-
1
-
-
76449098262
-
PHENIX: a comprehensive Python-based system for macromolecular structure solution
-
Adams, P.D., Afonine, P.V., Bunkóczi, G., Chen, V.B., Davis, I.W., Echols, N., Headd, J.J., Hung, L.-W., Kapral, G.J., Grosse-Kunstleve, R.W., et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66 (2010), 213–221.
-
(2010)
Acta Crystallogr. D Biol. Crystallogr.
, vol.66
, pp. 213-221
-
-
Adams, P.D.1
Afonine, P.V.2
Bunkóczi, G.3
Chen, V.B.4
Davis, I.W.5
Echols, N.6
Headd, J.J.7
Hung, L.-W.8
Kapral, G.J.9
Grosse-Kunstleve, R.W.10
-
2
-
-
80053642374
-
The Phenix software for automated determination of macromolecular structures
-
Adams, P.D., Afonine, P.V., Bunkóczi, G., Chen, V.B., Echols, N., Headd, J.J., Hung, L.-W., Jain, S., Kapral, G.J., Grosse Kunstleve, R.W., et al. The Phenix software for automated determination of macromolecular structures. Methods 55 (2011), 94–106.
-
(2011)
Methods
, vol.55
, pp. 94-106
-
-
Adams, P.D.1
Afonine, P.V.2
Bunkóczi, G.3
Chen, V.B.4
Echols, N.5
Headd, J.J.6
Hung, L.-W.7
Jain, S.8
Kapral, G.J.9
Grosse Kunstleve, R.W.10
-
3
-
-
84920973221
-
The human otubain2-ubiquitin structure provides insights into the cleavage specificity of poly-ubiquitin-linkages
-
Altun, M., Walter, T.S., Kramer, H.B., Herr, P., Iphöfer, A., Boström, J., David, Y., Komsany, A., Ternette, N., Navon, A., et al. The human otubain2-ubiquitin structure provides insights into the cleavage specificity of poly-ubiquitin-linkages. PLoS ONE, 10, 2015, e0115344.
-
(2015)
PLoS ONE
, vol.10
, pp. e0115344
-
-
Altun, M.1
Walter, T.S.2
Kramer, H.B.3
Herr, P.4
Iphöfer, A.5
Boström, J.6
David, Y.7
Komsany, A.8
Ternette, N.9
Navon, A.10
-
4
-
-
77953148666
-
Site-specific phosphorylation dynamics of the nuclear proteome during the DNA damage response
-
Bennetzen, M.V., Larsen, D.H., Bunkenborg, J., Bartek, J., Lukas, J., Andersen, J.S., Site-specific phosphorylation dynamics of the nuclear proteome during the DNA damage response. Mol. Cell. Proteomics 9 (2010), 1314–1323.
-
(2010)
Mol. Cell. Proteomics
, vol.9
, pp. 1314-1323
-
-
Bennetzen, M.V.1
Larsen, D.H.2
Bunkenborg, J.3
Bartek, J.4
Lukas, J.5
Andersen, J.S.6
-
5
-
-
84898754901
-
New insights into ubiquitin E3 ligase mechanism
-
Berndsen, C.E., Wolberger, C., New insights into ubiquitin E3 ligase mechanism. Nat. Struct. Mol. Biol. 21 (2014), 301–307.
-
(2014)
Nat. Struct. Mol. Biol.
, vol.21
, pp. 301-307
-
-
Berndsen, C.E.1
Wolberger, C.2
-
6
-
-
84900862275
-
Autoubiquitination of the 26S proteasome on Rpn13 regulates breakdown of ubiquitin conjugates
-
Besche, H.C., Sha, Z., Kukushkin, N.V., Peth, A., Hock, E.-M., Kim, W., Gygi, S., Gutierrez, J.A., Liao, H., Dick, L., Goldberg, A.L., Autoubiquitination of the 26S proteasome on Rpn13 regulates breakdown of ubiquitin conjugates. EMBO J. 33 (2014), 1159–1176.
-
(2014)
EMBO J.
, vol.33
, pp. 1159-1176
-
-
Besche, H.C.1
Sha, Z.2
Kukushkin, N.V.3
Peth, A.4
Hock, E.-M.5
Kim, W.6
Gygi, S.7
Gutierrez, J.A.8
Liao, H.9
Dick, L.10
Goldberg, A.L.11
-
7
-
-
84890300195
-
An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome
-
Bian, Y., Song, C., Cheng, K., Dong, M., Wang, F., Huang, J., Sun, D., Wang, L., Ye, M., Zou, H., An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome. J. Proteomics 96 (2014), 253–262.
