Protein aggregation due to nsSNP resulting in P56S VABP protein is associated with amyotrophic lateral sclerosis

Journal of Theoretical Biology

Volumn 354, Issue , 2014, Pages 72-80

  Vinay Kumar, Chundi ^a   Kumar, K M ^a   Swetha, Rayapadi ^a   Ramaiah, Sudha ^a   Anbarasu, Anand ^a  

^a VIT UNIVERSITY   (India)

Author keywords

ALS; Molecular dynamics simulation; SNP analysis; VAPB protein

Indexed keywords

PROTEIN IRE1; SYNAPTOBREVIN; X BOX BINDING PROTEIN 1; KCNIP1 PROTEIN, HUMAN; KV CHANNEL INTERACTING PROTEIN;

AGGREGATION; CHROMOSOME; CYTOGENETICS; MEMBRANE; MUTATION; PROTEIN;

AMYOTROPHIC LATERAL SCLEROSIS; ARTICLE; CYTOGENETICS; DISEASE ASSOCIATION; ENDOPLASMIC RETICULUM; GENE; GENE FUNCTION; GENE MUTATION; HUMAN; MOLECULAR DYNAMICS; NONSYNONYMOUS SINGLE NUCLEOTIDE POLYMORPHISM; PRIORITY JOURNAL; PROTEIN AGGREGATION; PROTEIN FUNCTION; PROTEIN STABILITY; PROTEIN STRUCTURE; SIGNAL TRANSDUCTION; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM; UNFOLDED PROTEIN RESPONSE; VABP GENE; AMINO ACID SUBSTITUTION; CHEMISTRY; GENETICS; INFORMATION PROCESSING; METABOLISM; MISSENSE MUTATION; PROTEINOSIS;

AMINO ACID SUBSTITUTION; AMYOTROPHIC LATERAL SCLEROSIS; DATASETS AS TOPIC; HUMANS; KV CHANNEL-INTERACTING PROTEINS; MOLECULAR DYNAMICS SIMULATION; MUTATION, MISSENSE; POLYMORPHISM, SINGLE NUCLEOTIDE; PROTEIN AGGREGATION, PATHOLOGICAL; UNFOLDED PROTEIN RESPONSE;

EID: 84897934338     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2014.03.027     Document Type: Article

References (54)

