-
1
-
-
84871031152
-
Ubiquitin chain conformation regulates recognition and activity of interacting proteins
-
Ye Y, et al. (2012) Ubiquitin chain conformation regulates recognition and activity of interacting proteins. Nature 492:266-270.
-
(2012)
Nature
, vol.492
, pp. 266-270
-
-
Ye, Y.1
-
2
-
-
84937395775
-
Lys63-linked ubiquitin chain adopts multiple conformational states for specific target recognition
-
Liu Z, et al. (2015) Lys63-linked ubiquitin chain adopts multiple conformational states for specific target recognition. eLife 4:e05767.
-
(2015)
ELife
, vol.4
, pp. e05767
-
-
Liu, Z.1
-
3
-
-
84971236561
-
The increasing complexity of the ubiquitin code
-
Yau R, Rape M (2016) The increasing complexity of the ubiquitin code. Nat Cell Biol 18:579-586.
-
(2016)
Nat Cell Biol
, vol.18
, pp. 579-586
-
-
Yau, R.1
Rape, M.2
-
4
-
-
84940783815
-
Expanding the ubiquitin code through post-translational modification
-
Herhaus L, Dikic I (2015) Expanding the ubiquitin code through post-translational modification. EMBO Rep 16:1071-1083.
-
(2015)
EMBO Rep
, vol.16
, pp. 1071-1083
-
-
Herhaus, L.1
Dikic, I.2
-
5
-
-
84961743030
-
Ubiquitin modifications
-
Swatek KN, Komander D (2016) Ubiquitin modifications. Cell Res 26:399-422.
-
(2016)
Cell Res
, vol.26
, pp. 399-422
-
-
Swatek, K.N.1
Komander, D.2
-
6
-
-
84901751574
-
Ubiquitin is phosphorylated by PINK1 to activate parkin
-
Koyano F, 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
-
7
-
-
84899539731
-
PINK1 phosphorylates ubiquitin to activate Parkin E3 ubiquitin ligase activity
-
Kane LA, et al. (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
-
8
-
-
84940792247
-
Phosphorylation of ubiquitin at Ser65 affects its polymerization, targets, and proteome-wide turnover
-
Swaney DL, Rodríguez-Mias RA, Villén J (2015) Phosphorylation of ubiquitin at Ser65 affects its polymerization, targets, and proteome-wide turnover. EMBO Rep 16:1131-1144.
-
(2015)
EMBO Rep
, vol.16
, pp. 1131-1144
-
-
Swaney, D.L.1
Rodríguez-Mias, R.A.2
Villén, J.3
-
9
-
-
84939795423
-
Mechanism of phosphoubiquitin-induced PARKIN activation
-
Wauer T, Simicek M, Schubert A, Komander D (2015) Mechanism of phosphoubiquitin-induced PARKIN activation. Nature 524:370-374.
-
(2015)
Nature
, vol.524
, pp. 370-374
-
-
Wauer, T.1
Simicek, M.2
Schubert, A.3
Komander, D.4
-
10
-
-
84944441112
-
A Ubl/ubiquitin switch in the activation of Parkin
-
Sauvé V, et al. (2015) A Ubl/ubiquitin switch in the activation of Parkin. EMBO J 34: 2492-2505.
-
(2015)
EMBO J
, vol.34
, pp. 2492-2505
-
-
Sauvé, V.1
-
11
-
-
84939804206
-
The ubiquitin kinase PINK1 recruits autophagy receptors to induce mitophagy
-
Lazarou M, et al. (2015) The ubiquitin kinase PINK1 recruits autophagy receptors to induce mitophagy. Nature 524:309-314.
-
(2015)
Nature
, vol.524
, pp. 309-314
-
-
Lazarou, M.1
-
12
-
-
85017499246
-
Parkin-phosphoubiquitin complex reveals cryptic ubiquitinbinding site required for RBR ligase activity
-
Kumar A, et al. (2017) Parkin-phosphoubiquitin complex reveals cryptic ubiquitinbinding site required for RBR ligase activity. Nat Struct Mol Biol 24:475-483.
