Dynamic behaviour of ubiquitin receptor S5a in free and complex with K48-linked diubiquitin

References

• Besche , H.C. , Peth , A. and Goldberg , A.L. 2009 . Getting to first base in proteasome assembly . Cell , 138 : 25 – 28 .
   PubMed Web of Science ®Google Scholar
• Pickart , C.M. and Cohen , R.E. 2004 . Proteasomes and their kin: Proteases in the machine age . Nature reviews. Mol. Cell Biol. , 5 : 177 – 187 .
   PubMed Web of Science ®Google Scholar
• Dikic , I. , Wakatsuki , S. and Walters , K.J. 2009 . Ubiquitin-binding domains – From structures to functions . Nature reviews. Mol. Cell Biol. , 10 : 659 – 671 .
   PubMed Web of Science ®Google Scholar
• Hoeller , D. and Dikic , I. 2009 . Targeting the ubiquitin system in cancer therapy . Nature , 458 : 438 – 444 .
   PubMed Web of Science ®Google Scholar
• Navon , A. and Ciechanover , A. 2009 . The 26 S proteasome: From basic mechanisms to drug targeting . J. Biol. Chem. , 284 : 33713 – 33718 .
   PubMed Web of Science ®Google Scholar
• Hartmann-Petersen , R. , Seeger , M. and Gordon , C. 2003 . Transferring substrates to the 26S proteasome . Trends Biochem. Sci. , 28 : 26 – 31 .
   PubMed Web of Science ®Google Scholar
• Chen , X. , Lee , B.H. , Finley , D. and Walters , K.J. 2010 . Structure of proteasome ubiquitin receptor hRpn13 and its activation by the scaffolding protein hRpn2 . Mol. Cell , 38 : 404 – 415 .
   PubMed Web of Science ®Google Scholar
• Wang , Q. , Young , P. and Walters , K.J. 2005 . Structure of S5a bound to monoubiquitin provides a model for polyubiquitin recognition . J. Biol. Chem. , 348 : 727 – 739 .
   Google Scholar
• Elangovan , M. , Shin , D.Y. and Yoo , Y.J. 2009 . The ubiquitin-interacting motifs of S5a as a unique upstream inhibitor of the 26S proteasome . Biochem. Biophys. Res. Comm. , 388 : 723 – 726 .
   Web of Science ®Google Scholar
• Schreiner , P. , Chen , X. , Husnjak , K. , Randles , L. , Zhang , N. , Elsasser , S. , Finley , D. , Dikic , I. , Walters , K.J. and Groll , M. 2008 . Ubiquitin docking at the proteasome through a novel pleckstrin-homology domain interaction . Nature , 453 : 548 – 552 .
   PubMed Web of Science ®Google Scholar
• Haririnia , A. , D'Onofrio , M. and Fushman , D. 2007 . Mapping the interactions between Lys48 and Lys63-linked di-ubiquitins and a ubiquitin-interacting motif of S5a . J. Mol. Biol. , 368 : 753 – 766 .
   Web of Science ®Google Scholar
• Besche , H.C. , Haas , W. , Gygi , S.P. and Goldberg , A.L. 2009 . Isolation of mammalian 26S proteasomes and p97/VCP complexes using the ubiquitin-like domain from HHR23B reveals novel proteasome-associated proteins . Biochemistry , 48 : 2538 – 2549 .
   PubMed Web of Science ®Google Scholar
• Goh , A.M. , Walters , K.J. , Elsasser , S. , Verma , R. , Deshaies , R.J. , Finley , D. and Howley , P.M. 2008 . Components of the ubiquitin-proteasome pathway compete for surfaces on Rad23 family proteins . BMC Biochem. , 9 : 4
   PubMedGoogle Scholar
• Dickinson , B.C. , Varadan , R. and Fushman , D. 2007 . Effects of cyclization on conformational dynamics and binding properties of Lys48-linked di-ubiquitin . Pro. Sci. , 16 : 369 – 378 .
   Web of Science ®Google Scholar
• Hirano , T. , Serve , O. , Yagi-Utsumi , M. , Takemoto , E. , Hiromoto , T. , Satoh , T. , Mizushima , T. and Kato , K. 2011 . Conformational dynamics of wild-type Lys-48-linked diubiquitin in solution . J. Biol. Chem. , 286 : 37496 – 37502 .
