Phylogenetic and in silico structural analysis of the Parkinson disease-related kinase PINK1

Human Mutation

Volumn 32, Issue 4, 2011, Pages 369-378

  Cardona, Fernando ^a,b   Sánchez Mut, Jose Vicente ^a   Dopazo, Hernán ^c   Pérez Tur, Jordi ^a,b  

^a INSTITUTO DE BIOMEDICINA DE VALENCIA   (Spain)

^b Centro de Investigación Príncipe Felipe ^*

^c BELLVITGE BIOMEDICAL RESEARCH INSTITUTE IDIBELL   (Spain)

Author keywords

CaMKI; CaMKII; DMPK; Kinase; Parkinson disease; Pathogenic mutations; Phylogeny; PINK1; Structure

Indexed keywords

AMINO ACID; MYOTONIC DYSTROPHY PROTEIN KINASE; PROTEIN KINASE; PTEN INDUCED KINASE 1; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; COMPUTER MODEL; ENZYME ACTIVITY; GENE MUTATION; GENETIC CONSERVATION; MOLECULAR EVOLUTION; MOLECULAR MODEL; MOLECULAR PHYLOGENY; NUCLEOTIDE SEQUENCE; PARKINSON DISEASE; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

BASE SEQUENCE; HUMANS; MOLECULAR SEQUENCE DATA; PARKINSON DISEASE; PHYLOGENY; PROTEIN CONFORMATION; PROTEIN KINASES; SEQUENCE ALIGNMENT;

EID: 79952770919     PISSN: 10597794     EISSN: 10981004     Source Type: Journal    
DOI: 10.1002/humu.21444     Document Type: Article

References (53)

