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Kimijima J, Inagawa A, Miyagawa A, Nasuno E, Uehara N. Probing the interaction between biomolecules under sub-zero temperature conditions by electrophoresis in ice grain boundaries. Anal Chim Acta 2024; 1311:342713. [PMID: 38816152 DOI: 10.1016/j.aca.2024.342713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/06/2024] [Accepted: 05/09/2024] [Indexed: 06/01/2024]
Abstract
BACKGROUND Psychrophiles can survive under cryogenic conditions because of various biomolecules. These molecules interact with cells, ice crystals, and lipid bilayers to enhance their functionality. Previous studies typically measured these interactions by thawing frozen samples and conducting biological assays at room temperature; however, studying these interactions under cryogenic conditions is crucial. This is because these biomolecules can function at lower temperatures. Therefore, a platform for measuring chemical interactions under sub-zero temperature conditions must be established. RESULTS The chemical interactions between biomolecules under sub-zero temperature conditions were evaluated within ice grain boundaries with a channel-like structure, which circumvents the need for thawing. An aqueous solution of sucrose was frozen within a microfluidic channel, facilitating the formation of freeze-concentrated solutions (FCSs) that functioned as size-tunable electrophoretic fields. Avidin proteins or single-stranded DNA (ssDNA) were introduced into the FCS in advance. Probe micro/nanospheres whose surfaces were modified with molecules complementary to the target analytes were introduced into the FCS. If the targets have functionalities under sub-zero temperature conditions, they interact with complementary molecules. The chemical interactions between the target molecules and nanospheres led to the aggregation of the particles. The size tunability of the diameter of the FCS channels enabled the recognition of aggregation levels, which is indicative of interaction reactivity. The avidin-biotin interaction and ssDNA hybridization served as models for chemical interactions, demonstrating interactivity under sub-zero temperature conditions. The results presented herein suggest the potential for in situ measurement of biochemical assays in the frozen state, elucidating the functionality of bio-related macromolecules at or slightly below 0 °C. SIGNIFICANCE This is the first methodology to evaluate chemical interactions under sub-zero temperature conditions without employing the freeze-and-thaw process. This method has the advantage of revealing the chemical interactions only at low temperatures. Therefore, it can be used to screen and evaluate the functionality of cryo-related biomolecules, including cold-shock and antifreeze proteins.
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Affiliation(s)
- Junya Kimijima
- School of Engineering, Utsunomiya University, 7-1-2, Yoto, Utsunomiya, Tochigi, 321-8585, Japan
| | - Arinori Inagawa
- School of Engineering, Utsunomiya University, 7-1-2, Yoto, Utsunomiya, Tochigi, 321-8585, Japan.
| | - Akihisa Miyagawa
- Department of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8571, Japan
| | - Eri Nasuno
- School of Engineering, Utsunomiya University, 7-1-2, Yoto, Utsunomiya, Tochigi, 321-8585, Japan
| | - Nobuo Uehara
- School of Engineering, Utsunomiya University, 7-1-2, Yoto, Utsunomiya, Tochigi, 321-8585, Japan
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2
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Thosar AU, Cai Y, Marks SM, Vicars Z, Choi J, Pallath A, Patel AJ. On the engulfment of antifreeze proteins by ice. Proc Natl Acad Sci U S A 2024; 121:e2320205121. [PMID: 38833468 PMCID: PMC11181090 DOI: 10.1073/pnas.2320205121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 04/16/2024] [Indexed: 06/06/2024] Open
Abstract
Antifreeze proteins (AFPs) are remarkable biomolecules that suppress ice formation at trace concentrations. To inhibit ice growth, AFPs must not only bind to ice crystals, but also resist engulfment by ice. The highest supercooling, [Formula: see text], for which AFPs are able to resist engulfment is widely believed to scale as the inverse of the separation, [Formula: see text], between bound AFPs, whereas its dependence on the molecular characteristics of the AFP remains poorly understood. By using specialized molecular simulations and interfacial thermodynamics, here, we show that in contrast with conventional wisdom, [Formula: see text] scales as [Formula: see text] and not as [Formula: see text]. We further show that [Formula: see text] is proportional to AFP size and that diverse naturally occurring AFPs are optimal at resisting engulfment by ice. By facilitating the development of AFP structure-function relationships, we hope that our findings will pave the way for the rational design of AFPs.
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Affiliation(s)
- Aniket U. Thosar
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA19104
| | - Yusheng Cai
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA19104
| | - Sean M. Marks
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA19104
| | - Zachariah Vicars
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA19104
| | - Jeongmoon Choi
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA19104
| | - Akash Pallath
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA19104
| | - Amish J. Patel
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA19104
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3
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Rahman R, Bheemasetti TV, Govil T, Sani R. Psychrophiles to control ice-water phase changes in frost-susceptible soils. Sci Rep 2024; 14:477. [PMID: 38177218 PMCID: PMC10766620 DOI: 10.1038/s41598-023-51060-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 12/29/2023] [Indexed: 01/06/2024] Open
Abstract
The phase changes of soil water or porous media have a crucial influence on the performance of natural and man-made infrastructures in cold regions. While various methods have been explored to address the impacts of frost-action arising from these phase changes, conventional approaches often rely on chemicals, mechanical techniques, and the reuse of waste materials, which often exhibit certain limitations and environmental concerns. In contrast, certain organisms produce ice-binding proteins (IBPs) or antifreeze proteins (AFPs) to adapt to low temperatures, which can inhibit ice crystal growth by lowering the freezing point and preventing ice crystallization without the need for external intervention. This study explores the potential of three psychrophilic microbes: Sporosarcina psychrophile, Sporosarcina globispora, and Polaromonas hydrogenivorans, to induce non-equilibrium freezing point depression and thermal hysteresis in order to control ice lens growth in frost-susceptible soils. We hypothesize that the AFPs produced by psychrophiles will alter the phase changes of porous media in frost-susceptible soils. The growth profiles of the microbes, the concentration of released proteins in the extracellular solution, and the thermal properties of the protein-mixed soils are monitored at an interval of three days. The controlled soil showed a freezing point of - 4.59 °C and thermal hysteresis of 4.62 °C, whereas protein-treated soil showed a maximum freezing point depression of - 8.54 °C and thermal hysteresis of 7.71 °C. Interestingly, except for the controlled sample, all the protein-treated soil samples were thawed at a negative temperature (minimum recorded at - 0.85 °C). Further analysis showed that the treated soils compared to porous media mixed soil freeze (1.25 °C vs. 0.51 °C) and thaw (2.75 °C vs. 1.72 °C) at extensive temperature gap. This freezing and thawing temperature gap is the temperature difference between the beginning of ice core formation and completed frozen, and the beginning of ice core thawing and completed thawed for the treated soil samples selected from different incubation days. Overall, this study presents a novel bio-mediated approach using psychrophilic microbes to control ice formation in frost-susceptible soils.
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Affiliation(s)
- Rashed Rahman
- Department of Civil and Architectural and Engineering Mechanics, University of Arizona, Tucson, AZ, 85721, USA
| | - Tejo V Bheemasetti
- Department of Civil and Architectural and Engineering Mechanics, University of Arizona, Tucson, AZ, 85721, USA.
| | - Tanvi Govil
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, 57701, USA
| | - Rajesh Sani
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, 57701, USA
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4
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Muraoka M. Measurement of Ice-Binding Protein Inhibition of Non-ice Crystal Growth. Methods Mol Biol 2024; 2730:155-167. [PMID: 37943457 DOI: 10.1007/978-1-0716-3503-2_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
The kinetic hydrate inhibitor (KHI) was developed to prevent the formation of undesirable gas hydrate crystals in natural gas pipelines. Studies of antifreeze proteins (AFPs) are gaining attention in the natural gas research field due to their performance in crystal growth inhibition, excellent biodegradation, and low toxicity. Studies of AFPs may provide clues for developing future commercial KHIs used offshore. This chapter presents a simple method of evaluating AFP inhibitory performance as a KHI on tetrahydrofuran (THF) hydrate growth with a unidirectional growth apparatus.
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Affiliation(s)
- Michihiro Muraoka
- Energy Process Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan.
