Submit to Biomolecules Review for Biomolecules Propose a Special Issue

Journal Browser

► Journal Browser

Antifreeze Protein: New Insight from Different Approaches

Special Issue Editors
Special Issue Information
Keywords
Published Papers

A special issue of Biomolecules (ISSN 2218-273X).

Deadline for manuscript submissions: closed (2 July 2019) | Viewed by 52117

Share This Special Issue

Special Issue Editors

Prof. Dr. Hidemasa Kondo

E-Mail Website
Guest Editor

Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)2-17-2-1 Tsukisamu-Higashi, Toyohira, Sapporo 062-8517, Japan
Interests: structural biology; industrial protein; antifreeze protein; industrial enzyme

Prof. Dr. Sakae Tsuda

E-Mail Website
Guest Editor

Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)2-17-2-1 Tsukisamu-Higashi, Toyohira, Sapporo 062-8517, Japan
Interests: antifreeze proteins (fish AFPI~III, fish AFGP, fungal beta-helical AFPs)

Special Issue Information

Dear Colleagues,

Antifreeze proteins (AFPs) or ice-binding proteins (IBPs) are polypeptides discovered from vertebrates, plants, fungi, and bacteria that survive in cold environments. Increasing evidence has shown that AFPs can bind to a set of waters constructing ice crystals to inhibit their growth and recrystallization at higher subzero temperatures. AFPs are also known to interact with membranes to elongate the life time of various cells near 0°C. Since these functions are related with various research fields and that is worth to be considered intensively, this Special Issue focuses on both basics and technological insights of AFPs. The issue welcomes articles on this unique category and its many different approaches, which may include AFP, IBP, antifreeze glycoprotein (AFGP), ice-binding, ice-plane affinity, thermal hysteresis, crystal growth, ice recrystallization, ice nucleation, AFP-mimetics, tandem repeats, structure, dynamics, water, hydration, molecular dynamics (MD) simulation, chemical synthesis, mass-preparation, evolution, lateral gene transfer, and cell and tissue preservation.

Prof. Dr. Sakae Tsuda
Prof. Dr. Hidemasa Kondo
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biomolecules is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

AFP
IBP
antifreeze glycoprotein (AFGP)
ice-binding
ice-plane affinity
thermal hysteresis
crystal growth
ice recrystallization
ice nucleation
AFP-mimetics
tandem repeats
structure
dynamics
water
hydration
molecular dynamics (MD) simulation
chemical synthesis
mass-preparation
evolution
lateral gene transfer
and cell and tissue preservation

Published Papers (11 papers)

Download All Papers

Research

Jump to: Review

15 pages, 2296 KiB

Open AccessArticle

An Ice-Binding Protein from an Antarctic Ascomycete Is Fine-Tuned to Bind to Specific Water Molecules Located in the Ice Prism Planes

by Akari Yamauchi, Tatsuya Arai, Hidemasa Kondo, Yuji C. Sasaki and Sakae Tsuda

Biomolecules 2020, 10(5), 759; https://doi.org/10.3390/biom10050759 - 13 May 2020

Cited by 7 | Viewed by 3408

Abstract

Many microbes that survive in cold environments are known to secrete ice-binding proteins (IBPs). The structure–function relationship of these proteins remains unclear. A microbial IBP denoted AnpIBP was recently isolated from a cold-adapted fungus, Antarctomyces psychrotrophicus. The present study identified an orbital illumination (prism ring) on a globular single ice crystal when soaked in a solution of fluorescent AnpIBP, suggesting that AnpIBP binds to specific water molecules located in the ice prism planes. In order to examine this unique ice-binding mechanism, we carried out X-ray structural analysis and mutational experiments. It appeared that AnpIBP is made of 6-ladder β-helices with a triangular cross section that accompanies an “ice-like” water network on the ice-binding site. The network, however, does not exist in a defective mutant. AnpIBP has a row of four unique hollows on the IBS, where the distance between the hollows (14.7 Å) is complementary to the oxygen atom spacing of the prism ring. These results suggest the structure of AnpIBP is fine-tuned to merge with the ice–water interface of an ice crystal through its polygonal water network and is then bound to a specific set of water molecules constructing the prism ring to effectively halt the growth of ice. Full article

(This article belongs to the Special Issue Antifreeze Protein: New Insight from Different Approaches)

