Structural basis for the binding of a globular antifreeze protein to ice

Jia, Zongchao; Deluca, C.I.; Chao, Heman; Davies, Peter L.

doi:10.1038/384285a0

Cited by 256 publications

(283 citation statements)

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“…50 All experimental data were collected on a Bruker Avance DRX600 spectrometer equipped with a cryogenic triple-resonance probe at a temperature of 3.0 C. 1 H and 15 N referencing was performed relative to DSS as described. 51 For the 15 Spectra were processed using NMRPipe, 52 and chemical shift assignments were made using the CCPNMR analysis software version 2.1. 53 Chemical shifts of rHPLC6 1 H and 15 N atoms were obtained from previously published studies on the synthetic protein, 28,54 and 15 N-TOCY and 15 N-NOESY experiments were used to assign resonances that underwent large chemical shifts in the rHPLC6-Arg 37 and rHPLC6-Ala 37 mutants.…”

Section: Circular Dichroism Spectroscopymentioning

confidence: 99%

“…How the AFP binds to the ice surface has been more difficult to determine as there are no consistently conserved motifs in AFP protein sequences or structures. The known and predicted structural folds include a single a-helical structure (Type I AFP), 11 lectin folds (Type II AFP), 12,13 mixed irregular a-helix and b-strand (Type III AFP), 14,15 a-helical bundle (Type IV AFP), 16 b-helical fold (some insect and plant AFPs), [17][18][19] and polyproline Type II fold (snow flea AFP). 20,21 The structures of Types II-IV AFPs and the insect AFPs are reviewed in Refs.…”

Section: Introductionmentioning

confidence: 99%

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Increased flexibility decreases antifreeze protein activity

Patel

Graether

2010

Protein Science

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Antifreeze proteins protect several cold-blooded organisms from subzero environments by preventing death from freezing. The Type I antifreeze protein (AFP) isoform from Pseudopleuronectes americanus, named HPLC6, is a 37-residue protein that is a single a-helix. Mutational analysis of the protein showed that its alanine-rich face is important for binding to and inhibiting the growth of macromolecular ice. Almost all structural studies of HPLC6 involve the use of chemically synthesized protein as it requires a native N-terminal aspartate and an amidated C-terminus for full activity. Here, we examine the role of C-terminal amide and C-terminal arginine side chain in the activity, structure, and dynamics of nonamidated Arg 37 HPLC6, nonamidated HPLC6 Ala 37 , amidated HPLC6 Ala 37 , and fully native HPLC6 using a recombinant bacterial system. The thermal hysteresis (TH) activities of the nonamidated mutants are 35% lower compared with amidated proteins, but analysis of the NMR data and circular dichroism spectra shows that they are all still a-helical. Relaxation data from the two nonamidated mutants indicate that the C-terminal residues are considerably more flexible than the rest of the protein because of the loss of the amide group, whereas the amidated Ala 37 mutant has a C-terminus that is as rigid as the wild-type protein and has high TH activity. We propose that an increase in flexibility of the AFP causes it to lose activity because its dynamic nature prevents it from binding strongly to the ice surface.

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Section: Circular Dichroism Spectroscopymentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Increased flexibility decreases antifreeze protein activity

Patel

Graether

2010

Protein Science

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“…Synthesis of antifreeze glycoproteins and peptides can further depress the freezing point of body fluids or cellular water. These proteins lower the freezing point by a noncolligative mechanism without altering the melting point significantly, and are therefore also referred to as thermal hysteresis proteins [1,2]. They were first discovered in the blood sera of Antarctic fish living perennially at about −1.9°C, but have been now reported in many organisms including plants, insects, fungi and bacteria [3][4][5].…”

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confidence: 99%

Psychrophilic enzymes: molecular basis of cold adaptation

Feller

Gerday

1997

CMLS, Cell. mol. life sci.

371

233

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Abstract. Psychrophilic organisms have successfully provides enhanced abilities to undergo conformational colonized polar and alpine regions and are able to grow changes during catalysis. Thermal instability of coldefficiently at sub-zero temperatures. At the enzymatic adapted enzymes is therefore regarded as a consequence level, such organisms have to cope with the reduction of of their conformational flexibility. A survey of the psychrophilic enzymes studied so far reveals only minor chemical reaction rates induced by low temperatures in alterations of the primary structure when compared to order to maintain adequate metabolic fluxes. Thermal compensation in cold-adapted enzymes is reached mesophilic or thermophilic homologues. However, all known structural factors and weak interactions inthrough improved turnover number and catalytic effivolved in protein stability are either reduced in number ciency. This optimization of the catalytic parameters can originate from a highly flexible structure which or modified in order to increase their flexibility.Key words. Psychrophiles; extremophiles; cold adaptation; microbial proteins; protein stability; weak interactions; Antarctic.Psychrophiles live at the lowest temperatures which allow the development of living organisms. These extremophilic organisms, either prokaryotic or eukaryotic, represent a major class of the living world if we consider the vast extent of permanently cold environments on Earth, such as polar and alpine regions or deep-sea waters. The successful colonization of such severe ecological niches by psychrophiles, their diversity and abundance are now well recognized. The lower temperature limit of life is commonly defined as the freezing point of cellular water. Although apparently simple by definition, this limit can drop significantly below 0°C, the freezing point of pure water. For instance, the freezing point of a typical marine teleost ranges between −0.5 and −0.9°C. Sodium chloride is responsible for about 85% of the freezing point depression, and the remaining 15% is due to other small solutes. Synthesis of antifreeze glycoproteins and peptides can further depress the freezing point of body fluids or cellular water. These proteins lower the freezing point by a noncolligative mechanism without altering the melting point significantly, and are therefore also referred to as thermal hysteresis proteins [1,2]. They were first discovered in the blood sera of Antarctic fish living perennially at about −1.9°C, but have been now reported in many organisms including plants, insects, fungi and bacteria [3][4][5]. Levels of thermal hysteresis activity generally range from 0.1 to 0.3°C in bacteria, from 0.2 to 0.5°C in plants, from 0.7 to 1.5°C in fish and from 3 to 6°C in insects. Besides the synthesis of cryoprotectants which lead to freeze avoidance, several organisms have developed mechanisms of freeze tolerance, involving drastic metabolic modifica-* Corresponding author.