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5
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Guerreiro BM, Lou LT, Rubinsky B, Freitas F. Ice modulatory effect of the polysaccharide FucoPol in directional freezing. SOFT MATTER 2023; 19:8978-8987. [PMID: 37964678 DOI: 10.1039/d3sm01154b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Directional freezing harnesses crystal growth development to create aligned solid structures or etchable patterns, useful for directed ice growth in cryobiology and cryoprinting for tissue engineering. We have delved into the ice-modulating properties of FucoPol, a fucose-rich, bio-based polysaccharide. Previous research on FucoPol revealed its non-colligative hysteresis in kinetic freezing point, reduced crystal dimensions and cryoprotective effect. Here, FucoPol reshaped developing sharp, anisotropic obloid ice dendrites into linearly-aligned, thin, isotropic spicules or tubules (cooling rate-dependent morphology). The effect was enhanced by increased concentration and decreased cooling rate, but major reshaping was observed with 5 μM and below. These structures boasted remarkable enhancements: uniform alignment (3-fold), tip symmetry (5.9-fold) and reduced thickness (5.3-fold). The ice-modulating capability of FucoPol resembles the Gibbs-Thomson effect of antifreeze proteins, in particular the ice reshaping profiles of type I antifreeze proteins and rattlesnake venom lectins, evidenced by a 52.6 ± 2.2° contact angle (θ) and spicular structure generation. The high viscosity of FucoPol solutions, notably higher than that of sucrose, plays a crucial role. This viscosity dynamically intensifies during directional freezing, leading to a diffusion-limited impediment that influences dendritic formation. Essentially, the ice-modulating prowess of FucoPol not only reinforces its established cryoprotective qualities but also hints at its potential utility in applications that harness advantageous ice growth for intentional structuring. For instance, its potential in cryobioprinting is noteworthy, offering an economical, biodegradable resource, of easy removal, sidestepping the need for toxic reagents. Moreover, FucoPol fine-tunes resulting ice structures, enabling the ice-etching of biologically relevant patterns within biocompatible matrices for advanced tissue engineering endeavors.
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Affiliation(s)
- Bruno M Guerreiro
- UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University Lisbon, Caparica, Portugal.
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Leo T Lou
- Department of Mechanical Engineering, University of California at Berkeley, Berkeley, CA, USA.
| | - Boris Rubinsky
- Department of Mechanical Engineering, University of California at Berkeley, Berkeley, CA, USA.
| | - Filomena Freitas
- UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University Lisbon, Caparica, Portugal.
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
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6
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William N, Mangan S, Ben RN, Acker JP. Engineered Compounds to Control Ice Nucleation and Recrystallization. Annu Rev Biomed Eng 2023; 25:333-362. [PMID: 37104651 DOI: 10.1146/annurev-bioeng-082222-015243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
One of the greatest concerns in the subzero storage of cells, tissues, and organs is the ability to control the nucleation or recrystallization of ice. In nature, evidence of these processes, which aid in sustaining internal temperatures below the physiologic freezing point for extended periods of time, is apparent in freeze-avoidant and freeze-tolerant organisms. After decades of studying these proteins, we now have easily accessible compounds and materials capable of recapitulating the mechanisms seen in nature for biopreser-vation applications. The output from this burgeoning area of research can interact synergistically with other novel developments in the field of cryobiology, making it an opportune time for a review on this topic.
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Affiliation(s)
- Nishaka William
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada;
| | - Sophia Mangan
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | - Rob N Ben
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | - Jason P Acker
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada;
- Innovation and Portfolio Management, Canadian Blood Services, Edmonton, Alberta, Canada
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7
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Takahashi H, Kono T, Sawada K, Kumano S, Tsuri Y, Maruyama M, Yoshimura M, Takahashi D, Kawamura Y, Uemura M, Nakabayashi S, Mori Y, Hosokawa Y, Yoshikawa HY. Spatiotemporal Control of Ice Crystallization in Supercooled Water via an Ultrashort Laser Impulse. J Phys Chem Lett 2023; 14:4394-4402. [PMID: 37154425 DOI: 10.1021/acs.jpclett.3c00414] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Focused irradiation with ultrashort laser pulses realized the fine spatiotemporal control of ice crystallization in supercooled water. An effective multiphoton excitation at the laser focus generated shockwaves and bubbles, which acted as an impulse for inducing ice crystal nucleation. The impulse that was localized close to the laser focus and accompanied by a small temperature elevation allowed the precise position control of ice crystallization and its observation with spatiotemporal resolution of micrometers and microseconds using a microscope. To verify the versatility of this laser method, we also applied it using various aqueous systems (e.g., plant extracts). The systematic study of crystallization probability revealed that laser-induced cavitation bubbles play a crucial role in inducing ice crystal nucleation. This method can be used as a tool for studying ice crystallization dynamics in various natural and biological phenomena.
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Affiliation(s)
- Hozumi Takahashi
- Department of Applied Physics, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Tatsuya Kono
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Kosuke Sawada
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Satoru Kumano
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Yuka Tsuri
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Mihoko Maruyama
- Division of Electrical, Electronics and Infocommunications Engineering, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
- Graduate School of Life and Environmental Science, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Masashi Yoshimura
- Institute of Laser Engineering (ILE), Osaka University, 2-6 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Daisuke Takahashi
- United Graduate School of Agricultural Sciences, Iwate University, Ueda 3-18-8, Morioka 020-8550, Japan
- Division of Life Science, Graduate School of Science & Engineering, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama City, Saitama 338-8570, Japan
| | - Yukio Kawamura
- United Graduate School of Agricultural Sciences, Iwate University, Ueda 3-18-8, Morioka 020-8550, Japan
- Department of Plant-bioscience, Faculty of Agriculture, Iwate University, Ueda 3-18-8, Morioka 020-8550, Japan
| | - Matsuo Uemura
- United Graduate School of Agricultural Sciences, Iwate University, Ueda 3-18-8, Morioka 020-8550, Japan
- Department of Plant-bioscience, Faculty of Agriculture, Iwate University, Ueda 3-18-8, Morioka 020-8550, Japan
| | - Seiichiro Nakabayashi
- Department of Chemistry, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama City, Saitama 338-8570, Japan
- Division of Strategic Research and Development, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama City, Saitama, 338-8570, Japan
| | - Yusuke Mori
- Division of Electrical, Electronics and Infocommunications Engineering, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Yoichiroh Hosokawa
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Hiroshi Y Yoshikawa
- Department of Applied Physics, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
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8
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Farag H, Peters B. Free energy barriers for anti-freeze protein engulfment in ice: Effects of supercooling, footprint size, and spatial separation. J Chem Phys 2023; 158:094501. [PMID: 36889941 DOI: 10.1063/5.0131983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Anti-freeze proteins (AFPs) protect organisms at freezing conditions by attaching to the ice surface and arresting its growth. Each adsorbed AFP locally pins the ice surface, resulting in a metastable dimple for which the interfacial forces counteract the driving force for growth. As supercooling increases, these metastable dimples become deeper, until metastability is lost in an engulfment event where the ice irreversibly swallows the AFP. Engulfment resembles nucleation in some respects, and this paper develops a model for the "critical profile" and free energy barrier for the engulfment process. Specifically, we variationally optimize the ice-water interface and estimate the free energy barrier as a function of the supercooling, the AFP footprint size, and the distance to neighboring AFPs on the ice surface. Finally, we use symbolic regression to derive a simple closed-form expression for the free energy barrier as a function of two physically interpretable, dimensionless parameters.
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Affiliation(s)
- Hossam Farag
- Nuclear, Plasma, and Radiological Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Baron Peters
- Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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9
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The Modification of Polyvinyl Alcohol for Ice Nucleation Based upon the Structures of Antifreeze Glycoproteins Found in Antarctic Fish. BIOPHYSICA 2022. [DOI: 10.3390/biophysica2040037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Various alternative compounds have been investigated to prevent icing, one of which includes poly(vinyl) alcohol (PVA), which has shown promising anti-freeze effects. However, determining the optimal structures and formulations of PVA for anti-icing applications has remained a challenge. Building upon our previous work, which used molecular dynamics simulations to assess the effects of hydroxyl group separation distance on ice nucleation, in this work, PVA was modified based upon the structures of antifreeze glycoproteins (AFGPs) found in Antarctic fish, and examined as a potential antifreeze compound. Four different PVA samples with different degrees of hydrolysis were fabricated and subsequently examined for their effects on ice crystallization. The results showed that the modified PVA samples with degrees of hydrolysis of 76% and 66% had an effect on ice crystallization, delaying ice crystallization by an average of approximately 20 min, and even preventing ice crystallization altogether in a small portion of the sample. Meanwhile, other samples with degrees of hydrolysis of 100% and 34% either showed no effect on ice crystallization, shortened the ice crystallization time, and appeared to promote ice nucleation.
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10
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Lee SY, Kim M, Won TK, Back SH, Hong Y, Kim BS, Ahn DJ. Janus regulation of ice growth by hyperbranched polyglycerols generating dynamic hydrogen bonding. Nat Commun 2022; 13:6532. [PMID: 36319649 PMCID: PMC9626502 DOI: 10.1038/s41467-022-34300-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 10/20/2022] [Indexed: 11/16/2022] Open
Abstract
In this study, a new phenomenon describing the Janus effect on ice growth by hyperbranched polyglycerols, which can align the surrounding water molecules, has been identified. Even with an identical polyglycerol, we not only induced to inhibit ice growth and recrystallization, but also to promote the growth rate of ice that is more than twice that of pure water. By investigating the polymer architecture and population, we found that the stark difference in the generation of quasi-structured H2O molecules at the ice/water interface played a crucial role in the outcome of these opposite effects. Inhibition activity was induced when polymers at nearly fixed loci formed steady hydrogen bonding with the ice surface. However, the formation-and-dissociation dynamics of the interfacial hydrogen bonds, originating from and maintained by migrating polymers, resulted in an enhanced quasi-liquid layer that facilitated ice growth. Such ice growth activity is a unique property unseen in natural antifreeze proteins or their mimetic materials.