-
(2014)
J. Proteomics
, vol.96
, pp. 253-262
-
-
Bian, Y.1
Song, C.2
Cheng, K.3
Dong, M.4
Wang, F.5
Huang, J.6
Sun, D.7
Wang, L.8
Ye, M.9
Zou, H.10
-
8
-
-
77955417276
-
Lys11-linked ubiquitin chains adopt compact conformations and are preferentially hydrolyzed by the deubiquitinase Cezanne
-
Bremm, A., Freund, S.M.V., Komander, D., Lys11-linked ubiquitin chains adopt compact conformations and are preferentially hydrolyzed by the deubiquitinase Cezanne. Nat. Struct. Mol. Biol. 17 (2010), 939–947.
-
(2010)
Nat. Struct. Mol. Biol.
, vol.17
, pp. 939-947
-
-
Bremm, A.1
Freund, S.M.V.2
Komander, D.3
-
9
-
-
70350013557
-
Mislocalized activation of oncogenic RTKs switches downstream signaling outcomes
-
Choudhary, C., Olsen, J.V., Brandts, C., Cox, J., Reddy, P.N.G., Böhmer, F.D., Gerke, V., Schmidt-Arras, D.-E., Berdel, W.E., Müller-Tidow, C., et al. Mislocalized activation of oncogenic RTKs switches downstream signaling outcomes. Mol. Cell 36 (2009), 326–339.
-
(2009)
Mol. Cell
, vol.36
, pp. 326-339
-
-
Choudhary, C.1
Olsen, J.V.2
Brandts, C.3
Cox, J.4
Reddy, P.N.G.5
Böhmer, F.D.6
Gerke, V.7
Schmidt-Arras, D.-E.8
Berdel, W.E.9
Müller-Tidow, C.10
-
10
-
-
84889072454
-
The E3 ubiquitin ligase UBE3C enhances proteasome processivity by ubiquitinating partially proteolyzed substrates
-
Chu, B.W., Kovary, K.M., Guillaume, J., Chen, L.-C., Teruel, M.N., Wandless, T.J., The E3 ubiquitin ligase UBE3C enhances proteasome processivity by ubiquitinating partially proteolyzed substrates. J. Biol. Chem. 288 (2013), 34575–34587.
-
(2013)
J. Biol. Chem.
, vol.288
, pp. 34575-34587
-
-
Chu, B.W.1
Kovary, K.M.2
Guillaume, J.3
Chen, L.-C.4
Teruel, M.N.5
Wandless, T.J.6
-
11
-
-
84937640135
-
The demographics of the ubiquitin system
-
Clague, M.J., Heride, C., Urbé, S., The demographics of the ubiquitin system. Trends Cell Biol. 25 (2015), 417–426.
-
(2015)
Trends Cell Biol.
, vol.25
, pp. 417-426
-
-
Clague, M.J.1
Heride, C.2
Urbé, S.3
-
12
-
-
80054787664
-
What genetics tells us about the causes and mechanisms of Parkinson's disease
-
Corti, O., Lesage, S., Brice, A., What genetics tells us about the causes and mechanisms of Parkinson's disease. Physiol. Rev. 91 (2011), 1161–1218.
-
(2011)
Physiol. Rev.
, vol.91
, pp. 1161-1218
-
-
Corti, O.1
Lesage, S.2
Brice, A.3
-
13
-
-
77949535720
-
Features and development of Coot
-
Emsley, P., Lohkamp, B., Scott, W.G., Cowtan, K., Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66 (2010), 486–501.
-
(2010)
Acta Crystallogr. D Biol. Crystallogr.
, vol.66
, pp. 486-501
-
-
Emsley, P.1
Lohkamp, B.2
Scott, W.G.3
Cowtan, K.4
-
14
-
-
84873085753
-
A strategy for modulation of enzymes in the ubiquitin system
-
Ernst, A., Avvakumov, G., Tong, J., Fan, Y., Zhao, Y., Alberts, P., Persaud, A., Walker, J.R., Neculai, A.-M., Neculai, D., et al. A strategy for modulation of enzymes in the ubiquitin system. Science 339 (2013), 590–595.
-
(2013)
Science
, vol.339
, pp. 590-595
-
-
Ernst, A.1
Avvakumov, G.2
Tong, J.3
Fan, Y.4
Zhao, Y.5
Alberts, P.6
Persaud, A.7
Walker, J.R.8
Neculai, A.-M.9
Neculai, D.10
-
15
-
-
84946231682
-
The missing links to link ubiquitin: Methods for the enzymatic production of polyubiquitin chains
-
Faggiano, S., Alfano, C., Pastore, A., The missing links to link ubiquitin: Methods for the enzymatic production of polyubiquitin chains. Anal. Biochem. 492 (2016), 82–90.
-
(2016)
Anal. Biochem.
, vol.492
, pp. 82-90
-
-
Faggiano, S.1
Alfano, C.2
Pastore, A.3
-
16
-
-
66549119395
-
Advances and pitfalls of protein structural alignment
-
Hasegawa, H., Holm, L., Advances and pitfalls of protein structural alignment. Curr. Opin. Struct. Biol. 19 (2009), 341–348.
