Structural Investigation of Supercooled Water Confined in Antifreeze Proteins: Models’ Performance Evaluation between Coarse Grained and Atomistic Simulation Models

  • Nghiep H.V.
  • Hung P.N.
  • Ly L.
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 8158)

Abstract

Antifreeze proteins (AFPs) play an important role as inhibitors of ice crystal growth in the body fluid of living organisms. Nonetheless, the exact mechanism of ice growth inhibition is still poorly understood to experimentally analyze the molecular-scale which strongly requires computer simulation for AFPs’ binding site to certain planes of ice crystal. In this research, Coarse-Grained simulation using MARTINI force field was utilized to evaluate stability of helix/β-helix restraints of M. americanus, L. perenne, M. primoryensis andC. Fumiferana were collected on the Protein Data Bank using high resolution of X-ray diffraction because the β-helix/helix in AFPs’ structure play an important role to face ice-binding residues with ice cluster, as receptor and ligand interactions. In results, the root mean square deviations have shown high identity of RMSF between AA-MD and CG-MD simulation in 1HG7 and 3P4G, exceptionally, 1N4I and 3ULT that can be further studied in detail using all-atoms molecular dynamics simulation (AA-MD).

Keywords

Antifreeze protein Coarse-Grained simulation helix/beta-helix MARTINI force field AA-MD 

