic desolvation energies from the structures of crystallized proteins. J Mol Biol, 1997, 267: 707–726
Yuan Z, Bailey T L, Teasdale R D. Prediction of protein B-factor profiles. Proteins, 2005, 58: 905–912
Ringe D, Petsko G A. Study of protein dynamics by X-ray diffraction. Methods Enzymol, 1986, 131: 389–433
Parthasarathy S, Murthy M R. Protein thermal stability: insights from atomic displacement parameters (B values). Protein Eng, 2000, 13: 9–13
Carlson H A, McCammon J A. Accommodating protein flexibility in computational drug design. Mol Pharmacol, 2000, 57: 213–218
Hinkle A, Tobacman L S. Folding and function of the troponin tail domain, effects of cardiomyopathic troponin T mutations. J Biol Chem, 2003, 278: 506–513
Suhre K, Sanejouand Y H. ElNe’mo: a normal mode web-server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Res, 2004, 32: 610–614
Teng S, Madej T, Panchenko A, et al. Modeling effects of human single nucleotide polymorphisms on protein-protein interactions. Biophys J, 2009, 96: 2178–2188
Elepeleg O N, Shaag A. The spectrum of mutations of the aspartoacylase gene in Canavan disease in Non-Jewish patients. J Inher Metab Dis, 1999, 22: 531–534
Hussain R, Daud S, Kakar N. A missense mutation (p.G274R) in gene ASPA causes Canavan disease in a Pakistani family. Mol Bio Rep, 2012, 39: 6197–6201
Sistermans E A, de Coo R F, van Beerendonk H M, et al. Mutation detection in the aspartoacylase gene in 17 patients with Canavan disease: four new mutations in the non-Jewish population. J Hum Genet, 2000, 8: 557–560
Olsen T R, Tranebjaerg L, Kvittingen E A, et al. Two novel aspartoacylase gene (ASPA) missense mutations specific to Norwegian and Swedish patients with Canavan disease. J Med Genet, 2002, 39: E55
Kaul R, Gao G P, Balamurugan K, et al. Cloning of the human aspartoacylase cDNA and a common missense mutation in Canavan disease. Nat Genet, 1993, 5: 118–123
Moore R A, Le Coq J, Faehnle C R. Purification and preliminary characterization of brain aspartoacylase. Arch Biochem Biophys, 2003, 413: 1–8
Kaul R, Gao G P, Aloya M. Canavan disease: mutations among Jewish and non-Jewish patients. Am J Hum Genet, 1994, 55: 34–41
Kumar P, Henikoff S, Ng P C. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc, 2009, 4: 1073–1081
Capriotti E, Fariselli P, Rossi I, et al. A three-state prediction of single point mutations on protein stability changes. BMC Bioinformatics, 2008, 9: S6
Adzhubei I A, Schmidt S, Peshkin L, et al. A method and server for predicting damaging missense mutations. Nat Methods, 2010, 7: 248–249
Author information
Authors and Affiliations
Corresponding authors
Additional information
This article is published with open access at Springerlink.com
Rights and permissions
Open Access This article is distributed under the terms of the Creative Commons Attribution 2.0 International License (https://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
About this article
Cite this article
Sreevishnupriya, K., Chandrasekaran, P., Senthilkumar, A. et al. Computational analysis of deleterious missense mutations in aspartoacylase that cause Canavan’s disease. Sci. China Life Sci. 55, 1109–1119 (2012). https://doi.org/10.1007/s11427-012-4406-8
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11427-012-4406-8