-
(2009)
Curr. Opin. Struct. Biol.
, vol.19
, pp. 341-348
-
-
Hasegawa, H.1
Holm, L.2
-
17
-
-
84867583216
-
Enhanced phosphoserine insertion during Escherichia coli protein synthesis via partial UAG codon reassignment and release factor 1 deletion
-
Heinemann, I.U., Rovner, A.J., Aerni, H.R., Rogulina, S., Cheng, L., Olds, W., Fischer, J.T., Söll, D., Isaacs, F.J., Rinehart, J., Enhanced phosphoserine insertion during Escherichia coli protein synthesis via partial UAG codon reassignment and release factor 1 deletion. FEBS Lett. 586 (2012), 3716–3722.
-
(2012)
FEBS Lett.
, vol.586
, pp. 3716-3722
-
-
Heinemann, I.U.1
Rovner, A.J.2
Aerni, H.R.3
Rogulina, S.4
Cheng, L.5
Olds, W.6
Fischer, J.T.7
Söll, D.8
Isaacs, F.J.9
Rinehart, J.10
-
18
-
-
84940783815
-
Expanding the ubiquitin code through post-translational modification
-
Herhaus, L., Dikic, I., Expanding the ubiquitin code through post-translational modification. EMBO Rep. 16 (2015), 1071–1083.
-
(2015)
EMBO Rep.
, vol.16
, pp. 1071-1083
-
-
Herhaus, L.1
Dikic, I.2
-
19
-
-
84877313192
-
Assembly, analysis and architecture of atypical ubiquitin chains
-
Hospenthal, M.K., Freund, S.M.V., Komander, D., Assembly, analysis and architecture of atypical ubiquitin chains. Nat. Struct. Mol. Biol. 20 (2013), 555–565.
-
(2013)
Nat. Struct. Mol. Biol.
, vol.20
, pp. 555-565
-
-
Hospenthal, M.K.1
Freund, S.M.V.2
Komander, D.3
-
20
-
-
84856801739
-
OTUB1 co-opts Lys48-linked ubiquitin recognition to suppress E2 enzyme function
-
Juang, Y.C., Landry, M.C., Sanches, M., Vittal, V., Leung, C.C., Ceccarelli, D.F., Mateo, A.R., Pruneda, J.N., Mao, D.Y., Szilard, R.K., et al. OTUB1 co-opts Lys48-linked ubiquitin recognition to suppress E2 enzyme function. Mol. Cell 45 (2012), 384–397.
-
(2012)
Mol. Cell
, vol.45
, pp. 384-397
-
-
Juang, Y.C.1
Landry, M.C.2
Sanches, M.3
Vittal, V.4
Leung, C.C.5
Ceccarelli, D.F.6
Mateo, A.R.7
Pruneda, J.N.8
Mao, D.Y.9
Szilard, R.K.10
-
21
-
-
79961000536
-
Protein standard absolute quantification (PSAQ) method for the measurement of cellular ubiquitin pools
-
Kaiser, S.E., Riley, B.E., Shaler, T.A., Trevino, R.S., Becker, C.H., Schulman, H., Kopito, R.R., Protein standard absolute quantification (PSAQ) method for the measurement of cellular ubiquitin pools. Nat. Methods 8 (2011), 691–696.
-
(2011)
Nat. Methods
, vol.8
, pp. 691-696
-
-
Kaiser, S.E.1
Riley, B.E.2
Shaler, T.A.3
Trevino, R.S.4
Becker, C.H.5
Schulman, H.6
Kopito, R.R.7
-
22
-
-
84899539731
-
PINK1 phosphorylates ubiquitin to activate Parkin E3 ubiquitin ligase activity
-
Kane, L.A., Lazarou, M., Fogel, A.I., Li, Y., Yamano, K., Sarraf, S.A., Banerjee, S., Youle, R.J., PINK1 phosphorylates ubiquitin to activate Parkin E3 ubiquitin ligase activity. J. Cell Biol. 205 (2014), 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
-
23
-
-
84899421556
-
Parkin is activated by PINK1-dependent phosphorylation of ubiquitin at Ser65
-
Kazlauskaite, A., Kondapalli, C., Gourlay, R., Campbell, D.G., Ritorto, M.S., Hofmann, K., Alessi, D.R., Knebel, A., Trost, M., Muqit, M.M.K., Parkin is activated by PINK1-dependent phosphorylation of ubiquitin at Ser65. Biochem. J. 460 (2014), 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.K.10
-
24
-
-
84878862687
-
OTULIN antagonizes LUBAC signaling by specifically hydrolyzing Met1-linked polyubiquitin
-
Keusekotten, K., Elliott, P.R., Glockner, L., Fiil, B.K., Damgaard, R.B., Kulathu, Y., Wauer, T., Hospenthal, M.K., Gyrd-Hansen, M., Krappmann, D., et al. OTULIN antagonizes LUBAC signaling by specifically hydrolyzing Met1-linked polyubiquitin. Cell 153 (2013), 1312–1326.
