-
1
-
-
34548154812
-
Small but versatile: the extraordinary functional and structural diversity of the beta-grasp fold
-
Burroughs A.M., Balaji S., Iyer L.M., Aravind L. Small but versatile: the extraordinary functional and structural diversity of the beta-grasp fold. Biol Direct 2007, 2:18.
-
(2007)
Biol Direct
, vol.2
, pp. 18
-
-
Burroughs, A.M.1
Balaji, S.2
Iyer, L.M.3
Aravind, L.4
-
3
-
-
70350150000
-
The emerging complexity of protein ubiquitination
-
Komander D. The emerging complexity of protein ubiquitination. Biochem Soc Trans 2009, 37:937-953.
-
(2009)
Biochem Soc Trans
, vol.37
, pp. 937-953
-
-
Komander, D.1
-
4
-
-
12744263121
-
Simultaneous determination of protein structure and dynamics
-
Lindorff-Larsen K., Best R.B., Depristo M.A., Dobson C.M., Vendruscolo M. Simultaneous determination of protein structure and dynamics. Nature 2005, 433:128.
-
(2005)
Nature
, vol.433
, pp. 128
-
-
Lindorff-Larsen, K.1
Best, R.B.2
Depristo, M.A.3
Dobson, C.M.4
Vendruscolo, M.5
-
5
-
-
0033613906
-
Native proteins are surface-molten solids: application of the Lindemann criterion for the solid versus liquid state
-
Zhou Y., Vitkup D., Karplus M. Native proteins are surface-molten solids: application of the Lindemann criterion for the solid versus liquid state. J Mol Biol 1999, 285:1371-1375.
-
(1999)
J Mol Biol
, vol.285
, pp. 1371-1375
-
-
Zhou, Y.1
Vitkup, D.2
Karplus, M.3
-
6
-
-
59149097931
-
Residual dipolar couplings as a tool to study molecular recognition of ubiquitin
-
Lakomek N.-A., Lange O.F., Walter K.F.A., Farès C., Egger D., Lunkenheimer P., Meiler J., Grubmüller H., Becker S., de Groot B.L., et al. Residual dipolar couplings as a tool to study molecular recognition of ubiquitin. Biochem Soc Trans 2008, 36:1433-1437.
-
(2008)
Biochem Soc Trans
, vol.36
, pp. 1433-1437
-
-
Lakomek, N.-A.1
Lange, O.F.2
Walter, K.F.A.3
Farès, C.4
Egger, D.5
Lunkenheimer, P.6
Meiler, J.7
Grubmüller, H.8
Becker, S.9
de Groot, B.L.10
-
7
-
-
45849131354
-
Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution
-
Lange O., Lakomek N.-A., Fares C., Schroder G., Walter K., Becker S., Meiler J., Grubmuller H., Griesinger C., De Groot B. Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution. Science 2008, 320:1471.
-
(2008)
Science
, vol.320
, pp. 1471
-
-
Lange, O.1
Lakomek, N.-A.2
Fares, C.3
Schroder, G.4
Walter, K.5
Becker, S.6
Meiler, J.7
Grubmuller, H.8
Griesinger, C.9
De Groot, B.10
-
8
-
-
73349117207
-
Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin
-
Wlodarski T., Zagrovic B. Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin. Proc Natl Acad Sci U S A 2009, 106:19346-19351.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 19346-19351
-
-
Wlodarski, T.1
Zagrovic, B.2
-
9
-
-
0001858251
-
Application of a theory of enzyme specificity to protein synthesis
-
Koshland D.E. Application of a theory of enzyme specificity to protein synthesis. Proc Natl Acad Sci U S A 1958, 44:98-104.
-
(1958)
Proc Natl Acad Sci U S A
, vol.44
, pp. 98-104
-
-
Koshland, D.E.1
-
10
-
-
70350340728
-
The role of dynamic conformational ensembles in biomolecular recognition
-
Boehr D.D., Nussinov R., Wright P.E. The role of dynamic conformational ensembles in biomolecular recognition. Nat Chem Biol 2009, 5:789-796.
