SCOPUS 정보 검색 플랫폼

Physical Chemistry Chemical Physics

Volumn 16, Issue 1, 2014, Pages 48-60

Decoding the patterns of ubiquitin recognition by ubiquitin-associated domains from free energy simulations

(1) Bouvier, Benjamin a

a INSTITUT DE BIOLOGIE ET CHIMIE DES PROTÉINES (France)

Author keywords

[No Author keywords available]

Indexed keywords

SOLVENT; UBIQUITIN; WATER;

AMINO ACID SEQUENCE; ARTICLE; CHEMISTRY; METABOLISM; MOLECULAR DYNAMICS; MOLECULAR GENETICS; PROTEIN BINDING; PROTEIN TERTIARY STRUCTURE; THERMODYNAMICS;

AMINO ACID SEQUENCE; MOLECULAR DYNAMICS SIMULATION; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; SOLVENTS; THERMODYNAMICS; UBIQUITIN; WATER;

EID: 84889017321 PISSN: 14639076 EISSN: None Source Type: Journal
DOI: 10.1039/c3cp52436a Document Type: Article

Times cited : (6)

References (54)

1
- 79961000536
- S. E. Kaiser B. E. Riley T. A. Shaler R. S. Trevino C. H. Becker H. Schulman R. R. Kopito Nat. Methods 2011 8 691
- (2011) Nat. Methods , vol.8 , pp. 691
- 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

2
- 84861783400
- K. Husnjak I. Dikic Annu. Rev. Biochem. 2012 81 291
- (2012) Annu. Rev. Biochem. , vol.81 , pp. 291
- Husnjak, K.¹ Dikic, I.²

3
- 84856138559
- E. R. Strieter D. A. Korasick ACS Chem. Biol. 2012 7 52
- (2012) ACS Chem. Biol. , vol.7 , pp. 52
- Strieter, E.R.¹ Korasick, D.A.²

4
- 9744227183
- C. M. Pickart M. J. Eddins Biochim. Biophys. Acta 2004 1695 55
- (2004) Biochim. Biophys. Acta , vol.1695 , pp. 55
- Pickart, C.M.¹ Eddins, M.J.²

5
- 0034602845
- J. S. Thrower L. Hoffman M. Rechsteiner C. M. Pickart EMBO J. 2000 19 94
- (2000) EMBO J. , vol.19 , pp. 94
- Thrower, J.S.¹ Hoffman, L.² Rechsteiner, M.³ Pickart, C.M.⁴

6
- 82955162702
- J. F. Trempe Curr. Opin. Struct. Biol. 2011 21 792
- (2011) Curr. Opin. Struct. Biol. , vol.21 , pp. 792
- Trempe, J.F.¹

7
- 70349441058
- I. Dikic S. Wakatsuki K. J. Walters Nat. Rev. Mol. Cell Biol. 2009 10 659
- (2009) Nat. Rev. Mol. Cell Biol. , vol.10 , pp. 659
- Dikic, I.¹ Wakatsuki, S.² Walters, K.J.³

8
- 77956551581
- J. F. Trempe N. R. Brown M. E. Noble J. A. Endicott Acta Crystallogr., Sect. F: Struct. Biol. Cryst. Commun. 2010 66 994
- (2010) Acta Crystallogr., Sect. F: Struct. Biol. Cryst. Commun. , vol.66 , pp. 994
- Trempe, J.F.¹ Brown, N.R.² Noble, M.E.³ Endicott, J.A.⁴

9
- 0026746290
- W. J. Cook L. C. Jeffrey M. Carson Z. Chen C. M. Pickart J. Biol. Chem. 1992 267 16467
- (1992) J. Biol. Chem. , vol.267 , pp. 16467
- Cook, W.J.¹ Jeffrey, L.C.² Carson, M.³ Chen, Z.⁴ Pickart, C.M.⁵

10
- 0036922992
- R. Varadan O. Walker C. Pickart D. Fushman J. Mol. Biol. 2002 324 637
- (2002) J. Mol. Biol. , vol.324 , pp. 637
- Varadan, R.¹ Walker, O.² Pickart, C.³ Fushman, D.⁴

