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* Department of Biochemistry and the
Protein Function Discovery Group, Queen's University, Kingston, Ontario K7L 3N6, Canada
Correspondence: Address reprint requests to Peter L. Davies, Dept. of Biochemistry, Queen's University, Kingston, ON K7L 3N6, Canada. Tel.: 613-533-2983; Fax: 613-533-2497; E-mail: daviesp{at}post.queensu.ca.
| ABSTRACT |
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| INTRODUCTION |
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Two antifreeze isoforms were isolated from the snow flea, which differ in mass (15.7 kDa and 6.5 kDa) (1
). Both of these proteins had potent thermal hysteresis activities of >2 C° at micromolar concentrations. They have very similar amino acid compositions. The short isoform (6.5 kDa) of snow flea AFP (sfAFP) contains 81 residues organized into a prominent repeat of Gly-x1-x2 where x1 is often a glycine, and x2 varies between a charged/hydrophilic residue and a small, hydrophobic residue (alanine/valine). This protein contains 37 glycines (45.7%) and the second most abundant residue is alanine (13.6%). The protein also contains four cysteines, which were found to form two disulfide bonds based on the mass difference after reduction and alkylation, although the bonding pattern is not known. Interestingly, the larger isoform has only two cysteines, and these are also disulfide bonded.
The amount of sfAFP that can be readily purified from natural sources is insufficient for conventional structure determination. It has proven difficult to collect even gram amounts of this organism (510,000 individuals/g) from which microgram quantities of AFP can be purified. Moreover, it is not easy to produce the AFP as a well-folded recombinant protein because of its unusual properties and thermal instability (data not shown). In the interim, we set out to model the protein structure ab initio.
| METHODS |
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A physical model was constructed using the HGS Biochemistry Molecular Model from Hinomoto Plastics (Tokyo, Japan).
Molecular dynamics
A virtual model was built using PyMOL 0.98 (7
). The model was solvated in a 5.1 nm x 3.6 nm x 3.4 nm box of water containing 1776 waters and had a net single positive charge. To neutralize the charge of the system and to provide an effective concentration of 0.1M NaCl, nine molecules of water were replaced by 4 Na+ and 5 Cl ions. The system was subjected to energy minimization by steepest descents, position restrained molecular dynamics to relax the solvent, followed by full molecular dynamics. All molecular mechanics calculations were done with GROMACS 3.3 (8
). GROMACS uses a triclinic unit cell for its periodic boundary conditions. For calculating short-range nonbonded interactions, only the nearest image is considered (8
). Long-range electrostatics is treated with the particle mesh Ewald method. The simulations were done under isothermal conditions using Berendsen temperature coupling. The GROMOS96 43a1 force field was chosen. The simulations were done independently at 4°C and 25°C using a timestep of 2 fs for a total duration of 10 ns at each temperature.
| RESULTS AND DISCUSSION |
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The third position (x2) is generally occupied by hydrophilic residues in segments 1, 3, and 5 and by small hydrophobic residues in segments 2, 4, and 6 (Fig. 1, B and C). This arrangement of hydrophilic and hydrophobic residues in the third position of the repeat causes the face formed by the even-numbered segments to be relatively hydrophobic, whereas the odd-numbered segments form a relatively hydrophilic surface (Fig. 2 A).
Circular dichroism spectrum analysis
The only biophysical evidence we have for this model (given the tiny amount of natural protein available) is its circular dichroism (CD) spectrum (Fig. 3). Deconvolution of this CD spectrum suggested a significant amount of random coil (1
). However, Sreerama and Woody (9
) have pointed out the difficulties of deconvoluting CD spectra of PPII-containing structures and in particular of distinguishing random coil or unstructured protein from PPII helix structure. Interestingly, there is increasing evidence that what has traditionally been considered as random coil may instead contain a significant amount of PPII structure (10
). The sfAFP CD spectrum is similar to those of other PPII-type structures (Fig. 3), especially since different peptides that contain PPII structure display a variety of minima and maxima in their CD spectra. Therefore, although we cannot conclude from the CD spectrum that sfAFP is predominantly formed of PPII helices, we can say the CD spectrum is consistent with such a structure.
