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Nooteboom SW, Okholm KR, Lamberti V, Oomen B, Sutherland DS, Zijlstra P. Rate-Engineered Plasmon-Enhanced Fluorescence for Real-Time Microsecond Dynamics of Single Biomolecules. NANO LETTERS 2024; 24:11641-11647. [PMID: 39248371 PMCID: PMC11421078 DOI: 10.1021/acs.nanolett.4c03220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/10/2024]
Abstract
Single-molecule fluorescence has revealed a wealth of biochemical processes but does not give access to submillisecond dynamics involved in transient interactions and molecular dynamics. Here we overcome this bottleneck and demonstrate record-high photon count rates of >107 photons/s from single plasmon-enhanced fluorophores. This is achieved by combining two conceptual novelties: first, we balance the excitation and decay rate enhancements by the antenna's volume, resulting in maximum fluorescence intensity. Second, we enhance the triplet decay rate using a multicomponent surface chemistry that minimizes microsecond blinking. We demonstrate applications to two exemplary molecular processes: we first reveal transient encounters and hybridization of DNA with a 1 μs temporal resolution. Second, we exploit the field gradient around the nanoparticle as a molecular ruler to reveal microsecond intramolecular dynamics of multivalent complexes. Our results pave the way toward real-time microsecond studies of biochemical processes using an implementation compatible with existing single-molecule fluorescence methods.
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Affiliation(s)
- Sjoerd W Nooteboom
- Department of Applied Physics and Science Education, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Kasper R Okholm
- Interdisciplinary Nanoscience Center, Aarhus University, 8000 Aarhus C, Denmark
- The Centre for Cellular Signal Patterns (CELLPAT), 8000 Aarhus C, Denmark
| | - Vincenzo Lamberti
- Department of Applied Physics and Science Education, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Bas Oomen
- Department of Applied Physics and Science Education, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Duncan S Sutherland
- Interdisciplinary Nanoscience Center, Aarhus University, 8000 Aarhus C, Denmark
- The Centre for Cellular Signal Patterns (CELLPAT), 8000 Aarhus C, Denmark
| | - Peter Zijlstra
- Department of Applied Physics and Science Education, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
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2
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Gerhäuser J, Hale J, Wefers D, Gaukel V. Furcellaran: Impact of Concentration, Rheological Properties, and Structure on Ice Recrystallization Inhibition Activity. Biomacromolecules 2024; 25:4535-4544. [PMID: 38973364 DOI: 10.1021/acs.biomac.4c00541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
Recrystallization is considered the main damaging mechanism during the frozen storage of biologic materials. In this study, furcellaran, a polysaccharide related to κ-carrageenan, was studied for its concentration-dependent effect on ice crystal growth and recrystallization. The structure and sulfate content of the utilized furcellaran was analyzed by 1H nuclear magnetic resonance spectroscopy, ion chromatography, and high-performance size-exclusion chromatography. Additionally, the rheological properties of furcellaran solutions were investigated. Our findings demonstrate that furcellaran inhibits ice growth as effectively as κ-carrageenan. Furthermore, the rheological properties change with increasing furcellaran concentration, resulting in a gel-like consistency at 5 g/L, which coincides with decreased recrystallization inhibition activity and larger crystals. This suggests that gel formation or a gel-like consistency has to be avoided for optimal recrystallization inhibition activity.
