Molecular dynamics simulation of winter flounder antifreeze protein variants in solution: correlation between side chain spacing and ice lattice.
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 degree 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 A during the 120 ps of simulation, but values simultaneously close to the repeat distance of 16.6 A between oxygen atoms along the [0112] direction in ice are observed. Furthermore, two engineered variants were studied using the same simulation protocol.
Jorgensen
H
H
Biotechnology Laboratory, Sumitomo Chemical Co., Ltd., Hyogo, Japan.
Mori
M
M
Matsui
H
H
Kanaoka
M
M
Yanagi
H
H
Yabusaki
Y
Y
Kikuzono
Y
Y
D000595:Amino Acid Sequence; D000818:Animals; D021301:Antifreeze Proteins; D002942:Circular Dichroism; D003198:Computer Simulation; D005432:Flounder; D005615:Freezing; D006023:Glycoproteins / Q000737:chemistry*; D006860:Hydrogen Bonding; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000737:chemistry*; D011487:Protein Conformation; D015202:Protein Engineering; D017433:Protein Structure, Secondary; D012984:Software; D012996:Solutions / Q000737:chemistry
D021301:Antifreeze Proteins; D006023:Glycoproteins; D010446:Peptide Fragments; D012996:Solutions