-
(2013)
Cell
, vol.153
, pp. 1312-1326
-
-
Keusekotten, K.1
Elliott, P.R.2
Glockner, L.3
Fiil, B.K.4
Damgaard, R.B.5
Kulathu, Y.6
Wauer, T.7
Hospenthal, M.K.8
Gyrd-Hansen, M.9
Krappmann, D.10
-
25
-
-
33745742269
-
Quantitative analysis of in vitro ubiquitinated cyclin B1 reveals complex chain topology
-
Kirkpatrick, D.S., Hathaway, N.A., Hanna, J., Elsasser, S., Rush, J., Finley, D., King, R.W., Gygi, S.P., Quantitative analysis of in vitro ubiquitinated cyclin B1 reveals complex chain topology. Nat. Cell Biol. 8 (2006), 700–710.
-
(2006)
Nat. Cell Biol.
, vol.8
, pp. 700-710
-
-
Kirkpatrick, D.S.1
Hathaway, N.A.2
Hanna, J.3
Elsasser, S.4
Rush, J.5
Finley, D.6
King, R.W.7
Gygi, S.P.8
-
27
-
-
68049084674
-
Breaking the chains: structure and function of the deubiquitinases
-
Komander, D., Clague, M.J., Urbé, S., Breaking the chains: structure and function of the deubiquitinases. Nat. Rev. Mol. Cell Biol. 10 (2009), 550–563.
-
(2009)
Nat. Rev. Mol. Cell Biol.
, vol.10
, pp. 550-563
-
-
Komander, D.1
Clague, M.J.2
Urbé, S.3
-
28
-
-
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, H.I., Campbell, D.G., Gourlay, R., Burchell, L., Walden, H., Macartney, T.J., Deak, M., et al. PINK1 is activated by mitochondrial membrane potential depolarization and stimulates Parkin E3 ligase activity by phosphorylating Serine 65. Open Biol., 2, 2012, 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
-
29
-
-
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., et al. Ubiquitin is phosphorylated by PINK1 to activate parkin. Nature 510 (2014), 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
-
30
-
-
84961288441
-
K29-selective ubiquitin binding domain reveals structural basis of specificity and heterotypic nature of k29 polyubiquitin
-
Kristariyanto, Y.A., Abdul Rehman, S.A., Campbell, D.G., Morrice, N.A., Johnson, C., Toth, R., Kulathu, Y., K29-selective ubiquitin binding domain reveals structural basis of specificity and heterotypic nature of k29 polyubiquitin. Mol. Cell 58 (2015), 83–94.
-
(2015)
Mol. Cell
, vol.58
, pp. 83-94
-
-
Kristariyanto, Y.A.1
Abdul Rehman, S.A.2
Campbell, D.G.3
Morrice, N.A.4
Johnson, C.5
Toth, R.6
Kulathu, Y.7
-
31
-
-
84864222562
-
Atypical ubiquitylation - the unexplored world of polyubiquitin beyond Lys48 and Lys63 linkages
-
Kulathu, Y., Komander, D., Atypical ubiquitylation - the unexplored world of polyubiquitin beyond Lys48 and Lys63 linkages. Nat. Rev. Mol. Cell Biol. 13 (2012), 508–523.
-
(2012)
Nat. Rev. Mol. Cell Biol.
, vol.13
, pp. 508-523
-
-
Kulathu, Y.1
Komander, D.2
-
32
-
-
78649575597
-
Total chemical synthesis of di-ubiquitin chains
-
Kumar, K.S.A., Spasser, L., Erlich, L.A., Bavikar, S.N., Brik, A., Total chemical synthesis of di-ubiquitin chains. Angew. Chem. Int. Ed. Engl. 49 (2010), 9126–9131.
-
(2010)
Angew. Chem. Int. Ed. Engl.
, vol.49
, pp. 9126-9131
-
-
Kumar, K.S.A.1
Spasser, L.2
Erlich, L.A.3
Bavikar, S.N.4
Brik, A.5
-
33
-
-
84944441665
-
Disruption of the autoinhibited state primes the E3 ligase parkin for activation and catalysis
-
Kumar, A., Aguirre, J.D., Condos, T.E.C., Martinez-Torres, R.J., Chaugule, V.K., Toth, R., Sundaramoorthy, R., Mercier, P., Knebel, A., Spratt, D.E., et al. Disruption of the autoinhibited state primes the E3 ligase parkin for activation and catalysis. EMBO J. 34 (2015), 2506–2521.
-
(2015)
EMBO J.