-
(2009)
Nat Chem Biol
, vol.5
, pp. 789-796
-
-
Boehr, D.D.1
Nussinov, R.2
Wright, P.E.3
-
11
-
-
69549120472
-
Conformational selection or induced fit: a flux description of reaction mechanism
-
Hammes G.G., Chang Y.C., Oas T.G. Conformational selection or induced fit: a flux description of reaction mechanism. Proc Natl Acad Sci U S A 2009, 106:13737-13741.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 13737-13741
-
-
Hammes, G.G.1
Chang, Y.C.2
Oas, T.G.3
-
12
-
-
65249090946
-
Selected-fit versus induced-fit protein binding: kinetic differences and mutational analysis
-
Weikl T.R., von Deuster C. Selected-fit versus induced-fit protein binding: kinetic differences and mutational analysis. Proteins 2009, 75:104-110.
-
(2009)
Proteins
, vol.75
, pp. 104-110
-
-
Weikl, T.R.1
von Deuster, C.2
-
13
-
-
34548861782
-
Protein-protein docking with backbone flexibility
-
Wang C., Bradley P., Baker D. Protein-protein docking with backbone flexibility. J Mol Biol 2007, 373:503-519.
-
(2007)
J Mol Biol
, vol.373
, pp. 503-519
-
-
Wang, C.1
Bradley, P.2
Baker, D.3
-
14
-
-
34547592557
-
MolProbity: all-atom contacts and structure validation for proteins and nucleic acids
-
Davis I.W., Leaver-Fay A., Chen V.B., Block J.N., Kapral G.J., Wang X., Murray L.W., Bryan W., Arendall I., Snoeyink J., et al. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res 2007, 35:W375.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Davis, I.W.1
Leaver-Fay, A.2
Chen, V.B.3
Block, J.N.4
Kapral, G.J.5
Wang, X.6
Murray, L.W.7
Bryan, W.8
Arendall, I.9
Snoeyink, J.10
-
15
-
-
0001933882
-
Integrated access to sequence and structural data
-
EEC, Bruxelles, Belgium, C. Saccone (Ed.)
-
Lesk A.M. Integrated access to sequence and structural data. Biosequences: Perspectives and User Services in Europe 1986, EEC, Bruxelles, Belgium, pp. 23-28. C. Saccone (Ed.).
-
(1986)
Biosequences: Perspectives and User Services in Europe
, pp. 23-28
-
-
Lesk, A.M.1
-
16
-
-
0028268603
-
Synthetic, structural and biological studies of the ubiquitin system: the total chemical synthesis of ubiquitin
-
Ramage R., Green J., Muir T.W., Ogunjobi O.M., Love S., Shaw K. Synthetic, structural and biological studies of the ubiquitin system: the total chemical synthesis of ubiquitin. Biochem J 1994, 299(Pt 1):151-158.
-
(1994)
Biochem J
, vol.299
, Issue.PART 1
, pp. 151-158
-
-
Ramage, R.1
Green, J.2
Muir, T.W.3
Ogunjobi, O.M.4
Love, S.5
Shaw, K.6
-
17
-
-
0023644679
-
Structure of ubiquitin refined at 1.8A resolution
-
Vijay-Kumar S., Bugg C.E., Cook W.J. Structure of ubiquitin refined at 1.8A resolution. J Mol Biol 1987, 194:531-544.
-
(1987)
J Mol Biol
, vol.194
, pp. 531-544
-
-
Vijay-Kumar, S.1
Bugg, C.E.2
Cook, W.J.3
-
18
-
-
0034663722
-
The penultimate rotamer library
-
Lovell S.C., Word J.M., Richardson J.S., Richardson D.C. The penultimate rotamer library. Proteins 2000, 40:389-408.
-
(2000)
Proteins
, vol.40
, pp. 389-408
-
-
Lovell, S.C.1
Word, J.M.2
Richardson, J.S.3
Richardson, D.C.4
-
19
-
-
52949132638
-
Cavities and atomic packing in protein structures and interfaces
-
Sonavane S., Chakrabarti P. Cavities and atomic packing in protein structures and interfaces. PLoS Comput Biol 2008, 4:e1000188.
