Structure of a peptide antifreeze and mechanism of adsorption to ice

Antifreeze proteins of teleost fishes

Marine teleosts at high latitudes can encounter ice-laden seawater that is approximately 1 degrees C colder than the colligative freezing point of their body fluids. They avoid freezing by producing small antifreeze proteins (AFPs) that adsorb to ice and halt its growth, thereby producing an additional non-colligative lowering of the freezing point. AFPs are typically secreted by the liver into the blood. Recently, however, it has become clear that AFP isoforms are produced in the epidermis (skin, scales, fin, and gills) and may serve as a first line of defense against ice propagation into the fish. The basis for the adsorption of AFPs to ice is something of a mystery and is complicated by the extreme structural diversity of the five antifreeze types. Despite the recent acquisition of several AFP three-dimensional structures and the definition of their ice-binding sites by mutagenesis, no common ice-binding motif or even theme is apparent except that surface-surface complementarity is important for binding. The remarkable diversity of antifreeze types and their seemingly haphazard phylogenetic distribution suggest that these proteins might have evolved recently in response to sea level glaciation occurring just 1-2 million years ago in the northern hemisphere and 10-30 million years ago around Antarctica. Not surprisingly, the expression of AFP genes from different origins can also be quite dissimilar. The most intensively studied system is that of the winter flounder, which has a built-in annual cycle of antifreeze expression controlled by growth hormone (GH) release from the pituitary in tune with seasonal cues. The signal transduction pathway, transcription factors, and promoter elements involved in this process are just beginning to be characterized.

Source of the ice-binding specificity of antifreeze protein type I

Antifreeze proteins (AFPs) are a group of structurally very diverse proteins with the unique capability of binding to the surface of seed ice crystals and inhibiting ice crystal growth. The AFPs bind with high affinity to specific planes of the ice crystal. Previously, this affinity of AFPs has been ascribed to the formation of multiple hydrogen bonds across the protein-ice interface, but more recently van der Waals interactions have been suggested to be the dominant energetic factors for the adsorption. To determine whether van der Waals interactions are also responsible for the binding specificities of AFPs, the protein-ice interaction of the helical AFP Type I from winter flounder (HPLC6) was studied using a Monte Carlo rigid body docking approach. HPLC6 binds in the [1102] direction of the [2021] plane, with the Thr-Ala-Asn surface comprising the protein's binding face. The binding of HPLC6 to this ice plane is highly preferred, but the protein is also found to bind favorably to the [1010] prism plane using a different protein surface comprised of Thr and Ala residues. The results show that van der Waals interactions, despite accounting for most of the intermolecular energy (>80%), are not sufficient to completely explain the AFP binding specificity.

A novel basic protein from human kidney which inhibits calcium oxalate crystal growth

OBJECTIVES

To isolate calcium oxalate-binding proteins from human kidney and characterize the functional properties.

MATERIALS AND METHODS

Calcium oxalate crystals were prepared and allowed to interact at two different pH values with Triton-extracted human kidney homogenate. The proteins in the homogenate were isolated and fractionated on a cellulose column, and purified by high-performance liquid chromatography. The protein with the greatest oxalate binding activity at pH 4.5 was analysed for its amino-acid composition and characterized by Scatchard plot analysis, crystal growth, nucleation and aggregation studies.

RESULTS

Three major protein fractions were eluted when calcium oxalate monohydrate was adsorbed at both pH values (designated as fractions I-III, according to their order of elution). The yield of fraction I and III was increased when adsorbed at an acidic pH. However, only fraction III had maximum oxalate binding activity at pH 4.5. When purified, this protein had maximum oxalate binding activity of approximately 270 pmol/mg protein and a molecular weight of approximately 23 kDa. Amino acid analysis showed that 18% of the total molar proportion was of basic amino acids, e.g. lysine and arginine, while acidic amino acids accounted for only 11%. Both alanine and glycine constituted approximately 41% of the total molar proportion. Modifications to the lysine group abolished oxalate-binding activity of the protein. The protein inhibited crystal growth by 82% at 0.8 micromol/L, while it inhibited the nucleation and aggregation of the crystals by 6% and 28%, respectively, at 49 nmol/L. The inhibition of both nucleation and aggregation was higher at pH 5.7 than at pH 7.4. Significantly, the protein induced the formation of intertwined calcium oxalate dihydrate crystals in a medium known to induce the formation of individual dihydrate crystals.

CONCLUSION

The protein described here is the first reported basic inhibitor of calcium oxalate crystal growth with oxalate-binding activity at pH 4.5 that modulates calcium oxalate crystallization. It is suggested that this protein may play a physiologically significant role in inhibiting stone formation in acidic urine.