11
- 33947411739
- Y. E. Ryabov D. Fushman J. Am. Chem. Soc. 2007 129 3315
- (2007) J. Am. Chem. Soc. , vol.129 , pp. 3315
- Ryabov, Y.E.¹ Fushman, D.²

12
- 33750555919
- J. H. Hurley S. Lee G. Prag Biochem. J. 2006 399 361
- (2006) Biochem. J. , vol.399 , pp. 361
- Hurley, J.H.¹ Lee, S.² Prag, G.³

13
- 80054809736
- T. Hirano O. Serve M. Yagi-Utsumi E. Takemoto T. Hiromoto T. Satoh T. Mizushima K. Kato J. Biol. Chem. 2011 286 37496
- (2011) J. Biol. Chem. , vol.286 , pp. 37496
- Hirano, T.¹ Serve, O.² Yagi-Utsumi, M.³ Takemoto, E.⁴ Hiromoto, T.⁵ Satoh, T.⁶ Mizushima, T.⁷ Kato, K.⁸

14
- 84861393827
- M. Wilhelm A. Mukherjee B. Bouvier K. Zakrzewska J. T. Hynes R. Lavery J. Am. Chem. Soc. 2012 134 8588
- (2012) J. Am. Chem. Soc. , vol.134 , pp. 8588
- Wilhelm, M.¹ Mukherjee, A.² Bouvier, B.³ Zakrzewska, K.⁴ Hynes, J.T.⁵ Lavery, R.⁶

15
- 67651232308
- B. Bouvier R. Lavery J. Am. Chem. Soc. 2009 131 9864
- (2009) J. Am. Chem. Soc. , vol.131 , pp. 9864
- Bouvier, B.¹ Lavery, R.²

16
- 27344436659
- J. C. Phillips R. Braun W. Wang J. Gumbart E. Tajkhorshid E. Villa C. Chipot R. D. Skeel L. Kalé K. Schulten J. Comput. Chem. 2005 26 1781
- (2005) J. Comput. Chem. , vol.26 , pp. 1781
- Phillips, J.C.¹ Braun, R.² Wang, W.³ Gumbart, J.⁴ Tajkhorshid, E.⁵ Villa, E.⁶ Chipot, C.⁷ Skeel, R.D.⁸ Kalé, L.⁹ Schulten, K.¹⁰

17
- 0032922174
- T. E. Cheatham P. Cieplak P. A. Kollman J. Biomol. Struct. Dyn. 1999 16 845
- (1999) J. Biomol. Struct. Dyn. , vol.16 , pp. 845
- Cheatham, T.E.¹ Cieplak, P.² Kollman, P.A.³

18
- 0004016501
- W. L. Jorgensen J. Chandrasekhar J. D. Madura R. W. Impey M. L. Klein J. Chem. Phys. 1983 79 926
- (1983) J. Chem. Phys. , vol.79 , pp. 926
- Jorgensen, W.L.¹ Chandrasekhar, J.² Madura, J.D.³ Impey, R.W.⁴ Klein, M.L.⁵

19
- 49449085241
- I. S. Joung T. E. Cheatham J. Phys. Chem. B 2008 112 9020
- (2008) J. Phys. Chem. B , vol.112 , pp. 9020
- Joung, I.S.¹ Cheatham, T.E.²

20
- 0037877123
- Yale University Press, New Haven, CT, USA
- A. T. Brünger, X-PLOR: A System for X-ray Crystallography and NMR, Yale University Press, New Haven, CT, USA, 1993
- (1993) X-PLOR: A System for X-ray Crystallography and NMR
- Brünger, A.T.¹

21
- 36449003554
- G. J. Martyna D. J. Tobias M. L. Klein J. Chem. Phys. 1994 101 4177
- (1994) J. Chem. Phys. , vol.101 , pp. 4177
- Martyna, G.J.¹ Tobias, D.J.² Klein, M.L.³

