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Graham LA, Davies PL. Fish antifreeze protein origin in sculpins by frameshifting within a duplicated housekeeping gene. FEBS J 2024. [PMID: 38923815 DOI: 10.1111/febs.17205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 03/25/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024]
Abstract
Antifreeze proteins (AFPs) are found in a variety of marine cold-water fishes where they prevent freezing by binding to nascent ice crystals. Their diversity (types I, II, III and antifreeze glycoproteins), as well as their scattered taxonomic distribution hint at their complex evolutionary history. In particular, type I AFPs appear to have arisen in response to the Late Cenozoic Ice Age that began ~ 34 million years ago via convergence in four different groups of fish that diverged from lineages lacking this AFP. The progenitor of the alanine-rich α-helical type I AFPs of sculpins has now been identified as lunapark, an integral membrane protein of the endoplasmic reticulum. Following gene duplication and loss of all but three of the 15 exons, the final exon, which encoded a glutamate- and glutamine-rich segment, was converted to an alanine-rich sequence by a combination of frameshifting and mutation. Subsequent gene duplications produced numerous isoforms falling into four distinct groups. The origin of the flounder type I AFP is quite different. Here, a small segment from the original antiviral protein gene was amplified and the rest of the coding sequence was lost, while the gene structure was largely retained. The independent origins of type I AFPs with up to 83% sequence identity in flounder and sculpin demonstrate strong convergent selection at the level of protein sequence for alanine-rich single alpha helices that bind to ice. Recent acquisition of these AFPs has allowed sculpins to occupy icy seawater niches with reduced competition and predation from other teleost species.
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Affiliation(s)
- Laurie A Graham
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Canada
| | - Peter L Davies
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Canada
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Rives N, Lamba V, Christina Cheng CH, Zhuang X. Diverse origins of near-identical antifreeze proteins in unrelated fish lineages provide insights into evolutionary mechanisms of new gene birth and protein sequence convergence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.12.584730. [PMID: 38559027 PMCID: PMC10980009 DOI: 10.1101/2024.03.12.584730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Determining the origins of novel genes and the genetic mechanisms underlying the emergence of new functions is challenging yet crucial for understanding evolutionary innovations. The novel fish antifreeze proteins, exemplifying convergent evolution, represent excellent opportunities to investigate the evolutionary origins and pathways of new genes. Particularly notable is the near-identical type I antifreeze proteins (AFPI) in four phylogenetically divergent fish taxa. This study tested the hypothesis of protein sequence convergence beyond functional convergence in three unrelated AFPI-bearing fish lineages, revealing different paths by which a similar protein arose from diverse genomic resources. Comprehensive comparative analyses of de novo sequenced genome of the winter flounder and grubby sculpin, available high-quality genome of the cunner, and those of 14 other relevant species found that the near-identical AFPI originated from a distinct genetic precursor in each lineage, and independently evolved coding regions for the novel ice-binding protein while retaining sequence identity in the regulatory regions with their respective ancestor. The deduced evolutionary processes and molecular mechanisms is consistent with the Innovation-Amplification-Divergence (IAD) model applicable to AFPI formation in all three lineages, a new Duplication-Degeneration-Divergence (DDD) model we propose for the sculpin lineage, and a DDD model with gene fission for the cunner lineage. This investigation illustrates the multiple ways by which a novel functional gene with sequence convergence at the protein level could evolve across divergent species, advancing our understanding of the mechanistic intricacies in new gene formation.
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Affiliation(s)
- Nathan Rives
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA
| | - Vinita Lamba
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA
| | - C.-H. Christina Cheng
- Department of Evolution, Ecology and Behavior, University of Illinois, Urbana-Champaign, IL, USA
| | - Xuan Zhuang
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA
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3
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Cui M, Li J, Li J, Wang F, Li X, Yu J, Huang Y, Liu Y. Screening and characterization of a novel antifreeze peptide from silver carp muscle hydrolysate. Food Chem 2023; 403:134480. [DOI: 10.1016/j.foodchem.2022.134480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/28/2022] [Accepted: 09/28/2022] [Indexed: 11/28/2022]
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Water-organizing motif continuity is critical for potent ice nucleation protein activity. Nat Commun 2022; 13:5019. [PMID: 36028506 PMCID: PMC9418140 DOI: 10.1038/s41467-022-32469-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 07/29/2022] [Indexed: 12/02/2022] Open
Abstract
Bacterial ice nucleation proteins (INPs) can cause frost damage to plants by nucleating ice formation at high sub-zero temperatures. Modeling of Pseudomonas borealis INP by AlphaFold suggests that the central domain of 65 tandem sixteen-residue repeats forms a beta-solenoid with arrays of outward-pointing threonines and tyrosines, which may organize water molecules into an ice-like pattern. Here we report that mutating some of these residues in a central segment of P. borealis INP, expressed in Escherichia coli, decreases ice nucleation activity more than the section’s deletion. Insertion of a bulky domain has the same effect, indicating that the continuity of the water-organizing repeats is critical for optimal activity. The ~10 C-terminal coils differ from the other 55 coils in being more basic and lacking water-organizing motifs; deletion of this region eliminates INP activity. We show through sequence modifications how arrays of conserved motifs form the large ice-nucleating surface required for potency. Ice nucleation proteins have the same tandemly arrayed water-organizing motifs seen in some antifreeze proteins, but on a larger scale. The authors show that mutation, interruption, and truncation of these arrays reduce ice nucleation activity indicating that the two protein types share a common mechanism.
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Antifreeze Proteins: Novel Applications and Navigation towards Their Clinical Application in Cryobanking. Int J Mol Sci 2022; 23:ijms23052639. [PMID: 35269780 PMCID: PMC8910022 DOI: 10.3390/ijms23052639] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 02/16/2022] [Accepted: 02/25/2022] [Indexed: 12/04/2022] Open
Abstract
Antifreeze proteins (AFPs) or thermal hysteresis (TH) proteins are biomolecular gifts of nature to sustain life in extremely cold environments. This family of peptides, glycopeptides and proteins produced by diverse organisms including bacteria, yeast, insects and fish act by non-colligatively depressing the freezing temperature of the water below its melting point in a process termed thermal hysteresis which is then responsible for ice crystal equilibrium and inhibition of ice recrystallisation; the major cause of cell dehydration, membrane rupture and subsequent cryodamage. Scientists on the other hand have been exploring various substances as cryoprotectants. Some of the cryoprotectants in use include trehalose, dimethyl sulfoxide (DMSO), ethylene glycol (EG), sucrose, propylene glycol (PG) and glycerol but their extensive application is limited mostly by toxicity, thus fueling the quest for better cryoprotectants. Hence, extracting or synthesizing antifreeze protein and testing their cryoprotective activity has become a popular topic among researchers. Research concerning AFPs encompasses lots of effort ranging from understanding their sources and mechanism of action, extraction and purification/synthesis to structural elucidation with the aim of achieving better outcomes in cryopreservation. This review explores the potential clinical application of AFPs in the cryopreservation of different cells, tissues and organs. Here, we discuss novel approaches, identify research gaps and propose future research directions in the application of AFPs based on recent studies with the aim of achieving successful clinical and commercial use of AFPs in the future.
