-
1
-
-
84986512474
-
CHARMM: a program for macromolecular energy, minimization, and dynamics calculations
-
Brooks BR, Olafson REB, States DJ, Swaminathan S, Karplus M. 1983. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 4:187-217.
-
(1983)
J Comput Chem
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Olafson, R.E.B.2
States, D.J.3
Swaminathan, S.4
Karplus, M.5
-
2
-
-
84867219321
-
Motion of transfer RNA from the A/T state into the A-site using docking and simulations
-
Caulfield T, Devkota B. 2012. Motion of transfer RNA from the A/T state into the A-site using docking and simulations. Proteins 80:2489-2500.
-
(2012)
Proteins
, vol.80
, pp. 2489-2500
-
-
Caulfield, T.1
Devkota, B.2
-
3
-
-
80053383964
-
Molecular dynamics simulations of human DNA methyltransferase 3B with selective inhibitor nanaomycin A
-
Caulfield T, Medina-Franco JL. 2011. Molecular dynamics simulations of human DNA methyltransferase 3B with selective inhibitor nanaomycin A. J Struct Biol 176:185-191.
-
(2011)
J Struct Biol
, vol.176
, pp. 185-191
-
-
Caulfield, T.1
Medina-Franco, J.L.2
-
4
-
-
79957906053
-
Examinations of tRNA range of motion using simulations of cryo-EM microscopy and X-ray data
-
Caulfield TR, Devkota B, Rollins GC. 2011. Examinations of tRNA range of motion using simulations of cryo-EM microscopy and X-ray data. J Biophys 2011:219515.
-
(2011)
J Biophys
, vol.2011
, pp. 219515
-
-
Caulfield, T.R.1
Devkota, B.2
Rollins, G.C.3
-
5
-
-
84912127688
-
Phosphorylation by PINK1 releases the UBL domain and initializes the conformational opening of the E3 ubiquitin ligase Parkin
-
Caulfield TR, Fiesel FC, Moussaud-Lamodiere EL, Dourado DF, Flores SC, Springer W. 2014. Phosphorylation by PINK1 releases the UBL domain and initializes the conformational opening of the E3 ubiquitin ligase Parkin. PLoS Comput Biol 10:e1003935.
-
(2014)
PLoS Comput Biol
, vol.10
, pp. e1003935
-
-
Caulfield, T.R.1
Fiesel, F.C.2
Moussaud-Lamodiere, E.L.3
Dourado, D.F.4
Flores, S.C.5
Springer, W.6
-
6
-
-
79960649509
-
Autoregulation of Parkin activity through its ubiquitin-like domain
-
Chaugule VK, Burchell L, Barber KR, Sidhu A, Leslie SJ, Shaw GS, Walden H. 2011. Autoregulation of Parkin activity through its ubiquitin-like domain. EMBO J 30:2853-2867.
-
(2011)
EMBO J
, vol.30
, pp. 2853-2867
-
-
Chaugule, V.K.1
Burchell, L.2
Barber, K.R.3
Sidhu, A.4
Leslie, S.J.5
Shaw, G.S.6
Walden, H.7
-
7
-
-
14244271476
-
Molecular dynamics simulation of nucleic acids: successes, limitations and promise
-
Cheatham III TE, Young MA. 2001. Molecular dynamics simulation of nucleic acids: successes, limitations and promise. Biopolymers 56:232-256.
-
(2001)
Biopolymers
, vol.56
, pp. 232-256
-
-
III Cheatham, T.E.1
Young, M.A.2
-
8
-
-
79957517961
-
Parkin mediates apparent E2-independent monoubiquitination in vitro and contains an intrinsic activity that catalyzes polyubiquitination
-
Chew KC, Matsuda N, Saisho K, Lim GG, Chai C, Tan HM, Tanaka K, Lim KL. 2011. Parkin mediates apparent E2-independent monoubiquitination in vitro and contains an intrinsic activity that catalyzes polyubiquitination. PLoS One 6:e19720.
-
(2011)
PLoS One
, vol.6
, pp. e19720
-
-
Chew, K.C.1
Matsuda, N.2
Saisho, K.3
Lim, G.G.4
Chai, C.5
Tan, H.M.6
Tanaka, K.7
Lim, K.L.8
-
9
-
-
0344011981
-
RING finger 1 mutations in Parkin produce altered localization of the protein
-
Cookson MR, Lockhart PJ, McLendon C, O'Farrell C, Schlossmacher M, Farrer MJ. 2003. RING finger 1 mutations in Parkin produce altered localization of the protein. Hum Mol Genet 12:2957-2965.