Similarity of the sfAFP model to synthetic glycine-rich protein structures
The glycine-rich composition of sfAFP means that this natural protein has considerable sequence identity to both poly-(ProGlyGly) and poly-glycine, two synthetic polymers. The polyglycine II structure, which was first proposed in 1955 by Crick and Rich (11
) is made up of parallel polyglycine chains that have a threefold screw axis with a vertical repeat (pitch) of 9.3 Å. The lack of side chains allows the main chains to be packed into a hexagonal array with each chain hydrogen-bonded to six neighbors through backbone amide groups (C=O and N-H) that project normal to the helical axis. The lack of chirality around the C
atom means that an antiparallel chain could fit into the bundle and still make the same hydrogen-bonding connections to its neighbors. In contrast, the poly-(ProGlyGly) structure has more constraints due to the presence of Pro in every third position (12
). It has characteristics of both the polyglycine II structure and the PPII structure, which is a left-handed helix with 3.0 residues per turn. Poly-(ProGlyGly) is also a left-handed helix with 3.0 residues per turn. It differs from polyglycine II in being only able to form two backbone-backbone NH...O hydrogen bonds per tripeptide to neighboring helical chains. This constrains the structure into double-layered sheets where the polarity of the strands in each sheet is the same but antiparallel to the other sheet. The crucial difference between the poly-(ProGlyGly) fold and that of the sfAFP model is that the former is held together by intermolecular interactions and the latter's interactions are intramolecular, including two pairs of disulfide bonds.
sfAFP does not adopt a collagen-like structure
The skewed amino acid composition of sfAFP means that it also has considerable sequence similarity to collagen (13
). Indeed, the CD spectra of sfAFP and collagen are alike, although the AFP spectrum is blue shifted (Fig. 3). The spectral similarities likely reflect similar backbone conformations. As in collagen, our model makes a left-handed helix with 3.0 residues per turn and hydrogen bonds to neighboring helices. However, in collagen three identical chains are coiled around each other with a common axis to form the collagen triple-helix. The contacting surface of the three collagen monomers is composed of glycine from the G-x-P repeat. This allows a compact structure to form between coils due to low steric hindrance.
We considered the theoretical possibility that sfAFP adopts a collagen-like triple-helix fold. However coiling three sfAFP around each other to form the triple-helix would obviously position the cysteines too far apart for intrachain disulfide bonding. Mass spectrometry clearly shows that sfAFP makes two intrachain disulfide bonds, with no hint of interchain Cys-Cys connections (1
).
To investigate the possibility that sfAFP forms an intramolecular triple-helix, the protein was subdivided into three segments, 1 + 2, 3 + 4, and 5 + 6. Three-segment collagen folding would require the middle segment to run antiparallel to the other two, whereas natural collagen monomers polymerize in a parallel fashion. This model would not be compatible with disulfide-bond formation. The spacing between the cysteines does not allow any combination of disulfide bonding to form in a three-segmented sequence. A scenario where the six segments form two independent collagen-like folds seems unlikely for similar reasons. We conclude from this analysis that sfAFP does not adopt a collagen-like fold.
Comparison with antifreeze glycoprotein
Another naturally occurring protein with which sfAFP can be usefully compared is antifreeze glycoprotein (AFGP). AFGPs exist as multiple isoforms of varying lengths of tandem repeats of the consensus sequence AlaAlaThr with the threonine glycosylated by a disaccharide moiety (Galb1-3GalNAca1-). Although the sequence itself is not similar to that of sfAFP, it does contain a tripeptide repeat. In the NMR structure analysis of synthetic AFGPs by Nishimura's lab, this simple tripeptide repeat assumes a PPII-like fold with the glycosylated threonine side chain extending out on one side and the two alanines on the opposite side of the PPII barrel (14
). This structure generates an amphipathic molecule where the alanine side chains form the hydrophobic face and the disaccharides make a more hydrophilic surface. AFGPs exhibit CD spectra resembling those of collagen and sfAFP, albeit with a much greater amplitude in the 190210-nm range (Fig. 3).