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Baskaran A, Kaari M, Venugopal G, Manikkam R, Joseph J, Bhaskar PV. Anti freeze proteins (Afp): Properties, sources and applications - A review. Int J Biol Macromol 2021; 189:292-305. [PMID: 34419548 DOI: 10.1016/j.ijbiomac.2021.08.105] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 11/17/2022]
Abstract
Extreme cold marine and freshwater temperatures (below 4 °C) induce massive deterioration to the cell membranes of organisms resulting in the formation of ice crystals, consequently causing organelle damage or cell death. One of the adaptive mechanisms organisms have evolved to thrive in cold environments is the production of antifreeze proteins with the functional capabilities to withstand frigid temperatures. Antifreeze proteins are extensively identified in different cold-tolerant species and they facilitate the persistence of cold-adapted organisms by decreasing the freezing point of their body fluids. Various structurally diverse types of antifreeze proteins detected possess the ability to modify ice crystal growth by thermal hysteresis and ice recrystallization inhibition. The unique properties of antifreeze proteins have made them a promising resource in industry, biomedicine, food storage and cryobiology. This review collates the findings of the various studies carried out in the past and the recent developments observed in the properties, functional mechanisms, classification, distinct sources and the ever-increasing applications of antifreeze proteins. This review also summarizes the possibilities of the way forward to identify new avenues of research on anti-freeze proteins.
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Affiliation(s)
- Abirami Baskaran
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600 119, Tamil Nadu, India
| | - Manigundan Kaari
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600 119, Tamil Nadu, India
| | - Gopikrishnan Venugopal
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600 119, Tamil Nadu, India
| | - Radhakrishnan Manikkam
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600 119, Tamil Nadu, India.
| | - Jerrine Joseph
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600 119, Tamil Nadu, India
| | - Parli V Bhaskar
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Vasco-da-Gama 403804, Goa, India
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Kozuch DJ, Stillinger FH, Debenedetti PG. Genetic Algorithm Approach for the Optimization of Protein Antifreeze Activity Using Molecular Simulations. J Chem Theory Comput 2020; 16:7866-7873. [PMID: 33201707 DOI: 10.1021/acs.jctc.0c00773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Antifreeze proteins (AFPs) are of much interest for their ability to inhibit ice growth at low concentrations. In this work, we present a genetic algorithm for the in silico design of AFP mutants with improved antifreeze activity, measured as the predicted thermal hysteresis at a fixed concentration, ΔTC. Central to the algorithm is our recently developed neural network method for predicting ΔTC from molecular simulations [Kozuch et al., PNAS, 115, 13252 (2018)]. Applying the algorithm to three structurally diverse AFPs, wfAFP, rQAE, and RiAFP, we find that significantly improved mutants are discovered for rQAE and RiAFP. Testing of the optimized mutants shows an increase in ΔTC of 0.572 ± 0.11 K (262 ± 50.6%) and 1.33 ± 0.14 K (39.9 ± 4.19%) over the native structures for rQAE and RiAFP, respectively. Structural analysis of the optimized mutants reveals that the algorithm is able to exploit two pathways for enhancing the predicted antifreeze activity of the mutants: (1) increasing the local order of surface waters by encouraging the formation of internal water channels in the protein and (2) increasing the total ice-binding area by improving the planar structure of the ice-binding surface. Additionally, analysis of all mutants explored by the algorithm reveals that a subset of residues, mainly nonpolar, are particularly helpful in improving antifreeze activity at the ice-binding surface.
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Affiliation(s)
- Daniel J Kozuch
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Frank H Stillinger
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Pablo G Debenedetti
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
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Hanson JM, Courtenay SC. Data Recovery from Old Filing Cabinets: Seasonal Diets of the Most Common Demersal Fishes in the Miramichi River Estuary (Atlantic Canada), 1991–1993. Northeast Nat (Steuben) 2020. [DOI: 10.1656/045.027.0302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- John Mark Hanson
- Science Branch, Gulf Fisheries Centre, Fisheries and Ocean Canada, PO Box 5030, Moncton, NB E1C 9B6, Canada
| | - Simon C. Courtenay
- Science Branch, Gulf Fisheries Centre, Fisheries and Ocean Canada, PO Box 5030, Moncton, NB E1C 9B6, Canada
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Lee H. Effects of hydrophobic and hydrogen-bond interactions on the binding affinity of antifreeze proteins to specific ice planes. J Mol Graph Model 2018; 87:48-55. [PMID: 30502671 DOI: 10.1016/j.jmgm.2018.11.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 11/17/2018] [Accepted: 11/19/2018] [Indexed: 11/26/2022]
Abstract
Tenebrio molitor antifreeze protein (TmAFP) was simulated with growing ice surfaces such as primary prism, secondary prism, basal, and pyramidal planes. The ice-binding site of TmAFP, which is full of threonine (Thr), binds to the primary-prism plane but does not bind to other ice planes, in agreement with experiments showing the fast adsorption of TmAFP to the primary-prism plane. To mimic the ice-binding site of shorthorn sculpin AFP (ssAFP; type I) that predominantly consists of alanine (Ala) and has the binding affinity to the secondary-prism plane, the ice-binding site of TmAFP was mutated by replacing a few Thr residues with Ala residues, showing that mutated TmAFP binds to the secondary-prism plane, similar to the ice-binding affinity of ssAFP. Ala residues are located at the cavity of ice, while Thr residues form hydrogen bonds with water molecules. When the mutated TmAFP is further modified by removing Thr, it does not bind to the secondary-prism plane. These findings indicate that simulations can successfully capture the experimentally observed binding affinity of AFP to specific ice planes, to an extent dependent on hydrophobicity of the ice-binding site. In particular, the addition of hydrophobic residues influences the ice-binding affinity of TmAFP, while a certain amount of hydrophilic residue is still required for hydrogen-bond interactions, which supports experimental observations regarding the key roles of hydrophobic and hydrophilic interactions on the AFP-ice binding.
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Affiliation(s)
- Hwankyu Lee
- Department of Chemical Engineering, Dankook University, Yongin-si, Gyeonggi-do, 16890, South Korea.