1. Adzhubei A., Schmidt S., Peshkin L., Ramensky V.E., Gerasimova A., Bork P., Kondrashov A.S., Sunyaev S.R. A method and server for predicting damaging missense mutations. Nat. Methods 2010, 7(4):248-249.
2. Amadei A., Linssen A.B.M., Berendsen H.J.C. Essential dynamics of proteins. Proteins 1993, 17(4):412-425.
3. Amberger J., Bocchini C.A., Scott A.F., Hamosh A., McKusick's Online Mendelian Inheritance in Man (OMIM). Nucleic Acids Res. 2009, 37(5):793-796.
4. Anbarasu A., Kundu A. Influence of SMAD1 gene in osteoporosis: a bioinformatics approach. Open Access Bioinform. 2010, 2:79-87.
5. Anbarasu A., Kundu A. Leucine to Proline substitution by SNP at position 197 in Caspase9 gene expression leads to neuroblastoma: a bioinformatics analysis. Interdiscip. Sci. 2012, 4(2):225-234.
6. Beleza-Meireles A., Al-Chalabi A. Genetic studies of amyotrophic lateral sclerosis: controversies and perspectives. Amyotroph. Lateral Scler. 2009, 10(1):1-14.
7. Berendsen H.J.C., Postma J.P.M., Gunsteren W.F.V., Hermans J. Interaction models for water in relation to protein hydration. Intermolecular forces 1981, 331-342. D. Riedel Publishing Company, Dordrecht, The Netherlands. B. Pullman (Ed.).
8. Bruijn L.I., Miller T.M., Cleveland D.W. Unraveling the mechanisms involved in motor neuron degeneration in ALS. Annu. Rev. Neurosci. 2004, 27:723-749.
9. Calabrese R., Capriotti E., Fariselli P., Martelli P.L., Casadio R. Functional annotations improve the predictive score of human disease-related mutations in proteins. Hum. Mutat. 2009, 30(8):1237-1244.
10. Capriotti E., Fariselli P., Rossi I., Casadio R. A three state prediction of single point mutations on protein stability changes. BMC Bioinform. 2008, 9(2):S6.
11. Capriotti E., Calabrese R., Casadio R Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information. Bioinformatics 2006, 22(22):2729-2734.
12. Carvalho M., Pino M.A., Karchin R., Beddor J., Godinho-Netto M., Mesquita R.D., Rodarte R.S., Vaz D.C., Monteiro V.A., Manoukian S., Colombo M., Ripamonti C.B., Rosenquist R., Suthers G., Borg A., Radice P., Grist S.A., Monteiro A.N., Billack B. Analysis of a set of missense, frameshift, and in-frame deletion variants of BRCA1. Mutat. Res. 2009, 660(1-2):1-11.
13. Carvalho M.A., Marsillac S.M., Karchin R., Manoukian S., Grist S., Swaby R.F., Urmenyi T.P., Rondinelli E., Silva R., Gayol L., Baumbach L., Sutphen R., Pickard-Brzosowicz J.L., Nathanson K.L., Sali A., Goldgar D., Couch F.J., Radice P., Monteiro A.N. Determination of cancer risk associated with germ line BRCA1 missense variants by functional analysis. Cancer Res. 2007, 67(4):1494-1501.
14. De Vos K.J., Morotz G.M., Stoica R., Tudor E.L., Lau K.F., Ackerly S., Warley A., Shaw C.E., Miller C.C. VAPB interacts with the mitochondrial protein PTPIP51 to regulate calcium homeostasis. Hum. Mol. Genet. 2012, 21(6):1299-1311.
15. Dixit A, Torkamani A., Schork N.J., Verkhivker G. Computational modeling of structurally conserved cancer mutations in the RET and MET kinase: the impact on protein structure, dynamics and stability. Biophys. J. 2009, 96(3):858-874.
16. Essmann U., Perera L., Berkowitz M.L., Darden T., Lee H., Pedersen L.G. A smooth particle mesh Ewald method. J. Chem. Phys. 1995, 103(19):8577-8593.
17. Gkogkas C., Middleton S., Kremer A.M., Wardrope C., Hannah M., Gillingwater T.H., Skehel P. VAPB interacts with and modulates the activity of ATF6. Hum. Mol. Genet. 2008, 17:1517-1526.
18. Goodall E.F., Morrison K.E. Amyotrophic lateral sclerosis (motor neuron disease): proposed mechanisms and pathways to treatment. Expert Rev. Mol. Med. 2006, 8(11):1-22.