► Show Figures

Graphical abstract

14 pages, 2157 KiB

Open AccessFeature PaperArticle

Fish-Derived Antifreeze Proteins and Antifreeze Glycoprotein Exhibit a Different Ice-Binding Property with Increasing Concentration

by Sakae Tsuda, Akari Yamauchi, N. M.-Mofiz Uddin Khan, Tatsuya Arai, Sheikh Mahatabuddin, Ai Miura and Hidemasa Kondo

Biomolecules 2020, 10(3), 423; https://doi.org/10.3390/biom10030423 - 09 Mar 2020

Cited by 18 | Viewed by 5288

Abstract

The concentration of a protein is highly related to its biochemical properties, and is a key determinant for its biotechnological applications. Antifreeze proteins (AFPs) and antifreeze glycoproteins (AFGPs) are structurally diverse macromolecules that are capable of binding to embryonic ice crystals below 0 °C, making them useful as protectants of ice-block formation. In this study, we examined the maximal solubility of native AFP I–III and AFGP with distilled water, and evaluated concentration dependence of their ice-binding property. Approximately 400 mg/mL (AFP I), 200 mg/mL (AFP II), 100 mg/mL (AFP III), and >1800 mg/mL (AFGP) of the maximal solubility were estimated, and among them AFGP’s solubility is much higher compared with that of ordinary proteins, such as serum albumin (~500 mg/mL). The samples also exhibited unexpectedly high thermal hysteresis values (2–3 °C) at 50–200 mg/mL. Furthermore, the analysis of fluorescence-based ice plane affinity showed that AFP II binds to multiple ice planes in a concentration-dependent manner, for which an oligomerization mechanism was hypothesized. The difference of concentration dependence between AFPs and AFGPs may provide a new clue to help us understand the ice-binding function of these proteins. Full article

(This article belongs to the Special Issue Antifreeze Protein: New Insight from Different Approaches)

► Show Figures

Graphical abstract

16 pages, 3656 KiB

Open AccessArticle

Ice Nucleation Properties of Ice-binding Proteins from Snow Fleas

by Akalabya Bissoyi, Naama Reicher, Michael Chasnitsky, Sivan Arad, Thomas Koop, Yinon Rudich and Ido Braslavsky

Biomolecules 2019, 9(10), 532; https://doi.org/10.3390/biom9100532 - 25 Sep 2019

Cited by 14 | Viewed by 5103

Abstract

Ice-binding proteins (IBPs) are found in many organisms, such as fish and hexapods, plants, and bacteria that need to cope with low temperatures. Ice nucleation and thermal hysteresis are two attributes of IBPs. While ice nucleation is promoted by large proteins, known as ice nucleating proteins, the smaller IBPs, referred to as antifreeze proteins (AFPs), inhibit the growth of ice crystals by up to several degrees below the melting point, resulting in a thermal hysteresis (TH) gap between melting and ice growth. Recently, we showed that the nucleation capacity of two types of IBPs corresponds to their size, in agreement with classical nucleation theory. Here, we expand this finding to additional IBPs that we isolated from snow fleas (the arthropod Collembola), collected in northern Israel. Chemical analyses using circular dichroism and Fourier-transform infrared spectroscopy data suggest that these IBPs have a similar structure to a previously reported snow flea antifreeze protein. Further experiments reveal that the ice-shell purified proteins have hyperactive antifreeze properties, as determined by nanoliter osmometry, and also exhibit low ice-nucleation activity in accordance with their size. Full article

(This article belongs to the Special Issue Antifreeze Protein: New Insight from Different Approaches)

► Show Figures

Figure 1

8 pages, 1730 KiB

Open AccessEditor’s ChoiceCommunication

The Impact of Salts on the Ice Recrystallization Inhibition Activity of Antifreeze (Glyco)Proteins