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10
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Wellig S, Hamm P. Solvation Layer of Antifreeze Proteins Analyzed with a Markov State Model. J Phys Chem B 2018; 122:11014-11022. [PMID: 29889528 DOI: 10.1021/acs.jpcb.8b04491] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Three structurally very different antifreeze proteins (AFPs) are studied, addressing the question as to what extent the hypothesized preordering-binding mechanism is still relevant in the second solvation layer of the protein and beyond. Assuming a two-state model of water, the solvation layers are analyzed with the help of molecular dynamics simulations together with a Markov state model, which investigates the local tedrahedrality of the water hydrogen-bond network around a given water molecule. It has been shown previously that this analysis can discriminate the high-entropy, high-density state of the liquid (HDL) from its more structured low-density state (LDL). All investigated proteins, regardless of whether they are an AFP or not, have a tendency to increase the amount of HDL in their second solvation layer. The ice binding site (IBS) of the antifreeze proteins counteracts that trend, with either a hole in the HDL layer or a true excess of LDL. The results correlate to a certain extent with recent experiments, which have observed ice-like vibrational (VSFG) spectra for the water atop the IBS of only a subset of antifreeze proteins. It is concluded that the preordering-binding mechanism indeed seems to play a role but is only part of the overall picture.
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Affiliation(s)
- Sebastian Wellig
- Department of Chemistry , University of Zurich , 8057 Zurich , Switzerland
| | - Peter Hamm
- Department of Chemistry , University of Zurich , 8057 Zurich , Switzerland
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11
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Stevens CA, Semrau J, Chiriac D, Litschko M, Campbell RL, Langelaan DN, Smith SP, Davies PL, Allingham JS. Peptide backbone circularization enhances antifreeze protein thermostability. Protein Sci 2017; 26:1932-1941. [PMID: 28691252 DOI: 10.1002/pro.3228] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 06/22/2017] [Accepted: 07/03/2017] [Indexed: 11/09/2022]
Abstract
Antifreeze proteins (AFPs) are a class of ice-binding proteins that promote survival of a variety of cold-adapted organisms by decreasing the freezing temperature of bodily fluids. A growing number of biomedical, agricultural, and commercial products, such as organs, foods, and industrial fluids, have benefited from the ability of AFPs to control ice crystal growth and prevent ice recrystallization at subzero temperatures. One limitation of AFP use in these latter contexts is their tendency to denature and irreversibly lose activity at the elevated temperatures of certain industrial processing or large-scale AFP production. Using the small, thermolabile type III AFP as a model system, we demonstrate that AFP thermostability is dramatically enhanced via split intein-mediated N- and C-terminal end ligation. To engineer this circular protein, computational modeling and molecular dynamics simulations were applied to identify an extein sequence that would fill the 20-Å gap separating the free ends of the AFP, yet impose little impact on the structure and entropic properties of its ice-binding surface. The top candidate was then expressed in bacteria, and the circularized protein was isolated from the intein domains by ice-affinity purification. This circularized AFP induced bipyramidal ice crystals during ice growth in the hysteresis gap and retained 40% of this activity even after incubation at 100°C for 30 min. NMR analysis implicated enhanced thermostability or refolding capacity of this protein compared to the noncyclized wild-type AFP. These studies support protein backbone circularization as a means to expand the thermostability and practical applications of AFPs.
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Affiliation(s)
- Corey A Stevens
- Protein Function Discovery Group and the Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - Joanna Semrau
- Protein Function Discovery Group and the Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - Dragos Chiriac
- Protein Function Discovery Group and the Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - Morgan Litschko
- Protein Function Discovery Group and the Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - Robert L Campbell
- Protein Function Discovery Group and the Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - David N Langelaan
- Protein Function Discovery Group and the Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - Steven P Smith
- Protein Function Discovery Group and the Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - Peter L Davies
- Protein Function Discovery Group and the Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - John S Allingham
- Protein Function Discovery Group and the Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, K7L 3N6, Canada
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12
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Blocking rapid ice crystal growth through nonbasal plane adsorption of antifreeze proteins. Proc Natl Acad Sci U S A 2016; 113:3740-5. [PMID: 26936953 DOI: 10.1073/pnas.1524109113] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Antifreeze proteins (AFPs) are a unique class of proteins that bind to growing ice crystal surfaces and arrest further ice growth. AFPs have gained a large interest for their use in antifreeze formulations for water-based materials, such as foods, waterborne paints, and organ transplants. Instead of commonly used colligative antifreezes such as salts and alcohols, the advantage of using AFPs as an additive is that they do not alter the physicochemical properties of the water-based material. Here, we report the first comprehensive evaluation of thermal hysteresis (TH) and ice recrystallization inhibition (IRI) activity of all major classes of AFPs using cryoscopy, sonocrystallization, and recrystallization assays. The results show that TH activities determined by cryoscopy and sonocrystallization differ markedly, and that TH and IRI activities are not correlated. The absence of a distinct correlation in antifreeze activity points to a mechanistic difference in ice growth inhibition by the different classes of AFPs: blocking fast ice growth requires rapid nonbasal plane adsorption, whereas basal plane adsorption is only relevant at long annealing times and at small undercooling. These findings clearly demonstrate that biomimetic analogs of antifreeze (glyco)proteins should be tailored to the specific requirements of the targeted application.
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13
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Davies PL. Ice-binding proteins: a remarkable diversity of structures for stopping and starting ice growth. Trends Biochem Sci 2014; 39:548-55. [DOI: 10.1016/j.tibs.2014.09.005] [Citation(s) in RCA: 268] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 09/24/2014] [Accepted: 09/25/2014] [Indexed: 12/01/2022]
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Graham LA, Hobbs RS, Fletcher GL, Davies PL. Helical antifreeze proteins have independently evolved in fishes on four occasions. PLoS One 2013; 8:e81285. [PMID: 24324684 PMCID: PMC3855684 DOI: 10.1371/journal.pone.0081285] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 10/21/2013] [Indexed: 12/25/2022] Open
Abstract
Alanine-rich α-helical (type I) antifreeze proteins (AFPs) are produced by a variety of fish species from three different orders to protect against freezing in icy seawater. Interspersed amongst and within these orders are fishes making AFPs that are completely different in both sequence and structure. The origin of this variety of types I, II, III and antifreeze glycoproteins (AFGPs) has been attributed to adaptation following sea-level glaciations that occurred after the divergence of most of the extant families of fish. The presence of similar types of AFPs in distantly related fishes has been ascribed to lateral gene transfer in the case of the structurally complex globular type II lectin-like AFPs and to convergent evolution for the AFGPs, which consist of a well-conserved tripeptide repeat. In this paper, we examine the genesis of the type I AFPs, which are intermediate in complexity. These predominantly α-helical peptides share many features, such as putative capping structures, Ala-richness and amphipathic character. We have added to the type I repertoire by cloning additional sequences from sculpin and have found that the similarities between the type I AFPs of the four distinct groups of fishes are not borne out at the nucleotide level. Both the non-coding sequences and the codon usage patterns are strikingly different. We propose that these AFPs arose via convergence from different progenitor helices with a weak affinity for ice and that their similarity is dictated by the propensity of specific amino acids to form helices and to align water on one side of the helix into an ice-like pattern.