1. Arbiza L, Duchi S, Montaner D, Burguet J, Pantoja-Uceda D, Pineda-Lucena A, Dopazo J, Dopazo H. 2006. Selective pressures at a codon-level predict deleterious mutations in human disease genes. J Mol Biol 358:1390-1404.
2. Bajaj K, Madhusudhan MS, Adkar BV, Chakrabarti P, Ramakrishnan C, Sali A, Varadarajan R. 2007. Stereochemical criteria for prediction of the effects of proline mutations on protein stability. PLoS Comput Biol 3:e241.
3. Beilina A, Van Der Brug M, Ahmad R, Kesavapany S, Miller DW, Petsko GA, Cookson MR. 2005. Mutations in PTEN-induced putative kinase 1 associated with recessive parkinsonism have differential effects on protein stability. Proc Natl Acad Sci USA 102:5703-5708.
4. 2+/calmodulin-dependent protein kinase II, improves recovery of cardiac function in the globally ischemic heart. Mol Cell Biochem 259:35-42.
5. Bonifati V, Rohe CF, Breedveld GJ, Fabrizio E, De Mari M, Tassorelli C, Tavella A, Marconi R, Nicholl DJ, Chien HF, Fincati E, Abbruzzese G, Marini P, De Gaetano A, Horstink MW, Maat-Kievit JA, Sampaio C, Antonini A, Stocchi F, Montagna P, Toni V, Guidi M, Dalla Libera A, Tinazzi M, De Pandis F, Fabbrini G, Goldwurm S, de Klein A, Barbosa E, Lopiano L, Martignoni E, Lamberti P, Vanacore N, Meco G, Oostra BA; Italian Parkinson Genetics Network. 2005. Early-onset parkinsonism associated with PINK1 mutations: frequency, genotypes, and phenotypes. Neurology 65:87-95.
6. Capriotti E, Fariselli P, Casadio R. 2005. I-Mutant 2.0: predicting stability changes upon mutation from the protein sequence or structure. Nucleic Acids Res 33:W306-W310.
7. Castresana J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17:540-552.
8. Castrignano T, De Meo PD, Cozzetto D, Talamo IG, Tramontano A. 2006. The PMDB Protein Model Database. Nucleic Acids Res 34:D306-D309.
9. Cheng J, Randall A, Baldi P. 2006. Prediction of protein stability changes for single-site mutations using support vector machines. Proteins 62:1125-1132.
10. Cipolletta E, Monaco S, Maione AS, Vitiello L, Campiglia P, Pastore L, Franchini C, Novellino E, Limongelli V, Bayer KU, Means AR, Rossi G, Trimarco B, Iaccarino G, Illario M. 2010. Calmodulin-dependent kinase II mediates vascular smooth muscle cell proliferation and is potentiated by extracellular signal regulated kinase. Endocrinology 151:2747-2759.
11. de Rijk MC, Launer LJ, Berger K, Breteler MM, Dartigues JF, Baldereschi M, Fratiglioni L, Lobo A, Martinez-Lage J, Trenkwalder C, Hofman A. 2000. Prevalence of Parkinson's disease in Europe: a collaborative study of population-based cohorts. Neurologic Diseases in the Elderly Research Group. Neurology 54(Suppl 5):S21-S23.
12. de Vries SJ, van Dijk M, Bonvin AM. 2010. The HADDOCK web server for data-driven biomolecular docking. Nat Protoc 5:883-897.
13. Deas E, Plun-Favreau H, Wood NW. 2009. PINK1 function in health and disease. EMBO Mol Med 1:152-165.
14. Do CB, Mahabhashyam MS, Brudno M, Batzoglou S. 2005. ProbCons: probabilistic consistency-based multiple sequence alignment. Genome Res 15:330-340.
15. Dubey S, Idicula-Thomas S, Anwaruddin M, Saravanan C, Varma RR, Maitra A. 2009. A novel 9-bp insertion detected in steroid 21-hydroxylase gene (CYP21A2): prediction of its structural and functional implications by computational methods. J Biomed Sci 16:3.
16. Eswar N, Eramian D, Webb B, Shen MY, Sali A. 2008. Protein structure modeling with MODELLER. Methods Mol Biol 426:145-159.
17. Gandhi S, Wood-Kaczmar A, Yao Z, Plun-Favreau H, Deas E, Klupsch K, Downward J, Latchman DS, Tabrizi SJ, Wood NW, Duchen MR, Abramov AY. 2009. PINK1-associated Parkinson's disease is caused by neuronal vulnerability to calcium-induced cell death. Mol Cell 33:627-638.
18. Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD, Bairoch A. 2003. ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res 31:3784-3788.
