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Intermolecular interaction studies of winter flounder antifreeze protein reveal the existence of thermally accessible binding state
Author(s) -
Nguyen Dat H.,
Colvin Michael E.,
Yeh Yin,
Feeney Robert E.,
Fink William H.
Publication year - 2004
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.20104
Subject(s) - chemistry , antifreeze protein , intermolecular force , solvation , antifreeze , chemical physics , molecule , antiparallel (mathematics) , solvophobic , winter flounder , molecular dynamics , context (archaeology) , thermodynamics , crystallography , computational chemistry , flounder , physics , organic chemistry , fish <actinopterygii> , biochemistry , quantum mechanics , fishery , magnetic field , biology , paleontology
Abstract The physical nature underlying intermolecular interactions between two rod‐like winter flounder antifreeze protein (AFP) molecules and their implication for the mechanism of antifreeze function are examined in this work using molecular dynamics simulations, augmented with free energy calculations employing a continuum solvation model. The energetics for different modes of interactions of two AFP molecules is examined in both vacuum and aqueous phases along with the water distribution in the region encapsulated by two antiparallel AFP backbones. The results show that in a vacuum two AFP molecules intrinsically attract each other in the antiparallel fashion, where their complementary charge side chains face each other directly. In the aqueous environment, this attraction is counteracted by both screening and entropic effects. Therefore, two nearly energetically degenerate states, an aggregated state and a dissociated state, result as a new aspect of intermolecular interaction in the paradigm for the mechanism of action of AFP. The relevance of these findings to the mechanism of function of freezing inhibition in the context of our work on Antarctic cod antifreeze glycoprotein (Nguyen et al., Biophysical Journal, 2002, Vol. 82, pp. 2892–2905) is discussed. © 2004 Wiley Periodicals, Inc. Biopolymers, 2004