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Affiliation(s)
- Laurie A. Graham
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
| | - Rod S. Hobbs
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Garth L. Fletcher
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Peter L. Davies
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
- * E-mail:
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15
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Haridas V, Naik S. Natural macromolecular antifreeze agents to synthetic antifreeze agents. RSC Adv 2013. [DOI: 10.1039/c3ra00081h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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16
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Middleton AJ, Marshall CB, Faucher F, Bar-Dolev M, Braslavsky I, Campbell RL, Walker VK, Davies PL. Antifreeze protein from freeze-tolerant grass has a beta-roll fold with an irregularly structured ice-binding site. J Mol Biol 2012; 416:713-24. [PMID: 22306740 DOI: 10.1016/j.jmb.2012.01.032] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 01/18/2012] [Indexed: 11/16/2022]
Abstract
The grass Lolium perenne produces an ice-binding protein (LpIBP) that helps this perennial tolerate freezing by inhibiting the recrystallization of ice. Ice-binding proteins (IBPs) are also produced by freeze-avoiding organisms to halt the growth of ice and are better known as antifreeze proteins (AFPs). To examine the structural basis for the different roles of these two IBP types, we have solved the first crystal structure of a plant IBP. The 118-residue LpIBP folds as a novel left-handed beta-roll with eight 14- or 15-residue coils and is stabilized by a small hydrophobic core and two internal Asn ladders. The ice-binding site (IBS) is formed by a flat beta-sheet on one surface of the beta-roll. We show that LpIBP binds to both the basal and primary-prism planes of ice, which is the hallmark of hyperactive AFPs. However, the antifreeze activity of LpIBP is less than 10% of that measured for those hyperactive AFPs with convergently evolved beta-solenoid structures. Whereas these hyperactive AFPs have two rows of aligned Thr residues on their IBS, the equivalent arrays in LpIBP are populated by a mixture of Thr, Ser and Val with several side-chain conformations. Substitution of Ser or Val for Thr on the IBS of a hyperactive AFP reduced its antifreeze activity. LpIBP may have evolved an IBS that has low antifreeze activity to avoid damage from rapid ice growth that occurs when temperatures exceed the capacity of AFPs to block ice growth while retaining the ability to inhibit ice recrystallization.
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Affiliation(s)
- Adam J Middleton
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada K7L 3N6
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Hobbs RS, Shears MA, Graham LA, Davies PL, Fletcher GL. Isolation and characterization of type I antifreeze proteins from cunner, Tautogolabrus adspersus, order Perciformes. FEBS J 2011; 278:3699-710. [DOI: 10.1111/j.1742-4658.2011.08288.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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18
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Bayer-Giraldi M, Weikusat I, Besir H, Dieckmann G. Characterization of an antifreeze protein from the polar diatom Fragilariopsis cylindrus and its relevance in sea ice. Cryobiology 2011; 63:210-9. [PMID: 21906587 DOI: 10.1016/j.cryobiol.2011.08.006] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Revised: 08/12/2011] [Accepted: 08/15/2011] [Indexed: 11/16/2022]
Abstract
Antifreeze proteins (AFPs), characterized by their ability to separate the melting and growth temperatures of ice and to inhibit ice recrystallization, play an important role in cold adaptation of several polar and cold-tolerant organisms. Recently, a multigene family of AFP genes was found in the diatom Fragilariopsis cylindrus, a dominant species within polar sea ice assemblages. This study presents the AFP from F. cylindrus set in a molecular and crystallographic frame. Differential protein expression after exposure of the diatoms to environmentally relevant conditions underlined the importance of certain AFP isoforms in response to cold. Analyses of the recombinant AFP showed freezing point depression comparable to the activity of other moderate AFPs and further enhanced by salt (up to 0.9°C in low salinity buffer, 2.5°C at high salinity). However, unlike other moderate AFPs, its fastest growth direction is perpendicular to the c-axis. The protein also caused strong inhibition of recrystallization at concentrations of 1.2 and 0.12 μM at low and high salinity, respectively. Observations of crystal habit modifications and pitting activity suggested binding of AFPs to multiple faces of the ice crystals. Further analyses showed striations caused by AFPs, interpreted as inclusion in the ice. We suggest that the influence on ice microstructure is the main characteristic of these AFPs in sea ice.
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19
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The triplet puzzle of homologies in receptor heteromers exists also in other types of protein-protein interactions. J Mol Neurosci 2011; 44:173-7. [PMID: 21416272 DOI: 10.1007/s12031-011-9511-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Accepted: 03/03/2011] [Indexed: 11/26/2022]
Abstract
Based on our theory, we point out main triplets of amino acid residues in the GABAB1 receptor, found in the central and peripheral nervous system, which seem to be critical for both receptor heterodimerization and chemokine binding. The obtained results suggest that these triplets may "guide-and-clasp" protein-protein interactions playing a role, e.g., in neuroinflammation disorders.
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20
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Patel SN, Graether SP. Structures and ice-binding faces of the alanine-rich type I antifreeze proteins. Biochem Cell Biol 2010; 88:223-9. [PMID: 20453925 DOI: 10.1139/o09-183] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Antifreeze proteins (AFPs) protect cold-blooded organisms from the damage caused by freezing through their ability to inhibit ice growth. The type I AFP family, found in several fish species, contains proteins that have a high alanine content (>60% of the sequence) and structures that are almost all alpha-helical. We examine the structure of the type I AFP isoforms HPLC6 from winter flounder, shorthorn sculpin 3, and the winter flounder hyperactive type I AFP. The HPLC6 isoform structure consists of a single alpha-helix that is 37 residues long, whereas the shorthorn sculpin 3 isoform consists of two helical regions separated by a kink. The high-resolution structure of the hyperactive type I AFP has yet to be determined, but circular dichroism data and analytical ultracentrifugation suggest that the 195 residue protein is a side-by-side dimer of two alpha-helices. The alanine-rich ice-binding faces of HPLC6 and hyperactive type I AFP are discussed, and we propose that the ice-binding face of the shorthorn sculpin 3 AFP contains Ala14, Ala19, and Ala25. We also propose that the denaturation of hyperactive type I AFP at room temperature is explained by the stabilization of the dimerization interface through hydrogen bonds.