, vol.34
, pp. 2506-2521
-
-
Kumar, A.1
Aguirre, J.D.2
Condos, T.E.C.3
Martinez-Torres, R.J.4
Chaugule, V.K.5
Toth, R.6
Sundaramoorthy, R.7
Mercier, P.8
Knebel, A.9
Spratt, D.E.10
-
34
-
-
84949520315
-
Phosphoproteomic screening identifies Rab GTPases as novel downstream targets of PINK1
-
Lai, Y.-C., Kondapalli, C., Lehneck, R., Procter, J.B., Dill, B.D., Woodroof, H.I., Gourlay, R., Peggie, M., Macartney, T.J., Corti, O., et al. Phosphoproteomic screening identifies Rab GTPases as novel downstream targets of PINK1. EMBO J. 34 (2015), 2840–2861.
-
(2015)
EMBO J.
, vol.34
, pp. 2840-2861
-
-
Lai, Y.-C.1
Kondapalli, C.2
Lehneck, R.3
Procter, J.B.4
Dill, B.D.5
Woodroof, H.I.6
Gourlay, R.7
Peggie, M.8
Macartney, T.J.9
Corti, O.10
-
35
-
-
84939804206
-
The ubiquitin kinase PINK1 recruits autophagy receptors to induce mitophagy
-
Lazarou, M., Sliter, D.A., Kane, L.A., Sarraf, S.A., Wang, C., Burman, J.L., Sideris, D.P., Fogel, A.I., Youle, R.J., The ubiquitin kinase PINK1 recruits autophagy receptors to induce mitophagy. Nature 524 (2015), 309–314.
-
(2015)
Nature
, vol.524
, pp. 309-314
-
-
Lazarou, M.1
Sliter, D.A.2
Kane, L.A.3
Sarraf, S.A.4
Wang, C.5
Burman, J.L.6
Sideris, D.P.7
Fogel, A.I.8
Youle, R.J.9
-
36
-
-
84863323068
-
Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues
-
Lundby, A., Secher, A., Lage, K., Nordsborg, N.B., Dmytriyev, A., Lundby, C., Olsen, J.V., Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues. Nat. Commun., 3, 2012, 876.
-
(2012)
Nat. Commun.
, vol.3
, pp. 876
-
-
Lundby, A.1
Secher, A.2
Lage, K.3
Nordsborg, N.B.4
Dmytriyev, A.5
Lundby, C.6
Olsen, J.V.7
-
37
-
-
70349974263
-
Quantitative analysis of the human spindle phosphoproteome at distinct mitotic stages
-
Malik, R., Lenobel, R., Santamaria, A., Ries, A., Nigg, E.A., Körner, R., Quantitative analysis of the human spindle phosphoproteome at distinct mitotic stages. J. Proteome Res. 8 (2009), 4553–4563.
-
(2009)
J. Proteome Res.
, vol.8
, pp. 4553-4563
-
-
Malik, R.1
Lenobel, R.2
Santamaria, A.3
Ries, A.4
Nigg, E.A.5
Körner, R.6
-
38
-
-
79953187997
-
Discovery of mouse spleen signaling responses to anthrax using label-free quantitative phosphoproteomics via mass spectrometry
-
M110.000927
-
Manes, N.P., Dong, L., Zhou, W., Du, X., Reghu, N., Kool, A.C., Choi, D., Bailey, C.L., Petricoin, E.F., Liotta, L.A., Popov, S.G., Discovery of mouse spleen signaling responses to anthrax using label-free quantitative phosphoproteomics via mass spectrometry. Mol. Cell. Proteomics, 10, 2011 M110.000927.
-
(2011)
Mol. Cell. Proteomics
, vol.10
-
-
Manes, N.P.1
Dong, L.2
Zhou, W.3
Du, X.4
Reghu, N.5
Kool, A.C.6
Choi, D.7
Bailey, C.L.8
Petricoin, E.F.9
Liotta, L.A.10
Popov, S.G.11
-
39
-
-
34447508216
-
Phaser crystallographic software
-
McCoy, A.J., Grosse-Kunstleve, R.W., Adams, P.D., Winn, M.D., Storoni, L.C., Read, R.J., Phaser crystallographic software. J. Appl. Cryst. 40 (2007), 658–674.
-
(2007)
J. Appl. Cryst.
, vol.40
, pp. 658-674
-
-
McCoy, A.J.1
Grosse-Kunstleve, R.W.2
Adams, P.D.3
Winn, M.D.4
Storoni, L.C.5
Read, R.J.6
-
40
-
-
84878832998
-
OTU deubiquitinases reveal mechanisms of linkage specificity and enable ubiquitin chain restriction analysis
-
Mevissen, T.E., Hospenthal, M.K., Geurink, P.P., Elliott, P.R., Akutsu, M., Arnaudo, N., Ekkebus, R., Kulathu, Y., Wauer, T., El Oualid, F., et al. OTU deubiquitinases reveal mechanisms of linkage specificity and enable ubiquitin chain restriction analysis. Cell 154 (2013), 169–184.
