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Protein Science (2004), 13:1524-1537. Published by Cold Spring Harbor Laboratory Press. Copyright © 2004 The Protein Society
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Theoretical study of interaction of winter flounder antifreeze protein with ice

Alexander Jorov, Boris S. Zhorov and Daniel S.C. Yang

Department of Biochemistry, McMaster University, Hamilton, Ontario L8N 3Z5, Canada

(RECEIVED January 19, 2004; FINAL REVISION March 16, 2004; ACCEPTED March 16, 2003)



Abstract

Antifreeze proteins (AFPs) are synthesized by various organisms to enable their cells to survive subzero environment. These proteins bind to small ice crystals and inhibit their growth, which if left uncontrolled would be fatal to cells. The crystal structures of a number of AFPs have been determined; however, crystallographic analysis of AFP–ice complex is nearly impossible. Molecular modeling studies of AFPs’ interaction with ice surface is therefore invaluable. Early models of AFP–ice interaction suggested H-bond as the primary driving force behind such interaction. Recent experimental evidence, however, suggested that hydrophobic interactions could be the main contributor to AFP–ice association. All computational studies published to date were carried out to verify the H-bond model, and no works attempting to verify the hydrophobic interaction model have been published. In this work, we Monte Carlo–minimized complexes of several AFPs with ice taking into account nonbonded interactions, H-bonds, and the hydration potential for proteins. Parameters of the hydration potential for ice were developed with the assumption that the free energy of the water–ice association should be close to zero at equilibrium melting temperature. Our calculations demonstrate that desolvation of hydrophobic groups in the AFPs upon their binding to the grooves at the ice surface is indeed the major stabilizing contributor to the free energy of AFP–ice binding. This study is consistent with available structural and mutation data on AFPs. In particular, it explains the paradoxical finding that substitution of Thr residues with Val does not affect the potency of winter flounder AFP whereas substitution with Ser abolished its antifreeze activity.

Keywords: antifreeze protein; ice; energy minimization; Monte Carlo minimization; hydrophobic interactions; structure–activity relationships

Abbreviations: AFP, antifreeze protein • WF, winter flounder • MC, Monte Carlo • MCM, Monte Carlo minimization • MD, molecular dynamics

Reprint requests to: Daniel S.C. Yang, Department of Biochemistry, McMaster University, 1200 Main Street West, Hamilton, Ontario L8N 3Z5, Canada; e-mail: yang{at}mcmaster.ca; fax: (905) 522-9033.

Article and publication are at http://www.proteinscience.org/cgi/doi/10.1110/ps.04641104.


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