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Affiliation(s)
- Shruti N Patel
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
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21
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Mok YF, Lin FH, Graham LA, Celik Y, Braslavsky I, Davies PL. Structural Basis for the Superior Activity of the Large Isoform of Snow Flea Antifreeze Protein. Biochemistry 2010; 49:2593-603. [DOI: 10.1021/bi901929n] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yee-Foong Mok
- Department of Biochemistry and Protein Function Discovery Group, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - Feng-Hsu Lin
- Department of Biochemistry and Protein Function Discovery Group, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - Laurie A. Graham
- Department of Biochemistry and Protein Function Discovery Group, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - Yeliz Celik
- Department of Physics and Astronomy, Ohio University, Athens, Ohio 45701
| | - Ido Braslavsky
- Department of Physics and Astronomy, Ohio University, Athens, Ohio 45701
| | - Peter L. Davies
- Department of Biochemistry and Protein Function Discovery Group, Queen’s University, Kingston, Ontario K7L 3N6, Canada
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22
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Tarakanov AO, Fuxe KG. Triplet Puzzle: Homologies of Receptor Heteromers. J Mol Neurosci 2009; 41:294-303. [DOI: 10.1007/s12031-009-9313-5] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2009] [Accepted: 11/12/2009] [Indexed: 11/27/2022]
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23
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Takamichi M, Nishimiya Y, Miura A, Tsuda S. Fully active QAE isoform confers thermal hysteresis activity on a defective SP isoform of type III antifreeze protein. FEBS J 2009; 276:1471-9. [PMID: 19187223 DOI: 10.1111/j.1742-4658.2009.06887.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Type III antifreeze protein is naturally expressed as a mixture of sulfopropyl-Sephadex (SP) and quaternary aminoethyl-Sephadex (QAE)-binding isoforms, whose sequence identity is approximately 55%. We studied the ice-binding properties of a SP isoform (nfeAFP6) and the differences from those of a QAE isoform (nfeAFP8); both of these isoforms have been identified from the Japanese fish Zoarces elongatus Kner. The two isoforms possessed ice-shaping ability, such as the creation of an ice bipyramid, but nfeAFP6 was unable to halt crystal growth and exhibited no thermal hysteresis activity. For example, the ice growth rate for nfeAFP6 was 1000-fold higher than that for nfeAFP8 when measured for 0.1 mm protein solution at 0.25 degrees C below the melting point. Nevertheless, nfeAFP6 exhibited full thermal hysteresis activity in the presence of only 1% nfeAFP8 (i.e. [nfeAFP8]/[nfeAFP6] = 0.01), the effectiveness of which was indistinguishable from that of nfeAFP8 alone. We also observed a burst of ice crystal growth from the tip of the ice bipyramid for both isoforms on lowering the temperature. These results suggest that the ice growth inhibitory activity of an antifreeze protein isoform lacking the active component is restored by the addition of a minute amount of the active isoform.
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Affiliation(s)
- Manabu Takamichi
- Functional Protein Research Group, Research Institute of Genome-based Biofactory, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
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24
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Petit-Haertlein I, Blakeley MP, Howard E, Hazemann I, Mitschler A, Haertlein M, Podjarny A. Perdeuteration, purification, crystallization and preliminary neutron diffraction of an ocean pout type III antifreeze protein. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:406-9. [PMID: 19342793 PMCID: PMC2664773 DOI: 10.1107/s1744309109008574] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2009] [Accepted: 03/09/2009] [Indexed: 11/10/2022]
Abstract
The highly homologous type III antifreeze protein (AFP) subfamily share the capability to inhibit ice growth at subzero temperatures. Extensive studies by X-ray crystallography have been conducted, mostly on AFPs from polar fishes. Although interactions between a defined flat ice-binding surface and a particular lattice plane of an ice crystal have now been identified, the fine structural features underlying the antifreeze mechanism still remain unclear owing to the intrinsic difficulty in identifying H atoms using X-ray diffraction data alone. Here, successful perdeuteration (i.e. complete deuteration) for neutron crystallographic studies of the North Atlantic ocean pout (Macrozoarces americanus) AFP in Escherichia coli high-density cell cultures is reported. The perdeuterated protein (AFP D) was expressed in inclusion bodies, refolded in deuterated buffer and purified by cation-exchange chromatography. Well shaped perdeuterated AFP D crystals have been grown in D(2)O by the sitting-drop method. Preliminary neutron Laue diffraction at 293 K using LADI-III at ILL showed that with a few exposures of 24 h a very low background and clear small spots up to a resolution of 1.85 A were obtained using a ;radically small' perdeuterated AFP D crystal of dimensions 0.70 x 0.55 x 0.35 mm, corresponding to a volume of 0.13 mm(3).
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Affiliation(s)
- Isabelle Petit-Haertlein
- ILL–EMBL Deuteration Laboratory, Partnership for Structural Biology, 6 Rue Jules Horowitz, 38042 Grenoble, France
- Institut Laue–Langevin, 6 Rue Jules Horowitz, 38042 Grenoble, France
| | | | | | | | - Andre Mitschler
- IGBMC, CNRS, INSERM, UdS, 1 Rue Laurent Fries, Illkirch, France
| | - Michael Haertlein
- ILL–EMBL Deuteration Laboratory, Partnership for Structural Biology, 6 Rue Jules Horowitz, 38042 Grenoble, France
- Institut Laue–Langevin, 6 Rue Jules Horowitz, 38042 Grenoble, France
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25
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Kristiansen E, Pedersen SA, Zachariassen KE. Salt-induced enhancement of antifreeze protein activity: A salting-out effect. Cryobiology 2008; 57:122-9. [DOI: 10.1016/j.cryobiol.2008.07.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2008] [Revised: 05/20/2008] [Accepted: 07/05/2008] [Indexed: 10/21/2022]
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26
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Nishimiya Y, Kondo H, Takamichi M, Sugimoto H, Suzuki M, Miura A, Tsuda S. Crystal structure and mutational analysis of Ca2+-independent type II antifreeze protein from longsnout poacher, Brachyopsis rostratus. J Mol Biol 2008; 382:734-46. [PMID: 18674542 DOI: 10.1016/j.jmb.2008.07.042] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2008] [Revised: 07/13/2008] [Accepted: 07/16/2008] [Indexed: 10/21/2022]
Abstract
We recently found that longsnout poacher (Brachyosis rostratus) produces a Ca(2+)-independent type II antifreeze protein (lpAFP) and succeeded in expressing recombinant lpAFP using Phichia pastoris. Here, we report, for the first time, the X-ray crystal structure of lpAFP at 1.34 A resolution. The lpAFP structure displayed a relatively planar surface, which encompasses two loop regions (Cys86-Lys89 and Asn91-Cys97) and a short beta-strand (Trp109-Leu112) with three unstructured segments (Gly57-Ile58, Ala103-Ala104, and Pro113-His118). Electrostatic calculation of the protein surface showed that the relatively planar surface was divided roughly into a hydrophobic area (composed of the three unstructured segments lacking secondary structure) and a hydrophilic area (composed of the loops and beta-strand). Site-directed mutation of Ile58 with Phe at the center of the hydrophobic area decreased activity significantly, whereas mutation of Leu112 with Phe at an intermediate area between the hydrophobic and hydrophilic areas retained complete activity. In the hydrophilic area, a peptide-swap mutant in the loops retained 60% activity despite simultaneous mutations of eight residues. We conclude that the epicenter of the ice-binding site of lpAFP is the hydrophobic region, which is centered by Ile58, in the relatively planar surface. We built an ice-binding model for lpAFP on the basis of a lattice match of ice and constrained water oxygen atoms surrounding the hydrophobic area in the lpAFP structure. The model in which lpAFP has been docked to a secondary prism (2-1-10) plane, which is different from the one determined for Ca(2+)-independent type II AFP from sea raven (11-21), appears to explain the results of the mutagenesis analysis.