Type I 'antifreeze' proteins. Structure-activity studies and mechanisms of ice growth inhibition

The type I 'antifreeze' proteins, found in the body fluids of fish inhabiting polar oceans, are alanine-rich alpha-helical proteins that are able to inhibit the growth of ice. Within this class there are two distinct subclasses of proteins: those related to the winter flounder sequence HPLC6 and which contain 11-residue repeat units commencing with threonine; and those from the sculpins that are unique in the N-terminal region that contains established helix breakers and lacks the 11-residue repeat structure present in the rest of the protein. Although 14 type I proteins have been isolated, almost all research has focused on HPLC6, the 37-residue protein from the winter flounder Pseudopleuronectes americanus. This protein modifies both the rate and shape (or 'habit') of ice crystal growth, displays hysteresis and accumulates specifically at the {2 0 2; 1} ice plane. Until very recently, all models to explain the mechanism for this specific interaction have relied on the interaction of the four threonine hydroxyls, which are spaced equally apart on one face of the helix, with the ice lattice. In contrast, proteins belonging to the sculpin family accumulate specifically at the {2 1; 1; 0} plane. The molecular origin of this difference in specificity between the flounder and sculpin proteins is not understood. This review will summarize the structure-activity and molecular modelling and dynamics studies on HPLC6, with an emphasis on recent studies in which the threonine residues have been mutated. These studies have identified important hydrophobic contributions to the ice growth inhibition mechanism. Some 50 mutants of HPLC6 have been reported and the data is consistent with the following requirements for ice growth inhibition: (a) a minimum length of approx. 25 residues; (b) an alanine-rich sequence in order to induce a highly helical conformation; (c) a hydrophobic face; (d) a number of charged/polar residues which are involved in solubility and/or interaction with the ice surface. The emerging picture, that requires further dynamics studies including accurate modelling of the ice/water interface, suggests that a hydrophobic interaction between the surface of the protein and ice is the key to explaining accumulation at specific ice planes, and thus the molecular level mechanism for ice growth inhibition.

Secretory expression and site-directed mutagenesis studies of the winter flounder skin-type antifreeze polypeptides

Winter flounder contains both liver-type, extracellular antifreeze polypeptides (wflAFPs) and less active skin-type, intracellular antifreeze polypeptides (wfsAFPs). The lower activity of wfsAFPs might be due to their lack of complete ice-binding motifs '-K-DT-'. In order to test the functional role of this putative ice-binding motif, mutations were introduced into the N-terminal or C-terminal regions of wfsAFP-2, which lack any presumptive ice-binding motifs. The wild-type and mutant wfsAFP-2 were secreted in Escherichia coli culture media as mature antifreeze proteins and purified to homogeneity. Surprisingly, the antifreeze activity decreased with the introduction of ice-binding motifs. However, there was a corresponding decrease in alpha-helical content as well as thermal stability and this would suggest a compromise in retaining helical structure with the presence of ice-binding motifs. These studies have brought new definitions of the roles of ice-binding motif residues in type I antifreeze proteins.

Alternative roles for putative ice-binding residues in type I antifreeze protein

Two sets of variants of type I antifreeze protein have been synthesized to investigate the role of Leu and Asn in the activity of this 37-residue alpha-helix. Leu and Asn flank the central two of four regularly spaced ice-binding Thr in the i-1 and i + 3 positions, respectively. All three residues project from the same side of the helix to form the protein's putative ice-adsorption site and are considered in some models to act together as an "ice-binding motif". Replacement of Asn by residues with shorter side chains resulted in either a small loss (Ala) or gain (Thr) of antifreeze activity. However, substitution of Asn by its slightly larger homologue (Gln) abolished thermal hysteresis activity. The Gln-containing peptide was very soluble, largely monomeric, and fully helical. Of the three variants in which Leu was replaced by Ala, two of the three were more active than their Leu-containing counterparts, but all three variants began to precipitate as the peptide concentration increased. None of the seven variants tested showed dramatic differences in ice crystal morphology from that established by the wild type. These results are consistent with a primary role for Leu in preventing peptide aggregation at the antifreeze protein concentrations (10 mg/mL) normally present in fish serum. Similarly the role for Asn may have more to do with enhancing the solubility of these rather hydrophobic peptides than of making a stereospecific hydrogen-bonding match to the ice lattice as traditionally thought. Nevertheless, the dramatic loss of activity in the Asn-to-Gln replacement demonstrates the steric restriction on residues in or near the ice-binding site of the peptide.

