Skip Navigation

This Article
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (33)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Jorgensen, H.
Right arrow Articles by Kikuzono, Y.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Jorgensen, H.
Right arrow Articles by Kikuzono, Y.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Protein Engineering vol. 6 no. 1 pp. 19-27, 1993
© 1993 Oxford University Press

RESEARCH-ARTICLE

Molecular dynamics simulation of winter flounder antifreeze protein variants in solution: correlation between side chain spacing and ice lattice

H. Jorgensen1,2,3, M. Mori1, H. Matsui2, M. Kanaoka1, H. Yanagi1, Y. Yabusaki1 and Y. Kikuzono2

1Biotechnology Laboratory, Takarazuka Research Center, Sumitomo Chemical Co., Ltd 4-2-1 Takatsukasa, Takarazuka Hyogo 665, Japan 2Process Systems Department, Sumitomo Chemical Co., Ltd Sumitomo Building 4-5-33 Kitahama, Chuo-ku, Osaka 541, Japan

3To whom correspondence should be addressed

The solution structure of the 38 amino acid C-terminal region of the precursor for the HPLC-6 antifreeze protein from winter flounder has been investigated with molecular dynamics using the AMBER software. The simulation for the peptide in aqueous solution was carried out at a constant temperature of 0°C and at atmospheric pressure. The simulation covered 120 ps and the results were analyzed based on data sampled upon reaching a stable equilibrium phase. Information has been obtained on the quality of constant temperature and pressure simulations, the solution structure and dynamics, the hydrogen bonding network, the helix-stabilizing role of terminal charges and the interaction with the surrounding water molecules. The Lys18–Glu22 interactions and the terminal charged residues are found to stabilize a helical structure with the side chains of Thr2, Thr13, Thr24 and Thr35 equally spaced on one side of the helix. The spacing between oxygen atoms in the hydroxyl group of the threonine side chains exhibits fluctuations of the order of 2–3 Å during the 120 ps of simulation, but values simultaneously close to the repeat distance of 16.6 Å between oxygen atoms along the [0112] direction in ice are observed. Furthermore, two engineered variants were studied using the same simulation protocol.

Keywords: antifreeze protein/molecular dynamics simulation/protein engineering/solution structure/structure—function relationship

Received August 28, 1992; accepted October 9, 1992.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 J. Biol. Chem.Home page
K. Fairley, B. J. Westman, L. H. Pham, A. D. J. Haymet, M. M. Harding, and J. P. Mackay
Type I Shorthorn Sculpin Antifreeze Protein. RECOMBINANT SYNTHESIS, SOLUTION CONFORMATION, AND ICE GROWTH INHIBITION STUDIES
J. Biol. Chem., June 28, 2002; 277(27): 24073 - 24080.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.