-
(2017)
Nat Struct Mol Biol
, vol.24
, pp. 475-483
-
-
Kumar, A.1
-
13
-
-
84922235969
-
Ubiquitin Ser65 phosphorylation affects ubiquitin structure, chain assembly and hydrolysis
-
Wauer T, et al. (2015) Ubiquitin Ser65 phosphorylation affects ubiquitin structure, chain assembly and hydrolysis. EMBO J 34:307-325.
-
(2015)
EMBO J
, vol.34
, pp. 307-325
-
-
Wauer, T.1
-
14
-
-
84937253640
-
A versatile strategy for the semisynthetic production of Ser65 phosphorylated ubiquitin and its biochemical and structural characterisation
-
Han C, Pao KC, Kazlauskaite A, Muqit MM, Virdee S (2015) A versatile strategy for the semisynthetic production of Ser65 phosphorylated ubiquitin and its biochemical and structural characterisation. ChemBioChem 16:1574-1579.
-
(2015)
ChemBioChem
, vol.16
, pp. 1574-1579
-
-
Han, C.1
Pao, K.C.2
Kazlauskaite, A.3
Muqit, M.M.4
Virdee, S.5
-
16
-
-
77955405903
-
Cytosolic pH is a second messenger for glucose and regulates the PKA pathway through V-ATPase
-
Dechant R, et al. (2010) Cytosolic pH is a second messenger for glucose and regulates the PKA pathway through V-ATPase. EMBO J 29:2515-2526.
-
(2010)
EMBO J
, vol.29
, pp. 2515-2526
-
-
Dechant, R.1
-
17
-
-
84867273800
-
ROS-induced mitochondrial depolarization initiates PARK2/PARKIN-dependent mitochondrial degradation by autophagy
-
Wang Y, Nartiss Y, Steipe B, McQuibban GA, Kim PK (2012) ROS-induced mitochondrial depolarization initiates PARK2/PARKIN-dependent mitochondrial degradation by autophagy. Autophagy 8:1462-1476.
-
(2012)
Autophagy
, vol.8
, pp. 1462-1476
-
-
Wang, Y.1
Nartiss, Y.2
Steipe, B.3
McQuibban, G.A.4
Kim, P.K.5
-
18
-
-
0023644679
-
Structure of ubiquitin refined at 1.8 A resolution
-
Vijay-Kumar S, Bugg CE, Cook WJ (1987) Structure of ubiquitin refined at 1.8 A resolution. J Mol Biol 194:531-544.
-
(1987)
J Mol Biol
, vol.194
, pp. 531-544
-
-
Vijay-Kumar, S.1
Bugg, C.E.2
Cook, W.J.3
-
19
-
-
0032528033
-
Validation of protein structure from anisotropic carbonyl chemical shifts in a dilute liquid crystalline phase
-
Cornilescu G, Marquardt JL, Ottiger M, Bax A (1998) Validation of protein structure from anisotropic carbonyl chemical shifts in a dilute liquid crystalline phase. J Am Chem Soc 120:6836-6837.
-
(1998)
J Am Chem Soc
, vol.120
, pp. 6836-6837
-
-
Cornilescu, G.1
Marquardt, J.L.2
Ottiger, M.3
Bax, A.4
-
20
-
-
0033377656
-
Random-coil chemical shifts of phosphorylated amino acids
-
Bienkiewicz EA, Lumb KJ (1999) Random-coil chemical shifts of phosphorylated amino acids. J Biomol NMR 15:203-206.
-
(1999)
J Biomol NMR
, vol.15
, pp. 203-206
-
-
Bienkiewicz, E.A.1
Lumb, K.J.2
-
21
-
-
84922003154
-
PH-dependent random coil (1)H, (13)C, and (15)N chemical shifts of the ionizable amino acids: A guide for protein pKa measurements
-
Platzer G, Okon M, McIntosh LP (2014) pH-dependent random coil (1)H, (13)C, and (15)N chemical shifts of the ionizable amino acids: A guide for protein pKa measurements. J Biomol NMR 60:109-129.