-
(2008)
PLoS Comput Biol
, vol.4
-
-
Sonavane, S.1
Chakrabarti, P.2
-
20
-
-
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., et al. Structural basis of ubiquitin recognition by the deubiquitinating protease USP2. Structure 2006, 14:1293-1302.
-
(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
-
21
-
-
1842421429
-
Ubiquitin recognition by the human TSG101 protein
-
Sundquist W.I., Schubert H.L., Kelly B.N., Hill G.C., Holton J.M., Hill C.P. Ubiquitin recognition by the human TSG101 protein. Mol Cell 2004, 13:783-789.
-
(2004)
Mol Cell
, vol.13
, pp. 783-789
-
-
Sundquist, W.I.1
Schubert, H.L.2
Kelly, B.N.3
Hill, G.C.4
Holton, J.M.5
Hill, C.P.6
-
22
-
-
44849136272
-
Structural basis for ubiquitin recognition by the Otu1 ovarian tumor domain protein
-
Messick T.E., Russell N.S., Iwata A.J., Sarachan K.L., Shiekhattar R., Shanks J.R., Reyes-Turcu F.E., Wilkinson K.D., Marmorstein R. Structural basis for ubiquitin recognition by the Otu1 ovarian tumor domain protein. J Biol Chem 2008, 283:11038-11049.
-
(2008)
J Biol Chem
, vol.283
, pp. 11038-11049
-
-
Messick, T.E.1
Russell, N.S.2
Iwata, A.J.3
Sarachan, K.L.4
Shiekhattar, R.5
Shanks, J.R.6
Reyes-Turcu, F.E.7
Wilkinson, K.D.8
Marmorstein, R.9
-
23
-
-
3142581995
-
Structural insights into endosomal sorting complex required for transport (ESCRT-I) recognition of ubiquitinated proteins
-
Teo H., Veprintsev D.B., Williams R.L. Structural insights into endosomal sorting complex required for transport (ESCRT-I) recognition of ubiquitinated proteins. J Biol Chem 2004, 279:28689-28696.
-
(2004)
J Biol Chem
, vol.279
, pp. 28689-28696
-
-
Teo, H.1
Veprintsev, D.B.2
Williams, R.L.3
-
24
-
-
33750603201
-
Structural basis for ubiquitin recognition by the human ESCRT-II EAP45 GLUE domain
-
Alam S.L., Langelier C., Whitby F.G., Koirala S., Robinson H., Hill C.P., Sundquist W.I. Structural basis for ubiquitin recognition by the human ESCRT-II EAP45 GLUE domain. Nat Struct Mol Biol 2006, 13:1029.
-
(2006)
Nat Struct Mol Biol
, vol.13
, pp. 1029
-
-
Alam, S.L.1
Langelier, C.2
Whitby, F.G.3
Koirala, S.4
Robinson, H.5
Hill, C.P.6
Sundquist, W.I.7
-
25
-
-
33644792262
-
Structural basis for ubiquitin recognition and autoubiquitination by Rabex-5
-
Lee S., Tsai Y.C., Mattera R., Smith W.J., Kostelansky M.S., Weissman A.M., Bonifacino J.S., Hurley J.H. Structural basis for ubiquitin recognition and autoubiquitination by Rabex-5. Nat Struct Mol Biol 2006, 13:264-271.
-
(2006)
Nat Struct Mol Biol
, vol.13
, pp. 264-271
-
-
Lee, S.1
Tsai, Y.C.2
Mattera, R.3
Smith, W.J.4
Kostelansky, M.S.5
Weissman, A.M.6
Bonifacino, J.S.7
Hurley, J.H.8
-
26
-
-
70349995780
-
Crystal structure of the NEMO ubiquitin-binding domain in complex with Lys 63-linked di-ubiquitin
-
Yoshikawa A., Sato Y., Yamashita M., Mimura H., Yamagata A., Fukai S. Crystal structure of the NEMO ubiquitin-binding domain in complex with Lys 63-linked di-ubiquitin. FEBS Lett 2009, 583:3317-3322.