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“…The proteins chosen for analysis and presented here are a subset of the selected entries and belong to one of the following functional groups: growth factors, serine protease inhibitors, antifreeze proteins, chaperones and proteins of unknown function (Table 1). The data for the analyzed structures were taken from investigations carried out using X-ray crystallography [26][27][28] and NMR techniques [29][30][31][32][33][34][35][36][37][38][39][40]. Additionally, the SH3 domain is discussed with respect to the various proteins that contain it and their different biological functions [41].…”

Section: Datamentioning

confidence: 99%

“…Some explanations of this phenomenon suggest the reduction of the solubility of the antifreeze proteins in the solution as one of the causes of hysteretic activity [63]. Other studies [26,64] identify N14, T18 and Q44 as the key residues for antifreeze protein (type III) -ice interaction and reveal the amphipathic character of the ice-binding site. Interaction with ice is of low specificity character.…”

Section: Antifreeze Proteinsmentioning

confidence: 99%

“Fuzzy oil drop” model applied to individual small proteins built of 70 amino acids

2010

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To cite this version:Katarzyna Prymula, Kinga Salapa, Irena Roterman. "Fuzzy oil drop" model applied to individual small proteins built of 70 amino acids. Journal of Molecular Modeling, Springer Verlag (Germany), 2010, 16 (7) Abstract: The proteins composed of short polypeptides (about 70 amino acid residues) representing the following functional groups (according to PDB notation): growth hormones, serine protease inhibitors, antifreeze proteins, chaperones and proteins of unknown function, were selected for structural and functional analysis. Classification based on the distribution of hydrophobicity in terms of deficiency/excess as the measure of structural and functional specificity is presented. The experimentally observed distribution of hydrophobicity in the protein body is compared to the idealized one expressed by a three-dimensional Gauss function. The differences between these two distributions reveal the specificity of structural/functional characteristics of the protein. The residues of hydrophobicity deficiency versus the idealized distribution are assumed to indicate cavities with the potential to bind ligands, while the residues of hydrophobicity excess are interpreted as potentially participating in protein-protein complexation. The distribution of hydrophobicity irregularity seems to be specific for particular structures and functions of proteins. A comparative analysis of such profiles is carried out to identify the potential biological activity of proteins of unknown function.Response to Reviewers: Comments to the reviewers Reviewer #1The sentence "protein structure determines its biological function" got changed to the form : "The spatial distribution of amino acid residues and particularly distribution of their specific hydrophobicity in a protein structure is assumed to influence the biological function". Reviewer #2Ad.1. The section INTRODUCTION has been modified making the problem of NBP less exposed. The paper describing the structures of NBP form is in press currently. The appearance of that paper will make clear the idea of NBP and the usefulness of the presented method. The real proteins available in PDB allowed the comparative analysis of the NBP proteins reveling some substantial differences and similarities between these two groups of proteins position #18 on the reference list (Prymula K, Piwowar M, Kochanczyk M, Flis L, Malawski M, Szepieniec T, Evangelista G, Minervini G, Polticelli F, Wisniowski Z, Salapa K, Matczynska E, and Roterman I (2009) In silico structural study of random amino acid sequence proteins not present in nature. Chem Biodivers, in press). Ad.2. The hydrophobicity scaleThe hydrophobicity scales (theoretical and experimental) were compared in details in respect to "fuzzy oil drop" model in other publication. The "fuzzy oil drop" estimates the hydrophobicity distribution in the very simplified and averaged form. In result, the relative distribution of hydrophobicity is under consideration. The differences observed between different scales get marginal in this st...

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Structural basis for the binding of a globular antifreeze protein to ice

Cited by 256 publications

References 20 publications

Increased flexibility decreases antifreeze protein activity

Increased flexibility decreases antifreeze protein activity

Psychrophilic enzymes: molecular basis of cold adaptation

“Fuzzy oil drop” model applied to individual small proteins built of 70 amino acids

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