Skin-type antifreeze protein from the shorthorn sculpin, Myoxocephalus scorpius. Expression and characterization of a Mr 9, 700 recombinant protein

A cDNA clone encoding a presumptive antifreeze protein was isolated from a skin library from shorthorn sculpin, Myoxocephalus scorpius. The clone encodes a 92-residue mature polypeptide (sssAFP-2) without any signal and prosequence, which suggests an intracellular localization. It is the largest alanine-rich, alpha-helical type I antifreeze protein known. A recombinant fusion protein containing an N-terminal-linked His-tag was produced and purified from Escherichia coli. This protein is alpha-helical at 0 degreesC and exhibits significant antifreeze activity. Northern blot and reverse transcription-polymerase chain reaction analyses indicate that sssAFP-2 mRNA has limited tissue distribution and is present in peripheral tissues such as skin and dorsal fin, but is notably absent in the liver. These studies reinforce recent evidence that indicate that the external tissues of cold water marine fishes are major organs for antifreeze protein synthesis and are likely the first line of defense against the threat of freezing.

Antifreeze proteins bind independently to ice

It has been suggested that cooperative interactions between antifreeze proteins (AFPs) on the ice surfaces are required for complete inhibition of ice crystal growth. To test this hypothesis, a 7-kDa type III AFP was linked through its N-terminus to thioredoxin (12 kDa) or maltose-binding protein (42 kDa). The resultant 20-kDa and 50-kDa fusion proteins were larger in diameter than free AFP and thus precluded any extensive AFP-AFP contacts on the ice surface. Both fusion proteins were at least as active as free AFP at virtually all concentrations tested. By these criteria, AFPs function independently of each other and do not require specific intermolecular interactions to bind tightly to ice.

A diminished role for hydrogen bonds in antifreeze protein binding to ice

The most abundant isoform (HPLC-6) of type I antifreeze protein (AFP1) in winter flounder is a 37-amino-acid-long, alanine-rich, alpha-helical peptide, containing four Thr spaced 11 amino acids apart. It is generally assumed that HPLC-6 binds ice through a hydrogen-bonding match between the Thr and neighboring Asx residues to oxygens atoms on the {2021} plane of the ice lattice. The result is a lowering of the nonequilibrium freezing point below the melting point (thermal hysteresis). HPLC-6, and two variants in which the central two Thr were replaced with either Ser or Val, were synthesized. The Ser variant was virtually inactive, while only a minor loss of activity was observed in the Val variant. CD, ultracentrifugation, and NMR studies indicated no significant structural changes or aggregation of the variants compared to HPLC-6. These results call into question the role of hydrogen bonds and suggest a much more significant role for entropic effects and van der Waals interactions in binding AFP to ice.

NMR characterization of side chain flexibility and backbone structure in the type I antifreeze protein at near freezing temperatures

The flexibility of the polar side chains in the alpha-helical Type I antifreeze protein (AFP) near the solution freezing temperature was investigated by two-dimensional nuclear magnetic resonance spectroscopy. These experiments were conducted to define the rotameric conformations of the proposed ice-binding groups, threonines and asparagines, in order to probe the molecular mechanism for ice binding. On the basis of the 3J alpha beta 2 NMR coupling constant values of 7.1, 8.5, 8.5, and 6.8 Hz for residues T2, T13, T24, and T35, respectively, it can be calculated that the regularly spaced ice-binding threonines sample many possible rotameric states prior to ice binding. The lack of a dominant side chain rotamer is further corroborated by nuclear Overhauser distance measurements for T13 and T24. N16 and N27, both with 3J alpha beta 2 and 3J alpha beta 3 coupling constants of 8.4 and 4.5 Hz, respectively, show a slight preference for the side chain conformation with a chi 1 of -60 degrees. These data suggest that prior to ice binding the threonine and asparagine side chains are free to rotate and that a unique preformed ice-binding structure in solution is not apparent. These observations do not support the rigid side chain model proposed recently by an X-ray study [Sicheri, F., & Yang, D. S. C. (1995) Nature 375, 427-431].

Effect of type III antifreeze protein dilution and mutation on the growth inhibition of ice

Mutation of residues at the ice-binding site of type III antifreeze protein (AFP) not only reduced antifreeze activity as indicated by the failure to halt ice crystal growth, but also altered ice crystal morphology to produce elongated hexagonal bipyramids. In general, the c axis to a axis ratio of the ice crystal increased from approximately 2 to over 10 with the severity of the mutation. It also increased during ice crystal growth upon serial dilution of the wild-type AFP. This is in marked contrast to the behavior of the alpha-helical type I AFPs, where neither dilution nor mutation of ice-binding residues increases the c:a axial ratio of the ice crystal above the standard 3.3. We suggest that the ice crystal morphology produced by type III AFP and its mutants can be accounted for by the protein binding to the prism faces of ice and operating by step growth inhibition. In this model a decrease in the affinity of the AFP for ice leads to filling in of individual steps at the prism surfaces, causing the ice crystals to grow with a longer c:a axial ratio.