-
(2003)
Hum Mol Genet
, vol.12
, pp. 2957-2965
-
-
Cookson, M.R.1
Lockhart, P.J.2
McLendon, C.3
O'Farrell, C.4
Schlossmacher, M.5
Farrer, M.J.6
-
10
-
-
84937730783
-
-
A second generation force field for the simulation of proteins and nucleic acids. PhD thesis, University of California, San Francisco, CA.
-
Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM Jr, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA. 1994. A second generation force field for the simulation of proteins and nucleic acids. PhD thesis, University of California, San Francisco, CA.
-
(1994)
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz Jr, K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
11
-
-
80054787664
-
What genetics tells us about the causes and mechanisms of Parkinson's disease
-
Corti O, Lesage S, Brice A. 2011. What genetics tells us about the causes and mechanisms of Parkinson's disease. Physiol Rev 91:1161-1218.
-
(2011)
Physiol Rev
, vol.91
, pp. 1161-1218
-
-
Corti, O.1
Lesage, S.2
Brice, A.3
-
12
-
-
84877727171
-
Parkin disease: a clinicopathologic entity?
-
Doherty KM, Silveira-Moriyama L, Parkkinen L, Healy DG, Farrell M, Mencacci NE, Ahmed Z, Brett FM, Hardy J, Quinn N, Counihan TJ, Lynch T, et al. 2013. Parkin disease: a clinicopathologic entity? JAMA Neurol 70:571-579.
-
(2013)
JAMA Neurol
, vol.70
, pp. 571-579
-
-
Doherty, K.M.1
Silveira-Moriyama, L.2
Parkkinen, L.3
Healy, D.G.4
Farrell, M.5
Mencacci, N.E.6
Ahmed, Z.7
Brett, F.M.8
Hardy, J.9
Quinn, N.10
Counihan, T.J.11
Lynch, T.12
-
13
-
-
84938664482
-
A multiscale approach to predicting affinity changes in protein-protein interfaces
-
Dourado DF, Flores SC. 2014. A multiscale approach to predicting affinity changes in protein-protein interfaces. Proteins 82:2681-2690.
-
(2014)
Proteins
, vol.82
, pp. 2681-2690
-
-
Dourado, D.F.1
Flores, S.C.2
-
14
-
-
0034848395
-
Lewy bodies and parkinsonism in families with parkin mutations
-
Farrer M, Chan P, Chen R, Tan L, Lincoln S, Hernandez D, Forno L, Gwinn-Hardy K, Petrucelli L, Hussey J, Singleton A, Tanner C, et al. 2001. Lewy bodies and parkinsonism in families with parkin mutations. Ann Neurol 50:293-300.
-
(2001)
Ann Neurol
, vol.50
, pp. 293-300
-
-
Farrer, M.1
Chan, P.2
Chen, R.3
Tan, L.4
Lincoln, S.5
Hernandez, D.6
Forno, L.7
Gwinn-Hardy, K.8
Petrucelli, L.9
Hussey, J.10
Singleton, A.11
Tanner, C.12
-
15
-
-
84906071009
-
A specific subset of E2 ubiquitin-conjugating enzymes regulate Parkin activation and mitophagy differently
-
Fiesel FC, Moussaud-Lamodiere EL, Ando M, Springer W. 2014. A specific subset of E2 ubiquitin-conjugating enzymes regulate Parkin activation and mitophagy differently. J Cell Sci 127:3488-3504.
-
(2014)
J Cell Sci
, vol.127
, pp. 3488-3504
-
-
Fiesel, F.C.1
Moussaud-Lamodiere, E.L.2
Ando, M.3
Springer, W.4
-
16
-
-
79960896331
-
Fast flexible modeling of macromolecular structure using internal coordinates
-
Flores S, Sherman M, Bruns C, Eastman P, Altman R. 2010. Fast flexible modeling of macromolecular structure using internal coordinates. IEEE Trans Comput Biol Bioinform 8:1247-1257.
-
(2010)
IEEE Trans Comput Biol Bioinform
, vol.8
, pp. 1247-1257
-
-
Flores, S.1
Sherman, M.2
Bruns, C.3
Eastman, P.4
Altman, R.5
-
17
-
-
79960896331
-
Fast flexible modeling of RNA structure using internal coordinates
-
Flores SC, Sherman MA, Bruns CM, Eastman P, Altman RB. 2011. Fast flexible modeling of RNA structure using internal coordinates. IEEE/ACM Trans Comput Biol Bioinform 8:1247-1257.
-
(2011)
IEEE/ACM Trans Comput Biol Bioinform
, vol.8
, pp. 1247-1257
-
-
Flores, S.C.1
Sherman, M.A.2
Bruns, C.M.3
Eastman, P.4
Altman, R.B.5
-
18
-
-
75949130828
-
PINK1/Parkin-mediated mitophagy is dependent on VDAC1 and p62/SQSTM1
-
Geisler S, Holmstrom KM, Skujat D, Fiesel FC, Rothfuss OC, Kahle PJ, Springer W. 2010. PINK1/Parkin-mediated mitophagy is dependent on VDAC1 and p62/SQSTM1. Nat Cell Biol 12:119-131.
