Ordered surface carbons distinguish antifreeze proteins and their ice-binding regions.
Antifreeze proteins (AFPs) are found in cold-adapted organisms and have the unusual ability to bind to and inhibit the growth of ice crystals. However, the underlying molecular basis of their ice-binding activity is unclear because of the difficulty of studying the AFP-ice interaction directly and the lack of a common motif, domain or fold among different AFPs. We have formulated a generic ice-binding model and incorporated it into a physicochemical pattern-recognition algorithm. It successfully recognizes ice-binding surfaces for a diverse range of AFPs, and clearly discriminates AFPs from other structures in the Protein Data Bank. The algorithm was used to identify a novel AFP from winter rye, and the antifreeze activity of this protein was subsequently confirmed. The presence of a common and distinct physicochemical pattern provides a structural basis for unifying AFPs from fish, insects and plants.
Doxey
Andrew C
AC
Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada.
Yaish
Mahmoud W
MW
Griffith
Marilyn
M
McConkey
Brendan J
BJ
D000465:Algorithms; D021301:Antifreeze Proteins / Q000145:classification / Q000302:isolation & purification*; D030562:Databases, Protein / Q000145:classification*; D008956:Models, Chemical; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017386:Sequence Homology, Amino Acid; D013329:Structure-Activity Relationship
D021301:Antifreeze Proteins