Details of the sfAFP model
The conceptual model was built into a physical model to determine three-dimensional coordinates. The final minimized structure is represented in stereo in Fig. 4 and in space-filling mode in Fig. 5. The modeled polypeptide fold closely matches the fold proposed by Traub for poly-(ProGlyGly) but is limited to the six internally hydrogen-bonded PPII helices. In the model, an extensive regular pattern of hydrogen bonding can be observed between helices as shown in Fig. 4. As indicated earlier, helices 3 and 4 each make hydrogen bonds to four neighboring helices, due to their high glycine content. Throughout molecular dynamics simulations, especially at 4°C, Lys-2 is predominantly in proximity to Asp-5 and Lys-72 is in proximity to Asp-75. This suggests the potential for salt links between these pairs of residues with an i, i + 3 relationship, corresponding to one turn down the PPII helices. All potential salt links are located on the hydrophilic side of the AFP. During simulations, the loops connecting the PPII helices are flexible relative to the helices themselves, but their movements do not distort the flat surfaces formed by the core of the structure.
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-helical type I AFPs of winter flounder (17
Molecular dynamics: 25°C simulation
During the 10-ns molecular dynamic simulation of the model at 25°C, the loop between segments 4 and 5 gradually breaks away from the hydrogen-bonded core. In addition, because the hydrogen bonding between internal glycines becomes more irregular than in the 4°C structure, the pattern of ridges of hydrophobic residues becomes blurred (Fig. 5). This result is consistent with the sfAFP's lack of stability at room temperature (data not shown). Despite the increased flexibility of the backbone fold in the 25°C model, salt links suggested by the 4°C simulation appear to be maintained.
Based on the simulations, the total energy of each system was plotted, and hydrogen bonding between peptide backbones was plotted in Fig. 6. Despite the fact that the total energy of the system and hydrogen bonding within the backbone chain remained constant throughout the simulations, significant differences can be observed between the structures at 4°C and 25°C. We suggest that the conformation(s) adopted at 25°C results in loss of ice surface complementarity at the ice-binding face. Moreover, the abundance of hydrogen bonding at 25°C makes it likely that this conformation will remain stable (locked in place) at lower temperatures, and it might account for some irreversible loss in thermal hysteresis after the protein is heated to 25°C.
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angles for the model are distributed in the most favored region of the upper left quadrant, which is where those of the optimized collagen monomer cluster. The tight clustering of the collagen data points reflects the extreme regularity of this polymer. Predicted points for sfAFP were more scattered and differ slightly from the synthetic collagen peptides. The bottom left quadrant residues include some glycines that are located close to the end of the helical segments. In less favored regions of the two right quadrants are residues that are present in the loops of the predicted structure. The flexibility of these loops at both 4°C and 25°C is illustrated in Fig. 8 by a plot of root mean-square fluctuation for each residue in the sequence. Fluctuation is greatest for residues in the loops and least for residues in the middle of the coiled segments. As mentioned earlier, the loop between segments 4 and 5 is particularly unstable and shows the greatest root mean-square fluctuation of all the loops.
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| SUMMARY OF THE SFAFP MODEL |
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The modeled protein has dimensions 47 Å x 17 Å x 13 Å and has distinct amphipathic character. As an AFP, the hydrophilic surface formed by the outer residues of segments 1, 3, and 5 is most likely to present to the solvent, and the hydrophobic surface formed by the outer residues of segments 2, 4, and 6 will bind to ice. On this hydrophobic surface, there are projections with regular spacing that offer the potential to interact with a crystalline surface with complementary spacing.
| SUPPLEMENTARY MATERIAL |
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| ACKNOWLEDGEMENTS |
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This research was funded by a grant to P.L.D. from the Canadian Institutes for Health Research. P.L.D. holds a Canada Research Chair in Protein Engineering.
Submitted on July 14, 2006; accepted for publication November 7, 2006.
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