19. Geisler S, Holmstrom KM, Skujat D, Fiesel FC, Rothfuss OC, Kahle PJ, Springer W. 2010a. PINK1/Parkin-mediated mitophagy is dependent on VDAC1 and p62/SQSTM1. Nat Cell Biol 12:119-131.
20. Geisler S, Holmstrom KM, Treis A, Skujat D, Weber SS, Fiesel FC, Kahle PJ, Springer W. 2010b. The PINK1/Parkin-mediated mitophagy is compromised by PD-associated mutations. Autophagy 6:871-878.
21. Giese KP, Fedorov NB, Filipkowski RK, Silva AJ. 1998. Autophosphorylation at Thr286 of the alpha calcium-calmodulin kinase II in LTP and learning. Science 279:870-873.
22. Gu X, Vander Velden K. 2002. DIVERGE: phylogeny-based analysis for functional-structural divergence of a protein family. Bioinformatics 18:500-501.
23. Guindon S, Lethiec F, Duroux P, Gascuel O. 2005. PHYML Online-a web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Res 33:W557-W559.
24. Hanks SK, Hunter T. 1995. Protein kinases 6. The eukaryotic protein kinase superfamily: kinase (catalytic) domain structure and classification. FASEB J 9:576-596.
25. Ibanez P, Lesage S, Lohmann E, Thobois S, De Michele G, Borg M, Agid Y, Durr A, Brice A. 2006. Mutational analysis of the PINK1 gene in early-onset parkinsonism in Europe and North Africa. Brain 129(Pt 3):686-694.
26. Kim Y, Park J, Kim S, Song S, Kwon SK, Lee SH, Kitada T, Kim JM, Chung J. 2008. PINK1 controls mitochondrial localization of Parkin through direct phosphorylation. Biochem Biophys Res Commun 377:975-980.
27. Kumazawa R, Tomiyama H, Li Y, Imamichi Y, Funayama M, Yoshino H, Yokochi F, Fukusako T, Takehisa Y, Kashihara K, Kondo T, Elibol B, Bostantjopoulou S, Toda T, Takahashi H, Yoshii F, Mizuno Y, Hattori N. 2008. Mutation analysis of the PINK1 gene in 391 patients with Parkinson disease. Arch Neurol 65:802-808.
28. Kuntal BK, Aparoy P, Reddanna P. 2010. EasyModeller: a graphical interface to MODELLER. BMC Res Notes 3:226.
29. Kwiek NC, Thacker DF, Haystead TA. 2007. Dual kinase-mediated regulation of PITK by CaMKII and GSK3. Cell Signal 19:593-599.
30. Lein ES, Hawrylycz MJ, Ao N, Ayres M, Bensinger A, Bernard A, Boe AF, Boguski MS, Brockway KS, Byrnes EJ, Chen L, Chen L, Chen TM, Chin MC, Chong J, Crook BE, Czaplinska A, Dang CN, Datta S, Dee NR, Desaki AL, Desta T, Diep E, Dolbeare TA, Donelan MJ, Dong HW, Dougherty JG, Duncan BJ, Ebbert AJ, Eichele G, Estin LK, Faber C, Facer BA, Fields R, Fischer SR, Fliss TP, Frensley C, Gates SN, Glattfelder KJ, Halverson KR, Hart MR, Hohmann JG, Howell MP, Jeung DP, Johnson RA, Karr PT, Kawal R, Kidney JM, Knapik RH, Kuan CL, Lake JH, Laramee AR, Larsen KD, Lau C, Lemon TA, Liang AJ, Liu Y, Luong LT, Michaels J, Morgan JJ, Morgan RJ, Mortrud MT, Mosqueda NF, Ng LL, Ng R, Orta GJ, Overly CC, Pak TH, Parry SE, Pathak SD, Pearson OC, Puchalski RB, Riley ZL, Rockett HR, Rowland SA, Royall JJ, Ruiz MJ, Sarno NR, Schaffnit K, Shapovalova NV, Sivisay T, Slaughterbeck CR, Smith SC, Smith KA, Smith BI, Sodt AJ, Stewart NN, Stumpf KR, Sunkin SM, Sutram M, Tam A, Teemer CD, Thaller C, Thompson CL, Varnam LR, Visel A, Whitlock RM, Wohnoutka PE, Wolkey CK, Wong VY, Wood M, Yaylaoglu MB, Young RC, Youngstrom BL, Yuan XF, Zhang B, Zwingman TA, Jones AR. 2007. Genome-wide atlas of gene expression in the adult mouse brain. Nature 445:168-176.
31. Lesage S, Brice A. 2009. Parkinson's disease: from monogenic forms to genetic susceptibility factors. Hum Mol Genet 18:R48-R59.
32. Lu J, Wu DM, Hu B, Zheng YL, Zhang ZF, Wang YJ. 2010. NGF-Dependent activation of TrkA pathway: a mechanism for the neuroprotective effect of troxerutin in D-galactose-treated mice. Brain Pathol 20:952-965.
33. Majewski J, Ott J. 2003. Amino acid substitutions in the human genome: evolutionary implications of single nucleotide polymorphisms. Gene 305:167-173.
34. Matsuda N, Sato S, Shiba K, Okatsu K, Saisho K, Gautier CA, Sou YS, Saiki S, Kawajiri S, Sato F, Kimura M, Komatsu M, Hattori N, Tanaka K. 2010. PINK1 stabilized by mitochondrial depolarization recruits Parkin to damaged mitochondria and activates latent Parkin for mitophagy. J Cell Biol 189:211-221.