-
(2010)
Nat Cell Biol
, vol.12
, pp. 119-131
-
-
Geisler, S.1
Holmstrom, K.M.2
Skujat, D.3
Fiesel, F.C.4
Rothfuss, O.C.5
Kahle, P.J.6
Springer, W.7
-
19
-
-
10744227945
-
The C289G and C418R missense mutations cause rapid sequestration of human Parkin into insoluble aggregates
-
Gu WJ, Corti O, Araujo F, Hampe C, Jacquier S, Lucking CB, Abbas N, Duyckaerts C, Rooney T, Pradier L, Ruberg M, Brice A. 2003. The C289G and C418R missense mutations cause rapid sequestration of human Parkin into insoluble aggregates. Neurobiol Dis 14:357-364.
-
(2003)
Neurobiol Dis
, vol.14
, pp. 357-364
-
-
Gu, W.J.1
Corti, O.2
Araujo, F.3
Hampe, C.4
Jacquier, S.5
Lucking, C.B.6
Abbas, N.7
Duyckaerts, C.8
Rooney, T.9
Pradier, L.10
Ruberg, M.11
Brice, A.12
-
20
-
-
0036291145
-
Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations
-
Guerois R, Nielsen JE, Serrano L. 2002. Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J Mol Biol 320:369-387.
-
(2002)
J Mol Biol
, vol.320
, pp. 369-387
-
-
Guerois, R.1
Nielsen, J.E.2
Serrano, L.3
-
21
-
-
33745280651
-
Biochemical analysis of Parkinson's disease-causing variants of Parkin, an E3 ubiquitin-protein ligase with monoubiquitylation capacity
-
Hampe C, Ardila-Osorio H, Fournier M, Brice A, Corti O. 2006. Biochemical analysis of Parkinson's disease-causing variants of Parkin, an E3 ubiquitin-protein ligase with monoubiquitylation capacity. Hum Mol Genet 15:2059-2075.
-
(2006)
Hum Mol Genet
, vol.15
, pp. 2059-2075
-
-
Hampe, C.1
Ardila-Osorio, H.2
Fournier, M.3
Brice, A.4
Corti, O.5
-
22
-
-
13244257325
-
Pathogenic mutations inactivate parkin by distinct mechanisms
-
Henn IH, Gostner JM, Lackner P, Tatzelt J, Winklhofer KF. 2005. Pathogenic mutations inactivate parkin by distinct mechanisms. J Neurochem 92:114-122.
-
(2005)
J Neurochem
, vol.92
, pp. 114-122
-
-
Henn, I.H.1
Gostner, J.M.2
Lackner, P.3
Tatzelt, J.4
Winklhofer, K.F.5
-
24
-
-
84881260124
-
Parkin catalyzed ubiquitin-ester transfer is triggered by PINK1-dependent phosphorylation
-
Iguchi M, Kujuro Y, Okatsu K, Koyano F, Kosako H, Kimura M, Suzuki N, Uchiyama S, Tanaka K, Matsuda N. 2013. Parkin catalyzed ubiquitin-ester transfer is triggered by PINK1-dependent phosphorylation. J Biol Chem 288:22019-22032.
-
(2013)
J Biol Chem
, vol.288
, pp. 22019-22032
-
-
Iguchi, M.1
Kujuro, Y.2
Okatsu, K.3
Koyano, F.4
Kosako, H.5
Kimura, M.6
Suzuki, N.7
Uchiyama, S.8
Tanaka, K.9
Matsuda, N.10
-
25
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. 1983. Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926-935.
-
(1983)
J Chem Phys
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
26
-
-
84899539731
-
PINK1 phosphorylates ubiquitin to activate Parkin E3 ubiquitin ligase activity
-
Kane LA, Lazarou M, Fogel AI, Li Y, Yamano K, Sarraf SA, Banerjee S, Youle RJ. 2014. PINK1 phosphorylates ubiquitin to activate Parkin E3 ubiquitin ligase activity. J Cell Biol 205:143-153.
-
(2014)
J Cell Biol
, vol.205
, pp. 143-153
-
-
Kane, L.A.1
Lazarou, M.2
Fogel, A.I.3
Li, Y.4
Yamano, K.5
Sarraf, S.A.6
Banerjee, S.7
Youle, R.J.8
-
27
-
-
84899454281
-
Phosphorylation of Parkin at Serine65 is essential for activation: elaboration of a Miro1 substrate-based assay of Parkin E3 ligase activity
-
Kazlauskaite A, Kelly V, Johnson C, Baillie C, Hastie CJ, Peggie M, Macartney T, Woodroof HI, Alessi DR, Pedrioli PG, Muqit MM. 2014a. Phosphorylation of Parkin at Serine65 is essential for activation: elaboration of a Miro1 substrate-based assay of Parkin E3 ligase activity. Open Biol 4:130213.