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Affiliation(s)
- Sang Yup Lee
- grid.222754.40000 0001 0840 2678KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, Republic of Korea ,grid.222754.40000 0001 0840 2678The w:i Interface Augmentation Center, Korea University, Seoul, Republic of Korea
| | - Minseong Kim
- grid.15444.300000 0004 0470 5454Department of Chemistry, Yonsei University, Seoul, Republic of Korea
| | - Tae Kyung Won
- grid.222754.40000 0001 0840 2678The w:i Interface Augmentation Center, Korea University, Seoul, Republic of Korea ,grid.222754.40000 0001 0840 2678Department of Chemical and Biological Engineering, Korea University, Seoul, Republic of Korea
| | - Seung Hyuk Back
- grid.222754.40000 0001 0840 2678The w:i Interface Augmentation Center, Korea University, Seoul, Republic of Korea ,grid.222754.40000 0001 0840 2678Department of Chemical and Biological Engineering, Korea University, Seoul, Republic of Korea
| | - Youngjoo Hong
- grid.15444.300000 0004 0470 5454Department of Chemistry, Yonsei University, Seoul, Republic of Korea
| | - Byeong-Su Kim
- grid.15444.300000 0004 0470 5454Department of Chemistry, Yonsei University, Seoul, Republic of Korea
| | - Dong June Ahn
- grid.222754.40000 0001 0840 2678KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, Republic of Korea ,grid.222754.40000 0001 0840 2678The w:i Interface Augmentation Center, Korea University, Seoul, Republic of Korea ,grid.222754.40000 0001 0840 2678Department of Chemical and Biological Engineering, Korea University, Seoul, Republic of Korea
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11
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Lee C, Lee Y, Jung WH, Kim TY, Kim T, Kim DN, Ahn DJ. Peptide-DNA origami as a cryoprotectant for cell preservation. SCIENCE ADVANCES 2022; 8:eadd0185. [PMID: 36306364 PMCID: PMC9616499 DOI: 10.1126/sciadv.add0185] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 09/12/2022] [Indexed: 05/21/2023]
Abstract
Cryopreservation of cells is essential for the conservation and cold chain of bioproducts and cell-based medicines. Here, we demonstrate that self-assembled DNA origami nanostructures have a substantial ability to protect cells undergoing freeze-thaw cycles; thereby, they can be used as cryoprotectant agents, because their nanoscale morphology and ice-philicity are tailored. In particular, a single-layered DNA origami nanopatch functionalized with antifreezing threonine peptides enabled the viability of HSC-3 cells to reach 56% after 1 month of cryopreservation, surpassing dimethyl sulfoxide, which produced 38% viability. It also exhibited minimal dependence on the cryopreservation period and freezing conditions. We attribute this outcome to the fact that the peptide-functionalized DNA nanopatches exert multisite actions for the retardation of ice growth in both intra- and extracellular regions and the protection of cell membranes during cryopreservation. This discovery is expected to deepen our fundamental understanding of cell survival under freezing environment and affect current cryopreservation technologies.
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Affiliation(s)
- Chanseok Lee
- Institute of Advanced Machines and Design, Seoul National University, Seoul 08826, Korea
- The w:i Interface Augmentation Center, Korea University, Seoul 02841, Korea
| | - Yedam Lee
- The w:i Interface Augmentation Center, Korea University, Seoul 02841, Korea
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Korea
| | - Woo Hyuk Jung
- The w:i Interface Augmentation Center, Korea University, Seoul 02841, Korea
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Korea
| | - Tae-Yeon Kim
- Department of Mechanical Engineering, Seoul National University, Seoul 08826, Korea
| | - Taehwi Kim
- Department of Mechanical Engineering, Seoul National University, Seoul 08826, Korea
| | - Do-Nyun Kim
- Institute of Advanced Machines and Design, Seoul National University, Seoul 08826, Korea
- The w:i Interface Augmentation Center, Korea University, Seoul 02841, Korea
- Department of Mechanical Engineering, Seoul National University, Seoul 08826, Korea
- Corresponding author. (D.J.A.); (D.-N.K.)
| | - Dong June Ahn
- The w:i Interface Augmentation Center, Korea University, Seoul 02841, Korea
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Korea
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Korea
- Corresponding author. (D.J.A.); (D.-N.K.)
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12
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Rizzuti B. Molecular simulations of proteins: From simplified physical interactions to complex biological phenomena. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140757. [PMID: 35051666 DOI: 10.1016/j.bbapap.2022.140757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 01/08/2022] [Accepted: 01/10/2022] [Indexed: 12/22/2022]
Abstract
Molecular dynamics simulation is the most popular computational technique for investigating the structural and dynamical behaviour of proteins, in search of the molecular basis of their function. Far from being a completely settled field of research, simulations are still evolving to best capture the essential features of the atomic interactions that govern a protein's inner motions. Modern force fields are becoming increasingly accurate in providing a physical description adequate to this purpose, and allow us to model complex biological systems under fairly realistic conditions. Furthermore, the use of accelerated sampling techniques is improving our access to the observation of progressively larger molecular structures, longer time scales, and more hidden functional events. In this review, the basic principles of molecular dynamics simulations and a number of key applications in the area of protein science are summarized, and some of the most important results are discussed. Examples include the study of the structure, dynamics and binding properties of 'difficult' targets, such as intrinsically disordered proteins and membrane receptors, and the investigation of challenging phenomena like hydration-driven processes and protein aggregation. The findings described provide an overall picture of the current state of this research field, and indicate new perspectives on the road ahead to the upcoming future of molecular simulations.
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Affiliation(s)
- Bruno Rizzuti
- CNR-NANOTEC, SS Rende (CS), Department of Physics, University of Calabria, 87036 Rende, Italy; Institute for Biocomputation and Physics of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, University of Zaragoza, 50018 Zaragoza, Spain.
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13
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Ghalamara S, Silva S, Brazinha C, Pintado M. Structural diversity of marine anti-freezing proteins, properties and potential applications: a review. BIORESOUR BIOPROCESS 2022; 9:5. [PMID: 38647561 PMCID: PMC10992025 DOI: 10.1186/s40643-022-00494-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/08/2022] [Indexed: 11/10/2022] Open
Abstract
Cold-adapted organisms, such as fishes, insects, plants and bacteria produce a group of proteins known as antifreeze proteins (AFPs). The specific functions of AFPs, including thermal hysteresis (TH), ice recrystallization inhibition (IRI), dynamic ice shaping (DIS) and interaction with membranes, attracted significant interest for their incorporation into commercial products. AFPs represent their effects by lowering the water freezing point as well as preventing the growth of ice crystals and recrystallization during frozen storage. The potential of AFPs to modify ice growth results in ice crystal stabilizing over a defined temperature range and inhibiting ice recrystallization, which could minimize drip loss during thawing, improve the quality and increase the shelf-life of frozen products. Most cryopreservation studies using marine-derived AFPs have shown that the addition of AFPs can increase post-thaw viability. Nevertheless, the reduced availability of bulk proteins and the need of biotechnological techniques for industrial production, limit the possible usage in foods. Despite all these drawbacks, relatively small concentrations are enough to show activity, which suggests AFPs as potential food additives in the future. The present work aims to review the results of numerous investigations on marine-derived AFPs and discuss their structure, function, physicochemical properties, purification and potential applications.
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Affiliation(s)
- Soudabeh Ghalamara
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal
| | - Sara Silva
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal
| | - Carla Brazinha
- LAQV/Requimte, Faculdade de Ciências E Tecnologia, Universidade Nova de Lisboa, Campus de Caparica, 2829-516, Caparica, Portugal
| | - Manuela Pintado
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal.
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14
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Gerhäuser J, Gaukel V. Detailed Analysis of the Ice Surface after Binding of an Insect Antifreeze Protein and Correlation with the Gibbs-Thomson Equation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:11716-11725. [PMID: 34585573 DOI: 10.1021/acs.langmuir.1c01620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Antifreeze proteins (AFPs) are able to influence the ice crystal growth and the recrystallization process due to the Gibbs-Thomson effect. The binding of the AFP leads to the formation of a curved ice surface and it is generally assumed that there is a critical radius between the proteins on the ice surface that determines the maximal thermal hysteresis. Up to now, this critical radius has not yet been proven beyond doubt or only in poor agreement with the Gibbs-Thomson equation. Using molecular dynamics (MD) simulations, the resulting three-dimensional surface structure is analyzed and the location of the critical radius is identified. Our results demonstrate that the correct analysis of the geometry of the ice surface is extremely important and cannot be guessed upfront a simulation. In contrary to earlier expectations from the literature, we could show that the critical radius is not located directly between the adsorbed proteins. In addition, we showed that the minimum temperature at which the system does not freeze is in very good agreement with the value calculated with the Gibbs-Thomson equation at the critical radius, as long as dynamic system conditions are taken into account. This proves on the one hand that the Gibbs-Thomson effect is the basis of thermal hysteresis and that MD simulations are suitable for the prediction of the melting point depression.
