Wuhan University Journal of Natural Sciences

, Volume 12, Issue 6, pp 1034–1038 | Cite as

Investigation of highly designable dented structures in HP model with hydrogen bond energy

  • Zhang Wei 
  • Huang Shengyou 
  • Yu Tao 
  • Zou Xianwu 


Some highly designable protein structures have dented on the surface of their native structures, and are not full compactly folded. According to hydrophobic-polar (HP) model the most designable structures are full compactly folded. To investigate the designability of the dented structures, we introduce the hydrogen bond energy in the secondary structures by using the secondary-structure-favored HP model proposed by Ou-yang etc. The result shows that the average designability increases with the strength of the hydrogen bond. The designabilities of the structures with same dented shape increase exponentially with the number of secondary structure sites. The dented structures can have the highest designabilities for a certain value of hydrogen bond energy density.

Key words

protein folding designability dented structure hydrogen bond energy HP model 

CLC number

O 469 Q 518.1 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. [1]
    Chen H, Zhou X, Ou-yang Z C. Secondary-Structure-Favored Hydrophobic-Polar Lattice Model of Protein Folding [J]. Phys Rev E, 2001, 64: 41905.CrossRefGoogle Scholar
  2. [2]
    Shih C T, Su Z Y, Gwan J F, et al. Mean-Field HP Model, Designability and Alpha-Helices in Protein Structures [J]. Phys Rev Lett, 2000, 20: 1883–1886.Google Scholar
  3. [3]
    Creighton T E. Protein Folding [M]. New York: Freeman, 1992.Google Scholar
  4. [4]
    Anfisen C. Principles that Govern the Folding of Protein Chains[J]. Science, 1973, 181: 223–230.CrossRefGoogle Scholar
  5. [5]
    Murzin A, Brenner S, Hubbard T, et al. SCOP-A Structure Classification of Proteins Database for the Investigation of Sequences and Structures [J]. J Mol Biol, 1995, 247: 536–540.CrossRefGoogle Scholar
  6. [6]
    Liu X S, Fan K, Wang W. The Number of Protein Folds and Their Distribution over Families in Nature [J]. Proteins, 2004, 54: 491–499.CrossRefGoogle Scholar
  7. [7]
    Li H, Tang C, Wingreen N S. Are Protein Folds Atypical? [J]. Biophysics, 1998, 95: 4987–4990.Google Scholar
  8. [8]
    Dill K A. Theory for the Folding and Stability of Globular Proteins [J]. Biochemistry, 1985, 24: 1501–1509.CrossRefGoogle Scholar
  9. [9]
    Zhang W, Sun Z B, Zou X W. Study of Protein Folding Using the Lattice Model with Unrestricted Boundary [J]. Mod Phys Lett B, 2003, 17: 1243–1252.CrossRefGoogle Scholar
  10. [10]
    Zhang W, Sun Z B, Zou X W. Designability of Protein Structures on the Hexagonal Lattice Model [J]. Chin Phys Lett, 2005, 22:2133–2136.CrossRefGoogle Scholar
  11. [11]
    Nemethy G, Pottle M S, Scheraga H A. Updating of Geometrical Parameters, Non-Bonding Interactions and Hydrogen Bonding [J]. J Phys Chem, 1983, 87: 1883–1887.CrossRefGoogle Scholar
  12. [12]
    Wang J, Wang W. A Computational Approach to Simplifying the Protein Folding Alphabet[J]. Nature Struct Biol, 1999, 6: 1033–1038.CrossRefGoogle Scholar

Copyright information

© Wuhan University 2007

Authors and Affiliations

  • Zhang Wei 
    • 1
  • Huang Shengyou 
    • 1
  • Yu Tao 
    • 1
  • Zou Xianwu 
    • 1
  1. 1.School of Physics and TechnologyWuhan UniversityWuhanChina

Personalised recommendations