-
(2014)
Open Biol
, vol.4
, pp. 130213
-
-
Kazlauskaite, A.1
Kelly, V.2
Johnson, C.3
Baillie, C.4
Hastie, C.J.5
Peggie, M.6
Macartney, T.7
Woodroof, H.I.8
Alessi, D.R.9
Pedrioli, P.G.10
Muqit, M.M.11
-
28
-
-
84899421556
-
Parkin is activated by PINK1-dependent phosphorylation of ubiquitin at Ser65
-
Kazlauskaite A, Kondapalli C, Gourlay R, Campbell DG, Ritorto MS, Hofmann K, Alessi DR, Knebel A, Trost M, Muqit MM. 2014b. Parkin is activated by PINK1-dependent phosphorylation of ubiquitin at Ser65. Biochem J 460:127-139.
-
(2014)
Biochem J
, vol.460
, pp. 127-139
-
-
Kazlauskaite, A.1
Kondapalli, C.2
Gourlay, R.3
Campbell, D.G.4
Ritorto, M.S.5
Hofmann, K.6
Alessi, D.R.7
Knebel, A.8
Trost, M.9
Muqit, M.M.10
-
29
-
-
0032499264
-
Mutations in the parkin gene cause autosomal recessive juvenile parkinsonism
-
Kitada T, Asakawa S, Hattori N, Matsumine H, Yamamura Y, Minoshima S, Yokochi M, Mizuno Y, Shimizu N. 1998. Mutations in the parkin gene cause autosomal recessive juvenile parkinsonism. Nature 392:605-608.
-
(1998)
Nature
, vol.392
, pp. 605-608
-
-
Kitada, T.1
Asakawa, S.2
Hattori, N.3
Matsumine, H.4
Yamamura, Y.5
Minoshima, S.6
Yokochi, M.7
Mizuno, Y.8
Shimizu, N.9
-
30
-
-
84864267876
-
PINK1 is activated by mitochondrial membrane potential depolarization and stimulates Parkin E3 ligase activity by phosphorylating Serine 65
-
Kondapalli C, Kazlauskaite A, Zhang N, Woodroof HI, Campbell DG, Gourlay R, Burchell L, Walden H, Macartney TJ, Deak M, Knebel A, Alessi DR, et al. 2012. PINK1 is activated by mitochondrial membrane potential depolarization and stimulates Parkin E3 ligase activity by phosphorylating Serine 65. Open Biol 2:120080.
-
(2012)
Open Biol
, vol.2
, pp. 120080
-
-
Kondapalli, C.1
Kazlauskaite, A.2
Zhang, N.3
Woodroof, H.I.4
Campbell, D.G.5
Gourlay, R.6
Burchell, L.7
Walden, H.8
Macartney, T.J.9
Deak, M.10
Knebel, A.11
Alessi, D.R.12
-
31
-
-
84901751574
-
Ubiquitin is phosphorylated by PINK1 to activate parkin
-
Koyano F, Okatsu K, Kosako H, Tamura Y, Go E, Kimura M, Kimura Y, Tsuchiya H, Yoshihara H, Hirokawa T, Endo T, Fon EA, et al. 2014. Ubiquitin is phosphorylated by PINK1 to activate parkin. Nature 510:162-166.
-
(2014)
Nature
, vol.510
, pp. 162-166
-
-
Koyano, F.1
Okatsu, K.2
Kosako, H.3
Tamura, Y.4
Go, E.5
Kimura, M.6
Kimura, Y.7
Tsuchiya, H.8
Yoshihara, H.9
Hirokawa, T.10
Endo, T.11
Fon, E.A.12
-
33
-
-
84855945977
-
Assignment of protonation states in proteins and ligands: combining pKa prediction with hydrogen bonding network optimization
-
Krieger E, Dunbrack RL Jr, Hooft RW, Krieger B. 2012. Assignment of protonation states in proteins and ligands: combining pKa prediction with hydrogen bonding network optimization. Methods Mol Biol 819:405-421.
-
(2012)
Methods Mol Biol
, vol.819
, pp. 405-421
-
-
Krieger, E.1
Dunbrack Jr, R.L.2
Hooft, R.W.3
Krieger, B.4
-
34
-
-
74249090260
-
Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: four approaches that performed well in CASP8
-
Krieger E, Joo K, Lee J, Lee J, Raman S, Thompson J, Tyka M, Baker D, Karplus K. 2009. Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: four approaches that performed well in CASP8. Proteins 77 Suppl 9:114-122.