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Affiliation(s)
- Julian Gerhäuser
- Section I: Food Process Engineering, KIT (Karlsruhe Institute of Technology), Institute of Process Engineering in Life Sciences, Kaiserstraße 12, Karlsruhe 76131, Germany
| | - Volker Gaukel
- Section I: Food Process Engineering, KIT (Karlsruhe Institute of Technology), Institute of Process Engineering in Life Sciences, Kaiserstraße 12, Karlsruhe 76131, Germany
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15
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Molecular dynamics simulation of the formation of methane hydrates in the presence of KHIs. Chem Eng Sci 2021. [DOI: 10.1016/j.ces.2021.116508] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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Abstract
Antifreeze glycoproteins (AFGPs) found in various fish are used by the organisms to prevent freezing. While these compounds have been studied for their ability to bind to, and prevent the complete crystallization of water, the exact mechanisms by which AFGPs prevent freezing are still undetermined. Therefore, building upon our previous work, this study uses molecular dynamics simulations to assess the effects of hydroxyl group separation distance on AFGP ice nucleation activity. Water droplet crystallization simulations showed that modified AFGP structures containing hydroxyl distances smaller than ~3.0 Å lost their ability to prevent ice crystallization. Furthermore, modified AFGP containing hydroxyl distances of 7.327 Å and 6.160 Å was correlated with a promotion in ice nucleation, as demonstrated by the changes in the energy of the system. This supports the notion that the distance, and therefore, geometry characteristics between the hydroxyl groups located on the saccharide structures play a key role in the ice crystallization inhibition properties of AFGP compounds.
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17
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Both AK, Gao Y, Zeng XC, Cheung CL. Gas hydrates in confined space of nanoporous materials: new frontier in gas storage technology. NANOSCALE 2021; 13:7447-7470. [PMID: 33876814 DOI: 10.1039/d1nr00751c] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Gas hydrates (clathrate hydrates, clathrates, or hydrates) are crystalline inclusion compounds composed of water and gas molecules. Methane hydrates, the most well-known gas hydrates, are considered a menace in flow assurance. However, they have also been hailed as an alternative energy resource because of their high methane storage capacity. Since the formation of gas hydrates generally requires extreme conditions, developing porous material hosts to synthesize gas hydrates with less-demanding constraints is a topic of great interest to the materials and energy science communities. Though reports of modeling and experimental analysis of bulk gas hydrates are plentiful in the literature, reliable phase data for gas hydrates within confined spaces of nanoporous media have been sporadic. This review examines recent studies of both experiments and theoretical modeling of gas hydrates within four categories of nanoporous material hosts that include porous carbons, metal-organic frameworks, graphene nanoslits, and carbon nanotubes. We identify challenges associated with these porous systems and discuss the prospects of gas hydrates in confined space for potential applications.
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Affiliation(s)
- Avinash Kumar Both
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA.
| | - Yurui Gao
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA.
| | - Xiao Cheng Zeng
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA.
| | - Chin Li Cheung
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA.
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18
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Arai N, Fujiwara A, Wakuda M, Fujimoto T, Nambu Y, Ishii T, Matsumiya K, Matsumura Y, Kawahara H, Ogino K. Anti-freeze effect of Enoki mushroom extract on the quality preservation of frozen whipped cream. J FOOD ENG 2021. [DOI: 10.1016/j.jfoodeng.2020.110285] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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19
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Zheng X, Liu J, Liu Z, Wang J. Bio-inspired Ice-controlling Materials for Cryopreservation of Cells and Tissues. ACTA CHIMICA SINICA 2021. [DOI: 10.6023/a21020043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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20
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Bianco V, Espinosa JR, Vega C. Antifreeze proteins and homogeneous nucleation: On the physical determinants impeding ice crystal growth. J Chem Phys 2020; 153:091102. [PMID: 32891082 DOI: 10.1063/5.0023211] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Antifreeze proteins (AFPs) are biopolymers capable of interfering with ice growth. Their antifreeze action is commonly understood considering that the AFPs, by pinning the ice surface, force the crystal-liquid interface to bend forming an ice meniscus, causing an increase in the surface free energy and resulting in a decrease in the freezing point ΔTmax. Here, we present an extensive computational study for a model protein adsorbed on a TIP4P/Ice crystal, computing ΔTmax as a function of the average distance d between AFPs, with simulations spanning over 1 µs. First, we show that the lower the d, the larger the ΔTmax. Then, we find that the water-ice-protein contact angle along the line ΔTmax(d) is always larger than 0°, and we provide a theoretical interpretation. We compute the curvature radius of the stable solid-liquid interface at a given supercooling ΔT ≤ ΔTmax, connecting it with the critical ice nucleus at ΔT. Finally, we discuss the antifreeze capability of AFPs in terms of the protein-water and protein-ice interactions. Our findings establish a unified description of the AFPs in the contest of homogeneous ice nucleation, elucidating key aspects of the antifreeze mechanisms and paving the way for the design of novel ice-controlling materials.
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Affiliation(s)
- Valentino Bianco
- Faculty of Chemistry, Chemical Physics Department, Universidad Complutense de Madrid, Plaza de las Ciencias, Ciudad Universitaria, Madrid 28040, Spain
| | - Jorge R Espinosa
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge CB3 0H3, United Kingdom
| | - Carlos Vega
- Faculty of Chemistry, Chemical Physics Department, Universidad Complutense de Madrid, Plaza de las Ciencias, Ciudad Universitaria, Madrid 28040, Spain
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21
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Gandini E, Sironi M, Pieraccini S. Modelling of short synthetic antifreeze peptides: Insights into ice-pinning mechanism. J Mol Graph Model 2020; 100:107680. [PMID: 32738619 DOI: 10.1016/j.jmgm.2020.107680] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/18/2020] [Accepted: 06/24/2020] [Indexed: 10/23/2022]
Abstract
Organisms living in icy environments produce antifreeze proteins to control ice growth and recrystallization. It has been proposed that these molecules pin the surface of ice crystals, thus inducing the formation of a curved surface that arrests crystal growth. Such proteins are very appealing for many potential applications in food industry, material science and cryoconservation of organs and tissues. Unfortunately, their structural complexity has seriously hampered their practical use, while efficient and accessible synthetic analogues are highly desirable. In this paper, we used molecular dynamics based techniques to model the interaction of three short antifreeze synthetic peptides with an ice surface. The employed protocols succeeded in reproducing the ice pinning action of antifreeze peptides and the consequent ice growth arrest, as well as in distinguishing between antifreeze and control peptides, for which no such effect was observed. Principal components analysis of peptides trajectories in different simulation settings permitted to highlight the main structural features associated to antifreeze activity. Modeling results are highly correlated with experimentally measured properties, and insights on ice-peptide interactions and on conformational patterns favoring antifreeze activity will prompt the design of new and improved antifreeze peptides.
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Affiliation(s)
- Enrico Gandini
- Dipartimento di Chimica, Università Degli Studi di Milano, Via Golgi 19, 20133, Milano, Italy
| | - Maurizio Sironi
- Dipartimento di Chimica, Università Degli Studi di Milano, Via Golgi 19, 20133, Milano, Italy; Istituto di Scienze e Tecnologie Chimiche "G. Natta" (SCITEC-CNR), CNR, INSTM, UdR Milano, Via Golgi 19, 20133, Milano, Italy.
| | - Stefano Pieraccini
- Dipartimento di Chimica, Università Degli Studi di Milano, Via Golgi 19, 20133, Milano, Italy; Istituto di Scienze e Tecnologie Chimiche "G. Natta" (SCITEC-CNR), CNR, INSTM, UdR Milano, Via Golgi 19, 20133, Milano, Italy.
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22
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Demonstration of the cryoprotective properties of the fucose-containing polysaccharide FucoPol. Carbohydr Polym 2020; 245:116500. [PMID: 32718611 DOI: 10.1016/j.carbpol.2020.116500] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 05/19/2020] [Accepted: 05/20/2020] [Indexed: 11/21/2022]
Abstract
We report the cryoprotective potential of FucoPol, a fucose-containing bacterial exopolysaccharide produced by Enterobacter A47. In vitro cryopreservation assays of Vero, Saos-2, HFFF2 and C2C12 cell lines exposed to a validated non-cytotoxic 2.5 mg/mL FucoPol concentration demonstrated a consistent post-thaw metabolic viability increase. Calorimetric analysis showed a non-colligative, FucoPol concentration-dependent increase of the freezing point (Tf), with minimal change in melting point (Tm). Freezing point variation was corroborated by Polarized Optical Microscopy studies, also showing a reduction of ice crystal dimensions. Its proven shear-thinning behaviour and polyanionicity favour interactivity between the polysaccharide and the water-ice interface, resulting in ice growth inhibition. These findings demonstrate FucoPol's high promise as a bio-based, biodegradable approach to be implemented into cryopreservation formulations.