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Affiliation(s)
- Yoshiyuki Nishimiya
- Functional Protein Research Group, Research Institute of Genome-based Biofactory, National Institute of Advanced Industrial Science and Technology, 2-17-2-1 Tsukisamu-Higashi, Toyohira, Sapporo 062-8517, Japan
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27
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A Ca2+-dependent bacterial antifreeze protein domain has a novel β-helical ice-binding fold. Biochem J 2008; 411:171-80. [DOI: 10.1042/bj20071372] [Citation(s) in RCA: 113] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
AFPs (antifreeze proteins) are produced by many organisms that inhabit ice-laden environments. They facilitate survival at sub-zero temperatures by binding to, and inhibiting, the growth of ice crystals in solution. The Antarctic bacterium Marinomonas primoryensis produces an exceptionally large (>1 MDa) hyperactive Ca2+-dependent AFP. We have cloned, expressed and characterized a 322-amino-acid region of the protein where the antifreeze activity is localized that shows similarity to the RTX (repeats-in-toxin) family of proteins. The recombinant protein requires Ca2+ for structure and activity, and it is capable of depressing the freezing point of a solution in excess of 2 °C at a concentration of 0.5 mg/ml, therefore classifying it as a hyperactive AFP. We have developed a homology-guided model of the antifreeze region based partly on the Ca2+-bound β-roll from alkaline protease. The model has identified both a novel β-helical fold and an ice-binding site. The interior of the β-helix contains a single row of bound Ca2+ ions down one side of the structure and a hydrophobic core down the opposite side. The ice-binding surface consists of parallel repetitive arrays of threonine and aspartic acid/asparagine residues located down the Ca2+-bound side of the structure. The model was tested and validated by site-directed mutagenesis. It explains the Ca2+-dependency of the region, as well its hyperactive antifreeze activity. This is the first bacterial AFP to be structurally characterized and is one of only five hyperactive AFPs identified to date.
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29
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Abstract
The glycine-rich antifreeze protein recently discovered in snow fleas exhibits strong freezing point depression activity without significantly changing the melting point of its solution (thermal hysteresis). BLAST searches did not detect any protein with significant similarity in current databases. Based on its circular dichroism spectrum, discontinuities in its tripeptide repeat pattern, and intramolecular disulfide bonding, a detailed theoretical model is proposed for the 6.5-kDa isoform. In the model, the 81-residue protein is organized into a bundle of six short polyproline type II helices connected (with one exception) by proline-containing turns. This structure forms two sheets of three parallel helices, oriented antiparallel to each other. The central helices are particularly rich in glycines that facilitate backbone carbonyl-amide hydrogen bonding to four neighboring helices. The modeled structure has similarities to polyglycine II proposed by Crick and Rich in 1955 and is a close match to the polyproline type II antiparallel sheet structure determined by Traub in 1969 for (Pro-Gly-Gly)(n). Whereas the latter two structures are formed by intermolecular interactions, the snow flea antifreeze is stabilized by intramolecular interactions between the helices facilitated by the regularly spaced turns and disulfide bonds. Like several other antifreeze proteins, this modeled protein is amphipathic with a putative hydrophobic ice-binding face.
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Affiliation(s)
- Feng-Hsu Lin
- Department of Biochemistry and the Protein Function Discovery Group, Queen's University, Kingston, Ontario K7L 3N6, Canada
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30
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Scotter AJ, Marshall CB, Graham LA, Gilbert JA, Garnham CP, Davies PL. The basis for hyperactivity of antifreeze proteins. Cryobiology 2006; 53:229-39. [PMID: 16887111 DOI: 10.1016/j.cryobiol.2006.06.006] [Citation(s) in RCA: 197] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2006] [Revised: 06/09/2006] [Accepted: 06/19/2006] [Indexed: 11/27/2022]
Abstract
Antifreeze proteins (AFPs) bind to the surface of ice crystals and lower the non-equilibrium freezing temperature of the icy solution below its melting point. We have recently reported the discovery of three novel hyperactive AFPs from a bacterium, a primitive insect and a fish, which, like two hyperactive AFPs previously recognized in beetles and moths, are considerably better at depressing the freezing point than most fish AFPs. When cooled below the non-equilibrium freezing temperature, ice crystals formed in the presence of any of five distinct, moderately active fish AFPs grow suddenly along the c-axis. Ice crystals formed in the presence of any of the five evolutionarily and structurally distinct hyperactive AFPs remain stable to lower temperatures, and then grow explosively in a direction normal to the c-axis when cooled below the freezing temperature. We argue that this one consistent distinction in the behaviour of these two classes of AFPs is the key to hyperactivity. Whereas both AFP classes bind irreversibly to ice, the hyperactive AFPs are better at preventing ice growth out of the basal planes.
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Affiliation(s)
- Andrew J Scotter
- Department of Biochemistry, Queen's University, Kingston, Ont., Canada K7L 3N6
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31
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Nishimiya Y, Kondo H, Yasui M, Sugimoto H, Noro N, Sato R, Suzuki M, Miura A, Tsuda S. Crystallization and preliminary X-ray crystallographic analysis of Ca2+-independent and Ca2+-dependent species of the type II antifreeze protein. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:538-41. [PMID: 16754975 PMCID: PMC2243089 DOI: 10.1107/s1744309106015570] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2006] [Accepted: 04/28/2006] [Indexed: 11/10/2022]
Abstract
Ca2+-independent and Ca2+-dependent species of the type II antifreeze protein (AFP) were both crystallized using the hanging-drop vapour-diffusion method. It appeared that the crystal of the Ca2+-independent species from Brachyosis rostratus belongs to space group P2(1)2(1)2(1), with unit-cell parameters a = 43.3, b = 48.4, c = 59.7 A, and diffraction data were collected to 1.34 A resolution. For the Ca2+-dependent type II AFP species from Hypomesus nipponensis, crystallization was carried out for its Ca2+-free and Ca2+-bound states. 1.25 A resolution data were collected from the crystal in the Ca(2+)-free state, which exhibited P3(1)21 (or P3(2)21) symmetry, with unit-cell parameters a = b = 66.0, c = 50.3 A. Data collection could be extended to 1.06 A resolution for the crystal in the Ca2+ -bound state, which appeared to be isomorphous to the crystal in the Ca2+-free state (unit-cell parameters a = b = 66.0, c = 49.8 A). These data will allow us to determine the high-resolution structures of the two species of type II AFP.