-
(2009)
Proteins
, vol.77
, pp. 114-122
-
-
Krieger, E.1
Joo, K.2
Lee, J.3
Lee, J.4
Raman, S.5
Thompson, J.6
Tyka, M.7
Baker, D.8
Karplus, K.9
-
35
-
-
84873045973
-
PINK1 drives Parkin self-association and HECT-like E3 activity upstream of mitochondrial binding
-
Lazarou M, Narendra DP, Jin SM, Tekle E, Banerjee S, Youle RJ. 2013. PINK1 drives Parkin self-association and HECT-like E3 activity upstream of mitochondrial binding. J Cell Biol 200:163-172.
-
(2013)
J Cell Biol
, vol.200
, pp. 163-172
-
-
Lazarou, M.1
Narendra, D.P.2
Jin, S.M.3
Tekle, E.4
Banerjee, S.5
Youle, R.J.6
-
36
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, et al. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102:3586-3616.
-
(1998)
J Phys Chem B
, vol.102
, pp. 3586-3616
-
-
MacKerell, A.D.1
Bashford, D.2
Bellott, M.3
Dunbrack, R.L.4
Evanseck, J.D.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph-McCarthy, D.11
Kuchnir, L.12
-
37
-
-
84937735761
-
-
Maestro 9.1. M. 9.1. New York, NY: Schrödinger, LLC.
-
Maestro-9.1. 2010. Maestro 9.1. M. 9.1. New York, NY: Schrödinger, LLC.
-
(2010)
-
-
-
38
-
-
33645635706
-
Diverse effects of pathogenic mutations of Parkin that catalyze multiple monoubiquitylation in vitro
-
Matsuda N, Kitami T, Suzuki T, Mizuno Y, Hattori N, Tanaka K. 2006. Diverse effects of pathogenic mutations of Parkin that catalyze multiple monoubiquitylation in vitro. J Biol Chem 281:3204-3209.
-
(2006)
J Biol Chem
, vol.281
, pp. 3204-3209
-
-
Matsuda, N.1
Kitami, T.2
Suzuki, T.3
Mizuno, Y.4
Hattori, N.5
Tanaka, K.6
-
39
-
-
77951181836
-
PINK1 stabilized by mitochondrial depolarization recruits Parkin to damaged mitochondria and activates latent Parkin for mitophagy
-
Matsuda N, Sato S, Shiba K, Okatsu K, Saisho K, Gautier CA, Sou YS, Saiki S, Kawajiri S, Sato F, Kimura M, Komatsu M, et al. 2010. PINK1 stabilized by mitochondrial depolarization recruits Parkin to damaged mitochondria and activates latent Parkin for mitophagy. J Cell Biol 189:211-221.
-
(2010)
J Cell Biol
, vol.189
, pp. 211-221
-
-
Matsuda, N.1
Sato, S.2
Shiba, K.3
Okatsu, K.4
Saisho, K.5
Gautier, C.A.6
Sou, Y.S.7
Saiki, S.8
Kawajiri, S.9
Sato, F.10
Kimura, M.11
Komatsu, M.12
-
40
-
-
78649300971
-
p62/SQSTM1 is required for Parkin-induced mitochondrial clustering but not mitophagy; VDAC1 is dispensable for both
-
Narendra D, Kane LA, Hauser DN, Fearnley IM, Youle RJ. 2010a. p62/SQSTM1 is required for Parkin-induced mitochondrial clustering but not mitophagy; VDAC1 is dispensable for both. Autophagy 6:1090-1106.
-
(2010)
Autophagy
, vol.6
, pp. 1090-1106
-
-
Narendra, D.1
Kane, L.A.2
Hauser, D.N.3
Fearnley, I.M.4
Youle, R.J.5
-
41
-
-
75749156257
-
PINK1 is selectively stabilized on impaired mitochondria to activate Parkin
-
Narendra DP, Jin SM, Tanaka A, Suen DF, Gautier CA, Shen J, Cookson MR, Youle RJ. 2010b. PINK1 is selectively stabilized on impaired mitochondria to activate Parkin. PLoS Biol 8:e1000298.
-
(2010)
PLoS Biol
, vol.8
, pp. e1000298
-
-
Narendra, D.P.1
Jin, S.M.2
Tanaka, A.3
Suen, D.F.4
Gautier, C.A.5
Shen, J.6
Cookson, M.R.7
Youle, R.J.8
-
42
-
-
77954695260
-
p62/SQSTM1 cooperates with Parkin for perinuclear clustering of depolarized mitochondria
-
Okatsu K, Saisho K, Shimanuki M, Nakada K, Shitara H, Sou YS, Kimura M, Sato S, Hattori N, Komatsu M, Tanaka K, Matsuda N. 2010. p62/SQSTM1 cooperates with Parkin for perinuclear clustering of depolarized mitochondria. Genes Cells 15:887-900.