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Affiliation(s)
- Julian Gerhäuser
- Institute of Process Engineering in Life Sciences, Food Process Engineering, Karlsruhe Institute of Technology, Kaiserstraße 12, 76131 Karlsruhe, Germany
| | - Julia Hale
- Institute of Applied Biosciences, Department of Food Chemistry and Phytochemistry, Karlsruhe Institute of Technology, Kaiserstraße 12, 76131 Karlsruhe, Germany
| | - Daniel Wefers
- Institute of Chemistry, Food Chemistry, Martin Luther University Halle Wittenberg, Universitätsplatz 10, 06108 Halle, Germany
| | - Volker Gaukel
- Institute of Process Engineering in Life Sciences, Food Process Engineering, Karlsruhe Institute of Technology, Kaiserstraße 12, 76131 Karlsruhe, Germany
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Yang T, Zhang Y, Guo L, Li D, Liu A, Bilal M, Xie C, Yang R, Gu Z, Jiang D, Wang P. Antifreeze Polysaccharides from Wheat Bran: The Structural Characterization and Antifreeze Mechanism. Biomacromolecules 2024; 25:3877-3892. [PMID: 38388358 DOI: 10.1021/acs.biomac.3c00958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Exploring a novel natural cryoprotectant and understanding its antifreeze mechanism allows the rational design of future sustainable antifreeze analogues. In this study, various antifreeze polysaccharides were isolated from wheat bran, and the antifreeze activity was comparatively studied in relation to the molecular structure. The antifreeze mechanism was further revealed based on the interactions of polysaccharides and water molecules through dynamic simulation analysis. The antifreeze polysaccharides showed distinct ice recrystallization inhibition activity, and structural analysis suggested that the polysaccharides were arabinoxylan, featuring a xylan backbone with a majority of Araf and minor fractions of Manp, Galp, and Glcp involved in the side chain. The antifreeze arabinoxylan, characterized by lower molecular weight, less branching, and more flexible conformation, could weaken the hydrogen bonding of the surrounding water molecules more evidently, thus retarding the transformation of water molecules into the ordered ice structure.
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Affiliation(s)
- Tao Yang
- College of Food Science and Technology, Whole Grain Food Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop Physiology, Ecology, and Management, Ministry of Agriculture/National Engineering and Technology Center for Information Agriculture, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Yining Zhang
- College of Food Science and Technology, Whole Grain Food Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Li Guo
- School of Materials Science and Engineering, Jiangsu University, Zhenjiang 212013, People's Republic of China
| | - Dandan Li
- College of Food Science and Technology, Whole Grain Food Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
- The Sanya Institute of Nanjing Agricultural University, Sanya 572024, People's Republic of China
| | - Anqi Liu
- College of Food Science and Technology, Whole Grain Food Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Muhammad Bilal
- College of Food Science and Technology, Whole Grain Food Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Chong Xie
- College of Food Science and Technology, Whole Grain Food Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
- The Sanya Institute of Nanjing Agricultural University, Sanya 572024, People's Republic of China
| | - Runqiang Yang
- College of Food Science and Technology, Whole Grain Food Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
- The Sanya Institute of Nanjing Agricultural University, Sanya 572024, People's Republic of China
| | - Zhenxin Gu
- College of Food Science and Technology, Whole Grain Food Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
- The Sanya Institute of Nanjing Agricultural University, Sanya 572024, People's Republic of China
| | - Dong Jiang
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop Physiology, Ecology, and Management, Ministry of Agriculture/National Engineering and Technology Center for Information Agriculture, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
- The Sanya Institute of Nanjing Agricultural University, Sanya 572024, People's Republic of China
| | - Pei Wang
- College of Food Science and Technology, Whole Grain Food Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop Physiology, Ecology, and Management, Ministry of Agriculture/National Engineering and Technology Center for Information Agriculture, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
- The Sanya Institute of Nanjing Agricultural University, Sanya 572024, People's Republic of China
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4
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Nagel M, Pence V, Ballesteros D, Lambardi M, Popova E, Panis B. Plant Cryopreservation: Principles, Applications, and Challenges of Banking Plant Diversity at Ultralow Temperatures. ANNUAL REVIEW OF PLANT BIOLOGY 2024; 75:797-824. [PMID: 38211950 DOI: 10.1146/annurev-arplant-070623-103551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
Progressive loss of plant diversity requires the protection of wild and agri-/horticultural species. For species whose seeds are extremely short-lived, or rarely or never produce seeds, or whose genetic makeup must be preserved, cryopreservation offers the only possibility for long-term conservation. At temperatures below freezing, most vegetative plant tissues suffer severe damage from ice crystal formation and require protection. In this review, we describe how increasing the concentration of cellular solutes by air drying or adding cryoprotectants, together with rapid cooling, results in a vitrified, highly viscous state in which cells can remain viable and be stored. On this basis, a range of dormant bud-freezing, slow-cooling, and (droplet-)vitrification protocols have been developed, but few are used to cryobank important agricultural/horticultural/timber and threatened species. To improve cryopreservation efficiency, the effects of cryoprotectants and molecular processes need to be understood and the costs for cryobanking reduced. However, overall, the long-term costs of cryopreservation are low, while the benefits are huge.