19. Gunsteren W.F.V., Billeter S.R., Eising A.A., Hunenberger P.H., Kruger P.K., Mark A.E., Scott W.R.P., Tironi I.G. Biomolecular Simulation: The GROMOS96 Manual and User Guide 1996, 1-1024. Verlag der Fachvereine, ZUrich.
20. Guo J., Ning L., Ren H., Liu H., Yao X. Influence of the pathogenic mutations T188K/R/A on the structural stability and misfolding of human prion protein: Insight from molecular dynamics simulations. Biochim. Biophys. Acta 2012, 1820(2):116-123.
21. Hess B., Bekker H., Berendsen H.J., Cfraaije J.G.E.M. LINCS: a linear constraint solver for molecular simulations. J. Comput. Chem. 1997, 18(13):1463-1472.
22. Hess B., Kutzner C., Van der Spoel D., Lindahl E. GROMACS 4:algorithms for highly efficient, load-balanced, and scalable molecular simulation. J. Chem. Theory Comput. 2008, 4(3):435-447.
23. Hicks S., Wheeler D.A., Plon S.E., Kimmel M. Prediction of missense mutation functionality depends on both the algorithm and sequence alignment employed. Hum. Mutat. 2011, 32(6):661-668.
24. Kanekura K., Nishimoto I., Aiso S., Matsuoka M. Characterization of amyotrophic lateral sclerosis-linked P56S mutation of vesicle-associated membrane protein-associated protein B (VAPB/ALS8). J. Biol. Chem. 2006, 281(40):30223-30233.
25. Kanekura K., Suzuki H., Aiso S., Matsuoka M. ER Stress and unfolded protein response in amyotrophic lateral sclerosis. Mol. Neurobiol. 2009, 39(2):81-89.
26. Klose D.P., Wallace B.A., Robert W., Janes 2Struc: the secondary structure server. Bioinformatics 2010, 26(20):2624-2625.
27. 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(7):1073-1081.
28. Kundu A., Anbarasu A. Analysis of single nuceleotide polymorphisms of collagen type I alpha 1 gene associated with osteoporosis: an in-silico study. J. OMICS Res. 2011, 1(1):32-40.
29. Kundu A., Anbarasu A. Computational study of ADD1 gene polymorphism associated with hypertension. Cell Biochem. Biophys. 2013, 65(1):13-19.
30. Kundu A., Bag S., Ramaish S., Anbarasu A. Leucine to Proline substitution by SNP at position 197 in Caspase9 gene expression leads to neuroblastoma: a bioinformatics analysis. 3 Biotech 2013, 3:225-234.
31. Kundu A., Ramaiah S., Anbarasu A. Mutation in Angiotensin II type 1 receptor disrupts its binding to Angiotensin II leading to hypotension: an insight into hydrogen bonding patterns. Front. Biol. 2012, 7(5):447-484.
32. Kundu A., Ramakrishnan P., Rajendran A., Dharwar N.V., Anbarasu A. Analysis of non-synonymous single-nucleotide polymorphisms and population variability of PLD2 gene associated with hypertension. Int. J. Bioinform. Res. Appl. 2013, 9(3):227-241.
33. Landers J.E., Leclerc A.L., Shi L., Virkud A., Cho T., Maxwell M.M., Henry A.F., Polak M., Glass J.D., Kwiatkowski T.J., Al-Chalabi A., Shaw C.E., Leigh P.N., Rodriguez-Leyza I., McKenna-Yasek D., Sapp P.C., Brown R.H. New VAPB deletion variant and exclusion of VAPB mutations in familial ALS. Neurology 2008, 70(14):1179-1185.
34. Li B., Krishnan V.G., Mort M.E., Xin F., Kamati K.K., Cooper D.N., Mooney S.D., Radivojac P. Automated inference of molecular mechanisms of disease from amino acid substitutions. Bioinformatics 2009, 25(21):2744-2750.
35. Mitne-Neto M., Ramos C.R., Pimenta D.C., Luz J.S., Nishimura A.L., Gonzales F.A., Oliveria C.C., Zatz M. A mutation in human VAP-B-MSP domain, present in ALS patients, affects the interaction with other cellular proteins. Protein Expr. Purif. 2007, 55(1):139-146.