   Web of Science ®Google Scholar
• Long , D. and Bruschweiler , R. 2011 . In silico elucidation of the recognition dynamics of ubiquitin . PLoS Comput. Biol. , 7 : e1002035
   Web of Science ®Google Scholar
• Tomoo , K. , Mukai , Y. , In , Y. , Miyagawa , H. , Kitamura , K. , Yamano , A. , Shindo , H. and Ishida , T. 2008 . Crystal structure and molecular dynamics simulation of ubiquitin-like domain of murine parkin . Biochim. Biophys. Acta , 1784 : 1059 – 1067 .
   Web of Science ®Google Scholar
• Kim , Y.C. and Hummer , G. 2008 . Coarse-grained models for simulations of multiprotein complexes: Application to ubiquitin binding . J. Mol. Biol. , 375 : 1416 – 1433 .
   PubMed Web of Science ®Google Scholar
• Segev , E. , Wyttenbach , T. , Bowers , M.T. and Gerber , R.B. 2008 . Conformational evolution of ubiquitin ions in electrospray mass spectrometry: Molecular dynamics simulations at gradually increasing temperatures . Phys. Chem. Chem. Phys. , 10 : 3077 – 3082 .
   Web of Science ®Google Scholar
• Zhang , N. , Wang , Q. , Ehlinger , A. , Randles , L. , Lary , J.W. , Kang , Y. , Haririnia , A. , Storaska , A.J. , Cole , J.L. , Fushman , D. and Walters , K.J. 2009 . Structure of the s5a:k48-linked diubiquitin complex and its interactions with rpn13 . Mol. Cell , 35 : 280 – 290 .
   PubMed Web of Science ®Google Scholar
• Jorgensen , W.L. , Chandrasekhar , J. , Madura , J.D. , Impey , R.W. and Klein , M.L. 1983 . Comparison of simple potential functions for simulating liquid water . J. Chem. Phys. , 79 : 926 – 935 .
   Web of Science ®Google Scholar
• Berendsen , H.J.C. , Vanderspoel , D. and Vandrunen , R. 1995 . Gromacs – A mssage-passing parallel molecular-dynamics implementation . Comput. Phys. Commun. , 91 : 43 – 56 .
   Web of Science ®Google Scholar
• Hess , B. , Kutzner , C. , van der Spoel , D. and Lindahl , E. 2008 . GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation . J. Chem. Theory Comput. , 4 : 435 – 447 .
   PubMed Web of Science ®Google Scholar
• MacKerell , A.D. and Foloppe , N. 2000 . All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data . J. Comput. Chem. , 21 : 86 – 104 .
   Web of Science ®Google Scholar
• MacKerell , A.D. and Banavali , N.K. 2000 . All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution . J. Comput. Chem. , 21 : 105 – 120 .
   Web of Science ®Google Scholar
• MacKerell , A.D. , Banavali , N. and Foloppe , N. 2000 . Development and current status of the CHARMM force field for nucleic acids . Biopolymers , 56 : 257 – 265 .
   PubMed Web of Science ®Google Scholar
• Bussi , G. , Donadio , D. and Parrinello , M. 2007 . Canonical sampling through velocity rescaling . J. Chem. Phys. , 126 : 014101
   PubMed Web of Science ®Google Scholar
• Berendsen , H.J.C. , Postma , J.P.M. , Vangunsteren , W.F. , Dinola , A. and Haak , J.R. 1984 . Molecular-dynamics with coupling to an external bath . J. Chem. Phys. , 81 : 3684 – 3690 .
   Web of Science ®Google Scholar
• Hess , B. , Bekker , H. , Berendsen , H.J.C. and Fraaije , J.G.E.M. 1997 . LINCS: A linear constraint solver for molecular simulations . J. Comput. Chem. , 18 : 1463 – 1472 .
   Web of Science ®Google Scholar
• Essmann , U. , Perera , L. , Berkowitz , M.L. , Darden , T. , Lee , H. and Pedersen , L.G. 1995 . A smooth particle mesh Ewald method . J. Chem. Phys. , 103 : 8577 – 8593 .
   Web of Science ®Google Scholar
• Kabsch , W. and Sander , C. 1983 . Dictionary of protein secondary structure – Pattern-recognition of hydrogen-bonded and Geometrical Features . Biopolymers , 22 : 2577 – 2637 .
   PubMed Web of Science ®Google Scholar