Nanomedicine: Nanotechnology, Biology and Medicine
Volume 1, Issue 1 , Pages 41-46 , March 2005

Clustering and diversity of fluctuations for proteins

  • Melik C. Demirel, PhD

      Affiliations

    • College of Engineering, Pennsylvania State University, University Park, Pennsylvania
    • Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
    • Corresponding Author InformationCorresponding author. 212 EES Bldg., School of Engineering, Pennsylvania State University, University Park, PA 16802.
  • ,
  • Dmitry Cherny, PhD

      Affiliations

    • Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany

Received 16 October 2004 ,Accepted 25 November 2004.

References 

  1. Taylor WR, May ACW, Brown NP, Aszodi A. Protein structure: Geometry, topology and classification. Rep Prog Phys. 2001;64:517–590
  2. Schwieters CD, Kuszewski JJ, Tjandra N, Clore GM. The XPLOR-NIH NMR molecular structure determination package. J Magn Reson. 2003;160:65–73
  3. Meiler J, Baker D. Rapid protein fold determination using unassigned NMR data. Proc Natl Acad Sci USA. 2003;100:15404–15409
  4. Vendruscolo M, Najmanovich R, Domany E. Protein folding in contact map space. Phys Rev Lett. 1999;82:656–659
  5. Hu J, Shen X, Shao Y, Bystroff C, Zaki MJ. Mining protein contact maps. Proceedings of the Workshop on Data Mining in Bioinformatics (with SIGKDD02 Conference); 2004 Aug 22-25.
  6. Park B, Levitt M. Energy functions that discriminate X-ray and near-native folds from well-constructed decoys. J Mol Biol. 1996;258:367–392
  7. Richardson JS. Beta-sheet topology and the relatedness of proteins. Nature. 1977;268:495–500
  8. Ptitsyn OB, Finkelstein AV. Similarities of protein topologies: Evolutionary divergence, functional convergence or principles of folding. Q Rev Biophys. 1980;13:339–386
  9. Efimov AV. Structural trees for protein super-families. Proteins Struc Func Genet. 1997;28:241–260
  10. Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM. CATH — a hierarchic classification of protein domain structures. Structure. 1997;5:1093–1108
  11. Taylor WR. A “periodic table” for protein structures. Nature. 2002;416:657–660
  12. Demirel M, Atilgan A, Jernigan R, Erman B, Bahar I. Identification of kinetically hot residues in proteins. Protein Sci. 1998;7:2522–2532
  13. Demirel M, Bahar I, Atilgan A. Predicting the ensemble of unfolding pathways for proteins: an updated incremental Lagrangean model. Biophys J. 1999;76:A176
  14. Atilgan A, Durell S, Jernigan R, Demirel M, Keskin O, Bahar I. Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys J. 2001;80:505–515
  15. Bahar I, Atilgan A, Demirel M, Erman B. Vibrational dynamics of folded proteins: significance of slow and fast motions in relation to function and stability. Phys Rev Lett. 1998;80:2733–2736
  16. Keskin O. Comparison of full-atomic and coarse-grained models to examine the molecular fluctuations of c-AMP dependent protein kinase. J Biomol Struc Dynamics. 2002;20:333–346
  17. Demirel MC, Keskin O. Protein interactions and fluctuations in a proteomic network using an elastic network model. J Biomol Struc Dynamics. 2005;22:381–386
  18. Flory PJ. Statistical thermodynamics of random networks. Proc R Soc London A. 1976;351:351–380
  19. Brunger AT, Clore GM, Gronenborn AM, Saffrich R, Nilges M. Assessing the quality of solution nuclear-magnetic-resonance structures by complete cross-validation. Science. 1993;261:328–331
  20. Fersht AR, Daggett V. Protein folding and unfolding at atomic resolution. Cell. 2002;108:573–582
  21. Mayor U, Johnson CM, Daggett V, Fersht AR. Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation. Proc Natl Acad Sci U S A. 2001;98:13518–13522
  22. Ptitsyn OB. How molten is the molten globule?. Nat Struc Biol. 1996;3:488–490
  23. Miyazawa S, Jernigan RL. Residue–residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J Mol Biol. 1996;256:623–644
  24. Baysal C, Atilgan AR. Coordination topology and stability for the native and binding conformers of chymotrypsin inhibitor 2. Proteins Struc Func Genet. 2001;45:62–70
  25. Humphrey W, Dalke A, Schulten K. VMD—visual molecular dynamics. J Mol Graphics. 1996;14:33–38

PII: S1549-9634(05)00008-0

doi: 10.1016/j.nano.2004.11.007

Nanomedicine: Nanotechnology, Biology and Medicine
Volume 1, Issue 1 , Pages 41-46 , March 2005