22
- 33846823909
- T. Darden D. York L. Pedersen J. Chem. Phys. 1993 98 10089
- (1993) J. Chem. Phys. , vol.98 , pp. 10089
- Darden, T.¹ York, D.² Pedersen, L.³

23
- 84986519238
- S. Kumar J. M. Rosenberg D. Bouzida R. H. Swendsen P. A. Kollman J. Comput. Chem. 1992 13 1011
- (1992) J. Comput. Chem. , vol.13 , pp. 1011
- Kumar, S.¹ Rosenberg, J.M.² Bouzida, D.³ Swendsen, R.H.⁴ Kollman, P.A.⁵

24
- 84855688941
- F. Zhu G. Hummer J. Comput. Chem. 2012 33 453
- (2012) J. Comput. Chem. , vol.33 , pp. 453
- Zhu, F.¹ Hummer, G.²

25
- 68049128318
- B. Bouvier R. Grünberg M. Nilges F. Cazals Proteins 2009 76 677
- (2009) Proteins , vol.76 , pp. 677
- Bouvier, B.¹ Grünberg, R.² Nilges, M.³ Cazals, F.⁴

26
- 33748171998
- F. Cazals F. Proust R. P. Bahadur J. Janin Protein Sci. 2006 15 2082
- (2006) Protein Sci. , vol.15 , pp. 2082
- Cazals, F.¹ Proust, F.² Bahadur, R.P.³ Janin, J.⁴

27
- 33749172039
- N. M. Glykos J. Comput. Chem. 2006 27 1765
- (2006) J. Comput. Chem. , vol.27 , pp. 1765
- Glykos, N.M.¹

28
- 3242877815
- S. R. Comeau D. W. Gatchell S. Vajda C. J. Camacho Nucleic Acids Res. 2004 32 W96
- (2004) Nucleic Acids Res. , vol.32 , pp. 96
- Comeau, S.R.¹ Gatchell, D.W.² Vajda, S.³ Camacho, C.J.⁴

29
- 77957963055
- D. Kozakov D. R. Hall D. Beglov R. Brenke S. R. Comeau Y. Shen K. Li J. Zheng P. Vakili I. C. h. Paschalidis S. Vajda Proteins 2010 78 3124
- (2010) Proteins , vol.78 , pp. 3124
- Kozakov, D.¹ Hall, D.R.² Beglov, D.³ Brenke, R.⁴ Comeau, S.R.⁵ Shen, Y.⁶ Li, K.⁷ Zheng, J.⁸ Vakili, P.⁹ Paschalidis, I.C.H.¹⁰ Vajda, S.¹¹

30
- 77957944014
- H. Hwang T. Vreven J. Janin Z. Weng Proteins 2010 78 3111
- (2010) Proteins , vol.78 , pp. 3111
- Hwang, H.¹ Vreven, T.² Janin, J.³ Weng, Z.⁴

31
- 84889013432
- T. Heijboer, WxTernary, 2012
- (2012) WxTernary
- Heijboer, T.¹

32
- 0029878720
- W. Humphrey A. Dalke K. Schulten J. Mol. Graphics Modell. 1996 14 33
- (1996) J. Mol. Graphics Modell. , vol.14 , pp. 33
- Humphrey, W.¹ Dalke, A.² Schulten, K.³

33
- 34247493236
- J. D. Hunter Comput. Sci. Eng. 2007 9 90
- (2007) Comput. Sci. Eng. , vol.9 , pp. 90
- Hunter, J.D.¹

34
- 17044420416
- A. Ohno J. Jee K. Fujiwara T. Tenno N. Goda H. Tochio H. Kobayashi H. Hiroaki M. Shirakawa Structure 2005 13 521
- (2005) Structure , vol.13 , pp. 521
- Ohno, A.¹ Jee, J.² Fujiwara, K.³ Tenno, T.⁴ Goda, N.⁵ Tochio, H.⁶ Kobayashi, H.⁷ Hiroaki, H.⁸ Shirakawa, M.⁹