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23
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Nian L, Cao A, Cai L. Investigation of the antifreeze mechanism and effect on quality characteristics of largemouth bass (Micropterus salmoides) during F-T cycles by hAFP. Food Chem 2020; 325:126918. [PMID: 32387943 DOI: 10.1016/j.foodchem.2020.126918] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 04/19/2020] [Accepted: 04/25/2020] [Indexed: 11/27/2022]
Abstract
The interaction between herring antifreeze protein (hAFP) and ice crystals was studied by molecular dynamics simulation in this paper. On this basis, the effect of hAFP on the quality attributes of largemouth bass after three freezing-thawing (F-T) cycles was studied. Scanning electron microscope was conducted to analyze the microstructure changes of muscle fibers. The content of dityrosine/total sulfhydryl/carbonyl and the Ca2+-ATPase activity were measured to explore the degree of protein oxidation. Raman and intrinsic fluorescence spectra were used to measure the protein secondary structure and tertiary conformation. Results showed that hAFP protected the organisms from freezing by binding to the ice crystals, decreasing the freezing point and inhibiting the recrystallization. Furthermore, hAFP combined with chitosan magnetic (CS@Fe3O4) nanoparticles or vacuum impregnation hAFP was shown to be an effective method to reduce the mechanical damage of ice crystals to samples, and decrease the oxidation degree of samples during F-T cycles.
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Affiliation(s)
- Linyu Nian
- College of Biosystems Engineering and Food Science, National & Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang University, Hangzhou 310058, China; Ningbo Research Institute, Zhejiang University, Ningbo 315100, China
| | - Ailing Cao
- Hangzhou Customs District, Hangzhou 310007, China.
| | - Luyun Cai
- College of Biosystems Engineering and Food Science, National & Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang University, Hangzhou 310058, China; Ningbo Research Institute, Zhejiang University, Ningbo 315100, China.
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24
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Inhibition Effect of Kinetic Hydrate Inhibitors on the Growth of Methane Hydrate in Gas–Liquid Phase Separation State. ENERGIES 2019. [DOI: 10.3390/en12234482] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The effect of kinetic hydrate inhibitors (KHIs) on the growth of methane hydrate in the gas–liquid phase separation state is studied at the molecular level. The simulation results show that the kinetic inhibitors, named PVP and PVP-A, show good inhibitory effects on the growth of methane hydrate under the gas–liquid phase separation state, and the initial position of the kinetic hydrate inhibitors has a major effect on the growth of methane hydrates. In addition, inhibitors at different locations exhibit different inhibition performances. When the inhibitor molecules are located at the gas–liquid phase interface, increasing the contact area between the groups of the inhibitor molecules and methane is beneficial to enhance the inhibitory performance of the inhibitors. When inhibitor molecules are located at the solid–liquid phase interface, the inhibitor molecules adsorbed on the surface of the hydrate nucleus and decreased the direct contact of hydrate nucleus with the surrounding water and methane molecules, which would delay the growth of hydrate nucleus. Moreover, the increase of hydrate surface curvature and the Gibbs–Thomson effect caused by inhibitors can also reduce the growth rate of methane hydrate.
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25
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Zhou D, Chen F, Handschuh‐Wang S, Gan T, Zhou X, Zhou X. Biomimetic Extreme‐Temperature‐ and Environment‐Adaptable Hydrogels. Chemphyschem 2019; 20:2139-2154. [DOI: 10.1002/cphc.201900545] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/10/2019] [Indexed: 12/31/2022]
Affiliation(s)
- Dan Zhou
- College of Chemistry and Environmental EngineeringShenzhen University, Shenzhen 518060 P. R. China
| | - Fan Chen
- College of Chemistry and Environmental EngineeringShenzhen University, Shenzhen 518060 P. R. China
| | - Stephan Handschuh‐Wang
- College of Chemistry and Environmental EngineeringShenzhen University, Shenzhen 518060 P. R. China
| | - Tiansheng Gan
- College of Chemistry and Environmental EngineeringShenzhen University, Shenzhen 518060 P. R. China
| | - Xiaohu Zhou
- College of Chemistry and Environmental EngineeringShenzhen University, Shenzhen 518060 P. R. China
| | - Xuechang Zhou
- College of Chemistry and Environmental EngineeringShenzhen University, Shenzhen 518060 P. R. China
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26
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Zhang B, Cao HJ, Lin HM, Deng SG, Wu H. Insights into ice-growth inhibition by trehalose and alginate oligosaccharides in peeled Pacific white shrimp (Litopenaeus vannamei) during frozen storage. Food Chem 2019; 278:482-490. [DOI: 10.1016/j.foodchem.2018.11.087] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 11/15/2018] [Accepted: 11/18/2018] [Indexed: 10/27/2022]
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27
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Kondo H, Mochizuki K, Bayer-Giraldi M. Multiple binding modes of a moderate ice-binding protein from a polar microalga. Phys Chem Chem Phys 2018; 20:25295-25303. [PMID: 30255887 DOI: 10.1039/c8cp04727h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Ice-binding proteins (IBPs) produced by cold-tolerant organisms interact with ice and strongly control crystal growth. The molecular basis for the different magnitudes of activity displayed by various IBPs (moderate and hyperactive) has not yet been clarified. Previous studies questioned whether the moderate activity of some IBPs relies on their weaker binding modus to the ice surface, compared to hyperactive IBPs, rather than relying on binding only to selected faces of the ice crystal. We present the structure of one moderate IBP from the sea-ice diatom Fragilariopsis cylindrus (fcIBP) as determined by X-ray crystallography and investigate the protein's binding modes to the growing ice-water interface using molecular dynamics simulations. The structure of fcIBP is the IBP-1 fold, defined by a discontinuous β-solenoid delimitated by three faces (A, B and C-faces) and braced by an α-helix. The fcIBP structure shows capping loops on both N- and C-terminal parts of the solenoid. We show that the protein adsorbs on both the prism and the basal faces of ice crystals, confirming experimental results. The fcIBP binds irreversibly to the prism face using the loop between the B and the C-faces, involving also the B-face in water immobilization despite its irregular structure. The α-helix attaches the protein to the basal face with a partly reversible modus. Our results suggest that fcIBP has a looser attachment to ice and that this weaker binding modus is the basis to explain the moderate activity of fcIBP.
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Affiliation(s)
- Hidemasa Kondo
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo 062-8517, Japan
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28
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Shimazu N, Takaiwa D, Suh D, Kawaguchi T, Fuse T, Kaneko T, Yasuoka K. Molecular Dynamics Simulation of Ice Crystal Growth Inhibition by Hexadecyl-trimethyl-ammonium Bromide. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:9330-9335. [PMID: 29989825 DOI: 10.1021/acs.langmuir.8b01903] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Recent experiments have found hexadecyl-trimethyl-ammonium bromide (CTAB) to have superior ice nucleation inhibition properties [ J. Phys. Chem. B 121, 6580]. The mechanism of how the inhibition takes place remains unclear. Therefore, molecular dynamics was used to simulate ice crystallization of a water/CTAB/ice system. The ice crystallization rate for a pure water system was compared for the basal [0001], first prism [101̅0], and secondary prism plane [112̅0], where the basal plane grew the slowest followed by the first prism plane. When CTAB was added to the ice-liquid water system, crystallization was clearly impeded. Even when ice starts growing away from the CTAB molecule, the hydrophilic head would at some point protrude and get caught in the water/ice interface. Once the head of the CTAB was encapsulated in the advancing interface, the hydrophobic body would wriggle around and disrupt the formation of hydrogen bond networks that are essential for ice growth. When the interface clears the length of the body of the CTAB molecule, ice crystallization resumes at its normal pace. In summary, the inhibition of ice growth is a combination of the hydrophilic head acting as an anchor and the dynamic motion of the hydrophobic tail hindering stable hydrogen bonding for ice growth.
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Affiliation(s)
- Naoya Shimazu
- Department of Mechanical Engineering , Keio University , 3-14-1 Hiyoshi , Kohoku-ku, Yokohama 223-8522 , Japan
| | - Daisuke Takaiwa
- Department of Mechanical Engineering , Keio University , 3-14-1 Hiyoshi , Kohoku-ku, Yokohama 223-8522 , Japan
| | - Donguk Suh
- Department of Mechanical Engineering , Keio University , 3-14-1 Hiyoshi , Kohoku-ku, Yokohama 223-8522 , Japan
| | - Touru Kawaguchi
- DENSO Corporation , 500-1 Minamiyama , Komenoki-cho, Nisshin-shi , Aichi 470-0111 , Japan
| | - Takuya Fuse
- DENSO Corporation , 500-1 Minamiyama , Komenoki-cho, Nisshin-shi , Aichi 470-0111 , Japan
| | - Takashi Kaneko
- DENSO Corporation , 500-1 Minamiyama , Komenoki-cho, Nisshin-shi , Aichi 470-0111 , Japan
| | - Kenji Yasuoka
- Department of Mechanical Engineering , Keio University , 3-14-1 Hiyoshi , Kohoku-ku, Yokohama 223-8522 , Japan
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29
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Eslami M, Shirali Hossein Zade R, Takalloo Z, Mahdevar G, Emamjomeh A, Sajedi RH, Zahiri J. afpCOOL: A tool for antifreeze protein prediction. Heliyon 2018; 4:e00705. [PMID: 30094375 PMCID: PMC6074609 DOI: 10.1016/j.heliyon.2018.e00705] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 07/20/2018] [Indexed: 11/16/2022] Open
Abstract
Various cold-adapted organisms produce antifreeze proteins (AFPs), which prevent the freezing of cell fluids by inhibiting the growth of ice crystals. AFPs are currently being recognized in various organisms, living in extremely low temperatures. AFPs have several important applications in increasing freeze tolerance of plants, maintaining the tissue in frozen conditions and producing cold-hardy plants by applying transgenic technology. Substantial differences in the sequence and structure of the AFPs, pose a challenge for researchers to identify these proteins. In this paper, we proposed a novel method to identify AFPs, using supportive vector machine (SVM) by incorporating 4 types of features. Results of the two used benchmark datasets, revealed the strength of the proposed method in AFP prediction. According to the results of an independent test setup, our method outperformed the current state-of-the-art methods. In addition, the comparison results of the discrimination power of different feature types revealed that physicochemical descriptors are the most contributing features in AFP detection. This method has been implemented as a stand-alone tool, named afpCOOL, for various operating systems to predict AFPs with a user friendly graphical interface.