-
(2014)
J Biomol NMR
, vol.60
, pp. 109-129
-
-
Platzer, G.1
Okon, M.2
McIntosh, L.P.3
-
22
-
-
63049125531
-
Quantitative proteomics reveals the function of unconventional ubiquitin chains in proteasomal degradation
-
Xu P, et al. (2009) Quantitative proteomics reveals the function of unconventional ubiquitin chains in proteasomal degradation. Cell 137:133-145.
-
(2009)
Cell
, vol.137
, pp. 133-145
-
-
Xu, P.1
-
23
-
-
84902663891
-
Single-molecule FRET of protein structure and dynamics-A primer
-
Schuler B (2013) Single-molecule FRET of protein structure and dynamics-A primer. J Nanobiotechnology 11(Suppl 1):S2.
-
(2013)
J Nanobiotechnology
, vol.11
, pp. S2
-
-
Schuler, B.1
-
24
-
-
84957427531
-
Deciphering complexity in molecular biophysics with single-molecule resolution
-
Deniz AA (2016) Deciphering complexity in molecular biophysics with single-molecule resolution. J Mol Biol 428:301-307.
-
(2016)
J Mol Biol
, vol.428
, pp. 301-307
-
-
Deniz, A.A.1
-
25
-
-
38749106195
-
Structure and mechanism of the M2 proton channel of influenza A virus
-
Schnell JR, Chou JJ (2008) Structure and mechanism of the M2 proton channel of influenza A virus. Nature 451:591-595.
-
(2008)
Nature
, vol.451
, pp. 591-595
-
-
Schnell, J.R.1
Chou, J.J.2
-
26
-
-
84870659973
-
PH-dependent conformational changes in proteins and their effect on experimental pK(a)s: The case of Nitrophorin 4
-
Di Russo NV, Estrin DA, Martí MA, Roitberg AE (2012) pH-dependent conformational changes in proteins and their effect on experimental pK(a)s: The case of Nitrophorin 4. PLOS Comput Biol 8:e1002761.
-
(2012)
PLOS Comput Biol
, vol.8
, pp. e1002761
-
-
Di Russo, N.V.1
Estrin, D.A.2
Martí, M.A.3
Roitberg, A.E.4
-
27
-
-
84882600742
-
Protons as second messenger regulators of G protein signaling
-
Isom DG, et al. (2013) Protons as second messenger regulators of G protein signaling. Mol Cell 51:531-538.
-
(2013)
Mol Cell
, vol.51
, pp. 531-538
-
-
Isom, D.G.1
-
28
-
-
80054809736
-
Conformational dynamics of wild-type Lys-48-linked diubiquitin in solution
-
Hirano T, et al. (2011) Conformational dynamics of wild-type Lys-48-linked diubiquitin in solution. J Biol Chem 286:37496-37502.
-
(2011)
J Biol Chem
, vol.286
, pp. 37496-37502
-
-
Hirano, T.1
-
29
-
-
84866998027
-
Structural and biochemical studies of the open state of Lys48-linked diubiquitin
-
LaiMY, Zhang D, Laronde-Leblanc N, Fushman D (2012) Structural and biochemical studies of the open state of Lys48-linked diubiquitin. Biochim Biophys Acta 1823:2046-2056.
-
(2012)
Biochim Biophys Acta
, vol.1823
, pp. 2046-2056
-
-
Lai, M.Y.1
Zhang, D.2
Laronde-Leblanc, N.3
Fushman, D.4
-
30
-
-
84964557331
-
Cytosolic PINK1 promotes the targeting of ubiquitinated proteins to the aggresome-autophagy pathway during proteasomal stress
-
Gao J, et al. (2016) Cytosolic PINK1 promotes the targeting of ubiquitinated proteins to the aggresome-autophagy pathway during proteasomal stress. Autophagy 12:632-647.