-
(2013)
Cell
, vol.154
, pp. 169-184
-
-
Mevissen, T.E.1
Hospenthal, M.K.2
Geurink, P.P.3
Elliott, P.R.4
Akutsu, M.5
Arnaudo, N.6
Ekkebus, R.7
Kulathu, Y.8
Wauer, T.9
El Oualid, F.10
-
41
-
-
84949989892
-
Assembly and specific recognition of k29- and k33-linked polyubiquitin
-
Michel, M.A., Elliott, P.R., Swatek, K.N., Simicek, M., Pruneda, J.N., Wagstaff, J.L., Freund, S.M.V., Komander, D., Assembly and specific recognition of k29- and k33-linked polyubiquitin. Mol. Cell 58 (2015), 95–109.
-
(2015)
Mol. Cell
, vol.58
, pp. 95-109
-
-
Michel, M.A.1
Elliott, P.R.2
Swatek, K.N.3
Simicek, M.4
Pruneda, J.N.5
Wagstaff, J.L.6
Freund, S.M.V.7
Komander, D.8
-
42
-
-
84922241634
-
Ubiquitin acetylation inhibits polyubiquitin chain elongation
-
Ohtake, F., Saeki, Y., Sakamoto, K., Ohtake, K., Nishikawa, H., Tsuchiya, H., Ohta, T., Tanaka, K., Kanno, J., Ubiquitin acetylation inhibits polyubiquitin chain elongation. EMBO Rep. 16 (2015), 192–201.
-
(2015)
EMBO Rep.
, vol.16
, pp. 192-201
-
-
Ohtake, F.1
Saeki, Y.2
Sakamoto, K.3
Ohtake, K.4
Nishikawa, H.5
Tsuchiya, H.6
Ohta, T.7
Tanaka, K.8
Kanno, J.9
-
43
-
-
84929691103
-
Defining roles of PARKIN and ubiquitin phosphorylation by PINK1 in mitochondrial quality control using a ubiquitin replacement strategy
-
Ordureau, A., Heo, J.-M., Duda, D.M., Paulo, J.A., Olszewski, J.L., Yanishevski, D., Rinehart, J., Schulman, B.A., Harper, J.W., Defining roles of PARKIN and ubiquitin phosphorylation by PINK1 in mitochondrial quality control using a ubiquitin replacement strategy. Proc. Natl. Acad. Sci. USA 112 (2015), 6637–6642.
-
(2015)
Proc. Natl. Acad. Sci. USA
, vol.112
, pp. 6637-6642
-
-
Ordureau, A.1
Heo, J.-M.2
Duda, D.M.3
Paulo, J.A.4
Olszewski, J.L.5
Yanishevski, D.6
Rinehart, J.7
Schulman, B.A.8
Harper, J.W.9
-
44
-
-
80052165817
-
Expanding the genetic code of Escherichia coli with phosphoserine
-
Park, H.-S., Hohn, M.J., Umehara, T., Guo, L.-T., Osborne, E.M., Benner, J., Noren, C.J., Rinehart, J., Söll, D., Expanding the genetic code of Escherichia coli with phosphoserine. Science 333 (2011), 1151–1154.
-
(2011)
Science
, vol.333
, pp. 1151-1154
-
-
Park, H.-S.1
Hohn, M.J.2
Umehara, T.3
Guo, L.-T.4
Osborne, E.M.5
Benner, J.6
Noren, C.J.7
Rinehart, J.8
Söll, D.9
-
45
-
-
80053374337
-
Proteomic and phosphoproteomic comparison of human ES and iPS cells
-
Phanstiel, D.H., Brumbaugh, J., Wenger, C.D., Tian, S., Probasco, M.D., Bailey, D.J., Swaney, D.L., Tervo, M.A., Bolin, J.M., Ruotti, V., et al. Proteomic and phosphoproteomic comparison of human ES and iPS cells. Nat. Methods 8 (2011), 821–827.
-
(2011)
Nat. Methods
, vol.8
, pp. 821-827
-
-
Phanstiel, D.H.1
Brumbaugh, J.2
Wenger, C.D.3
Tian, S.4
Probasco, M.D.5
Bailey, D.J.6
Swaney, D.L.7
Tervo, M.A.8
Bolin, J.M.9
Ruotti, V.10
-
46
-
-
33746827805
-
Structural basis of ubiquitin recognition by the deubiquitinating protease USP2
-
Renatus, M., Parrado, S.G., D'Arcy, A., Eidhoff, U., Gerhartz, B., Hassiepen, U., Pierrat, B., Riedl, R., Vinzenz, D., Worpenberg, S., Kroemer, M., Structural basis of ubiquitin recognition by the deubiquitinating protease USP2. Structure 14 (2006), 1293–1302.