by Romà Surís-Valls and Ilja K. Voets

Biomolecules 2019, 9(8), 347; https://doi.org/10.3390/biom9080347 - 06 Aug 2019

Cited by 18 | Viewed by 4582

Abstract

Antifreeze (glyco)proteins (AF(G)Ps) have received increasing attention as potential cryopreservation agents since their discovery in the 1970s. While cryopreservation strategies for specific cells (such as red blood cells) are successful and widely implemented, preservation of other cell types, tissues and whole organs remains challenging. This is due to the multifactorial nature of the freeze-thaw damage, the complexity of preserving biological matter and the (country-to-country) variability of the employed procedures and regulations. AF(G)Ps are well-known for their ability to modulate ice crystal growth morphology and ice recrystallization inhibition (IRI), both of which are considered key contributors to freeze-thaw damage. To date, however, the impact of AF(G)Ps on cell survival remains at best partially understood as conflicting results on the benefits or disadvantages of including AF(G)P in cryopreservation strategies remain unelucidated. We hypothesize that variability in the additives in the cryopreservation media contributes to the observed discrepancies. To critically examine this idea, we monitored the inhibition of ice recrystallization by AF(G)P in the presence of various salts using a quantitative analysis of optical microscopy images via the Lifshitz-Slyozov-Wagner (LSW) theory for Oswald ripening. We found that the addition of salts, which are used in culture and cryopreservation media, enhances the IRI activity of AF(G)Ps, and that the magnitude of the enhancement was in line with the Hofmeister series. The size of ice crystals grown in AFGP_1–5 and type III AFP samples containing chloride, phosphate and citrate ions were statistically smaller after 90 min of incubation than crystals grown in the absence of these salts. The ice recrystallization rates (k_d) of AFGP_1–5 and type III AFP samples prepared at a fixed overall ionic strength of 100 mM progressively decreased following the Hofmeister series for anions. Our results demonstrate that the performance of AF(G)Ps is significantly influenced by additives present in common cryopreservation media. It is thus important to conduct excipient compatibility experiments to identify potential incompatibilities between additives and AF(G)Ps in cryopreservation formulations. Full article

(This article belongs to the Special Issue Antifreeze Protein: New Insight from Different Approaches)

► Show Figures

Figure 1

22 pages, 4049 KiB

Open AccessArticle

The Ensemble of Conformations of Antifreeze Glycoproteins (AFGP8): A Study Using Nuclear Magnetic Resonance Spectroscopy

by Cheenou Her, Yin Yeh and Viswanathan V. Krishnan

Biomolecules 2019, 9(6), 235; https://doi.org/10.3390/biom9060235 - 17 Jun 2019

Cited by 9 | Viewed by 3824

Abstract

The primary sequence of antifreeze glycoproteins (AFGPs) is highly degenerate, consisting of multiple repeats of the same tripeptide, Ala–Ala–Thr*, in which Thr* is a glycosylated threonine with the disaccharide beta-d-galactosyl-(1,3)-alpha-N-acetyl-d-galactosamine. AFGPs seem to function as intrinsically disordered proteins, presenting challenges in determining their native structure. In this work, a different approach was used to elucidate the three-dimensional structure of AFGP8 from the Arctic cod Boreogadus saida and the Antarctic notothenioid Trematomus borchgrevinki. Dimethyl sulfoxide (DMSO), a non-native solvent, was used to make AFGP8 less dynamic in solution. Interestingly, DMSO induced a non-native structure, which could be determined via nuclear magnetic resonance (NMR) spectroscopy. The overall three-dimensional structures of the two AFGP8s from two different natural sources were different from a random coil ensemble, but their “compactness” was very similar, as deduced from NMR measurements. In addition to their similar compactness, the conserved motifs, Ala–Thr*–Pro–Ala and Ala–Thr*–Ala–Ala, present in both AFGP8s, seemed to have very similar three-dimensional structures, leading to a refined definition of local structural motifs. These local structural motifs allowed AFGPs to be considered functioning as effectors, making a transition from disordered to ordered upon binding to the ice surface. In addition, AFGPs could act as dynamic linkers, whereby a short segment folds into a structural motif, while the rest of the AFGPs could still be disordered, thus simultaneously interacting with bulk water molecules and the ice surface, preventing ice crystal growth. Full article

(This article belongs to the Special Issue Antifreeze Protein: New Insight from Different Approaches)

► Show Figures

Figure 1

12 pages, 5495 KiB

Open AccessFeature PaperArticle

Laboratory-Scale Isolation of Insect Antifreeze Protein for Cryobiology

by Heather E. Tomalty, Laurie A. Graham, Robert Eves, Audrey K. Gruneberg and Peter L. Davies