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Affiliation(s)
- Manuela Nagel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Seeland, Germany;
| | - Valerie Pence
- Lindner Center for Conservation and Research of Endangered Wildlife (CREW), Cincinnati Zoo & Botanical Garden, Cincinnati, Ohio, USA
| | - Daniel Ballesteros
- Department of Botany and Geology, Universitat de València, Burjassot, Spain
- Royal Botanic Gardens, Kew, Wakehurst Place, West Sussex, United Kingdom
| | - Maurizio Lambardi
- Institute of BioEconomy (IBE), National Research Council (CNR), Florence, Italy
| | - Elena Popova
- Department of Cell Biology and Biotechnology, K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Bart Panis
- The Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), KU Leuven, Leuven, Belgium
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5
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Song J, Tas RP, Martens MCM, Ritten MVM, Wu H, Jones ER, Lebouille JGJL, Vis M, Voets IK, Tuinier R. Freezing-mediated formation of supraproteins using depletion forces. J Colloid Interface Sci 2024; 665:622-633. [PMID: 38552579 DOI: 10.1016/j.jcis.2024.03.088] [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] [Received: 12/04/2023] [Revised: 02/16/2024] [Accepted: 03/11/2024] [Indexed: 04/17/2024]
Abstract
Hypothesis Long-acting formulations such as microparticles, injectable depots and implantable devices can realize spatiotemporally controlled delivery of protein drugs to extend their therapeutic in vivo half-lives. To efficiently encapsulate the protein drugs into such drug delivery systems, (sub)micron-sized protein particles are needed. The formation of micronized supraproteins can be induced through the synergistic combination of attractive depletion forces and freezing. The size of the supraproteins can be fine-tuned from submicron to several microns by adjusting the ice crystallization rate through the freeze-quench depth, which is set by the target temperature. Methods Supraprotein micron structures were prepared from protein solutions under various conditions in the presence and absence of nonadsorbing polyethylene glycol. Scanning electron microscopy and dynamic light scattering were employed to determine the sizes of the supraproteins and real-time total internal reflection fluorescent microscopy was used to follow the supraprotein formation during freezing. The protein secondary structure was measured before and after micronization by circular dichroism. A phase diagram of a protein-polyethylene glycol mixture was theoretically predicted to investigate whether the depletion interaction can elucidate the phase behavior. Findings Micronized protein supraparticles could be prepared in a controlled manner by rapid freeze-drying of aqueous mixtures of bovine serum albumin, horseradish peroxidase and lysozyme mixed with polyethylene glycol. Upon freezing, the temperature quench initiates a phase separation process which is reminiscent of spinodal decomposition. This demixing is subsequently arrested during droplet phase separation to form protein-rich microstructures. The final size of the generated protein microparticles is determined by a competition between phase separation and cooling rate, which can be controlled by target temperature. The experimental phase diagram of the aqueous protein-polyethylene glycol dispersion aligns with predictions from depletion theory for charged colloids and nonadsorbing polymers.
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Affiliation(s)
- Jiankang Song
- Laboratory of Physical Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, the Netherlands; Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, the Netherlands.
| | - Roderick P Tas
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, the Netherlands; Laboratory of Self-organizing Soft Matter, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, the Netherlands
| | - Max C M Martens
- Laboratory of Physical Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, the Netherlands; Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, the Netherlands
| | - Manon V M Ritten
- Laboratory of Physical Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, the Netherlands; Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, the Netherlands
| | - Hanglong Wu
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, the Netherlands; Bio-Organic Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, the Netherlands
| | | | | | - Mark Vis
- Laboratory of Physical Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, the Netherlands; Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, the Netherlands
| | - Ilja K Voets
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, the Netherlands; Laboratory of Self-organizing Soft Matter, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, the Netherlands
| | - Remco Tuinier
- Laboratory of Physical Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, the Netherlands; Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, the Netherlands.