-
(2006)
Structure
, vol.14
, pp. 1293-1302
-
-
Renatus, M.1
Parrado, S.G.2
D'Arcy, A.3
Eidhoff, U.4
Gerhartz, B.5
Hassiepen, U.6
Pierrat, B.7
Riedl, R.8
Vinzenz, D.9
Worpenberg, S.10
Kroemer, M.11
-
47
-
-
84907358982
-
Screening of DUB activity and specificity by MALDI-TOF mass spectrometry
-
Ritorto, M.S., Ewan, R., Perez-Oliva, A.B., Knebel, A., Buhrlage, S.J., Wightman, M., Kelly, S.M., Wood, N.T., Virdee, S., Gray, N.S., et al. Screening of DUB activity and specificity by MALDI-TOF mass spectrometry. Nat. Commun., 5, 2014, 4763.
-
(2014)
Nat. Commun.
, vol.5
, pp. 4763
-
-
Ritorto, M.S.1
Ewan, R.2
Perez-Oliva, A.B.3
Knebel, A.4
Buhrlage, S.J.5
Wightman, M.6
Kelly, S.M.7
Wood, N.T.8
Virdee, S.9
Gray, N.S.10
-
48
-
-
84931565890
-
Efficient genetic encoding of phosphoserine and its nonhydrolyzable analog
-
Rogerson, D.T., Sachdeva, A., Wang, K., Haq, T., Kazlauskaite, A., Hancock, S.M., Huguenin-Dezot, N., Muqit, M.M.K., Fry, A.M., Bayliss, R., Chin, J.W., Efficient genetic encoding of phosphoserine and its nonhydrolyzable analog. Nat. Chem. Biol. 11 (2015), 496–503.
-
(2015)
Nat. Chem. Biol.
, vol.11
, pp. 496-503
-
-
Rogerson, D.T.1
Sachdeva, A.2
Wang, K.3
Haq, T.4
Kazlauskaite, A.5
Hancock, S.M.6
Huguenin-Dezot, N.7
Muqit, M.M.K.8
Fry, A.M.9
Bayliss, R.10
Chin, J.W.11
-
49
-
-
52149103164
-
Structural basis for specific cleavage of Lys 63-linked polyubiquitin chains
-
Sato, Y., Yoshikawa, A., Yamagata, A., Mimura, H., Yamashita, M., Ookata, K., Nureki, O., Iwai, K., Komada, M., Fukai, S., Structural basis for specific cleavage of Lys 63-linked polyubiquitin chains. Nature 455 (2008), 358–362.
-
(2008)
Nature
, vol.455
, pp. 358-362
-
-
Sato, Y.1
Yoshikawa, A.2
Yamagata, A.3
Mimura, H.4
Yamashita, M.5
Ookata, K.6
Nureki, O.7
Iwai, K.8
Komada, M.9
Fukai, S.10
-
50
-
-
84924269252
-
Structures of CYLD USP with Met1- or Lys63-linked diubiquitin reveal mechanisms for dual specificity
-
Sato, Y., Goto, E., Shibata, Y., Kubota, Y., Yamagata, A., Goto-Ito, S., Kubota, K., Inoue, J., Takekawa, M., Tokunaga, F., Fukai, S., Structures of CYLD USP with Met1- or Lys63-linked diubiquitin reveal mechanisms for dual specificity. Nat. Struct. Mol. Biol. 22 (2015), 222–229.
-
(2015)
Nat. Struct. Mol. Biol.
, vol.22
, pp. 222-229
-
-
Sato, Y.1
Goto, E.2
Shibata, Y.3
Kubota, Y.4
Yamagata, A.5
Goto-Ito, S.6
Kubota, K.7
Inoue, J.8
Takekawa, M.9
Tokunaga, F.10
Fukai, S.11
-
51
-
-
84922537688
-
Ultradeep human phosphoproteome reveals a distinct regulatory nature of Tyr and Ser/Thr-based signaling
-
Sharma, K., D'Souza, R.C.J., Tyanova, S., Schaab, C., Wiśniewski, J.R., Cox, J., Mann, M., Ultradeep human phosphoproteome reveals a distinct regulatory nature of Tyr and Ser/Thr-based signaling. Cell Rep. 8 (2014), 1583–1594.
-
(2014)
Cell Rep.
, vol.8
, pp. 1583-1594
-
-
Sharma, K.1
D'Souza, R.C.J.2
Tyanova, S.3
Schaab, C.4
Wiśniewski, J.R.5
Cox, J.6
Mann, M.7
-
52
-
-
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., PINK1-mediated phosphorylation of the Parkin ubiquitin-like domain primes mitochondrial translocation of Parkin and regulates mitophagy. Sci. Rep., 2, 2012, 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
-
53
-
-
84869065540
-
Revised AMBER parameters for bioorganic phosphates
-
Steinbrecher, T., Latzer, J., Case, D.A., Revised AMBER parameters for bioorganic phosphates. J. Chem. Theory Comput. 8 (2012), 4405–4412.