35
- 37249016853
- G. Kozlov L. Nguyen T. Lin G. De Crescenzo M. Park K. Gehring J. Biol. Chem. 2007 282 35787
- (2007) J. Biol. Chem. , vol.282 , pp. 35787
- Kozlov, G.¹ Nguyen, L.² Lin, T.³ De Crescenzo, G.⁴ Park, M.⁵ Gehring, K.⁶

36
- 26944465404
- S. Raasi R. Varadan D. Fushman C. M. Pickart Nat. Struct. Mol. Biol. 2005 12 708
- (2005) Nat. Struct. Mol. Biol. , vol.12 , pp. 708
- Raasi, S.¹ Varadan, R.² Fushman, D.³ Pickart, C.M.⁴

37
- 33744461058
- Y. G. Chang A. X. Song Y. G. Gao Y. H. Shi X. J. Lin X. T. Cao D. H. Lin H. Y. Hu Protein Sci. 2006 15 1248
- (2006) Protein Sci. , vol.15 , pp. 1248
- Chang, Y.G.¹ Song, A.X.² Gao, Y.G.³ Shi, Y.H.⁴ Lin, X.J.⁵ Cao, X.T.⁶ Lin, D.H.⁷ Hu, H.Y.⁸

38
- 20444391345
- R. Varadan M. Assfalg S. Raasi C. Pickart D. Fushman Mol. Cell 2005 18 687
- (2005) Mol. Cell , vol.18 , pp. 687
- Varadan, R.¹ Assfalg, M.² Raasi, S.³ Pickart, C.⁴ Fushman, D.⁵

39
- 34547195241
- P. Peschard G. Kozlov T. Lin I. A. Mirza A. M. Berghuis S. Lipkowitz M. Park K. Gehring Mol. Cell 2007 27 474
- (2007) Mol. Cell , vol.27 , pp. 474
- 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

40
- 1542346459
- N. Chim W. E. Gall J. Xiao M. P. Harris T. R. Graham A. M. Krezel Proteins 2004 54 784
- (2004) Proteins , vol.54 , pp. 784
- Chim, N.¹ Gall, W.E.² Xiao, J.³ Harris, M.P.⁴ Graham, T.R.⁵ Krezel, A.M.⁶

41
- 36448991500
- M. A. Larkin G. Blackshields N. P. Brown R. Chenna P. A. McGettigan H. McWilliam F. Valentin I. M. Wallace A. Wilm R. Lopez J. D. Thompson T. J. Gibson D. G. Higgins Bioinformatics 2007 23 2947
- (2007) Bioinformatics , vol.23 , pp. 2947
- Larkin, M.A.¹ Blackshields, G.² Brown, N.P.³ Chenna, R.⁴ McGettigan, P.A.⁵ McWilliam, H.⁶ Valentin, F.⁷ Wallace, I.M.⁸ Wilm, A.⁹ Lopez, R.¹⁰ Thompson, J.D.¹¹ Gibson, T.J.¹² Higgins, D.G.¹³

42
- 79960017777
- B. Bouvier K. Zakrzewska R. Lavery Angew. Chem., Int. Ed. 2011 50 6516
- (2011) Angew. Chem., Int. Ed. , vol.50 , pp. 6516
- Bouvier, B.¹ Zakrzewska, K.² Lavery, R.³

43
- 23144452091
- L. Hicke H. L. Schubert C. P. Hill Nat. Rev. Mol. Cell Biol. 2005 6 610
- (2005) Nat. Rev. Mol. Cell Biol. , vol.6 , pp. 610
- Hicke, L.¹ Schubert, H.L.² Hill, C.P.³

44
- 10744226141
- K. Fujiwara T. Tenno K. Sugasawa J. G. Jee I. Ohki C. Kojima H. Tochio H. Hiroaki F. Hanaoka M. Shirakawa J. Biol. Chem. 2004 279 4760
- (2004) J. Biol. Chem. , vol.279 , pp. 4760
- Fujiwara, K.¹ Tenno, T.² Sugasawa, K.³ Jee, J.G.⁴ Ohki, I.⁵ Kojima, C.⁶ Tochio, H.⁷ Hiroaki, H.⁸ Hanaoka, F.⁹ Shirakawa, M.¹⁰