Biomolecules 2019, 9(5), 180; https://doi.org/10.3390/biom9050180 - 09 May 2019

Cited by 23 | Viewed by 5391

Abstract

Micromolar concentrations of hyperactive antifreeze proteins (AFPs) from insects can prevent aqueous solutions from freezing down to at least −6 °C. To explore cryopreservation of cells, tissues and organs at these temperatures without ice formation, we have developed a protocol to reliably produce ultrapure Tenebrio molitor AFP from cold-acclimated beetle larvae reared in the laboratory. The AFP was prepared from crude larval homogenates through five cycles of rotary ice-affinity purification, which can be completed in one day. Recovery of the AFP at each step was >90% and no impurities were detected in the final product. The AFP is a mixture of isoforms that are more active in combination than any one single component. Toxicity testing of the purified AFP in cell culture showed no inhibition of cell growth. The production process can easily be scaled up to industrial levels, and the AFP used in cryobiology applications was recovered for reuse in good yield and with full activity. Full article

(This article belongs to the Special Issue Antifreeze Protein: New Insight from Different Approaches)

► Show Figures

Graphical abstract

14 pages, 2555 KiB

Open AccessArticle

Calcium-Binding Generates the Semi-Clathrate Waters on a Type II Antifreeze Protein to Adsorb onto an Ice Crystal Surface

by Tatsuya Arai, Yoshiyuki Nishimiya, Yasushi Ohyama, Hidemasa Kondo and Sakae Tsuda

Biomolecules 2019, 9(5), 162; https://doi.org/10.3390/biom9050162 - 27 Apr 2019

Cited by 15 | Viewed by 3454

Abstract

Hydration is crucial for a function and a ligand recognition of a protein. The hydration shell constructed on an antifreeze protein (AFP) contains many organized waters, through which AFP is thought to bind to specific ice crystal planes. For a Ca²⁺-dependent species of AFP, however, it has not been clarified how 1 mol of Ca²⁺-binding is related with the hydration and the ice-binding ability. Here we determined the X-ray crystal structure of a Ca²⁺-dependent AFP (jsAFP) from Japanese smelt, Hypomesus nipponensis, in both Ca²⁺-bound and -free states. Their overall structures were closely similar (Root mean square deviation (RMSD) of Cα = 0.31 Å), while they exhibited a significant difference around their Ca²⁺-binding site. Firstly, the side-chains of four of the five Ca²⁺-binding residues (Q92, D94 E99, D113, and D114) were oriented to be suitable for ice binding only in the Ca²⁺-bound state. Second, a Ca²⁺-binding loop consisting of a segment D94–E99 becomes less flexible by the Ca²⁺-binding. Third, the Ca²⁺-binding induces a generation of ice-like clathrate waters around the Ca²⁺-binding site, which show a perfect position-match to the waters constructing the first prism plane of a single ice crystal. These results suggest that generation of ice-like clathrate waters induced by Ca²⁺-binding enables the ice-binding of this protein. Full article

(This article belongs to the Special Issue Antifreeze Protein: New Insight from Different Approaches)

► Show Figures

Graphical abstract

13 pages, 5702 KiB

Open AccessArticle

Freeze Tolerance in Sculpins (Pisces; Cottoidea) Inhabiting North Pacific and Arctic Oceans: Antifreeze Activity and Gene Sequences of the Antifreeze Protein

by Aya Yamazaki, Yoshiyuki Nishimiya, Sakae Tsuda, Koji Togashi and Hiroyuki Munehara

Biomolecules 2019, 9(4), 139; https://doi.org/10.3390/biom9040139 - 06 Apr 2019

Cited by 6 | Viewed by 4254

Abstract

Many marine species inhabiting icy seawater produce antifreeze proteins (AFPs) to prevent their body fluids from freezing. The sculpin species of the superfamily Cottoidea are widely found from the Arctic to southern hemisphere, some of which are known to express AFP. Here we clarified DNA sequence encoding type I AFP for 3 species of 2 families (Cottidae and Agonidae) belonging to Cottoidea. We also examined antifreeze activity for 3 families and 32 species of Cottoidea (Cottidae, Agonidae, and Rhamphocottidae). These fishes were collected in 2013–2015 from the Arctic Ocean, Alaska, Japan. We could identify 8 distinct DNA sequences exhibiting a high similarity to those reported for Myoxocephalus species, suggesting that Cottidae and Agonidae share the same DNA sequence encoding type I AFP. Among the 3 families, Rhamphocottidae that experience a warm current did not show antifreeze activity. The species inhabiting the Arctic Ocean and Northern Japan that often covered with ice floe showed high activity, while those inhabiting Alaska, Southern Japan with a warm current showed low/no activity. These results suggest that Cottoidea acquires type I AFP gene before dividing into Cottidae and Agonidae, and have adapted to each location with optimal antifreeze activity level. Full article