A natural variant of type I antifreeze protein with four ice-binding repeats is a particularly potent antifreeze

A 4.3-kDa variant of Type I antifreeze protein (AFP9) was purified from winter flounder serum by size exclusion chromatography and reversed-phase HPLC. By the criteria of mass, amino acid composition, and N-terminal sequences of tryptic peptides, this variant is the posttranslationally modified product of the previously characterized AFP gene 21a. It has 52 amino acids and contains four 11-amino acid repeats, one more than the major serum AFP components. The larger protein is completely alpha-helical at 0 degree C, with a melting temperature of 18 degrees C. It is considerably more active as an antifreeze than the three-repeat winter flounder AFP and the four-repeat yellowtail flounder AFP, both on a molar and a mg/mL basis. Several structural features of the four-repeat winter flounder AFP, including its larger size, additional ice-binding residues, and differences in ice-binding motifs might contribute to its greater activity. Its abundance in flounder serum, together with its potency as an antifreeze, suggest that AFP9 makes a significant contribution to the overall freezing point depression of the host.

Low temperature persistence of type I antifreeze protein is mediated by cold-specific mRNA stability

In winter flounder, the levels of type I antifreeze protein (AFP) and its mRNA vary seasonally by as much as 1000-fold. Elevated levels in the fall are prompted by the loss of long day-lengths, while higher spring temperatures correlate with AFP clearance. We have investigated the role of temperature on AFP accumulation using transgenic Drosophila melanogaster by expressing multiple AFP genes under control of the heat-inducible hsp70 promoter. AFP and AFP mRNA persisted far longer in flies reared at 10 degrees C compared to 22 degrees C. This difference appears to be mediated by cold-specific mRNA stability since no such temperature effect was observed with either an endogenous heat-inducible mRNA or a constitutively expressed mRNA.

Antifreeze peptide heterogeneity in an antarctic eel pout includes an unusually large major variant comprised of two 7 kDa type III AFPs linked in tandem

The structural heterogeneity of the major antifreeze peptides (AFPs) from the antarctic eel pout, Lycodichthys dearborni (formerly classified as Rhigophila dearborni) was characterized. Three major AFPs designated as RD1, RD2 and RD3, and five minor ones were isolated from the fish plasma. RD1 and RD2 are both 64 residues in length, about 7 kDa, and thus similar in size to all characterized type III AFPs, while RD3 is twice as large, about 14 kDa, and represents the first example of a disparately large size variant within the same fish for the three known types of antifreeze peptides. RD3 was found to be 134 residues in length, arranged as a 64-residue N-terminal half and a 61-residue C-terminal half of similar sequence to each other and to the 7 kDa type III AFPs, linked by a 9-residue connector of unmatched sequence. RD3 has slightly lower antifreeze activity than its 7 kDa counterparts, with a melting-freezing point difference of about 0.81 degrees C at 10 mg/ml versus 0.95 degrees C and 0.90 degrees C for RD1 and RD2, respectively. RD1 and RD2 are 94% identical in sequence to each other. They are 98% and 94%, respectively identical to N-terminal half of RD3, and 85% and 77%, respectively, identical to C-terminal half of RD3. By sequence comparison, a previously characterized AFP from this fish [1] was identified to be RD2.

Calorimetric determination of inhibition of ice crystal growth by antifreeze protein in hydroxyethyl starch solutions

Differential scanning calorimetry and cryomicroscopy were used to investigate the effects of type I antifreeze protein (AFP) from winter flounder on 58% solutions of hydroxyethyl starch. The glass, devitrification, and melt transitions noted during rewarming were unaffected by 100 micrograms/ml AFP. Isothermal annealing experiments were undertaken to detect the effects of AFP-induced inhibition of ice crystal growth using calorimetry. A premelt endothermic peak was detected during warming after the annealing procedure. Increasing the duration or the temperature of the annealing for the temperature range from -28 and -18 degrees C resulted in a gradual increase in the enthalpy of the premelt endotherm. This transition was unaffected by 100 micrograms/ml AFP. Annealing between -18 and -10 degrees C resulted in a gradual decrease in the premelt peak enthalpy. This process was inhibited by 100 micrograms/ml AFP. Cryomicroscopic examination of the samples revealed that AFP inhibited ice recrystallization during isothermal annealing at -10 degrees C. Annealing at lower temperatures resulted in minimal ice recrystallization and no visible effect of AFP. Thus, the 100 micrograms/ml AFP to have a detectable influence on thermal events in the calorimeter, conditions must be used that result in significant ice growth without AFP and visible inhibition of this process by AFP.