-
(2009)
FEBS Lett
, vol.583
, pp. 3317-3322
-
-
Yoshikawa, A.1
Sato, Y.2
Yamashita, M.3
Mimura, H.4
Yamagata, A.5
Fukai, S.6
-
27
-
-
21644473663
-
Molecular mechanism of ubiquitin recognition by GGA3 GAT domain
-
Kawasaki M., Shiba T., Shiba Y., Yamaguchi Y., Matsugaki N., Igarashi N., Suzuki M., Kato R., Kato K., Nakayama K., et al. Molecular mechanism of ubiquitin recognition by GGA3 GAT domain. Genes Cells 2005, 10:639-654.
-
(2005)
Genes Cells
, vol.10
, pp. 639-654
-
-
Kawasaki, M.1
Shiba, T.2
Shiba, Y.3
Yamaguchi, Y.4
Matsugaki, N.5
Igarashi, N.6
Suzuki, M.7
Kato, R.8
Kato, K.9
Nakayama, K.10
-
28
-
-
67349231313
-
Molecular discrimination of structurally equivalent Lys 63-linked and linear polyubiquitin chains
-
Komander D., Reyes-Turcu F., Licchesi J.D.F., Odenwaelder P., Wilkinson K.D., Barford D. Molecular discrimination of structurally equivalent Lys 63-linked and linear polyubiquitin chains. EMBO Rep 2009, 10:466.
-
(2009)
EMBO Rep
, vol.10
, pp. 466
-
-
Komander, D.1
Reyes-Turcu, F.2
Licchesi, J.D.F.3
Odenwaelder, P.4
Wilkinson, K.D.5
Barford, D.6
-
29
-
-
12544253837
-
Structure of the ubiquitin hydrolase UCH-L3 complexed with a suicide substrate
-
Misaghi S., Galardy P.J., Meester W.J.N., Ovaa H., Ploegh H.L., Gaudet R. Structure of the ubiquitin hydrolase UCH-L3 complexed with a suicide substrate. J Biol Chem 2005, 280:1512-1520.
-
(2005)
J Biol Chem
, vol.280
, pp. 1512-1520
-
-
Misaghi, S.1
Galardy, P.J.2
Meester, W.J.N.3
Ovaa, H.4
Ploegh, H.L.5
Gaudet, R.6
-
30
-
-
0038820382
-
Mechanism of ubiquitin recognition by the CUE domain of Vps9p
-
Prag G., Misra S., Jones E.A., Ghirlando R., Davies B.A., Horazdovsky B.F., Hurley J.H. Mechanism of ubiquitin recognition by the CUE domain of Vps9p. Cell 2003, 113:609-620.
-
(2003)
Cell
, vol.113
, pp. 609-620
-
-
Prag, G.1
Misra, S.2
Jones, E.A.3
Ghirlando, R.4
Davies, B.A.5
Horazdovsky, B.F.6
Hurley, J.H.7
-
31
-
-
33644787880
-
Double-sided ubiquitin binding of Hrs-UIM in endosomal protein sorting
-
Hirano S., Kawasaki M., Ura H., Kato R., Raiborg C., Stenmark H., Wakatsuki S. Double-sided ubiquitin binding of Hrs-UIM in endosomal protein sorting. Nat Struct Mol Biol 2006, 13:272-277.
-
(2006)
Nat Struct Mol Biol
, vol.13
, pp. 272-277
-
-
Hirano, S.1
Kawasaki, M.2
Ura, H.3
Kato, R.4
Raiborg, C.5
Stenmark, H.6
Wakatsuki, S.7
-
32
-
-
25844509373
-
Structural basis for recognition of ubiquitinated cargo by Tom1-GAT domain
-
Akutsu M., Kawasaki M., Katoh Y., Shiba T., Yamaguchi Y., Kato R., Kato K., Nakayama K., Wakatsuki S. Structural basis for recognition of ubiquitinated cargo by Tom1-GAT domain. FEBS Lett 2005, 579:5385-5391.
