Skip to main content
SpringerLink
Log in

Computational simulations on the fish-type-II antifreeze protein-ice-solvent system

  • Research Article
  • Published:
Frontiers of Biology in China

Abstract

Based on the computational simulation with the vacuum environment for the fish-type-II antifreeze proteinice-solvent (water) system, the multi-complex system of the antifreeze protein-ice-water has been constructed and calculated. We have studied the interaction of such proteinice system with water solvent through the dynamics simulation with 350 ps. By employing the Molecular Dynamics simulation and semi-empirical method calculation, we have further investigated the interface properties of the antifreeze protein and ice crystal combined system. Consequently, a water solvent affects significantly the properties of this combined system.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Brooks B R, Bruccolei R E, Olafson B D, States D J, Swaminathan S, Karplus M (1983). CHARMM: A program for marcromolecular energy, minimization, and dynamics calculations. J Comput Chem, 4(2): 187–217

    Article  CAS  Google Scholar 

  • Chen G, Jia Z (1999). Ice-binding surface of fish type III antifreeze. Biophys J, 77: 1602–1608

    PubMed  CAS  Google Scholar 

  • Cheng Y H, Yang Z Y, Tan H W, Liu R Z, Chen G J, Jia Z C (2002). Analysis of ice-binding sites in fish type II antifreeze protein by quantum mechanics. Biophys J, 83: 2202–2210

    Article  PubMed  CAS  Google Scholar 

  • Cornell W D, Cleplak P, Bayly C I, Gould I R, Merz K M, Ferguson D M, Spellmeyer D C, Fox T, Caldwell J W, Kollman P A (1995). A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc, 117: 5179–5197

    Article  CAS  Google Scholar 

  • Dewar M J S, Thiel W (1977). Ground states of molecules. 38. The MNDO method. Approximations and parameters. J Am Chem Soc, 99: 4899

    Article  CAS  Google Scholar 

  • Ewart K V, Rubinsky B, Fletcher G L (1992). Structural and functional similarity between Æsh antifreeze proteins and calcium-dependent lectins. Biochem Biophys Res Commun, 185(1): 335–340

    PubMed  CAS  Google Scholar 

  • Gronwald W, Loewen M C, Lix B, Daugulis A J, Sönnichsen F D, Davies P L, Sykes B D (1998). The solution structure of type II antifreeze protein reveals a new member of the lectin family. Biochemistry, 37(14): 4712–4721

    Article  PubMed  CAS  Google Scholar 

  • Jocoby S L S, Kowalik J S, Pizzo J T (1972). Iterative Methods for Nonlinear Optimization Problems. Englewwood Cliffs, New Jersey: Prentice Hall

    Google Scholar 

  • John B (2001). Thermal hysteresis proteins. The Interaction Journal of Biochemistry and Cell Biology, 33: 105–117

    Article  Google Scholar 

  • Jorgensen W L, Chandrasekhar J, Madura J D (1983). comparison of simple potential functions of simulating liquid water. J Chem Phys, 79: 926–935

    Article  CAS  Google Scholar 

  • Kollman P A (1993). Free energy calculations: Applications to chemical and biochemical phenomena. Chem Rev, 93: 2395–2417

    Article  CAS  Google Scholar 

  • Sönnichsen F D, Sykes B D, Davies P L (1995). Comparative modeling of the three-dimensional structure of type II antifreeze protein. Protein Sci, 4(3): 460–471

    Article  PubMed  Google Scholar 

  • Wen D, Laursen R A (1993). An-antifreeze polypeptide displays the same activity as its natural L-enantiomer. FEBS Lett, 317(1–2): 3134

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. College of Life Sciences, Beijing Normal University, Beijing, 100875, China

    Liu Kai

  2. College of Chemistry, Beijing Normal University, Beijing, 100875, China

    Wang Yan, Tan Hongwei & Chen Guangju

  3. Technical Institute of Physics and Chemistry, Chinese Academy of Sciences and Graduate School of the Chinese Academy of Sciences, Beijing, 100039, China

    Tong Zhenhe

Authors
  1. Liu Kai
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Wang Yan
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Tan Hongwei
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Chen Guangju
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Tong Zhenhe
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Chen Guangju.

Additional information

__________

Translated from Journal of Beijing Normal University (Natural Science), 2006, 42(1): 74–77 [译自: 北京师范大学学报]

Rights and permissions

Reprints and permissions

About this article

Cite this article

Liu, K., Wang, Y., Tan, H. et al. Computational simulations on the fish-type-II antifreeze protein-ice-solvent system. Front. Biol. China 2, 180–183 (2007). https://doi.org/10.1007/s11515-007-0025-3

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11515-007-0025-3

Keywords

Search

Navigation