PDBsum entry 1j5b

Antifreeze protein

PDB id: 1j5b

Contents

Protein chain

38 a.a.

References listed in PDB file

Key reference

Title

Solution structure of a hydrophobic analogue of the winter flounder antifreeze protein.

Authors

E.Liepinsh, G.Otting, M.M.Harding, L.G.Ward, J.P.Mackay, A.D.Haymet.

Ref.

Eur J Biochem, 2002, 269, 1259-1266. [DOI no: 10.1046/j.1432-1033.2002.02766.x]

PubMed id

11856360

Abstract

The solution structure of a synthetic mutant type I antifreeze protein (AFP I) was determined in aqueous solution at pH 7.0 using nuclear magnetic resonance (NMR) spectroscopy. The mutations comprised the replacement of the four Thr residues by Val and the introduction of two additional Lys-Glu salt bridges. The antifreeze activity of this mutant peptide, VVVV2KE, has been previously shown to be similar to that of the wild type protein, HPLC6 (defined here as TTTT). The solution structure reveals an alphahelix bent in the same direction as the more bent conformer of the published crystal structure of TTTT, while the side chain chi1 rotamers of VVVV2KE are similar to those of the straighter conformer in the crystal of TTTT. The Val side chains of VVVV2KE assume the same orientations as the Thr side chains of TTTT, confirming the conservative nature of this mutation. The combined data suggest that AFP I undergoes an equilibrium between straight and bent helices in solution, combined with independent equilibria between different side chain rotamers for some of the amino acid residues. The present study presents the first complete sequence-specific resonance assignments and the first complete solution structure determination by NMR of any AFP I protein.

Figure 1.
Fig. 1. Analytical ultracentifugation data for VVVV2KE at concentrations of 1 mm (diamonds), 0.3 mm (squares) and 0.1 mm (circles). Top panel shows fits of data to an ideal-single species model and bottom panel shows residuals derived from this fit.

Figure 3.
Fig. 3. Stereo views of the solution structure of VVVV2KE. (A)Superposition of the 20 conformers representing the NMR structure of VVVV2KE (left panel) and single conformer closest to the average structure (right panel). The line drawings include all heavy atoms. -Carbon positions are identified by spheres, and the location of approximately every tenth residue is labeled by its number in the amino acid sequence. (B) Stereo views of the N-cap (left panel) and C-cap (right panel) in the NMR structure of VVVV2KE. The backbone atoms of the first five and last six residues, respectively, were superimposed for minimum r.m.s.d. Only bonds with backbone atoms and backbone carbonyl atoms are displayed, except for the side chain of Asp1. The N- and C-terminal ends are identified and hydrogen bonds drawn with dotted lines. The N-cap hydrogen bond between the carboxyl group of Asp1 and the backbone amide of Ser4 is identified in bold.

The above figures are reprinted by permission from the Federation of European Biochemical Societies: Eur J Biochem (2002, 269, 1259-1266) copyright 2002.