Antifreeze protein pseudogenes

Three members, 11-3, F2 and 5a, of the type-I antifreeze protein (AFP) multigene family in winter flounder were sequenced. All three belong to the subset of AFP genes that are linked, but irregularly spaced, and show significant differences from the functional genes in tandem repeats. 11-3 and F2 appear to be pseudogenes. Their intron, 3'-exon and 3'-flanking DNAs are similar to those of other AFP genes, but their 5'-exon is either missing or extensively modified, and has stop codons present in all three reading frames. Based on a comparison of intron sequences of family members, 11-3/F2 may represent a residual progenitor AFP gene which was duplicated after reaching pseudogene status. The third gene, 5a, is remarkable in having a 3'-exon that encodes an exceptionally long, Ala-rich sequence that lacks any semblance of the 11-amino acid repeats found in 11-3, F2 and functional AFP genes. 5a might also be a pseudogene, because its presumed TATA box appears to have mutated.

Energy-optimized structure of antifreeze protein and its binding mechanism

A combination of Monte Carlo simulated annealing and energy minimization was utilized to determine the conformation of the antifreeze protein from the fish winter flounder. It was found from the energy-optimized structure that the hydroxyl groups of its four threonine residues, i.e. Thr2, Thr13, Thr24, Thr35, are aligned on almost the same line parallel to the helix axis and separated successively by 16.1, 16.0 and 16.2 A, respectively, very close to the 16.6 A repeat spacing along [0112] in ice. Based on such a space match, a zipper-like model is proposed to elucidate the binding mechanism of the antifreeze protein to ice crystals. According to the current model, the antifreeze protein may bind to an ice nucleation structure in a zipper-like fashion through hydrogen bonding of the hydroxyl groups of these four Thr residues to the oxygen atoms along the [0112] direction in ice lattice, subsequently stopping or retarding the growth of ice pyramidal planes so as to depress the freeze point. The calculated results and the binding mechanism thus derived accord with recent experimental observations. The mechanistic implications derived from such a special antifreeze molecule might be generally applied to elucidate the structure-function relationship of other antifreeze proteins with the following two common features: (1) recurrence of a Thr residue (or any other polar amino acid residue whose side-chain can form a hydrogen bond with water) in an 11-amino-acid period along the sequence concerned; and (2) a high percentage of Ala residue component therein. Further experiments are suggested to test the ice binding model.

Protein interaction with ice

Many organisms have evolved novel mechanisms to minimize freezing injury due to extracellular ice formation. This article reviews our present knowledge on the structure and mode of action of two types of proteins capable of ice interaction. The antifreeze proteins inhibit ice crystal formation and alter ice growth habits. The ice nucleation proteins, on the other hand, provide a proper template to stimulate ice growth. The potential applications of these proteins in different industries are discussed.

The effect of enhanced alpha-helicity on the activity of a winter flounder antifreeze polypeptide

The antifreeze polypeptide (AFP) from the winter flounder displays partial alpha-helix formation at lower temperatures. To investigate the relationship between antifreeze activity and alpha-helical structure, we designed and then chemically synthesized an AFP analog with enhanced alpha-helicity, and compared its conformation and antifreeze properties with those of the native AFP. The synthetic analog was more helical than the native AFP; however, the antifreeze activity of both peptides were identical. The antifreeze activity of the peptides displayed a strong pH dependence, which paralleled pH-induced changes in helix content. At pH 8.5, the antifreeze activity of both peptides displayed identical concentration dependences. In addition to antifreeze activity measurements, the effects of the peptides on the rate of ice crystal growth were also measured. While both peptides affected the a- and c-axis growth rates of ice crystals, the highly helical analog was able to exert its effect on ice crystal growth rates at 7-8-fold lower concentrations than the native AFP. These data indicate that there is a direct but complex relationship between alpha-helicity and antifreeze activity.

Expression of antifreeze proteins in transgenic plants

The quality of frozen fruits and vegetables can be compromised by the damaging effects of ice crystal growth within the frozen tissue. Antifreeze proteins in the blood of some polar fishes have been shown to inhibit ice recrystallization at low concentrations. In order to determine whether expression of genes of this type confers improved freezing properties to plant tissue, we have produced transgenic tobacco and tomato plants which express genes encoding antifreeze proteins. The afa3 antifreeze gene was expressed at high steady-state mRNA levels in leaves from transformed plants, but we did not detect inhibition of ice recrystallization in tissue extracts. However, both mRNA and fusion proteins were detectable in transgenic tomato tissue containing a chimeric gene encoding a fusion protein truncated staphylococcal protein A and antifreeze protein. Furthermore, ice recrystallization inhibition was detected in this transgenic tissue.