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Affiliation(s)
- Yoshiyuki Nishimiya
- Functional Protein Research Group, Research Institute of Genome-based Biofactory, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira, Sapporo 062-8517, Japan
| | - Hidemasa Kondo
- Functional Protein Research Group, Research Institute of Genome-based Biofactory, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira, Sapporo 062-8517, Japan
| | - Masanori Yasui
- Functional Protein Research Group, Research Institute of Genome-based Biofactory, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira, Sapporo 062-8517, Japan
- Division of Biological Sciences, Graduate School of Science, Hokkaido University, N8W5, Kita, Sapporo 060-0808, Japan
| | - Hiroshi Sugimoto
- Biometal Science Laboratory, Riken SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Natsuko Noro
- Functional Protein Research Group, Research Institute of Genome-based Biofactory, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira, Sapporo 062-8517, Japan
| | - Ryoko Sato
- Functional Protein Research Group, Research Institute of Genome-based Biofactory, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira, Sapporo 062-8517, Japan
| | - Mamoru Suzuki
- Insititute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Ai Miura
- Functional Protein Research Group, Research Institute of Genome-based Biofactory, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira, Sapporo 062-8517, Japan
| | - Sakae Tsuda
- Functional Protein Research Group, Research Institute of Genome-based Biofactory, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira, Sapporo 062-8517, Japan
- Division of Biological Sciences, Graduate School of Science, Hokkaido University, N8W5, Kita, Sapporo 060-0808, Japan
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32
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Affiliation(s)
- Ninad Prabhu
- Johnson Research Foundation, Dept. of Biochemistry and Biophysics, University of Pennsylvania
| | - Kim Sharp
- Johnson Research Foundation, Dept. of Biochemistry and Biophysics, University of Pennsylvania
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33
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Evans RP, Fletcher GL. Type I antifreeze proteins expressed in snailfish skin are identical to their plasma counterparts. FEBS J 2005; 272:5327-36. [PMID: 16218962 DOI: 10.1111/j.1742-4658.2005.04929.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Type I antifreeze proteins (AFPs) are usually small, Ala-rich alpha-helical polypeptides found in right-eyed flounders and certain species of sculpin. These proteins are divided into two distinct subclasses, liver type and skin type, which are encoded by separate gene families. Blood plasma from Atlantic (Liparis atlanticus) and dusky (Liparis gibbus) snailfish contain type I AFPs that are significantly larger than all previously described type I AFPs. In this study, full-length cDNA clones that encode snailfish type I AFPs expressed in skin tissues were generated using a combination of library screening and PCR-based methods. The skin clones, which lack both signal and pro-sequences, produce proteins that are identical to circulating plasma AFPs. Although all fish examined consistently express antifreeze mRNA in skin tissue, there is extreme individual variation in liver expression - an unusual phenomenon that has never been reported previously. Furthermore, genomic Southern blot analysis revealed that snailfish AFPs are products of multigene families that consist of up to 10 gene copies per genome. The 113-residue snailfish AFPs do not contain any obvious amino acid repeats or continuous hydrophobic face which typify the structure of most other type I AFPs. These structural differences might have implications for their ice-crystal binding properties. These results are the first to demonstrate a dual liver/skin role of identical type I AFP expression which may represent an evolutionary intermediate prior to divergence into distinct gene families.
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Affiliation(s)
- Robert P Evans
- Ocean Sciences Centre, Memorial University of Newfoundland, St. John's, Newfoundland, Canada.
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34
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Kristiansen E, Zachariassen KE. The mechanism by which fish antifreeze proteins cause thermal hysteresis. Cryobiology 2005; 51:262-80. [PMID: 16140290 DOI: 10.1016/j.cryobiol.2005.07.007] [Citation(s) in RCA: 124] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2004] [Revised: 08/19/2004] [Accepted: 07/18/2005] [Indexed: 10/25/2022]
Abstract
Antifreeze proteins are characterised by their ability to prevent ice from growing upon cooling below the bulk melting point. This displacement of the freezing temperature of ice is limited and at a sufficiently low temperature a rapid ice growth takes place. The separation of the melting and freezing temperature is usually referred to as thermal hysteresis, and the temperature of ice growth is referred to as the hysteresis freezing point. The hysteresis is supposed to be the result of an adsorption of antifreeze proteins to the crystal surface. This causes the ice to grow as convex surface regions between adjacent adsorbed antifreeze proteins, thus lowering the temperature at which the crystal can visibly expand. The model requires that the antifreeze proteins are irreversibly adsorbed onto the ice surface within the hysteresis gap. This presupposition is apparently in conflict with several characteristic features of the phenomenon; the absence of superheating of ice in the presence of antifreeze proteins, the dependence of the hysteresis activity on the concentration of antifreeze proteins and the different capacities of different types of antifreeze proteins to cause thermal hysteresis at equimolar concentrations. In addition, there are structural obstacles that apparently would preclude irreversible adsorption of the antifreeze proteins to the ice surface; the bond strength necessary for irreversible adsorption and the absence of a clearly defined surface to which the antifreeze proteins may adsorb. This article deals with these apparent conflicts between the prevailing theory and the empirical observations. We first review the mechanism of thermal hysteresis with some modifications: we explain the hysteresis as a result of vapour pressure equilibrium between the ice surface and the ambient fluid fraction within the hysteresis gap due to a pressure build-up within the convex growth zones, and the ice growth as the result of an ice surface nucleation event at the hysteresis freezing point. We then go on to summarise the empirical data to show that the dependence of the hysteresis on the concentration of antifreeze proteins arises from an equilibrium exchange of antifreeze proteins between ice and solution at the melting point. This reversible association between antifreeze proteins and the ice is followed by an irreversible adsorption of the antifreeze proteins onto a newly formed crystal plane when the temperature is lowered below the melting point. The formation of the crystal plane is due to a solidification of the interfacial region, and the necessary bond strength is provided by the protein "freezing" to the surface. In essence: the antifreeze proteins are "melted off" the ice at the bulk melting point and "freeze" to the ice as the temperature is reduced to subfreezing temperatures. We explain the different hysteresis activities caused by different types of antifreeze proteins at equimolar concentrations as a consequence of their solubility features during the phase of reversible association between the proteins and the ice, i.e., at the melting point; a low water solubility results in a large fraction of the proteins being associated with the ice at the melting point. This leads to a greater density of irreversibly adsorbed antifreeze proteins at the ice surface when the temperature drops, and thus to a greater hysteresis activity. Reference is also made to observations on insect antifreeze proteins to emphasise the general validity of this approach.