45
- 33745032291
- Y. Levy J. N. Onuchic Annu. Rev. Biophys. Biomol. Struct. 2006 35 389
- (2006) Annu. Rev. Biophys. Biomol. Struct. , vol.35 , pp. 389
- Levy, Y.¹ Onuchic, J.N.²

46
- 0035819175
- H. Xu B. J. Berne J. Phys. Chem. B 2001 105 11929
- (2001) J. Phys. Chem. B , vol.105 , pp. 11929
- Xu, H.¹ Berne, B.J.²

47
- 45849131354
- O. F. Lange N. A. Lakomek C. Farès G. F. Schröder K. F. A. Walter S. Becker J. Meiler H. Grubmüller C. Griesinger B. L. de Groot Science 2008 320 1471
- (2008) Science , vol.320 , pp. 1471
- Lange, O.F.¹ Lakomek, N.A.² Farès, C.³ Schröder, G.F.⁴ Walter, K.F.A.⁵ Becker, S.⁶ Meiler, J.⁷ Grubmüller, H.⁸ Griesinger, C.⁹ De Groot, B.L.¹⁰

48
- 39649120317
- D. Zhang S. Raasi D. Fushman J. Mol. Biol. 2008 377 162
- (2008) J. Mol. Biol. , vol.377 , pp. 162
- Zhang, D.¹ Raasi, S.² Fushman, D.³

49
- 0037646406
- S. Raasi C. M. Pickart J. Biol. Chem. 2003 278 8951
- (2003) J. Biol. Chem. , vol.278 , pp. 8951
- Raasi, S.¹ Pickart, C.M.²

50
- 4143061786
- S. Raasi I. Orlov K. G. Fleming C. M. Pickart J. Mol. Biol. 2004 341 1367
- (2004) J. Mol. Biol. , vol.341 , pp. 1367
- Raasi, S.¹ Orlov, I.² Fleming, K.G.³ Pickart, C.M.⁴

51
- 25144507198
- J. F. Trempe N. R. Brown E. D. Lowe C. Gordon I. D. Campbell M. E. Noble J. A. Endicott EMBO J. 2005 24 3178
- (2005) EMBO J. , vol.24 , pp. 3178
- Trempe, J.F.¹ Brown, N.R.² Lowe, E.D.³ Gordon, C.⁴ Campbell, I.D.⁵ Noble, M.E.⁶ Endicott, J.A.⁷

52
- 79951953321
- R. C. Wilson S. P. Edmondson J. W. Flatt K. Helms P. D. Twigg Biochem. Biophys. Res. Commun. 2011 405 662
- (2011) Biochem. Biophys. Res. Commun. , vol.405 , pp. 662
- Wilson, R.C.¹ Edmondson, S.P.² Flatt, J.W.³ Helms, K.⁴ Twigg, P.D.⁵

53
- 41949134141
- J. Long T. R. Gallagher J. R. Cavey P. W. Sheppard S. H. Ralston R. Layfield M. S. Searle J. Biol. Chem. 2008 283 5427
- (2008) J. Biol. Chem. , vol.283 , pp. 5427
- Long, J.¹ Gallagher, T.R.² Cavey, J.R.³ Sheppard, P.W.⁴ Ralston, S.H.⁵ Layfield, R.⁶ Searle, M.S.⁷

54
- 67349231313
- D. Komander F. Reyes-Turcu J. D. Licchesi P. Odenwaelder K. D. Wilkinson D. Barford EMBO Rep. 2009 10 466
- (2009) EMBO Rep. , vol.10 , pp. 466
- Komander, D.¹ Reyes-Turcu, F.² Licchesi, J.D.³ Odenwaelder, P.⁴ Wilkinson, K.D.⁵ Barford, D.⁶

* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.