References

  1. 1.
    Atıcı, O., Nalbantoglu, B.: Antifreeze proteins in higher plants. Phytochemistry 64, 1187–1196 (2003)CrossRefGoogle Scholar
  2. 2.
    Griffith, M., Yaish, M.W.F.: Antifreeze proteins in overwintering plants: a tale of two activities. Trends Plant Sci. 9, 399–405 (2004)CrossRefGoogle Scholar
  3. 3.
    DeVries, A.L., Komatsu, S.K., Feeney, R.E.: Chemical and physical proper-ties of freezing-point depressing glycoproteins from antarctic fishes. J. Biol. Chem. 245, 2901–2908 (1970)Google Scholar
  4. 4.
    Davies, P.L., Hew, C.L., Fletcher, G.L.: Fish antifreeze proteins: physiology and evolutionary biology. Can. J. Zool. 66, 2611–2617 (1980)CrossRefGoogle Scholar
  5. 5.
    Marshall, C.B., Fletcher, G.L., Davies, P.L.: Hyperactive antifreeze protein in a fish. Nature 429, 153 (2004)CrossRefGoogle Scholar
  6. 6.
    Hew, C.L., Kao, M.H., So, Y.-P., Lim, K.-P.: Presence of cystine-containing antifreeze proteins in the spruce budworm, Choristoneura fumirana. Can. J. Zool. 61, 2324–2328 (1983)CrossRefGoogle Scholar
  7. 7.
    Schneppenheim, R., Theede, H.: Isolation and characterization of freezing-point depressing peptides from larvae of Tenebrio molitor. Comp. Biochem. Phys. B. Biochem. Mol. Biol. 67, 561–568 (1980)CrossRefGoogle Scholar
  8. 8.
    Duman, J.G., Bennett, V., Sformo, T., Hochstrasser, R., Barnes, B.M.: Anti-freeze proteins in alaskan insects and spiders. J. Insect Physiol. 50, 259–266 (2004)CrossRefGoogle Scholar
  9. 9.
    Muryoi, N., Sato, M., Kaneko, S., Kawahara, H., Obata, H., Yaish, M.W.F., Yeh, Y., Feeney, R.E.: Antifreeze proteins: structures and mechanisms of function. Chem. Rev. 96, 601–618 (1996)CrossRefGoogle Scholar
  10. 10.
    Yeh, Y., Feeney, R.E.: Antifreeze proteins: structures and mechanisms of function. Chem. Rev. 96, 601–618 (1996)CrossRefGoogle Scholar
  11. 11.
    Ewart, K.V., Lin, Q., Hew, C.L.: Structure, function and evolution of antifreeze protein. Cellular and Molecular Life Sciences (CMLS) 55(2) (1999)Google Scholar
  12. 12.
    Bale, J.S.: Insects and Low Temperatures: From Molecular Biology to Distri-butions and Abundance. Biological Sciences 357(1423), 849–862 (2002)CrossRefGoogle Scholar
  13. 13.
    Block, W.: To Freeze or Not to Freeze? Invertebrate Survival of Sub-Zero Temperatures. Functional Ecology 5(2), 284–290 (1991)CrossRefGoogle Scholar
  14. 14.
    Duman, J.G., Wu, D.W., Xu, L., Tursman, D., Olsen, T.M.: Adaptations of In-sects to Subzero Temperatures. The Quarterly Review of Biology 66(4) (1991)Google Scholar
  15. 15.
    Dalal, P., Knickelbein, J., Haymet, A.D.J., Sönnichsen, F.D., Madura, J.D.: Hydrogen bond analysis of Type 1 antifreeze protein in water and the ice/water interface. Physical Chemistry Communications 7, 1–5 (2001)Google Scholar
  16. 16.
    Griffith, M., Lumb, C., Wiseman, S.B., Wisniewski, M., Johnson, R.W., Ma-rangoni, A.G.: Antifreeze Proteins Modify the Freezing Process in Planta. Plant Physiology 138(1), 330–340 (2005)CrossRefGoogle Scholar
  17. 17.
    Hightower, R., Baden, C., Penzes, E., Lund, P., Dunsmuir, P.: Expression of antifreeze proteins in transgenic plants. Plant Molecular Biology 17, 1013–1021 (1991)CrossRefGoogle Scholar
  18. 18.
    Hiroki, N., Yoshinori, F.: Antifreeze proteins: computer simulation studies on the mechanism of ice growth inhibition. Polymer Journal 44, 690–698 (2012)CrossRefGoogle Scholar
  19. 19.
    Jia, Z.C., Davies, P.L.: Antifreeze proteins: an unusual receptor-ligand interac-tion. Trends Biochem. Sci. 27, 101–106 (2002)CrossRefGoogle Scholar
  20. 20.
    Chao, H., Hodges, R.S., Kay, C.M., Gauthier, S.Y., Davies, P.L.: A natural variant of type I antifreeze protein with four ice-binding repeats is a particularly potent antifreeze. Protein Sci. 5, 1150–1156 (1996)CrossRefGoogle Scholar
  21. 21.
    Leinala, E.K., Davies, P.L., Doucet, D., Tyshenko, M.G., Walker, V.K., Jia, Z.C.: A beta-helical antifreeze protein isoform with increased activity—Structural and functional insights. J. Biol. Chem. 277, 33349–33352 (2002)CrossRefGoogle Scholar
  22. 22.
    Marshall, C.B., Daley, M.E., Sykes, B.D., Davies, P.L.: Enhancing the activity of a beta-helical antifreeze protein by the engineered addition of coils. Biochemistry 43, 11637–11646 (2004)CrossRefGoogle Scholar
  23. 23.
    Haymet, A.D., Ward, L.G., Harding, M.M., Knight, C.A.: Valine substituted-winter flounder ‘antifreeze’: preservation of ice growth hysteresis. FEBS Lett. 3(430), 301–306 (1998)CrossRefGoogle Scholar
  24. 24.
    Nolan, B.H., Yoshiyuki, N., Sakae, T., Frank, D.S.: Activity of a two-domain antifreeze protein is not dependent on linker sequence. Biophysical Journal 92, 541–546 (2007)CrossRefGoogle Scholar
  25. 25.
    Rose, P.W., Bi, C., Bluhm, W.F., Christie, C.H., Dimitropoulos, D., Dutta, S., Bourne, P.E.: The RCSB Protein Data Bank: new resources for research and education. Nucleic Acids Res. 41(Database issue), D475–D482 (2013)CrossRefGoogle Scholar
  26. 26.
    Gilbert, J.A., Christine, P.J., Dodd, E.R., Layborn-Parry, J.: Demonstration of Antifreeze Protein Activity in Antarctic Lake Bacteria. Microbiology 150, 171–180 (2004)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Nghiep H.V.
    • 1
  • Hung P.N.
    • 2
  • Ly L.
    • 1
    • 2
  1. 1.School of Biotechnology, International University – Vietnam National University, HCMCVietnam
  2. 2.Institute for Computational Science and Technology at Ho Chi Minh CityVietnam

Personalised recommendations