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Affiliation(s)
- Erlend Kristiansen
- Department of Biology, Realfagsbygget, Norwegian University of Science and Technology, N-7491 Trondheim, Norway.
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35
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36
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Baardsnes J, Davies PL. Contribution of hydrophobic residues to ice binding by fish type III antifreeze protein. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1601:49-54. [PMID: 12429502 DOI: 10.1016/s1570-9639(02)00431-4] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Type III antifreeze protein (AFP) is a 7-kDa globular protein with a flat ice-binding face centered on Ala 16. Neighboring hydrophilic residues Gln 9, Asn 14, Thr 15, Thr 18 and Gln 44 have been implicated by site-directed mutagenesis in binding to ice. These residues have the potential to form hydrogen bonds with ice, but the tight packing of side chains on the ice-binding face limits the number and strength of possible hydrogen bond interactions. Recent work with alpha-helical AFPs has emphasized the hydrophobicity of their ice-binding sites and suggests that hydrophobic interactions are important for antifreeze activity. To investigate the contribution of hydrophobic interactions between type III AFP and ice, Leu, Ile and Val residues on the rim of the ice-binding face were changed to alanine. Mutant AFPs with single alanine substitutions, L19A, V20A, and V41A, showed a 20% loss in activity. Doubly substituted mutants, L19A/V41A and L10A/I13A, had less than 50% of the activity of the wild type. Thus, side chain substitutions that leave a cavity or undercut the contact surface are almost as deleterious to antifreeze activity as those that lengthen the side chain. These mutations emphasize the importance of maintaining a specific surface contour on the ice-binding face for docking to ice.
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Affiliation(s)
- Jason Baardsnes
- Department of Biochemistry, Queen's University, Stuart St., Kingston, ON, Canada K7L 3N6
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Marshall CB, Daley ME, Graham LA, Sykes BD, Davies PL. Identification of the ice-binding face of antifreeze protein from Tenebrio molitor. FEBS Lett 2002; 529:261-7. [PMID: 12372611 DOI: 10.1016/s0014-5793(02)03355-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The beetle Tenebrio molitor produces several isoforms of a highly disulfide-bonded beta-helical antifreeze protein with one surface comprised of an array of Thr residues that putatively interacts with ice. In order to use mutagenesis to identify the ice-binding face, we have selected an isoform that folds well and is tolerant of amino acid substitution, and have developed a heating test to monitor refolding. Three different types of steric mutations made to the putative ice-binding face reduced thermal hysteresis activity substantially while a steric mutation on an orthogonal surface had little effect. NMR spectra indicated that all mutations affected protein folding to a similar degree and demonstrated that most of the protein folded well. The large reductions in activity associated with steric mutations in the Thr array strongly suggest that this face of the protein is responsible for ice binding.
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Abstract
Plants are able to survive prolonged exposure to sub-zero temperatures; this ability is enhanced by pre-exposure to low, but above-zero temperatures. This process, known as cold acclimation, is briefly reviewed from the perception of cold, through transduction of the low-temperature signal to functional analysis of cold-induced gene products. The stresses that freezing of apoplastic water imposes on plant cells is considered and what is understood about the mechanisms that plants use to combat those stresses discussed, with particular emphasis on the role of the extracellular matrix.
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Affiliation(s)
- Maggie Smallwood
- Centre for Novel Agricultural Products, Department of Biology, PO Box 373, University of York, York YO1 5YW, UK.
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39
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Davies PL, Baardsnes J, Kuiper MJ, Walker VK. Structure and function of antifreeze proteins. Philos Trans R Soc Lond B Biol Sci 2002; 357:927-35. [PMID: 12171656 PMCID: PMC1692999 DOI: 10.1098/rstb.2002.1081] [Citation(s) in RCA: 208] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
High-resolution three-dimensional structures are now available for four of seven non-homologous fish and insect antifreeze proteins (AFPs). For each of these structures, the ice-binding site of the AFP has been defined by site-directed mutagenesis, and ice etching has indicated that the ice surface is bound by the AFP. A comparison of these extremely diverse ice-binding proteins shows that they have the following attributes in common. The binding sites are relatively flat and engage a substantial proportion of the protein's surface area in ice binding. They are also somewhat hydrophobic -- more so than that portion of the protein exposed to the solvent. Surface-surface complementarity appears to be the key to tight binding in which the contribution of hydrogen bonding seems to be secondary to van der Waals contacts.
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Affiliation(s)
- Peter L Davies
- Department of Biochemistry, Queen's University, Kingston, Ontario, Canada K7L 3N6.
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40
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Fairley K, Westman BJ, Pham LH, Haymet ADJ, Harding MM, Mackay JP. Type I shorthorn sculpin antifreeze protein: recombinant synthesis, solution conformation, and ice growth inhibition studies. J Biol Chem 2002; 277:24073-80. [PMID: 11940576 DOI: 10.1074/jbc.m200307200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
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 15N-labeled recombinant polypeptide, show that the polypeptides are alpha-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 degrees 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.
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Affiliation(s)
- Kayesh Fairley
- School of Chemistry and the Department of Biochemistry, University of Sydney, New South Wales 2006, Australia
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41
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Leinala EK, Davies PL, Jia Z. Crystal structure of beta-helical antifreeze protein points to a general ice binding model. Structure 2002; 10:619-27. [PMID: 12015145 DOI: 10.1016/s0969-2126(02)00745-1] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
Reported here is the 2.3 A resolution crystal structure of spruce budworm (Choristoneura fumiferana) antifreeze protein (CfAFP), solved by single anomalous scattering. The structure reveals an extremely regular left-handed beta-helical platform consisting of 15-amino acid loops with a repetitive Thr-X-Thr motif displayed on one of the helix's three faces. This motif results in a two-dimensional array of threonine residues in an identical orientation to those in the nonhomologous, right-handed beta-helical beetle AFP from Tenebrio molitor (TmAFP). The CfAFP structure led us to reevaluate our ice binding model, and the analysis of three possible modes of docking gives rise to a binding mechanism based on surface complementarity. This general mechanism is applicable to both fish and insect AFPs.
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Affiliation(s)
- Eeva K Leinala
- Department of Biochemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
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