Enhanced survival of yeast expressing an antifreeze gene analogue after freezing

Yeast, like most organisms, survives poorly under freezing conditions. It has been proposed that after rapid cooling yeast suffers a loss in viability from the recrystallization of intracellular ice. Antifreeze proteins found in the blood of certain polar fishes have been shown to be potent inhibitors of ice recrystallization at very low concentrations. We have examined the feasibility of protecting rapidly cooled yeast cells from freezing damage by inhibiting the recrystallization of intracellular ice through in vivo expression of an antifreeze analogue gene. A chemically synthesized gene encoding a protein similar to but differing from the antifreeze proteins of the fish Pseudopleuronectes americanus (winter flounder) was genetically fused to the 3' end of a truncated staphylococcal Protein A gene. When the fused gene was expressed in the budding yeast Saccharomyces cerevisiae, its cells were shown to produce a new chimeric protein that inhibited the recrystallization of ice in vitro. Yeast cells expressing the chimeric antifreeze protein showed a twofold increase in survival after rapid freezing (95 degrees C/min to -196 degrees C) and moderate rates of warming (26 to 64 degrees C/min) compared to cells lacking the chimeric protein.

An antifreeze glycopeptide gene from the antarctic cod Notothenia coriiceps neglecta encodes a polyprotein of high peptide copy number

The antarctic fish Notothenia coriiceps neglecta synthesizes eight antifreeze glycopeptides (AFGP 1-8; Mr 2600-34,000) to avoid freezing in its ice-laden freezing habitat. We report here the sequence of one of its AFGP genes. The structural gene contains 46 tandemly repeated segments, each encoding one AFGP peptide plus a 3-amino acid spacer. Most of the repeats (44/46) code for peptides of AFGP 8; the remaining 2 code for peptides of AFGP 7. At least 2 of the 3 amino acids in the spacers could act as substrate for chymotrypsin-like proteases. The nucleotide sequence between the translation initiation codon (ATG) and the first AFGP-coding segment is G + T-rich and encodes a presumptive 37-residue signal peptide of unusual sequence. Primer extension establishes the transcription start site at nucleotide 43 upstream from ATG. CAAT and TATA boxes begin at nucleotides 53 and 49, respectively, upstream from the transcription start site. The polyadenylylation signal, AATAAA, is located approximately 240 nucleotides downstream from the termination codon. A mRNA (approximately 3 kilobases) was found that matches the size of this AFGP gene. Thus, this AFGP gene encodes a secreted, high-copy-number polyprotein that is processed posttranslationally to produce active AFGPs.

Seasonal cycle and regulation by temperature of antifreeze protein mRNA in a Long Island population of winter flounder

The seasonal cycle and regulation by temperature of antifreeze protein mRNA (AF mRNA) were investigated in a Long Island population of winter flounder (Pseudopleuronectes americanus) by Northern blot hybridization and by in vitro translation of liver RNA. AF mRNA was expressed at high levels in the fall and winter (Nov.-Feb.) and at low or undetectable levels in the summer. The time of accumulation of AF mRNA coincides with the time during which water temperature and photoperiod decrease to 4°C and 9 h of light per day, respectively. A temperature and photoperiod decrease in the laboratory during this time also resulted in high levels of AF mRNA. The levels of other mRNAs, as assayed by in vitro translation, were relatively constant during both seasonal acclimation and laboratory acclimation. The seasonal cycle of AF mRNA in Long Island winter flounder is similar to that of a more northern, Newfoundland population of winter flounder and different from that of an intermediate, New Brunswick population. These similarities and dissimilarities are discussed in light of potentially different exogenous and endogenous regulatory cues in the different populations.

Structures of antifreeze peptides from the antarctic eel pout, Austrolycicthys brachycephalus

The antarctic eel pout, Austrolycicthys brachycephalus, synthesizes two predominant antifreeze peptides (AFPs) which, based on purification yields, make up about 94 and 6%, respectively, of the antifreezes in its serum. The amino acid sequences of these two AFPs, AB1 and AB2, were determined using automated sequencing, and compositional analyses of peptide fragments from enzymatic digests, and verified by molecular masses obtained with Fast Atom Bombardment Mass spectrometry. Substantial homologies in amino acid sequence exist between the AFPs of Austrolycicthys and those of other Southern and Northern eel pouts. 72% of the residues of AB1, and 84% of AB2, are identical to those of an AFP from another antarctic eel pout, Rhigophila dearborni. Between AB1 and AB2, 83% of the residues are identical. Secondary structure data based on circular dichroism studies indicated AB1 to be a random chain, but a sharp thermal transition of CD spectra around 30 degrees C suggested the presence of definite secondary or tertiary structure.

