Analysis of shorthorn sculpin antifreeze protein stereospecific binding to (2–1 0) faces of ice

Wierzbicki, Andrzej; Taylor, Mark; Knight, Charles; Madura, Jeffry D.; Harrington, John P.; Sikes, C. Steven

doi:10.1016/s0006-3495(96)79204-4

Cited by 72 publications

(96 citation statements)

References 18 publications

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“…For comparison, vacuum modeling has predicted that SS8 adopts a fully ␣-helical conformation (34), whereas more recent molecular dynamics calculations on SS8 have predicted that the N-terminal cap structure folds the N terminus up and away from the Ala-rich surface of the protein (35). Although direct comparisons between the conformation of residues 1-10 of SS3 and SS8 cannot be made, our results suggest that the first 10 residues of SS3 are aligned approximately parallel to the ␣-helix formed by residues 11-33, with no significant deviation similar to that predicted for SS8 (35).…”

Section: Discussionmentioning

confidence: 99%

“…It has been estimated using CD spectroscopy that XSS8, the major component, is more helical than XSS3, and it has been proposed that there are two different structural and possibly functional do-mains, the nine-residue N terminus and the alanine-rich helical region between residues 8 and 42 (3). Vacuum phase molecular dynamics studies on SS8, a closely related sequence to XSS8, concluded that the polypeptide conformation resembles an idealized ␣-helix, except for a short section of the N-terminal region (34). This study also proposed that SS8 acts via insertion of the side chains of the Arg and Lys residues into the ice lattice.…”

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confidence: 99%

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Type I Shorthorn Sculpin Antifreeze Protein

Fairley¹,

Westman²,

Pham³

et al. 2002

Journal of Biological Chemistry

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A number of structurally diverse classes of "antifreeze" proteins that allow fish to survive in sub-zero ice-laden waters have been isolated from the blood plasma of cold water teleosts. However, despite receiving a great deal of attention, the one or more mechanisms through which these proteins act are not fully understood. In this report we have synthesized a type I antifreeze polypeptide (AFP) from the shorthorn sculpin Myoxocephalus scorpius using recombinant methods. Construction of a synthetic gene with optimized codon usage and expression as a glutathione S-transferase fusion protein followed by purification yielded milligram amounts of polypeptide with two extra residues appended to the N terminus. Circular dichroism and NMR experiments, including residual dipolar coupling measurements on a 15 N-labeled recombinant polypeptide, show that the polypeptides are ␣-helical with the first four residues being more flexible than the remainder of the sequence. Both the recombinant and synthetic polypeptides modify ice growth, forming facetted crystals just below the freezing point, but display negligible thermal hysteresis. Acetylation of Lys-10, Lys-20, and Lys-21 as well as the N terminus of the recombinant polypeptide gave a derivative that displays both thermal hysteresis (0.4°C at 15 mg/ml) and ice crystal faceting. These results confirm that the N terminus of wild-type polypeptide is functionally important and support our previously proposed mechanism for all type I proteins, in which the hydrophobic face is oriented toward the ice at the ice/water interface.The type I AFPs 1 found in the blood of cold water teleosts (1-3) have attracted significant interest, due to the potential applications of such compounds in biotechnology and medicine (4 -9). These compounds are alanine-rich ␣-helical proteins of 33-47 residues in length (for reviews see Refs. 10 -13). Although 14 type I proteins have been identified in nature (summarized in Ref. 12), almost all studies to date have centered on HPLC6, the 37-residue protein from the winter flounder (see Table I below) (14). This protein is characterized as an AFP, because it modifies both the rate and shape of ice crystal growth and displays thermal hysteresis, i.e. a positive difference between the ice growth temperature and the equilibrium melting temperature of ice.During the last decade, significant progress has been made in elucidating the structural features of HPLC6 that are required to give antifreeze activity. Structure-activity studies have identified the importance of the Thr residues at positions 2, 13, 24, and 35 plus surrounding residues, for ice growth inhibition activity. Although the Thr residues were assumed to be involved in hydrogen-bonding interactions with ice for many years (15-19), more recent mutations have identified the hydrophobicity provided by the ␥-methyl group of Thr as a key factor related to the ability to inhibit ice growth (20 -24). Hydrogen bonding and other roles for the surrounding residues have also been considered (24 -29). Howe...

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Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

Type I Shorthorn Sculpin Antifreeze Protein

Fairley¹,

Westman²,

Pham³

et al. 2002

Journal of Biological Chemistry

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“…Jorov et al 34 used Monte Carlo simulation to investigate the effect of hydrophobic interactions between wfAFP and the pyramidal plane on the stability of binding. Similarly, computer simulation has been used to investigate energetically stable binding conformations at ice crystal surfaces for shorthorn sculpin type-I AFP, 35 eelpout type-III AFP, 36,37 sbwAFP 38 and tenebrio molitor AFP. 59 However, in real-world systems, AFPs bind to ice-water interfaces rather than to planes of ice crystals, and AFPs interact strongly not only with ice, but also with water.…”

Section: Computer Simulations Of Afp Binding To Ice Crystalsmentioning

confidence: 99%

“…Thus far, several research groups have used computer simulation for investigating the stable binding conformations of AFP at an ice crystal plane. [30][31][32][33][34][35][36][37] Recently, we also used MD simulation to analyze the molecular-scale growth kinetics at an ice-water interface to which AFP was bound. 38,39 These computer simulation studies have contributed to the understanding of the molecular-scale mechanism of ice growth inhibition by AFPs.…”

Section: Introductionmentioning

confidence: 99%

Antifreeze proteins: computer simulation studies on the mechanism of ice growth inhibition

Nada

Furukawa

2012

Polym J

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Antifreeze proteins (AFPs), which are present in the bodily fluids of organisms inhabiting cold environments, function as inhibitors of ice growth by binding to certain planes of ice crystals. However, the exact mechanism of ice growth inhibition is still poorly understood as it is exceedingly difficult to experimentally analyze the molecular-scale growth kinetics of ice crystals at the planes to which the proteins bind. This review paper focuses on computer simulation studies on the mechanism of ice growth inhibition by AFPs. Recent molecular dynamics simulations of a growing ice-water interface to which protein is bound have indicated that, when the protein is stably bound to the interface, the growth rate of ice surrounding the protein decreases drastically, owing to depression of the ice melting point through the Gibbs-Thomson effect. The observed decrease in growth rate is expected to correspond to ice growth inhibition in real-world systems. In addition to presenting published simulation studies on the mechanism of ice growth inhibition by AFPs, this review also outlines the direction of future simulation studies in this field.

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“…Similar to the AFPs, AFGP researchers have been divided over the importance of hydrogen bonding and its role in the mechanism of action. While it has been proposed that the hydrophilic interactions between polar hydroxy groups and the water molecules on the ice surface are extremely important, 170 others have invoked the idea that entropic and enthalpic contributions from hydrophobic residues are crucial in the binding of an AFGP to an ice surface. Despite the fact that significant entropic contributions are likely to be gained upon the exclusion of water from the protein and ice surfaces, a definitive mechanism invoking hydrophobic and/or hydrophilic interactions with emphasis on the role they play in adsorption of the antifreeze to the ice surface has failed to emerge.…”

Section: Antifreeze Proteinsmentioning

confidence: 99%