36. Nishimura A.L., Mitne-Neto M., Silva H.C., Richieri-Costa A., Middleton S., Cascio D., Kok F., Oliveira J.R., Gillingwater T., Webb J., Skehel P., Zatz M. A mutation in the vesicle-trafficking protein VAPB causes late-onset spinal muscular atrophy and amyotrophic lateral sclerosis. Am. J. Hum. Genet. 2004, 75(5):822-831.
37. Nishimura Y., Hayashi M., Inada H., Tanaka T. Molecular cloning and characterization of mammalian homologues of vesicle-associated membrane protein-associated [VAMP-associated] proteins. Biochem. Biophys. Res. Commun. 1999, 254(1):21-26.
38. Oostenbrink C., Villa A., Mark A.E., Gunsteren W.F.V. A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6. J. Comput. Chem. 2004, 25(13):1656-1676.
39. Pasinelli P., Brown R.H. Molecular biology of amyotrophic lateral sclerosis: insights from genetics. Nat. Rev. Neurosci. 2006, 7(9):710-723.
40. Prosser D.C., Tran D., Gougeon P.Y., Verly C., Ngsee J.K. FFAT rescues VAPA-mediated inhibition of ER-to-Golgi transport and VAPB-mediated ER aggregation. J. Cell Sci. 2008, 121(9):3052-3061.
41. Ratnaparkhi A., Lawless G.M., Schweizer F.E., Golshani P., Jackson G.R. A Drosophila model of ALS: human ALS-associated mutation in VAP33A suggests a dominant negative mechanism. PLoS One 2008, 3(6):e2334.
42. Rowland L.P., Shneider N.A. Amyotrophic lateral sclerosis. N. Engl. J. Med. 2001, 3:1688-1700.
43. Sherry S.T., Ward M.H., Kholodov M., Baker J., Phan L., Smigielski E.M., Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001, 29(1):308-311.
44. Shixiong, L., 2012, Structure and Function Studies of Vesicles-associated Membrane Protein Associated Protein B Associated With Amyotrophic Lateral Sclerosis (Thesis), National University of Singapore.
45. Skehel P.A., Fabian-Fine R., Kandel E.R. Mouse VAP33 is associated with the endoplasmic reticulum and microtubules. Proc. Natl. Acad. Sci. USA 2000, 97(3):1101-1106.
46. Skehel P.A., Martin K.C., Kandel E.R., Bartsch D. A VAMP-binding protein from Aplysia required for neurotransmitter release. Science 1995, 269(5230):1580-1583.
47. Suzuki H., Kanekura K., Levine T.P., Kohno K., Olkkonen V.M., Aiso A., Matsuoka M. ALS-linked P56S-VAPB, an aggregated loss-of-function mutant of VAPB, predisposes motor neurons to ER stress-related death by inducing aggregation of co-expressed wild-type VAPB. J. Neurochem. 2009, 108(4):973-985.
48. Teuling E., Ahmed S., Haasdijk E., Demmers J., Steinmetz M.O., Akhmanova A., Jaarsma D., Hoogenraad C.C. Motor neuron disease-associated mutant vesicle-associated membrane protein associated-protein (VAP) B recruits wild-type VAPs into endoplasmic reticulum-derived tubular aggregates. J. Neurosci. 2007, 27(36):9801-9815.
49. Thusberg J., Vihinen M. Pathogenic or not? and if so, then how? Studying the effects of missense mutations using bioinformatics methods. Hum. Mutat. 2009, 30(5):703-714.
50. Tran, D., 2010, The ALS8-Associated P56S Mutation of VAPB Alters ER Morphology and ER Function (Thesis), University of Ottawa.
51. Turner, P.J., 2005, XMGRACE, Version 5.1.19. central for costal and Land-Margin Research; Oregon Graduate Institute of Science and Technology. Beaverton, ORE, USA.
52. Van Der Spoel, Lindahl D., Hess E., Groenhof B., Mark G., Berendsen A.E GROMACS: fast flexible, and free. J. Comput. Chem. 2005, 26(16):1701-1718.
53. Wu X., Yang G., Zu Y., Fu Y., Zhou L., Yuan X. The Trp-cage miniprotein with single-site mutations: studies of stability and dynamics using molecular dynamics. Comput. Theor. Chem. 2011, 973(1-3):1-8.
54. Zhang K.H., Li Z., Lei J., Pang T., Xu B., Jiang W.Y., Li H.Y. Oculocutaneous Albinism type 3 (OCA3): analysis of two novel mutations in TYRP1 gene in two Chinese patients. Cell Biochem. Biophys. 2011, 61(3):523-529.