-
(2010)
Genes Cells
, vol.15
, pp. 887-900
-
-
Okatsu, K.1
Saisho, K.2
Shimanuki, M.3
Nakada, K.4
Shitara, H.5
Sou, Y.S.6
Kimura, M.7
Sato, S.8
Hattori, N.9
Komatsu, M.10
Tanaka, K.11
Matsuda, N.12
-
43
-
-
84922434418
-
Quantitative proteomics reveal a feedforward mechanism for mitochondrial PARKIN translocation and ubiquitin chain synthesis
-
Ordureau A, Sarraf SA, Duda DM, Heo JM, Jedrychowski MP, Sviderskiy VO, Olszewski JL, Koerber JT, Xie T, Beausoleil SA, Wells JA, Gygi SP, et al. 2014. Quantitative proteomics reveal a feedforward mechanism for mitochondrial PARKIN translocation and ubiquitin chain synthesis. Mol Cell 56:360-375.
-
(2014)
Mol Cell
, vol.56
, pp. 360-375
-
-
Ordureau, A.1
Sarraf, S.A.2
Duda, D.M.3
Heo, J.M.4
Jedrychowski, M.P.5
Sviderskiy, V.O.6
Olszewski, J.L.7
Koerber, J.T.8
Xie, T.9
Beausoleil, S.A.10
Wells, J.A.11
Gygi, S.P.12
-
44
-
-
0029633186
-
AMBER, a computer program for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to elucidate the structures and energies of molecules
-
Pearlman DA, Case DA, Caldwell JW, Ross WR, Cheatham TE III, DeBolt S, Ferguson D, Seibel G, Kollman P. 1995. AMBER, a computer program for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to elucidate the structures and energies of molecules. Comp Phys Commun 91:1-41.
-
(1995)
Comp Phys Commun
, vol.91
, pp. 1-41
-
-
Pearlman, D.A.1
Case, D.A.2
Caldwell, J.W.3
Ross, W.R.4
Cheatham, T.E.5
DeBolt, S.6
Ferguson, D.7
Seibel, G.8
Kollman, P.9
-
45
-
-
84875277277
-
Monogenic Parkinson's disease and parkinsonism: clinical phenotypes and frequencies of known mutations
-
Puschmann A. 2013. Monogenic Parkinson's disease and parkinsonism: clinical phenotypes and frequencies of known mutations. Parkinsonism Relat Disord 19:407-415.
-
(2013)
Parkinsonism Relat Disord
, vol.19
, pp. 407-415
-
-
Puschmann, A.1
-
46
-
-
36849057065
-
Conformations of flanking bases in HIV-1 RNA DIS kissing complexes studied by molecular dynamics
-
Reblova K, Fadrna E, Sarzynska J, Kulinski T, Kulhanek P, Ennifar E, Koca J, Sponer J. 2007. Conformations of flanking bases in HIV-1 RNA DIS kissing complexes studied by molecular dynamics. Biophys J 93:3932-3949.
-
(2007)
Biophys J
, vol.93
, pp. 3932-3949
-
-
Reblova, K.1
Fadrna, E.2
Sarzynska, J.3
Kulinski, T.4
Kulhanek, P.5
Ennifar, E.6
Koca, J.7
Sponer, J.8
-
47
-
-
33746388359
-
Structure, dynamics, and elasticity of free 16s rRNA helix 44 studied by molecular dynamics simulations
-
Reblova K, Lankas F, Razga F, Krasovska MV, Koca J, Sponer J. 2006. Structure, dynamics, and elasticity of free 16s rRNA helix 44 studied by molecular dynamics simulations. Biopolymers 82:504-520.
-
(2006)
Biopolymers
, vol.82
, pp. 504-520
-
-
Reblova, K.1
Lankas, F.2
Razga, F.3
Krasovska, M.V.4
Koca, J.5
Sponer, J.6
-
48
-
-
84879674444
-
Structure and function of Parkin E3 ubiquitin ligase reveals aspects of RING and HECT ligases
-
Riley BE, Lougheed JC, Callaway K, Velasquez M, Brecht E, Nguyen L, Shaler T, Walker D, Yang Y, Regnstrom K, Diep L, Zhang Z, et al. 2013. Structure and function of Parkin E3 ubiquitin ligase reveals aspects of RING and HECT ligases. Nature Commun 4:1982.
