Intermolecular interaction studies of winter flounder antifreeze protein reveal the existence of thermally accessible binding state
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 calcul...
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crwiley:10.1002/bip.20104 2024-06-02T07:57:58+00:00 Intermolecular interaction studies of winter flounder antifreeze protein reveal the existence of thermally accessible binding state Nguyen, Dat H. Colvin, Michael E. Yeh, Yin Feeney, Robert E. Fink, William H. 2004 http://dx.doi.org/10.1002/bip.20104 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1002%2Fbip.20104 https://onlinelibrary.wiley.com/doi/pdf/10.1002/bip.20104 en eng Wiley http://onlinelibrary.wiley.com/termsAndConditions#vor Biopolymers volume 75, issue 2, page 109-117 ISSN 0006-3525 1097-0282 journal-article 2004 crwiley https://doi.org/10.1002/bip.20104 2024-05-03T11:04:41Z 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 Article in Journal/Newspaper Antarc* Antarctic Wiley Online Library Antarctic Biopolymers 75 2 109 117 |
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Wiley Online Library |
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English |
description |
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 |
format |
Article in Journal/Newspaper |
author |
Nguyen, Dat H. Colvin, Michael E. Yeh, Yin Feeney, Robert E. Fink, William H. |
spellingShingle |
Nguyen, Dat H. Colvin, Michael E. Yeh, Yin Feeney, Robert E. Fink, William H. Intermolecular interaction studies of winter flounder antifreeze protein reveal the existence of thermally accessible binding state |
author_facet |
Nguyen, Dat H. Colvin, Michael E. Yeh, Yin Feeney, Robert E. Fink, William H. |
author_sort |
Nguyen, Dat H. |
title |
Intermolecular interaction studies of winter flounder antifreeze protein reveal the existence of thermally accessible binding state |
title_short |
Intermolecular interaction studies of winter flounder antifreeze protein reveal the existence of thermally accessible binding state |
title_full |
Intermolecular interaction studies of winter flounder antifreeze protein reveal the existence of thermally accessible binding state |
title_fullStr |
Intermolecular interaction studies of winter flounder antifreeze protein reveal the existence of thermally accessible binding state |
title_full_unstemmed |
Intermolecular interaction studies of winter flounder antifreeze protein reveal the existence of thermally accessible binding state |
title_sort |
intermolecular interaction studies of winter flounder antifreeze protein reveal the existence of thermally accessible binding state |
publisher |
Wiley |
publishDate |
2004 |
url |
http://dx.doi.org/10.1002/bip.20104 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1002%2Fbip.20104 https://onlinelibrary.wiley.com/doi/pdf/10.1002/bip.20104 |
geographic |
Antarctic |
geographic_facet |
Antarctic |
genre |
Antarc* Antarctic |
genre_facet |
Antarc* Antarctic |
op_source |
Biopolymers volume 75, issue 2, page 109-117 ISSN 0006-3525 1097-0282 |
op_rights |
http://onlinelibrary.wiley.com/termsAndConditions#vor |
op_doi |
https://doi.org/10.1002/bip.20104 |
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Biopolymers |
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75 |
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2 |
container_start_page |
109 |
op_container_end_page |
117 |
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1800741201277616128 |