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Affiliation(s)
- Morteza Eslami
- Department of Computer Engineering, Arak University, Arak, Iran
| | | | - Zeinab Takalloo
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ghasem Mahdevar
- Department of Mathematics, Faculty of Sciences, University of Isfahan, Isfahan, Iran
| | - Abbasali Emamjomeh
- Laboratory of Computational Biotechnology and Bioinformatics (CBB), Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Zabol, Iran
| | - Reza H Sajedi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Javad Zahiri
- Bioinformatics and Computational Omics Lab (BioCOOL), Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.,School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), P.O. Box 19395-5746, Tehran, Iran
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30
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Lee H. Structures, dynamics, and hydrogen-bond interactions of antifreeze proteins in TIP4P/Ice water and their dependence on force fields. PLoS One 2018; 13:e0198887. [PMID: 29879205 PMCID: PMC5991737 DOI: 10.1371/journal.pone.0198887] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 05/27/2018] [Indexed: 12/13/2022] Open
Abstract
Tenebrio molitor antifreeze protein (TmAFP) was simulated with growing ice-water interfaces at a realistic melting temperature using TIP4P/Ice water model. To test compatibility of protein force fields (FFs) with TIP4P/Ice water, CHARMM, AMBER, and OPLS FFs were applied. CHARMM and AMBER FFs predict more β-sheet structure and lower diffusivity of TmAFP at the ice-water interface than does OPLS FF, indicating that β-sheet structure is important for the TmAFP-interface binding and antifreeze activity. In particular, CHARMM FF more clearly distinguishes the strengths of hydrogen bonds in the ice-binding and non-ice-binding sites of TmAFP than do other FFs, in agreement with experiments, implying that CHARMM FF can be a reasonable choice to simulate proteins with TIP4P/Ice water. Simulations of mutated TmAFPs show that for the same density of Thr residues, continuous arrangement of Thr with the distance of 0.4~0.6 nm induces the higher extent of antifreeze activity than does intermittent arrangement of Thr with larger distances. These findings suggest the choice of CHARMM FF for AFP-TIP4P/Ice simulations and help explain the relationship between Thr-residue arrangement and antifreeze activity.
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Affiliation(s)
- Hwankyu Lee
- Department of Chemical Engineering, Dankook University, Yongin-si, Gyeonggi-do, South Korea
- * E-mail:
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31
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Does Marine Surface Tension Have Global Biogeography? Addition for the OCEANFILMS Package. ATMOSPHERE 2018. [DOI: 10.3390/atmos9060216] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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32
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Inagawa A, Okada Y, Okada T. Electrophoresis in ice surface grooves for probing protein affinity to a specific plane of ice crystal. Talanta 2018; 183:345-351. [DOI: 10.1016/j.talanta.2017.12.073] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 12/20/2017] [Accepted: 12/21/2017] [Indexed: 01/26/2023]
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Polypentagonal ice-like water networks emerge solely in an activity-improved variant of ice-binding protein. Proc Natl Acad Sci U S A 2018; 115:5456-5461. [PMID: 29735675 PMCID: PMC6003529 DOI: 10.1073/pnas.1800635115] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Polypentagonal water networks were recently observed in a protein capable of binding to ice crystals, or ice-binding protein (IBP). To examine such water networks and clarify their role in ice-binding, we determined X-ray crystal structures of a 65-residue defective isoform of a Zoarcidae-derived IBP (wild type, WT) and its five single mutants (A20L, A20G, A20T, A20V, and A20I). Polypentagonal water networks composed of ∼50 semiclathrate waters were observed solely on the strongest A20I mutant, which appeared to include a tetrahedral water cluster exhibiting a perfect position match to the [Formula: see text] first prism plane of a single ice crystal. Inclusion of another symmetrical water cluster in the polypentagonal network showed a perfect complementarity to the waters constructing the [Formula: see text] pyramidal ice plane. The order of ice-binding strength was A20L < A20G < WT < A20T < A20V < A20I, where the top three mutants capable of binding to the first prism and the pyramidal ice planes commonly contained a bifurcated γ-CH3 group. These results suggest that a fine-tuning of the surface of Zoarcidae-derived IBP assisted by a side-chain group regulates the holding property of its polypentagonal water network, the function of which is to freeze the host protein to specific ice planes.
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Yagasaki T, Matsumoto M, Tanaka H. Adsorption of Kinetic Hydrate Inhibitors on Growing Surfaces: A Molecular Dynamics Study. J Phys Chem B 2018; 122:3396-3406. [PMID: 29278335 DOI: 10.1021/acs.jpcb.7b10356] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We investigate the mechanism of a typical kinetic hydrate inhibitor (KHI), polyvinylcaprolactam (PVCap), which has been applied to prevent hydrate plugs from forming in gas pipe lines, using molecular dynamics simulations of crystal growth of ethylene oxide hydrate. Water-soluble ethylene oxide is chosen as a guest species to avoid problems associated with the presence of the gas phase in the simulation cell such as slow crystal growth. A PVCap dodecamer adsorbs irreversibly on the hydrate surface which grows at supercooling of 3 K when the hydrophobic part of two pendent groups are trapped in open cages at the surface. The amide hydrogen bonds make no contribution to the adsorption. PVCap can adsorb on various crystallographic planes of sI hydrate. This is in contrast to antifreeze proteins, each of which prefers a specific plane of ice. The trapped PVCap gives rise to necessarily the concave surface of the hydrate. The crystal growth rate decreases with increasing surface curvature, indicating that the inhibition by PVCap is explained by the Gibbs-Thomson effect.
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Affiliation(s)
- Takuma Yagasaki
- Research Institute for Interdisciplinary Science , Okayama University , Okayama 700-8530 , Japan
| | - Masakazu Matsumoto
- Research Institute for Interdisciplinary Science , Okayama University , Okayama 700-8530 , Japan
| | - Hideki Tanaka
- Research Institute for Interdisciplinary Science , Okayama University , Okayama 700-8530 , Japan
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35
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Mochizuki K, Molinero V. Antifreeze Glycoproteins Bind Reversibly to Ice via Hydrophobic Groups. J Am Chem Soc 2018; 140:4803-4811. [PMID: 29392937 DOI: 10.1021/jacs.7b13630] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Antifreeze molecules allow organisms to survive in subzero environments. Antifreeze glycoproteins (AFGPs), produced by polar fish, are the most potent inhibitors of ice recrystallization. To date, the molecular mechanism by which AFGPs bind to ice has not yet been elucidated. Mutation experiments cannot resolve whether the binding occurs through the peptide, the saccharides, or both. Here, we use molecular simulations to determine the mechanism and driving forces for binding of AFGP8 to ice, its selectivity for the primary prismatic plane, and the molecular origin of its exceptional ice recrystallization activity. Consistent with experiments, AFGP8 in simulations preferentially adopts the PPII helix secondary structure in solution. We show that the segregation of hydrophilic and hydrophobic groups in the PPII helix is vital for ice binding. Binding occurs through adsorption of methyl groups of the peptide and disaccharides to ice, driven by the entropy of dehydration of the hydrophobic groups as they nest in the cavities at the ice surface. The selectivity to the primary prismatic plane originates in the deeper cavities it has compared to the basal plane. We estimate the free energy of binding of AFGP8 and the longer AFGPs4-6, and find them to be consistent with the reversible binding demonstrated in experiments. The simulations reveal that AFGP8 binds to ice through a myriad of conformations that it uses to diffuse through the ice surface and find ice steps, to which it strongly adsorbs. We interpret that the existence of multiple, weak binding sites is the key for the exceptional ice recrystallization inhibition activity of AFGPs.
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Affiliation(s)
- Kenji Mochizuki
- Department of Chemistry , The University of Utah , Salt Lake City , Utah 84112-0580 , United States.,Institute for Fiber Engineering , Shinshu University , Ueda , Nagano 386-8567 , Japan
| | - Valeria Molinero
- Department of Chemistry , The University of Utah , Salt Lake City , Utah 84112-0580 , United States
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36
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Zhang B, Zhang XL, Shen CL, Deng SG. Understanding the influence of carrageenan oligosaccharides and xylooligosaccharides on ice-crystal growth in peeled shrimp (Litopenaeus vannamei) during frozen storage. Food Funct 2018; 9:4394-4403. [DOI: 10.1039/c8fo00364e] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cryoprotective saccharides are widely accepted antifreeze additives that reduce thawing loss, maintain texture, and retard protein denaturation in frozen seafood.