-
(2013)
Nature Commun
, vol.4
, pp. 1982
-
-
Riley, B.E.1
Lougheed, J.C.2
Callaway, K.3
Velasquez, M.4
Brecht, E.5
Nguyen, L.6
Shaler, T.7
Walker, D.8
Yang, Y.9
Regnstrom, K.10
Diep, L.11
Zhang, Z.12
-
49
-
-
79953182301
-
Impact of autosomal recessive juvenile Parkinson's disease mutations on the structure and interactions of the parkin ubiquitin-like domain
-
Safadi SS, Barber KR, Shaw GS. 2011. Impact of autosomal recessive juvenile Parkinson's disease mutations on the structure and interactions of the parkin ubiquitin-like domain. Biochemistry 50:2603-2610.
-
(2011)
Biochemistry
, vol.50
, pp. 2603-2610
-
-
Safadi, S.S.1
Barber, K.R.2
Shaw, G.S.3
-
50
-
-
84876296881
-
Landscape of the PARKIN-dependent ubiquitylome in response to mitochondrial depolarization
-
Sarraf SA, Raman M, Guarani-Pereira V, Sowa ME, Huttlin EL, Gygi SP, Harper JW. 2013. Landscape of the PARKIN-dependent ubiquitylome in response to mitochondrial depolarization. Nature 496:372-376.
-
(2013)
Nature
, vol.496
, pp. 372-376
-
-
Sarraf, S.A.1
Raman, M.2
Guarani-Pereira, V.3
Sowa, M.E.4
Huttlin, E.L.5
Gygi, S.P.6
Harper, J.W.7
-
51
-
-
46649117176
-
Aberrant folding of pathogenic Parkin mutants: aggregation versus degradation
-
Schlehe JS, Lutz AK, Pilsl A, Lammermann K, Grgur K, Henn IH, Tatzelt J, Winklhofer KF. 2008. Aberrant folding of pathogenic Parkin mutants: aggregation versus degradation. J Biol Chem 283:13771-13779.
-
(2008)
J Biol Chem
, vol.283
, pp. 13771-13779
-
-
Schlehe, J.S.1
Lutz, A.K.2
Pilsl, A.3
Lammermann, K.4
Grgur, K.5
Henn, I.H.6
Tatzelt, J.7
Winklhofer, K.F.8
-
52
-
-
84937733974
-
-
Suite 2012. New York, NY: Schrödinger, LLC.
-
Schrödinger. 2012. Suite 2012. New York, NY: Schrödinger, LLC.
-
(2012)
-
-
-
53
-
-
84937731686
-
-
Biologics Suite. BioLuminate, version 1.1. New York, NY: Schrödinger, LLC.
-
Schrödinger. 2013. Biologics Suite. BioLuminate, version 1.1. New York, NY: Schrödinger, LLC.
-
(2013)
-
-
-
54
-
-
84871891737
-
PINK1-mediated phosphorylation of the Parkin ubiquitin-like domain primes mitochondrial translocation of Parkin and regulates mitophagy
-
Shiba-Fukushima K, Imai Y, Yoshida S, Ishihama Y, Kanao T, Sato S, Hattori N. 2012. PINK1-mediated phosphorylation of the Parkin ubiquitin-like domain primes mitochondrial translocation of Parkin and regulates mitophagy. Sci Rep 2:1002.
-
(2012)
Sci Rep
, vol.2
, pp. 1002
-
-
Shiba-Fukushima, K.1
Imai, Y.2
Yoshida, S.3
Ishihama, Y.4
Kanao, T.5
Sato, S.6
Hattori, N.7
-
55
-
-
0033933048
-
Familial Parkinson disease gene product, parkin, is a ubiquitin-protein ligase
-
Shimura H, Hattori N, Kubo S, Mizuno Y, Asakawa S, Minoshima S, Shimizu N, Iwai K, Chiba T, Tanaka K, Suzuki T. 2000. Familial Parkinson disease gene product, parkin, is a ubiquitin-protein ligase. Nat Genet 25:302-305.
-
(2000)
Nat Genet
, vol.25
, pp. 302-305
-
-
Shimura, H.1
Hattori, N.2
Kubo, S.3
Mizuno, Y.4
Asakawa, S.5
Minoshima, S.6
Shimizu, N.7
Iwai, K.8
Chiba, T.9
Tanaka, K.10
Suzuki, T.11
-
56
-
-
24144470504
-
Familial-associated mutations differentially disrupt the solubility, localization, binding and ubiquitination properties of parkin
-
Sriram SR, Li X, Ko HS, Chung KK, Wong E, Lim KL, Dawson VL, Dawson TM. 2005. Familial-associated mutations differentially disrupt the solubility, localization, binding and ubiquitination properties of parkin. Hum Mol Genet 14:2571-2586.