-
(2005)
FEBS Lett
, vol.579
, pp. 5385-5391
-
-
Akutsu, M.1
Kawasaki, M.2
Katoh, Y.3
Shiba, T.4
Yamaguchi, Y.5
Kato, R.6
Kato, K.7
Nakayama, K.8
Wakatsuki, S.9
-
33
-
-
37249016853
-
Structural basis of ubiquitin recognition by the ubiquitin-associated (UBA) domain of the ubiquitin ligase EDD
-
Kozlov G., Nguyen L., Lin T., De Crescenzo G., Park M., Gehring K. Structural basis of ubiquitin recognition by the ubiquitin-associated (UBA) domain of the ubiquitin ligase EDD. J Biol Chem 2007, 282:35787-35795.
-
(2007)
J Biol Chem
, vol.282
, pp. 35787-35795
-
-
Kozlov, G.1
Nguyen, L.2
Lin, T.3
De Crescenzo, G.4
Park, M.5
Gehring, K.6
-
34
-
-
34547195241
-
Structural basis for ubiquitin-mediated dimerization and activation of the ubiquitin protein ligase Cbl-b
-
Peschard P., Kozlov G., Lin T., Mirza I.A., Berghuis A.M., Lipkowitz S., Park M., Gehring K. Structural basis for ubiquitin-mediated dimerization and activation of the ubiquitin protein ligase Cbl-b. Mol Cell 2007, 27:474-485.
-
(2007)
Mol Cell
, vol.27
, pp. 474-485
-
-
Peschard, P.1
Kozlov, G.2
Lin, T.3
Mirza, I.A.4
Berghuis, A.M.5
Lipkowitz, S.6
Park, M.7
Gehring, K.8
-
35
-
-
72449162040
-
Structural basis for specific recognition of Lys 63-linked polyubiquitin chains by NZF domains of TAB2 and TAB3
-
Sato Y., Yoshikawa A., Yamashita M., Yamagata A., Fukai S. Structural basis for specific recognition of Lys 63-linked polyubiquitin chains by NZF domains of TAB2 and TAB3. EMBO J 2009, 28:3903.
-
(2009)
EMBO J
, vol.28
, pp. 3903
-
-
Sato, Y.1
Yoshikawa, A.2
Yamashita, M.3
Yamagata, A.4
Fukai, S.5
-
36
-
-
71449095149
-
Two-sided ubiquitin binding explains specificity of the TAB2 NZF domain
-
Kulathu Y., Akutsu M., Bremm A., Hofmann K., Komander D. Two-sided ubiquitin binding explains specificity of the TAB2 NZF domain. Nat Struct Mol Biol 2009, 16:1328-1330.
-
(2009)
Nat Struct Mol Biol
, vol.16
, pp. 1328-1330
-
-
Kulathu, Y.1
Akutsu, M.2
Bremm, A.3
Hofmann, K.4
Komander, D.5
-
37
-
-
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 2008, 455:358-362.
-
(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
-
38
-
-
33847395453
-
Structure of a herpesvirus-encoded cysteine protease reveals a unique class of deubiquitinating enzymes
-
Schlieker C., Weihofen W.A., Frijns E., Kattenhorn L.M., Gaudet R., Ploegh H.L. Structure of a herpesvirus-encoded cysteine protease reveals a unique class of deubiquitinating enzymes. Mol Cell 2007, 25:677-687.
-
(2007)
Mol Cell
, vol.25
, pp. 677-687
-
-
Schlieker, C.1
Weihofen, W.A.2
Frijns, E.3
Kattenhorn, L.M.4
Gaudet, R.5
Ploegh, H.L.6
-
39
-
-
33646066025
-
The ubiquitin binding domain ZnF UBP recognizes the C-terminal diglycine motif of unanchored ubiquitin
-
Reyes-Turcu F.E., Horton J.R., Mullally J.E., Heroux A., Cheng X., Wilkinson K.D. The ubiquitin binding domain ZnF UBP recognizes the C-terminal diglycine motif of unanchored ubiquitin. Cell 2006, 124:1197-1208.
-
(2006)
Cell
, vol.124
, pp. 1197-1208
-
-
Reyes-Turcu, F.E.1
Horton, J.R.2
Mullally, J.E.3
Heroux, A.4
Cheng, X.5
Wilkinson, K.D.6
|