-
(2016)
Autophagy
, vol.12
, pp. 632-647
-
-
Gao, J.1
-
31
-
-
84940776745
-
(Patho-)Physiological relevance of PINK1-dependent ubiquitin phosphorylation
-
Fiesel FC, et al. (2015) (Patho-)Physiological relevance of PINK1-dependent ubiquitin phosphorylation. EMBO Rep 16:1114-1130.
-
(2015)
EMBO Rep
, vol.16
, pp. 1114-1130
-
-
Fiesel, F.C.1
-
32
-
-
0034523187
-
Mitochondria-dependent apoptosis and cellular pH regulation
-
Matsuyama S, Reed JC (2000) Mitochondria-dependent apoptosis and cellular pH regulation. Cell Death Differ 7:1155-1165.
-
(2000)
Cell Death Differ
, vol.7
, pp. 1155-1165
-
-
Matsuyama, S.1
Reed, J.C.2
-
33
-
-
84976507272
-
Tight coupling of astrocyte pH dynamics to epileptiform activity revealed by genetically encoded pH sensors
-
Raimondo JV, et al. (2016) Tight coupling of astrocyte pH dynamics to epileptiform activity revealed by genetically encoded pH sensors. J Neurosci 36:7002-7013.
-
(2016)
J Neurosci
, vol.36
, pp. 7002-7013
-
-
Raimondo, J.V.1
-
35
-
-
4544246352
-
Alterations of intracellular pH homeostasis in apoptosis: Origins and roles
-
Lagadic-Gossmann D, Huc L, Lecureur V (2004) Alterations of intracellular pH homeostasis in apoptosis: Origins and roles. Cell Death Differ 11:953-961.
-
(2004)
Cell Death Differ
, vol.11
, pp. 953-961
-
-
Lagadic-Gossmann, D.1
Huc, L.2
Lecureur, V.3
-
36
-
-
28844462033
-
Controlled synthesis of polyubiquitin chains
-
Pickart CM, Raasi S (2005) Controlled synthesis of polyubiquitin chains. Methods Enzymol 399:21-36.
-
(2005)
Methods Enzymol
, vol.399
, pp. 21-36
-
-
Pickart, C.M.1
Raasi, S.2
-
37
-
-
84958526656
-
Ensemble structure description of Lys63-linked diubiquitin
-
Liu Z, Tang C (2016) Ensemble structure description of Lys63-linked diubiquitin. Data Brief 7:81-88.
-
(2016)
Data Brief
, vol.7
, pp. 81-88
-
-
Liu, Z.1
Tang, C.2
-
40
-
-
33644753023
-
AMBER force-field parameters for phosphorylated amino acids in different protonation states: Phosphoserine, phosphothreonine, phosphotyrosine, and phosphohistidine
-
Homeyer N, Horn AH, Lanig H, Sticht H (2006) AMBER force-field parameters for phosphorylated amino acids in different protonation states: Phosphoserine, phosphothreonine, phosphotyrosine, and phosphohistidine. J Mol Model 12:281-289.
-
(2006)
J Mol Model
, vol.12
, pp. 281-289
-
-
Homeyer, N.1
Horn, A.H.2
Lanig, H.3
Sticht, H.4
-
41
-
-
84855443948
-
Noncovalent dimerization of ubiquitin
-
Liu Z, et al. (2012) Noncovalent dimerization of ubiquitin. Angew Chem Int Ed Engl 51:469-472.
-
(2012)
Angew Chem Int Ed Engl
, vol.51
, pp. 469-472
-
-
Liu, Z.1
-
42
-
-
84870852782
-
A toolkit and benchmark study for FRET-restrained highprecision structural modeling
-
Kalinin S, et al. (2012) A toolkit and benchmark study for FRET-restrained highprecision structural modeling. Nat Methods 9:1218-1225.