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 4405-4412
-
-
Steinbrecher, T.1
Latzer, J.2
Case, D.A.3
-
54
-
-
84940792247
-
Phosphorylation of ubiquitin at Ser65 affects its polymerization, targets, and proteome-wide turnover
-
Swaney, D.L., Rodríguez-Mias, R.A., Villén, J., Phosphorylation of ubiquitin at Ser65 affects its polymerization, targets, and proteome-wide turnover. EMBO Rep. 16 (2015), 1131–1144.
-
(2015)
EMBO Rep.
, vol.16
, pp. 1131-1144
-
-
Swaney, D.L.1
Rodríguez-Mias, R.A.2
Villén, J.3
-
55
-
-
2442668926
-
Hereditary early-onset Parkinson's disease caused by mutations in PINK1
-
Valente, E.M., Abou-Sleiman, P.M., Caputo, V., Muqit, M.M.K., Harvey, K., Gispert, S., Ali, Z., Del Turco, D., Bentivoglio, A.R., Healy, D.G., et al. Hereditary early-onset Parkinson's disease caused by mutations in PINK1. Science 304 (2004), 1158–1160.
-
(2004)
Science
, vol.304
, pp. 1158-1160
-
-
Valente, E.M.1
Abou-Sleiman, P.M.2
Caputo, V.3
Muqit, M.M.K.4
Harvey, K.5
Gispert, S.6
Ali, Z.7
Del Turco, D.8
Bentivoglio, A.R.9
Healy, D.G.10
-
56
-
-
0023644679
-
Structure of ubiquitin refined at 1.8 A resolution
-
Vijay-Kumar, S., Bugg, C.E., Cook, W.J., Structure of ubiquitin refined at 1.8 A resolution. J. Mol. Biol. 194 (1987), 531–544.
-
(1987)
J. Mol. Biol.
, vol.194
, pp. 531-544
-
-
Vijay-Kumar, S.1
Bugg, C.E.2
Cook, W.J.3
-
57
-
-
33846785485
-
Large-scale phosphorylation analysis of mouse liver
-
Villén, J., Beausoleil, S.A., Gerber, S.A., Gygi, S.P., Large-scale phosphorylation analysis of mouse liver. Proc. Natl. Acad. Sci. USA 104 (2007), 1488–1493.
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 1488-1493
-
-
Villén, J.1
Beausoleil, S.A.2
Gerber, S.A.3
Gygi, S.P.4
-
58
-
-
77956903406
-
Engineered diubiquitin synthesis reveals Lys29-isopeptide specificity of an OTU deubiquitinase
-
Virdee, S., Ye, Y., Nguyen, D.P., Komander, D., Chin, J.W., Engineered diubiquitin synthesis reveals Lys29-isopeptide specificity of an OTU deubiquitinase. Nat. Chem. Biol. 6 (2010), 750–757.
-
(2010)
Nat. Chem. Biol.
, vol.6
, pp. 750-757
-
-
Virdee, S.1
Ye, Y.2
Nguyen, D.P.3
Komander, D.4
Chin, J.W.5
-
59
-
-
84922235969
-
Ubiquitin Ser65 phosphorylation affects ubiquitin structure, chain assembly and hydrolysis
-
Wauer, T., Swatek, K.N., Wagstaff, J.L., Gladkova, C., Pruneda, J.N., Michel, M.A., Gersch, M., Johnson, C.M., Freund, S.M., Komander, D., Ubiquitin Ser65 phosphorylation affects ubiquitin structure, chain assembly and hydrolysis. EMBO J. 34 (2015), 307–325.
-
(2015)
EMBO J.
, vol.34
, pp. 307-325
-
-
Wauer, T.1
Swatek, K.N.2
Wagstaff, J.L.3
Gladkova, C.4
Pruneda, J.N.5
Michel, M.A.6
Gersch, M.7
Johnson, C.M.8
Freund, S.M.9
Komander, D.10
-
60
-
-
84874093507
-
Toward a comprehensive characterization of a human cancer cell phosphoproteome
-
Zhou, H., Di Palma, S., Preisinger, C., Peng, M., Polat, A.N., Heck, A.J.R., Mohammed, S., Toward a comprehensive characterization of a human cancer cell phosphoproteome. J. Proteome Res. 12 (2013), 260–271.
-
(2013)
J. Proteome Res.
, vol.12
, pp. 260-271
-
-
Zhou, H.1
Di Palma, S.2
Preisinger, C.3
Peng, M.4
Polat, A.N.5
Heck, A.J.R.6
Mohammed, S.7
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