Abstract
The possible interaction models for an antifreeze protein from Tenebrio molitar (TmAFP) have been systematically studied using the methods of molecular mechanics, molecular dynamics and quantum chemistry. It is hoped that these approaches would provide insights into the nature of interaction between protein monomers through sampling a number of interaction possibilities and evaluating their interaction energies between two monomers in the course of recognition. The results derived from the molecular mechanics indicate that monomerś β-sheets would be involved in interaction area and the side chains on two p-faces can match each other at the two-dimensional level. The results from molecular mechanics and ONIOM methods show that the strongest interaction energy could be gained through the formation of H-bonds when the twoβ-sheets are involved in the interaction model. Furthermore, the calculation of DFT and analysis of van der Waals bond charge density confirm further that recognition between the two TCTs mainly depends on inter-molecular hydroxyls. Therefore, our results demonstrate that during the course of interaction the most favorable association of TmAFPs is via their β-sheets.
Similar content being viewed by others
References
Mckee, T., Mckee, J. R., Biochemistry: An Introduction, 2nd ed., Beijing: Science Press, 2000, 94–106.
Sergeev, Y. V., Wingfield, P. T., Hejtmancik, J. F., Monomer-dimer equilibrium of normal and modified beta A3-crystallins: experimental determination and molecular modeling, Biochemistry, 2000,39: 15799–15806.
Falconi, M., Cambria, M. T., Cambria, A. et al., Structure and stability of the insulin dimer investigated by molecular dynamics simulation, J. Biomol. Struct. Dyn., 2001, 18: 761–772.
Liou, Y. C., Tocilj, A., Davies, P. L. et al., Mimicry of ice structure by surface hydroxyls and water of a p-helix antifreeze protein, Nature, 2000, 406:322–324.
Liou, Y. C., Daley, M. E., Graham, L. A. et al., Folding and structural characterization of highly disulfide-bonded beetle antifreeze protein produced in bacteria, Protein Expr. Purif., 2000, 19: 148- 157.
Cornell, W. D., Cleplak, P., Bayly, C. I. et al., A second generation force field for the simulation of proteins and nucleic acids, J. Am. Chem. Soc., 1995, 117: 5179–5197.
Svensson, M., Humbel, S., Froese, R. D. J. et al., Oniom: Amultilayered integrated MO+MM method for geometry optimizations and single point energy predictions, A test for Diels-Alder reactions and Pt(P(t-Bu)3)2+H2 oxidative addition, J. Phys. Chem., 1996,100: 19357–19363.
Stewart, J. J. P., Optimization of parameters for semi-empirical methods I-method, J. Comp. Chem., 1989, 10: 209–220.
Becke, A. D., Density-functional thermochemistry, III. The role of exact exchange, J. Phys. Chem., 1993, 98: 5648–5652.
Lee, C., Duman, W., Parr, R. G., Development of the colle-salvettti correlation-energy formula into a functional of the electron density, Phys. Rev. B, 1988, 37: 785–789.
Chen, G. J., Jia, Z. C., Ice-binding surface offish type III antifreeze, Biophys. J., 1999, 77: 1602–1608.
Kollman, P. A., Allen, L. C., The theory of the hydrogen bond, Chem. Rev., 1972, 72: 283–325.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Yang, Z., Jia, Z., Liu, R. et al. Molecular and quantum mechanical studies on the monomer recognition of a highly-regular β-helical antifreeze protein. Sc. China Ser. B-Chem. 47, 34–40 (2004). https://doi.org/10.1360/03yb0025
Received:
Issue Date:
DOI: https://doi.org/10.1360/03yb0025