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Affiliation(s)
- Bin Zhang
- Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province
- College of Food Science and Pharmacy
- Zhejiang Ocean University
- Zhoushan
- 316022 P. R. China
| | - Xiao-li Zhang
- Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province
- College of Food Science and Pharmacy
- Zhejiang Ocean University
- Zhoushan
- 316022 P. R. China
| | - Chun-lei Shen
- Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province
- College of Food Science and Pharmacy
- Zhejiang Ocean University
- Zhoushan
- 316022 P. R. China
| | - Shang-gui Deng
- Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province
- College of Food Science and Pharmacy
- Zhejiang Ocean University
- Zhoushan
- 316022 P. R. China
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37
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Verreault D, Alamdari S, Roeters SJ, Pandey R, Pfaendtner J, Weidner T. Ice-binding site of surface-bound type III antifreeze protein partially decoupled from water. Phys Chem Chem Phys 2018; 20:26926-26933. [DOI: 10.1039/c8cp03382j] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Combined SFG/MD analysis together with spectral calculations revealed that type III antifreeze proteins adsorbed at the air–water interface maintains a native state and adopts an orientation that leads to a partial decoupling of its ice-binding site from water.
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Affiliation(s)
| | - Sarah Alamdari
- Department of Chemical Engineering
- University of Washington
- Seattle
- USA
| | | | - Ravindra Pandey
- Department of Chemistry
- Indian Institute of Technology
- Roorkee 247667
- India
| | - Jim Pfaendtner
- Department of Chemical Engineering
- University of Washington
- Seattle
- USA
| | - Tobias Weidner
- Department of Chemistry
- Aarhus University
- 8000 Aarhus C
- Denmark
- Department of Chemical Engineering
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38
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Lopez Ortiz JI, Torres P, Quiroga E, Narambuena CF, Ramirez-Pastor AJ. Adsorption of three-domain antifreeze proteins on ice: a study using LGMMAS theory and Monte Carlo simulations. Phys Chem Chem Phys 2017; 19:31377-31388. [PMID: 29155905 DOI: 10.1039/c7cp06618j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the present work, the adsorption of three-domain antifreeze proteins on ice is studied by combining a statistical thermodynamics based theory and Monte Carlo simulations. The three-domain protein is modeled by a trimer, and the ice surface is represented by a lattice of adsorption sites. The statistical theory, obtained from the exact partition function of non-interacting trimers adsorbed in one dimension and its extension to two dimensions, includes the configuration of the molecule in the adsorbed state, and allows the existence of multiple adsorption states for the protein. We called this theory "lattice-gas model of molecules with multiple adsorption states" (LGMMAS). The main thermodynamics functions (partial and total adsorption isotherms, Helmholtz free energy and configurational entropy) are obtained by solving a non-linear system of j equations, where j is the total number of possible adsorption states of the protein. The theoretical results are contrasted with Monte Carlo simulations, and a modified Langmuir model (MLM) where the arrangement of the adsorption sites in space is immaterial. The formalism introduced here provides exact results in one-dimensional lattices, and offers a very accurate description in two dimensions (2D). In addition, the scheme is capable of predicting the proportion between coverage degrees corresponding to different conformations in the same energetic state. In contrast, the MLM does not distinguish between different adsorption states, and shows severe discrepancies with the 2D simulation results. These findings indicate that the adsorbate structure and the lattice geometry play fundamental roles in determining the statistics of multistate adsorbed molecules, and consequently, must be included in the theory.
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Affiliation(s)
- Juan Ignacio Lopez Ortiz
- Departamento de Física, Instituto de Física Aplicada, Universidad Nacional de San Luis-CONICET, Ejército de Los Andes 950, D5700BWS San Luis, Argentina.
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39
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Wang C, Pakhomova S, Newcomer ME, Christner BC, Luo BH. Structural basis of antifreeze activity of a bacterial multi-domain antifreeze protein. PLoS One 2017; 12:e0187169. [PMID: 29108002 PMCID: PMC5673226 DOI: 10.1371/journal.pone.0187169] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 10/13/2017] [Indexed: 01/05/2023] Open
Abstract
Antifreeze proteins (AFPs) enhance the survival of organisms inhabiting cold environments by affecting the formation and/or structure of ice. We report the crystal structure of the first multi-domain AFP that has been characterized. The two ice binding domains are structurally similar. Each consists of an irregular β-helix with a triangular cross-section and a long α-helix that runs parallel on one side of the β-helix. Both domains are stabilized by hydrophobic interactions. A flat plane on the same face of each domain’s β-helix was identified as the ice binding site. Mutating any of the smaller residues on the ice binding site to bulkier ones decreased the antifreeze activity. The bulky side chain of Leu174 in domain A sterically hinders the binding of water molecules to the protein backbone, partially explaining why antifreeze activity by domain A is inferior to that of domain B. Our data provide a molecular basis for understanding differences in antifreeze activity between the two domains of this protein and general insight on how structural differences in the ice-binding sites affect the activity of AFPs.
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Affiliation(s)
- Chen Wang
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Svetlana Pakhomova
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Marcia E. Newcomer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Brent C. Christner
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
- Department of Microbiology and Cell Science, Biodiversity Institute, University of Florida, Gainesville, Florida, United States of America
| | - Bing-Hao Luo
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
- * E-mail:
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40
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Balance between hydration enthalpy and entropy is important for ice binding surfaces in Antifreeze Proteins. Sci Rep 2017; 7:11901. [PMID: 28928396 PMCID: PMC5605524 DOI: 10.1038/s41598-017-11982-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 08/29/2017] [Indexed: 11/21/2022] Open
Abstract
Antifreeze Proteins (AFPs) inhibit the growth of an ice crystal by binding to it. The detailed binding mechanism is, however, still not fully understood. We investigated three AFPs using Molecular Dynamics simulations in combination with Grid Inhomogeneous Solvation Theory, exploring their hydration thermodynamics. The observed enthalpic and entropic differences between the ice-binding sites and the inactive surface reveal key properties essential for proteins in order to bind ice: While entropic contributions are similar for all sites, the enthalpic gain for all ice-binding sites is lower than for the rest of the protein surface. In contrast to most of the recently published studies, our analyses show that enthalpic interactions are as important as an ice-like pre-ordering. Based on these observations, we propose a new, thermodynamically more refined mechanism of the ice recognition process showing that the appropriate balance between entropy and enthalpy facilitates ice-binding of proteins. Especially, high enthalpic interactions between the protein surface and water can hinder the ice-binding activity.
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41
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Halder S, Mukhopadhyay C. Effect of glycosylation on hydration behavior at the ice-binding surface of the Ocean Pout type III antifreeze protein: a molecular dynamics simulation. J Biomol Struct Dyn 2016; 35:3591-3604. [PMID: 27882844 DOI: 10.1080/07391102.2016.1264888] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Antifreeze proteins (AFPs), found in certain vertebrates, plants, fungi and bacteria have the ability to permit their survival in subzero environments by thermal hysteresis mechanism. However, the exact mechanism of ice growth inhibition is still not clearly understood. Here, four long explicit molecular dynamics (MD) simulations have been carried out at two different temperatures (277 and 298 K) with and without glycan to study the conformational rigidity of the Ocean pout type III antifreeze protein in aqueous medium and the structural arrangements of water molecules hydrating its ice-binding surface. It is found that irrespective of the temperature the ice-binding surface (IBS) of the protein is relatively more rigid than its non ice-binding surface (NonIBS) in its native and glycosylated form. Hydrophilic residues N14, T18 and Q44 are essential to antifreeze activity. Radial distribution, density distribution function and nearest neighbor orientation plots with respect to individual two surfaces confirm that density of water molecule near these binding surface in native and glycosylated form are relatively more than the nonbinding surface. The glycosylated form shows a strong peak than the native one. From rotational auto correlation function of water molecules around ice-binding sites, it is prominent that with increase in temperature, strong interaction between the water oxygen and the hydrogen bond acceptor group on the protein-binding surface decreases. This provides a possible molecular reason behind the ice-binding activity of ocean pout at the prism plane of ice.
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Affiliation(s)
- Swagata Halder
- a Department of Chemistry , University of Calcutta , 92, A. P. C. Road, Kolkata 700009 , India
| | - Chaitali Mukhopadhyay
- a Department of Chemistry , University of Calcutta , 92, A. P. C. Road, Kolkata 700009 , India
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42
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Okada T. Micro- and Nano-Liquid Phases Coexistent with Ice as Separation and Reaction Media. CHEM REC 2016; 17:415-428. [PMID: 27709788 DOI: 10.1002/tcr.201600097] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Indexed: 12/21/2022]
Abstract
Ice has a variety of scientifically interesting features, some of which have not been reasonably interpreted despite substantial efforts by researchers. Most chemical studies of ice have focused on the elucidation of its physicochemical nature and its roles in the natural environment. Ice often contains impurities, such as salts, and in such cases, a liquid phase coexists with solid ice over a wide temperature range. This impure ice also acts as a cryoreactor, governing the circulation of chemical species of environmental importance. Reactions and phenomena occurring in this liquid phase show features different from those seen in normal bulk aqueous solutions. In the present account, we discuss the chemical characteristics of the liquid phase that develops in a frozen aqueous phase and show how novel analytical systems can be designed based on he features of the liquid phase which are predictable in some cases but unpredictable in others.