35. Mi H, Dong Q, Muruganujan A, Gaudet P, Lewis S, Thomas PD. 2010. PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. Nucleic Acids Res 38:D204-D210.
36. Mills RD, Sim CH, Mok SS, Mulhern TD, Culvenor JG, Cheng HC. 2008. Biochemical aspects of the neuroprotective mechanism of PTEN-induced kinase-1 (PINK1). J Neurochem 105:18-33.
37. Narendra DP, Jin SM, Tanaka A, Suen DF, Gautier CA, Shen J, Cookson MR, Youle RJ. 2010. PINK1 is selectively stabilized on impaired mitochondria to activate Parkin. PLoS Biol 8:e1000298.
38. Ng PC, Henikoff S. 2003. SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res 31:3812-3814.
39. Ramirez A, Heimbach A, Grundemann J, Stiller B, Hampshire D, Cid LP, Goebel I, Mubaidin AF, Wriekat AL, Roeper J and others. 2006. Hereditary parkinsonism with dementia is caused by mutations in ATP13A2, encoding a lysosomal type 5 P-type ATPase. Nat Genet 38:1184-1191.
40. Rogaeva E, Johnson J, Lang AE, Gulick C, Gwinn-Hardy K, Kawarai T, Sato C, Morgan A, Werner J, Nussbaum R, Petit A, Okun MS, McInerney A, Mandel R, Groen JL, Fernandez HH, Postuma R, Foote KD, Salehi-Rad S, Liang Y, Reimsnider S, Tandon A, Hardy J, St George-Hyslop P, Singleton AB. 2004. Analysis of the PINK1 gene in a large cohort of cases with Parkinson disease. Arch Neurol 61:1898-1904.
41. Ronquist F, Huelsenbeck JP. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.
42. Silvestri L, Caputo V, Bellacchio E, Atorino L, Dallapiccola B, Valente EM, Casari G. 2005. Mitochondrial import and enzymatic activity of PINK1 mutants associated to recessive parkinsonism. Hum Mol Genet 14:3477-3492.
43. Sim CH, Lio DS, Mok SS, Masters CL, Hill AF, Culvenor JG, Cheng HC. 2006. C-terminal truncation and Parkinson's disease-associated mutations down-regulate the protein serine/threonine kinase activity of PTEN-induced kinase-1. Hum Mol Genet 15:3251-3262.
44. Tamura K, Dudley J, Nei M, Kumar S. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596-1599.
45. Tan EK, Skipper LM. 2007. Pathogenic mutations in Parkinson disease. Hum Mutat 28:641-653.
46. Tarraga J, Medina I, Arbiza L, Huerta-Cepas J, Gabaldon T, Dopazo J, Dopazo H. 2007. Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics. Nucleic Acids Res 35:W38-W42.
47. Valente EM, Salvi S, Ialongo T, Marongiu R, Elia AE, Caputo V, Romito L, Albanese A, Dallapiccola B, Bentivoglio AR. 2004. PINK1 mutations are associated with sporadic early-onset parkinsonism. Ann Neurol 56:336-341.
48. van der Ven PF, Jansen G, van Kuppevelt TH, Perryman MB, Lupa M, Dunne PW, ter Laak HJ, Jap PH, Veerkamp JH, Epstein HF, Wieringa B. 1993. Myotonic dystrophy kinase is a component of neuromuscular junctions. Hum Mol Genet 2:1889-1894.
49. Vives-Bauza C, Zhou C, Huang Y, Cui M, de Vries RL, Kim J, May J, Tocilescu MA, Liu W, Ko HS, Magrané J, Moore DJ, Dawson VL, Grailhe R, Dawson TM, Li C, Tieu K, Przedborski S. 2010. PINK1-dependent recruitment of Parkin to mitochondria in mitophagy. Proc Natl Acad Sci USA 107:378-383.
50. Wang WY, Hao LY, Minobe E, Saud ZA, Han DY, Kameyama M. 2009. CaMKII phosphorylates a threonine residue in the C-terminal tail of Cav1.2 Ca(2+) channel and modulates the interaction of the channel with calmodulin. J Physiol Sci 59:283-290.
51. Wayman GA, Lee YS, Tokumitsu H, Silva AJ, Soderling TR. 2008. Calmodulin-kinases: modulators of neuronal development and plasticity. Neuron 59:914-931.
52. Xue Y, Liu Z, Cao J, Ma Q, Gao X, Wang Q, Jin C, Zhou Y, Wen L, Ren J. 2010. GPS 2.1: enhanced prediction of kinase-specific phosphorylation sites with an algorithm of motif length selection. Protein Eng Des Sel.
53. Zhou C, Huang Y, Shao Y, May J, Prou D, Perier C, Dauer W, Schon EA, Przedborski S. 2008. The kinase domain of mitochondrial PINK1 faces the cytoplasm. Proc Natl Acad Sci USA 105:12022-12027.