-
(2005)
Hum Mol Genet
, vol.14
, pp. 2571-2586
-
-
Sriram, S.R.1
Li, X.2
Ko, H.S.3
Chung, K.K.4
Wong, E.5
Lim, K.L.6
Dawson, V.L.7
Dawson, T.M.8
-
57
-
-
84879251778
-
Structure of Parkin reveals mechanisms for ubiquitin ligase activation
-
Trempe JF, Sauve V, Grenier K, Seirafi M, Tang MY, Menade M, Al-Abdul-Wahid S, Krett J, Wong K, Kozlov G, Nagar B, Fon EA, et al. 2013. Structure of Parkin reveals mechanisms for ubiquitin ligase activation. Science 340:1451-1455.
-
(2013)
Science
, vol.340
, pp. 1451-1455
-
-
Trempe, J.F.1
Sauve, V.2
Grenier, K.3
Seirafi, M.4
Tang, M.Y.5
Menade, M.6
Al-Abdul-Wahid, S.7
Krett, J.8
Wong, K.9
Kozlov, G.10
Nagar, B.11
Fon, E.A.12
-
58
-
-
0035957112
-
Clinical and pathologic abnormalities in a family with parkinsonism and parkin gene mutations
-
van de Warrenburg BP, Lammens M, Lucking CB, Denefle P, Wesseling P, Booij J, Praamstra P, Quinn N, Brice A, Horstink MW. 2001. Clinical and pathologic abnormalities in a family with parkinsonism and parkin gene mutations. Neurology 56:555-557.
-
(2001)
Neurology
, vol.56
, pp. 555-557
-
-
van de Warrenburg, B.P.1
Lammens, M.2
Lucking, C.B.3
Denefle, P.4
Wesseling, P.5
Booij, J.6
Praamstra, P.7
Quinn, N.8
Brice, A.9
Horstink, M.W.10
-
59
-
-
75949098487
-
PINK1-dependent recruitment of Parkin to mitochondria in mitophagy
-
Vives-Bauza C, Zhou C, Huang Y, Cui M, de Vries RL, Kim J, May J, Tocilescu MA, Liu W, Ko HS, Magrane J, Moore DJ, et al. 2010. PINK1-dependent recruitment of Parkin to mitochondria in mitophagy. Proc Natl Acad Sci USA 107:378-383.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, pp. 378-383
-
-
Vives-Bauza, C.1
Zhou, C.2
Huang, Y.3
Cui, M.4
de Vries, R.L.5
Kim, J.6
May, J.7
Tocilescu, M.A.8
Liu, W.9
Ko, H.S.10
Magrane, J.11
Moore, D.J.12
-
60
-
-
84865656962
-
Regulation of Parkin E3 ubiquitin ligase activity
-
Walden H, Martinez-Torres RJ. 2012. Regulation of Parkin E3 ubiquitin ligase activity. Cell Mol Life Sci 69:3053-3067.
-
(2012)
Cell Mol Life Sci
, vol.69
, pp. 3053-3067
-
-
Walden, H.1
Martinez-Torres, R.J.2
-
61
-
-
84881477223
-
Structure of the human Parkin ligase domain in an autoinhibited state
-
Wauer T, Komander D. 2013. Structure of the human Parkin ligase domain in an autoinhibited state. EMBO J 32:2099-2112.
-
(2013)
EMBO J
, vol.32
, pp. 2099-2112
-
-
Wauer, T.1
Komander, D.2
-
62
-
-
79957949190
-
UBCH7 reactivity profile reveals parkin and HHARI to be RING/HECT hybrids
-
Wenzel DM, Lissounov A, Brzovic PS, Klevit RE. 2011. UBCH7 reactivity profile reveals parkin and HHARI to be RING/HECT hybrids. Nature 474:105-108.
-
(2011)
Nature
, vol.474
, pp. 105-108
-
-
Wenzel, D.M.1
Lissounov, A.2
Brzovic, P.S.3
Klevit, R.E.4
-
64
-
-
84906315018
-
PINK1 triggers autocatalytic activation of Parkin to specify cell fate decisions
-
Zhang C, Lee S, Peng Y, Bunker E, Giaime E, Shen J, Zhou Z, Liu X. 2014. PINK1 triggers autocatalytic activation of Parkin to specify cell fate decisions. Curr Biol 24:1854-1865.
-
(2014)
Curr Biol
, vol.24
, pp. 1854-1865
-
-
Zhang, C.1
Lee, S.2
Peng, Y.3
Bunker, E.4
Giaime, E.5
Shen, J.6
Zhou, Z.7
Liu, X.8
-
65
-
-
84879885169
-
Parkin mitochondrial translocation is achieved through a novel catalytic activity coupled mechanism
-
Zheng X, Hunter T. 2013. Parkin mitochondrial translocation is achieved through a novel catalytic activity coupled mechanism. Cell Res 23:886-897.
-
(2013)
Cell Res
, vol.23
, pp. 886-897
-
-
Zheng, X.1
Hunter, T.2
|