Protein inhibitors of crystal growth

Nephrocalcin is a urinary glycopeptide that may be a physiological inhibitor of nephrolithiasis. Monomeric nephrocalcin purified from ethylenediaminetetracetic acid-treated urine is 14,000 daltons. Compositional analyses indicate that nephrocalcin is 10 per cent carbohydrate by weight and that 25 per cent of the amino acid residues are acidic (glutamic acid, aspartic acid and gamma-carboxyglutamic acid). Nephrocalcin binds reversibly to calcium oxalate crystals with a dissociation constant of about 0.5 microM. The high collapse pressure of nephrocalcin, 41.5 dynes per cm., measured for a monolayer at the air-water interface, suggests a highly organized structure in which hydrophilic and hydrophobic regions occupy separate regions on the surface of the inhibitor. Nephrocalcin contains the unusual amino acid, gamma-carboxyglutamic acid. Nephrocalcin isolated from urine of stone formers and from kidney stones does not contain gamma-carboxyglutamic acid and it has altered surface properties compared to normal nephrocalcin. The presence of the gamma-carboxyglutamic acid modification and the ability to form stable films with high collapse pressures may be important factors enabling nephrocalcin to prevent stone formation in vivo. The blood of cold water fishes contains antifreeze glycopeptides and/or peptides to prevent it from freezing. The structure of one such antifreeze peptide and its interactions with the crystal lattice of hexagonal ice are discussed as a model for how nephrocalcin might interact with calcium oxalate crystals and arrest their growth in urine.

Crystal structure of an antifreeze polypeptide and its mechanistic implications

The X-ray crystallographic structure of an antifreeze polypeptide from the fish winter flounder, has been determined at 2.5 A by an analysis of the Patterson function. This is the first report of a polypeptide of this size that is a single alpha-helix. A proposed mechanism of antifreeze binding to ice surfaces is given which requires: first, that the dipole moment from the helical structure dictates the preferential alignment of the peptide to the c-axis of ice nuclei; second, amphiphilicity of the helix; and third, torsional freedom of the side chains to facilitate hydrogen bonding to ice surfaces.

Structural variations in the alanine-rich antifreeze proteins of the pleuronectinae

The sequence and activity of antifreeze proteins from two right eye flounder species were compared to assess the influence of structural variations on antifreeze capacity. The cDNA encoding the major serum antifreeze protein in the yellowtail flounder (Limanda ferruginea) was cloned from liver tissue. Its DNA sequence shows that the precursor to the antifreeze is a 97-residue preproportion. Edman degradation identified the N-terminus of the 48-amino-acid mature serum antifreeze protein and confirmed the sequence of the first 36 residues. A comparison with the previously determined winter flounder antifreeze protein and mRNA sequences shows strong homology through the 5' and 3' untranslated regions and in the peptide region. The mature protein section has the greatest sequence variation. Specifically, the yellowtail antifreeze protein, in contrast to that of the winter flounder, contains a fourth 11-amino-acid repeat and lacks several of the hydrophilic residues that have been postulated to aid in the binding of the protein to ice crystals. Intramolecular salt bridges are present in the antifreeze proteins from both species but in different registries with respect to the 11-amino-acid repeats. On a mass basis the yellowtail flounder antifreeze, though longer than that of the winter flounder, is only 80% as effective at depressing the freezing temperature of aqueous solutions. This lower activity might be due to the reduced number of hydrophilic ice-binding residues per molecule.

Primary and secondary structure of antifreeze peptides from arctic and antarctic zoarcid fishes

Antifreeze peptides were isolated from Rhigophila dearborni, an antarctic eel pout, and Lycodes polaris, an arctic eel pout (both from the family Zoarcidae). The primary structures of two peptides, one from each species, were determined using a combination of Edman degradation and mass spectrometric techniques. The two sequences show a high degree of homology with nearly 80% of the residues being identical. These peptides are also homologous to antifreeze peptides from a third eel pout which inhabits the north Atlantic Ocean. The CD spectra of all of these peptides are also very similar. Unlike the antifreeze peptides of cottid fishes, the structures of antifreeze peptides from zoarcid fishes appear to be highly conserved, despite the large geographic distances which separate the different species. The zoarcid peptides also appear to have structures very different from other fish antifreezes.

A developmentally regulated gvpABC operon is involved in the formation of gas vesicles in the cyanobacterium Calothrix 7601

In the filamentous cyanobacterium Calothrix PCC7601, gas-vesicle (GV) formation is restricted to specialized filaments, called hormogonia. The differentiation of these cells is controlled by environmental factors, such as light intensity and/or wavelength. The structural gene (gvpA) encoding a GV protein in this cyanobacterium has been previously cloned and sequenced. Two other genes, gvpB and gvpC have been found in the sequence downstream from gvpA. The gvpB gene corresponds to a second copy of gvpA, encoding an identical protein. Unlike the GV protein, the product of the gvpC gene is predominantly hydrophilic, as deduced from nucleotide sequence. Interestingly, the internal part of the gvpC gene is composed of four contiguous repeats, each containing 99 bp, forming highly homologous repeats in the deduced amino acid sequence. Another kind of periodicity has been detected inside the 99-bp repeats, suggesting that the gvpC gene might have evolved by amplification of a 33-bp-long primordial building block. The function of this gene remains to be elucidated. Finally, we have shown that the three genes, gvpA, gvpB, and gvpC, are organized in an operon that is exclusively expressed during GV formation in hormogonia.

