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Original Articles

Identification of dynamic structural domains in proteins, analysis of local bond flexibility and application for interpretation of NMR experiments

Pages 729-732 | Received 15 Jul 2009, Accepted 14 Aug 2009, Published online: 25 Sep 2009

References

  • Aloy , P. and Russell , R.B. 2006 . Structural systems biology: Modelling protein interactions . Nat. Rev. Mol. Cell Biol. , 7 : 188 – 197 .
  • Tozzini , V. 2005 . Coarse-grained models for proteins . Curr. Opin. Struct. Biol. , 15 : 144 – 150 .
  • Bahar , I. and Rader , A.J. 2005 . Coarse-grained normal mode analysis in structural biology . Curr. Opin. Struct. Biol. , 15 : 586 – 592 .
  • Yesylevsky , S.O. , Kharkyanen , V.N. and Demchenko , A.P. 2006 . Dynamic protein domains: Identification, interdependence, and stability . Biophys. J. , 91 : 670 – 685 .
  • Hayward , S. , Kitao , A. and Berendsen , H. 1997 . Model-free methods of analyzing domain motions in proteins from simulation: A comparison of normal mode analysis and molecular dynamics simulation of lysozyme . Proteins , 27 : 425 – 437 .
  • Hayward , S. and Berendsen , H. 1998 . Systematic analysis of domain motions in proteins from conformational change; New results on citrate synthase and T4 lysozyme . Proteins , 30 : 144 – 154 .
  • Hinsen , K. 1998 . Analysis of domain motions by approximate normal mode calculations . Proteins , 33 : 417 – 429 .
  • Hinsen , K. , Thomas , A. and Field , M.J. 1999 . Analysis of domain motions in large proteins . Proteins , 34 : 369 – 382 .
  • Stepanova , M. 2007 . Dynamics of essential collective motions in proteins: Theory . Phys. Rev. E , 76 051918
  • Blinov , N. , Berjanskii , M. , Wishart , D. and Stepanova , M. 2009 . Structural domains and main-chain flexibility in prion proteins . Biochemistry , 48 : 1488 – 1497 .
  • Kitao , A. , Hirata , F. and Go , N. 1991 . The effects of solvent on the conformation and the collective motions of protein: Normal mode analysis and molecular dynamics simulations of melittin in water and in vacuum . Chem. Phys. , 158 : 447 – 472 .
  • H. Mori, Transport, collective motion, and Brownian motion, Prog. Theor. Phys. 33 (1965), pp. 423–455; H. Mori, A continued fraction representation of the time-correlation functions, Prog. Theor. Phys. 34 (1965), pp. 399–416
  • Humphrey , W. , Dalke , A. and Schulten , K. 1966 . VMD: Visual molecular dynamics . J. Mol. Graph. , 14 : 33 – 38 .
  • Stone , M.J. , Gupta , S. , Snyder , N. and Regan , L. 2001 . Comparison of protein backbone entropy and â-sheet stability: NMR-derived dynamics of protein G B1 domain mutants . J. Am. Chem. Soc. , 123 : 185 – 186 .
  • Bouvignies , G. , Bernado , P. , Meier , S. , Cho , K. , Grzesiek , S. , Brüschweiler , R. and Blackledge , M. 2005 . Identification of slow correlated motions in proteins using residual dipolar and hydrogen-bond scalar couplings . Proc. Natl Acad. Sci. USA , 102 : 13885 – 13890 .
  • Zahn , R. , Liu , A. , Lührs , T. , Riek , R. , von Schroetter , C. , López García , F. , Billeter , M. , Calzolai , L. , Wider , G. and Wüthrich , K. 2000 . NMR solution structure of the human prion protein . Proc. Natl Acad. Sci. USA , 97 : 145 – 150 .
  • Calzolai , L. , Lysek , D.A. , Pérez , D.R. , Güntert , P. and Wüthrich , K. 2005 . Prion protein NMR structures of chickens, turtles, and frogs . Proc. Natl Acad. Sci. USA , 102 : 651 – 655 .

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