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Affiliation(s)
- Tetsuo Okada
- Department of Chemistry, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152 - 8551, Japan
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43
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Kar RK, Bhunia A. Biophysical and biochemical aspects of antifreeze proteins: Using computational tools to extract atomistic information. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 119:194-204. [DOI: 10.1016/j.pbiomolbio.2015.09.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 09/04/2015] [Indexed: 01/09/2023]
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44
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Coarse grained simulation reveals antifreeze properties of hyperactive antifreeze protein from Antarctic bacterium Colwellia sp. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.08.042] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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45
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Duboué-Dijon E, Laage D. Comparative study of hydration shell dynamics around a hyperactive antifreeze protein and around ubiquitin. J Chem Phys 2015; 141:22D529. [PMID: 25494800 DOI: 10.1063/1.4902822] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The hydration layer surrounding a protein plays an essential role in its biochemical function and consists of a heterogeneous ensemble of water molecules with different local environments and different dynamics. What determines the degree of dynamical heterogeneity within the hydration shell and how this changes with temperature remains unclear. Here, we combine molecular dynamics simulations and analytic modeling to study the hydration shell structure and dynamics of a typical globular protein, ubiquitin, and of the spruce budworm hyperactive antifreeze protein over the 230-300 K temperature range. Our results show that the average perturbation induced by both proteins on the reorientation dynamics of water remains moderate and changes weakly with temperature. The dynamical heterogeneity arises mostly from the distribution of protein surface topographies and is little affected by temperature. The ice-binding face of the antifreeze protein induces a short-ranged enhancement of water structure and a greater slowdown of water reorientation dynamics than the non-ice-binding faces whose effect is similar to that of ubiquitin. However, the hydration shell of the ice-binding face remains less tetrahedral than the bulk and is not "ice-like". We finally show that the hydrogen bonds between water and the ice-binding threonine residues are particularly strong due to a steric confinement effect, thereby contributing to the strong binding of the antifreeze protein on ice crystals.
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Affiliation(s)
- Elise Duboué-Dijon
- Département de Chimie, École Normale Supérieure-PSL Research University, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, 24, rue Lhomond, 75005 Paris, France
| | - Damien Laage
- Département de Chimie, École Normale Supérieure-PSL Research University, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, 24, rue Lhomond, 75005 Paris, France
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46
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Kuiper MJ, Morton CJ, Abraham SE, Gray-Weale A. The biological function of an insect antifreeze protein simulated by molecular dynamics. eLife 2015; 4. [PMID: 25951514 PMCID: PMC4442126 DOI: 10.7554/elife.05142] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 05/06/2015] [Indexed: 11/16/2022] Open
Abstract
Antifreeze proteins (AFPs) protect certain cold-adapted organisms from freezing to death by selectively adsorbing to internal ice crystals and inhibiting ice propagation. The molecular details of AFP adsorption-inhibition is uncertain but is proposed to involve the Gibbs–Thomson effect. Here we show by using unbiased molecular dynamics simulations a protein structure-function mechanism for the spruce budworm Choristoneura fumiferana AFP, including stereo-specific binding and consequential melting and freezing inhibition. The protein binds indirectly to the prism ice face through a linear array of ordered water molecules that are structurally distinct from the ice. Mutation of the ice binding surface disrupts water-ordering and abolishes activity. The adsorption is virtually irreversible, and we confirm the ice growth inhibition is consistent with the Gibbs–Thomson law. DOI:http://dx.doi.org/10.7554/eLife.05142.001 Water expands as it freezes. If this happens to the water inside plants and animals, the resulting ice crystals can rupture cells. To prevent this, many plants and animals that live in cold climates have evolved ‘antifreeze proteins’. When a small particle of ice first starts to form, the antifreeze proteins bind to it and prevent the water around it freezing, hence preventing the growth of an ice crystal. There are many different types of antifreeze protein, and some are more active than others. For example, some insects including the spruce budworm are exposed to extremely cold temperatures—sometimes below −30°C—and these insects have antifreeze proteins that are highly active. It is not fully understood how different antifreeze proteins interact with ice and prevent the growth of ice crystals. This is largely because, as yet, there are no experimental techniques that make it possible to see how antifreeze proteins and water molecules arrange themselves at the surface of a growing particle of ice. Instead, scientists have developed computer simulations to investigate this process. While many of these studies have provided valuable information, the computational methods used have only recently become powerful enough to analyze how the antifreeze proteins approach the surface of the ice particle. Kuiper et al. carried out simulations involving a highly active antifreeze protein from the spruce budworm. The results of these simulations revealed that this antifreeze protein does not bind directly to ice; instead, water molecules at the surface of the protein act as a bridge between the protein and the ice. These water molecules are highly ordered and though they have similarities with how water is structured in the ice, they are distinct from the ice lattice itself. Furthermore, this arrangement appears to be important for allowing the spruce budworm antifreeze protein to interact with the ice. This study provides detailed insights as to how a highly active antifreeze protein helps to prevent ice crystals forming. In the future, the computational simulations used here may be extended to study the dynamics of other antifreeze proteins, and also how crystals of other materials form. DOI:http://dx.doi.org/10.7554/eLife.05142.002
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Affiliation(s)
- Michael J Kuiper
- Victorian Life Sciences Computation Initiative, The University of Melbourne, Carlton, Australia
| | - Craig J Morton
- ACRF Rational Drug Discovery Centre, St Vincent's Institute of Medical Research, Fitzroy, Australia
| | - Sneha E Abraham
- School of Chemistry, The University of Melbourne, Melbourne, Australia
| | - Angus Gray-Weale
- School of Chemistry, The University of Melbourne, Melbourne, Australia
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47
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Qu H, Arai Y, Harada M, Okada T. Freeze Enrichment Protocol Based on Voltammetric Probing of Liquid-Phase Growth in Frozen Aqueous Electrolyte Solutions. Anal Chem 2015; 87:4314-20. [DOI: 10.1021/acs.analchem.5b00747] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hui Qu
- Department of Chemistry, Tokyo Institute of Technology, Meguro-ku,
Tokyo 152-8551, Japan
| | - Yuta Arai
- Department of Chemistry, Tokyo Institute of Technology, Meguro-ku,
Tokyo 152-8551, Japan
| | - Makoto Harada
- Department of Chemistry, Tokyo Institute of Technology, Meguro-ku,
Tokyo 152-8551, Japan
| | - Tetsuo Okada
- Department of Chemistry, Tokyo Institute of Technology, Meguro-ku,
Tokyo 152-8551, Japan
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48
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Nada H. Importance of water in the control of calcite crystal growth by organic molecules. Polym J 2014. [DOI: 10.1038/pj.2014.87] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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49
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Kutschan B, Morawetz K, Thoms S. Dynamical mechanism of antifreeze proteins to prevent ice growth. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 90:022711. [PMID: 25215762 DOI: 10.1103/physreve.90.022711] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Indexed: 06/03/2023]
Abstract
The fascinating ability of algae, insects, and fishes to survive at temperatures below normal freezing is realized by antifreeze proteins (AFPs). These are surface-active molecules and interact with the diffusive water-ice interface thus preventing complete solidification. We propose a dynamical mechanism on how these proteins inhibit the freezing of water. We apply a Ginzburg-Landau-type approach to describe the phase separation in the two-component system (ice, AFP). The free-energy density involves two fields: one for the ice phase with a low AFP concentration and one for liquid water with a high AFP concentration. The time evolution of the ice reveals microstructures resulting from phase separation in the presence of AFPs. We observed a faster clustering of pre-ice structure connected to a locking of grain size by the action of AFP, which is an essentially dynamical process. The adsorption of additional water molecules is inhibited and the further growth of ice grains stopped. The interfacial energy between ice and water is lowered allowing the AFPs to form smaller critical ice nuclei. Similar to a hysteresis in magnetic materials we observe a thermodynamic hysteresis leading to a nonlinear density dependence of the freezing point depression in agreement with the experiments.
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Affiliation(s)
- B Kutschan
- Münster University of Applied Science, Stegerwaldstrasse 39, 48565 Steinfurt, Germany
| | - K Morawetz
- Münster University of Applied Science, Stegerwaldstrasse 39, 48565 Steinfurt, Germany and International Institute of Physics (IIP), Federal University of Rio Grande do Norte, Av. Odilon Gomes de Lima 1722, 59078-400 Natal, Brazil and Max-Planck-Institute for the Physics of Complex Systems, 01187 Dresden, Germany
| | - S Thoms
- Alfred Wegener Institut, Am Handelshafen 12, D-27570 Bremerhaven, Germany
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50
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Nguyen H, Le L, Ho TB. Computational study on ice growth inhibition of Antarctic bacterium antifreeze protein using coarse grained simulation. J Chem Phys 2014; 140:225101. [DOI: 10.1063/1.4881895] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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