Conserved repeats in diverged ice nucleation structural genes from two species of Pseudomonas

Sequence analysis shows that an ice nucleation gene (inaW) from Pseudomonas fluorescens is related to the inaZ gene of Pseudomonas syringae. The two genes have diverged by many amino acid substitutions, and have effectively randomized the third bases of homologous codons. By reference to their potential for change, it is shown that certain conserved features must have been maintained by selection pressure. In particular, their conservation of internal sequence repetition, with three orders of repeat periodicity in each gene, suggests that the pattern of repetition is significant to the gene products' function. We propose models for the structure of the gene products in which each order of periodicity would be required for the nucleation function.

Biosynthesis of antifreeze polypeptides in the winter flounder. Characterization and seasonal occurrence of precursor polypeptides

The precursor proteins for winter flounder antifreeze polypeptide (AFP) were isolated from liver using gel filtration chromatography and reverse-phase high-performance liquid chromatography. Two major pro-antifreezes (Mr 5000), corresponding to the precursors for AFP-6 and AFP-8, were characterized by amino acid analyses and automated Edman degradation. These precursors showed significant antifreeze activity. The pro-antifreezes were synthesized in the liver seasonally as demonstrated by immunoblotting and in vitro liver incorporation studies. No mature AFP were detected in liver, thus indicating that the processing of pro-antifreezes, including amidation of the C-termini, occurred mainly in the serum. The function(s) of the prosequences, if any, remain unclear.

Structures of shorthorn sculpin antifreeze polypeptides

The amino acid sequences of the two major antifreeze polypeptides (AFP) from the shorthorn sculpin have been determined using an automatic protein sequencer and enzymic digestion. These two polypeptides, SS-3 and SS-8, consist of 33 and 45 amino acid residues respectively. The N-terminal methionyl residue is blocked in both the polypeptides. When aligned for maximum structural similarity these two AFP are 80% homologous, and there appears a deletion of 12 amino acid residues at the N-terminal portion of SS-3. Like the winter flounder AFP, both the sculpin AFP also contain the 11-amino-acid repeat sequences. The secondary structure of the sculpin AFP is mainly alpha-helical as deduced from circular dichroic spectral data. The helical content of SS-8 is high (73%), while that of SS-3 is moderate (about 45%). The latter exhibits a relatively weak antifreeze activity. Removal of the blocked N-terminal residue in SS-8 did not alter the helical content significantly but did reduce the antifreeze activity. Helical contents of proteolytically generated fragments of AFP are much lower, and they are devoid of activity. The alpha-helix in the SS-8 component is seen to be amphiphilic in character. The relevance of this feature to the mechanism of the antifreeze action is briefly discussed.

Antifreeze protein genes are tandemly linked and clustered in the genome of the winter flounder

We have used genomic Southern blots and restriction maps of genomic clones to examine the organization of the antifreeze protein multigene family in the winter flounder. The majority of the approximately equal to 40 antifreeze protein (AFP) genes in this fish are present in 7- to 8-kilobase-pair (kbp) elements of DNA, which are iterated as tandem direct repeats. Each repeat contains a single antifreeze protein gene that is 1 kbp long, and all of these genes have the same transcriptional orientation. Although the repeated elements are highly homologous, they do show some restriction site and restriction length polymorphisms. When flounder genomic DNA is digested with restriction endonucleases that do not cut within the repeats, most of the antifreeze protein genes reside in fragments that are at least 40 kbp long, representing clusters of five or more repeats in tandem. After genomic DNA is digested with Xba I or Xho I, these genes are present in fragments of exceptionally high molecular weight, suggesting that the clusters themselves are grouped together in the genome. The AFP gene locus may have evolved by gene amplification as recently as 10(6) years ago in response to the onset of the Cenozoic ice age.

Sequence of an antifreeze protein precursor

The amino acid sequence of the precursor to the second-most-abundant serum antifreeze protein (B) in the winter flounder has been determined by a combination of protein and DNA sequencing. The precursor is an 82-residue preproprotein which differs in only three positions from the amino acid sequence of the precursor for the most-abundant serum antifreeze protein (A). The base changes responsible for these substitutions, as well as several silent changes, are all clustered within the DNA coding for the mature protein portion. Among the post-translational modifications that the precursor undergoes is the removal of the c-terminal glycine residue. Cloning of full-length antifreeze protein cDNA has enabled us to identify the transcription initiation site which occurs 49 nucleotides upstream from the initiation codon.