-
(2012)
Nat Methods
, vol.9
, pp. 1218-1225
-
-
Kalinin, S.1
-
43
-
-
0029400480
-
NMRPipe: A multidimensional spectral processing system based on UNIX pipes
-
Delaglio F, et al. (1995) NMRPipe: A multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6:277-293.
-
(1995)
J Biomol NMR
, vol.6
, pp. 277-293
-
-
Delaglio, F.1
-
44
-
-
19444382397
-
The CCPN data model for NMR spectroscopy: Development of a software pipeline
-
Vranken WF, et al. (2005) The CCPN data model for NMR spectroscopy: Development of a software pipeline. Proteins 59:687-696.
-
(2005)
Proteins
, vol.59
, pp. 687-696
-
-
Vranken, W.F.1
-
45
-
-
0031760503
-
Tunable alignment of macromolecules by filamentous phage yields dipolar coupling interactions
-
Hansen MR, Mueller L, Pardi A (1998) Tunable alignment of macromolecules by filamentous phage yields dipolar coupling interactions. Nat Struct Biol 5:1065-1074.
-
(1998)
Nat Struct Biol
, vol.5
, pp. 1065-1074
-
-
Hansen, M.R.1
Mueller, L.2
Pardi, A.3
-
46
-
-
0037551646
-
Alignment of biological macromolecules in novel nonionic liquid crystalline media for NMR experiments
-
Rücket M, Otting G (2000) Alignment of biological macromolecules in novel nonionic liquid crystalline media for NMR experiments. J Am Chem Soc 122:7793-7797.
-
(2000)
J Am Chem Soc
, vol.122
, pp. 7793-7797
-
-
Rücket, M.1
Otting, G.2
-
47
-
-
0032042263
-
Measurement of J and dipolar couplings from simplified two-dimensional NMR spectra
-
Ottiger M, Delaglio F, Bax A (1998) Measurement of J and dipolar couplings from simplified two-dimensional NMR spectra. J Magn Reson 131:373-378.
-
(1998)
J Magn Reson
, vol.131
, pp. 373-378
-
-
Ottiger, M.1
Delaglio, F.2
Bax, A.3
-
48
-
-
68349093958
-
TALOS+: A hybrid method for predicting protein backbone torsion angles from NMR chemical shifts
-
Shen Y, Delaglio F, Cornilescu G, Bax A (2009) TALOS+: A hybrid method for predicting protein backbone torsion angles from NMR chemical shifts. J Biomol NMR 44:213-223.
-
(2009)
J Biomol NMR
, vol.44
, pp. 213-223
-
-
Shen, Y.1
Delaglio, F.2
Cornilescu, G.3
Bax, A.4
-
49
-
-
12044259775
-
Quantitative J correlation: A new approach for measuring homonuclear three-bond J(H(N)H(alpha)) coupling constants in 15N-enriched proteins
-
Vuister GW, Bax A (1993) Quantitative J correlation: A new approach for measuring homonuclear three-bond J(H(N)H(alpha)) coupling constants in 15N-enriched proteins. J Am Chem Soc 115:7772-7777.
-
(1993)
J Am Chem Soc
, vol.115
, pp. 7772-7777
-
-
Vuister, G.W.1
Bax, A.2
-
50
-
-
44949111363
-
A pseudopotential for improving the packing of ellipsoidal protein structures determined from NMR data
-
Schwieters CD, Clore GM (2008) A pseudopotential for improving the packing of ellipsoidal protein structures determined from NMR data. J Phys Chem B 112:6070-6073.
-
(2008)
J Phys Chem B
, vol.112
, pp. 6070-6073
-
-
Schwieters, C.D.1
Clore, G.M.2
-
51
-
-
84870371264
-
Smooth statistical torsion angle potential derived from a large conformational database via adaptive kernel density estimation improves the quality of NMR protein structures
-
Bermejo GA, Clore GM, Schwieters CD (2012) Smooth statistical torsion angle potential derived from a large conformational database via adaptive kernel density estimation improves the quality of NMR protein structures. Protein Sci 21:1824-1836.
