Well we’re freezing our butts off here in sunny New England, so it’s time to discourse upon the chemical ingenuity of antifreeze proteins. They’ve long been known, with most found in fish living in arctic waters. A very unusual structure is found in a 79 amino acid protein from an insect living near Lake Ontario. It contains 79 amino acids with a set of 10 amino acid tandem repeats making up most of the protein. Here is the the repeat.
X X Cys X Gly X Tyr Cys X Gly ; X = any amino acid.
Can you as a computational chemistry expert figure out what it forms?
The 10 amino acids form a complete circle with the peptide backbone looking nothing like an alpha helix, a beta sheet or anything else I’ve seen. It just sort of wanders around for 360 degrees. In cross section the ‘circle’ resembles the Greek letter theta with a disulfide bond between the two cysteines forming a crossbar inside the circle. This puts all 7 tyrosines from the 7 repeats in a row on one side of the circle, where they form the presumed ice binding site. The solenoid is reinforced by intrachain hydrogen bonds, and side chain salt bridges. You can read about it and see some pictures in Proc. Natl. Acad. Sci. vol. 112 pp. 737 – 742 ’15 ].
The chemical ingenuity of some of these proteins is remarkable. None of them (except one) appear to have been figured out before their structures were determined.
[ Proc. Natl. Acad. Sci. vol. 108 pp. 7281 – 7282 ’11 ] Even now, the structural differences between the surface of ice nuclei and liquid water are poorly characterized (we don’t even know how many hydrogen bonds are involved), yet antifreeze proteins somehow recognize it. Some 12 different structural motifs have been found in antifreeze proteins. 3 are given — one is a small globular protein (sea pout) another is an alpha helix (winter flounder), and the third is a stack of left handed PolyProtein-II helices (snow flea). The present work gives a fourth example — a right handed parallel beta helix from (Marinomonas primoyensis). It is a 34 kiloDalton domain — it is a calcium bound parallel beta helix, with an extensive array of icelike surface waters that are anchored via hydrogen bonds directly to the protein backbone and adjacent side chains. The bound waters make an excellent 3 dimensional match to the primary prism and basal planes of ice.
Probably the most counterintuitive antifreeze protein is the following. It stands a lot of what we thought we knew about protein structure on its head.
[ Science vol. 343 pp. 743 – 744, 795 – 798 ’14 ] Almost all globular proteins reported to date have a dry protein core (e.g. water free). An antifreeze protein called Maxi from the winter flounder (Pseudopleuronectes americanus) has been found with a water filled core. It is a 3 kiloDalton alanine rich 4 helix bundle 145 Angstroms long. The periodicity of the alpha helices is 11 amino acids. A single turn of an alpha helix is 5.4 Angstroms high and 11 Angstroms wide. So 11 amino acids fairly neatly comes out to 16 Angstroms in length (because each helical turn is 3.7 residues (vs. the normal 3.6 in the classic alpha helix). The ice binding residues are Threonine at position i, Alanine at position i+4 and Alanine at position i + 8 (putting them along one face of the helix). The protein is a dimer of monomers each containing two helices. The core is comprised of 400 (yes 400 !) highly organized water molecules. The water is interleaved as a roughly two molecule thick layer between both intra and intermonomer helix interfaces, extending to the ice binding surfaces. Maxi must bind ice nuclei and inhibit their growth. The water molecules inside the bundle form pentagons ! ! ! Amazingly, this was predicted 50 years ago by Scheraga . The 5 membered water rings form cages around individual amino acid side chains, illustrating their semi-clathrate structure — rather than ice. Most of the carbonyls are involved in hydrogen bonding interactions with water — helping to keep the protein soluble. The protein denatures at low temperatures (16 C)
Ordered water can be found in most high resolution Xray crystallograpy protein structures, but they are usually between the proteins. Maxi retains the very structure of water.
Removal of water has been proposed as a potential rate limiting step in protein folding. Maxi folds to the point where water not in direct contact with the protein chain is removed from its core. It then arrests further folding to retain a beautifully ordered core of water interleaved between the protein helices.
Amazing! No one would ever have predicted something like Maxi (except Sheraga).