(This article belongs to the Special Issue Antifreeze Protein: New Insight from Different Approaches)

► Show Figures

Figure 1

9 pages, 889 KiB

Open AccessArticle

Effect of Antifreeze Glycoproteins on Organoid Survival during and after Hypothermic Storage

by Guizela Huelsz-Prince, Arthur L. DeVries, Huib J. Bakker, Jeroen S. van Zon and Konrad Meister

Biomolecules 2019, 9(3), 110; https://doi.org/10.3390/biom9030110 - 19 Mar 2019

Cited by 12 | Viewed by 4651

Abstract

We study the effect of antifreeze glycoproteins (AFGPs) on the survival of organoids under hypothermic conditions. We find that the survival of organoids in cold conditions depends on their developmental stage. Mature organoids die within 24 h when being stored at 4 °C, while cystic organoids can survive up to 48 h. We find that in the presence of AFGPs, the organoid survival is prolonged up to 72 h, irrespective of their developmental stage. Fluorescence microscopy experiments reveal that the AFGPs predominately localize at the cell surface and cover the cell membranes. Our findings support a mechanism in which the positive effect of AFGPs on cell survival during hypothermic storage involves the direct interaction of AFGPs with the cell membrane. Our research highlights organoids as an attractive multicellular model system for studying the action of AFGPs that bridges the gap between single-cell and whole-organ studies. Full article

(This article belongs to the Special Issue Antifreeze Protein: New Insight from Different Approaches)

► Show Figures

Graphical abstract

12 pages, 5257 KiB

Open AccessArticle

Effects of Winter Flounder Antifreeze Protein on the Growth of Ice Particles in an Ice Slurry Flow in Mini-Channels

by Yuki Takeshita, Tomonori Waku, Peter W. Wilson and Yoshimichi Hagiwara

Biomolecules 2019, 9(2), 70; https://doi.org/10.3390/biom9020070 - 18 Feb 2019

Cited by 4 | Viewed by 3470

Abstract

The control of ice growth in ice slurry is important for many fields, including (a) the cooling of the brain during cardiac arrest, (b) the storage and transportation of fresh fish and fruits, and (c) the development of distributed air-conditioning systems. One of the promising methods for the control is to use a substance such as antifreeze protein. We have observed and report here growth states of ice particles in both quiescent and flowing aqueous solutions of winter flounder antifreeze proteins in mini-channels with a microscope. We also measured ice growth rates. Our aim was to improve the levels of ice growth inhibition by subjecting the antifreeze protein solution both to preheating and to concentrating by ultrafiltration. We have found that the ice growth inhibition by the antifreeze protein decreased in flowing solutions compared with that in quiescent solutions. In addition, unlike unidirectional freezing experiments, the preheating of the antifreeze protein solution reduced the ice growth inhibition properties. This is because the direction of flow, containing HPLC6 and its aggregates, to the ice particle surfaces can change as the ice particle grows, and thus the probability of interaction between HPLC6 and ice surfaces does not increase. In contrast to this, ultrafiltration after preheating the solution improved the ice growth inhibition. This may be due to the interaction between ice surfaces and many aggregates in the concentrates. Full article

(This article belongs to the Special Issue Antifreeze Protein: New Insight from Different Approaches)

► Show Figures

Figure 1

Review

Jump to: Research

12 pages, 890 KiB

Open AccessEditor’s ChoiceReview

The Use of Antifreeze Proteins in the Cryopreservation of Gametes and Embryos

by Vanesa Robles, David G. Valcarce and Marta F. Riesco

Biomolecules 2019, 9(5), 181; https://doi.org/10.3390/biom9050181 - 09 May 2019

Cited by 61 | Viewed by 6573

Abstract

The cryopreservation of gametes and embryos is a technique widely used in reproductive biology. This technology helps in the reproductive management of domesticated animals, and it is an important tool for gene banking and for human-assisted reproductive technologies. Antifreeze proteins are naturally present in several organisms exposed to subzero temperatures. The ability for these proteins to inhibit ice recrystallization together with their ability to interact with biological membranes makes them interesting molecules to be used in cryopreservation protocols. This mini-review provides a general overview about the use of antifreeze proteins to improve the short and long term storage of gametes and embryos. Full article

(This article belongs to the Special Issue Antifreeze Protein: New Insight from Different Approaches)

► Show Figures