-
(2012)
Protein Sci
, vol.21
, pp. 1824-1836
-
-
Bermejo, G.A.1
Clore, G.M.2
Schwieters, C.D.3
-
52
-
-
3242886771
-
PDB2PQR: An automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations
-
Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA (2004) PDB2PQR: An automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res 32:W665-W667.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. W665-W667
-
-
Dolinsky, T.J.1
Nielsen, J.E.2
McCammon, J.A.3
Baker, N.A.4
-
53
-
-
0034687122
-
Interaction of the lantibiotic nisin with mixed lipid bilayers: A 31P and 2H NMR study
-
Bonev BB, Chan WC, Bycroft BW, Roberts GC,Watts A (2000) Interaction of the lantibiotic nisin with mixed lipid bilayers: A 31P and 2H NMR study. Biochemistry 39:11425-11433.
-
(2000)
Biochemistry
, vol.39
, pp. 11425-11433
-
-
Bonev, B.B.1
Chan, W.C.2
Bycroft, B.W.3
Roberts, G.C.4
Watts, A.5
-
55
-
-
22144492905
-
Accurate FRET measurements within single diffusing biomolecules using alternating-laser excitation
-
Lee NK, et al. (2005) Accurate FRET measurements within single diffusing biomolecules using alternating-laser excitation. Biophys J 88:2939-2953.
-
(2005)
Biophys J
, vol.88
, pp. 2939-2953
-
-
Lee, N.K.1
-
56
-
-
84923805315
-
Accuracy of maximum likelihood estimates of a two-state model in single-molecule FRET
-
Gopich IV (2015) Accuracy of maximum likelihood estimates of a two-state model in single-molecule FRET. J Chem Phys 142:034110.
-
(2015)
J Chem Phys
, vol.142
, pp. 034110
-
-
Gopich, I.V.1
-
57
-
-
8744307994
-
Multimodel inference: Understanding AIC and BIC in model selection
-
Burnham KP, Anderson DR (2004) Multimodel inference: Understanding AIC and BIC in model selection. Sociol Methods Res 33:261-304.
-
(2004)
Sociol Methods Res
, vol.33
, pp. 261-304
-
-
Burnham, K.P.1
Anderson, D.R.2
-
58
-
-
0000120766
-
Estimating the dimension of a model
-
Schwarz G (1978) Estimating the dimension of a model. Ann Stat 6:461-464.
-
(1978)
Ann Stat
, vol.6
, pp. 461-464
-
-
Schwarz, G.1
-
59
-
-
0016355478
-
A new look at the statistical model identification
-
Akaike H (1974) A new look at the statistical model identification. IEEE Trans Automat Contr 19:716-723.
-
(1974)
IEEE Trans Automat Contr
, vol.19
, pp. 716-723
-
-
Akaike, H.1
-
60
-
-
53549084075
-
A reducing and oxidizing system minimizes photobleaching and blinking of fluorescent dyes
-
Vogelsang J, et al. (2008) A reducing and oxidizing system minimizes photobleaching and blinking of fluorescent dyes. Angew Chem Int Ed Engl 47:5465-5469.
-
(2008)
Angew Chem Int Ed Engl
, vol.47
, pp. 5465-5469
-
-
Vogelsang, J.1
-
61
-
-
0030339738
-
AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR
-
Laskowski RA, Rullmannn JA, MacArthur MW, Kaptein R, Thornton JM (1996) AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR. J Biomol NMR 8:477-486.
-
(1996)
J Biomol NMR
, vol.8
, pp. 477-486
-
-
Laskowski, R.A.1
Rullmannn, J.A.2
MacArthur, M.W.3
Kaptein, R.4
Thornton, J.M.5
|