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6
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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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7
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Zhu S, Jin Y, Yu J, Yang W, Lian J, Wei Z, Zhang D, Ding Y, Zhou X. Composition-antifreeze property relationships of gelatin and the corresponding mechanisms. Int J Biol Macromol 2024; 268:131941. [PMID: 38685545 DOI: 10.1016/j.ijbiomac.2024.131941] [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] [Received: 08/12/2023] [Revised: 04/08/2024] [Accepted: 04/26/2024] [Indexed: 05/02/2024]
Abstract
The inherent functional fractions (gelation and ice-affinitive fractions) of gelatin enable it as a promising cryoprotectant alternative. However, the composition-antifreeze property relationships of gelatin remain to be investigated. In this study, the HW-PSG and LW-PSG fractions of gelatin from fish scales were obtained, according to the critical gelation conditions and ice-binding measurements, respectively. Thermal hysteresis (THA) value, associated with ice nucleation, of LW-PSG was higher than that of HW-PSG. Besides, the relatively low-sized ice crystals (210-550 μm2) indicated that HW-PSG showed strong ice recrystallization inhibition (IRI) ability, compared to other groups. These results suggested that LW-PSG inhibited ice nucleation, while HW-PSG displayed the strong IRI ability. Furthermore, the antifreeze mechanisms were clarified through IRI measurements and molecular dynamics simulation. The minimum size of ice crystals was found for HW-PSG gels with dense microstructure, suggesting the HW-PSG retarded the growth of ice crystals by restricting the migration and phase transformation of water molecules. The hydrogen bond interactions between the ice crystal surface and ASN1294 and PRO1433 residues of LW-PSG, and hydrophobic interactions contributed to inhibiting the nucleation of ice crystals. This study provided some references to further enhance antifreeze performance of gelatin by modulating fragment composition.
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Affiliation(s)
- Shichen Zhu
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou, China; Zhejiang Key Laboratory of Green, Low-carbon and Efficient Development of Marine Fishery Resources, Hangzhou 310014, China; National R&D Branch Center for Pelagic Aquatic Products Processing (Hangzhou), Hangzhou, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - Yan Jin
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou, China; Zhejiang Key Laboratory of Green, Low-carbon and Efficient Development of Marine Fishery Resources, Hangzhou 310014, China; National R&D Branch Center for Pelagic Aquatic Products Processing (Hangzhou), Hangzhou, China
| | - Jiehang Yu
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou, China; Zhejiang Key Laboratory of Green, Low-carbon and Efficient Development of Marine Fishery Resources, Hangzhou 310014, China; National R&D Branch Center for Pelagic Aquatic Products Processing (Hangzhou), Hangzhou, China
| | - Wenting Yang
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou, China; Zhejiang Key Laboratory of Green, Low-carbon and Efficient Development of Marine Fishery Resources, Hangzhou 310014, China; National R&D Branch Center for Pelagic Aquatic Products Processing (Hangzhou), Hangzhou, China
| | - Jing Lian
- Comprehensive service center of market supervision and management of Rongcheng, Shandong, China
| | - Zhengpeng Wei
- Taixiang Group, Rongcheng Taixiang Food Products Co., Ltd., Ministry of Agriculture, Key Laboratory of Frozen Prepared Marine Foods Processing, Rongcheng 264300, China
| | - Dong Zhang
- College of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Yuting Ding
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou, China; Zhejiang Key Laboratory of Green, Low-carbon and Efficient Development of Marine Fishery Resources, Hangzhou 310014, China; National R&D Branch Center for Pelagic Aquatic Products Processing (Hangzhou), Hangzhou, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - Xuxia Zhou
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou, China; Zhejiang Key Laboratory of Green, Low-carbon and Efficient Development of Marine Fishery Resources, Hangzhou 310014, China; National R&D Branch Center for Pelagic Aquatic Products Processing (Hangzhou), Hangzhou, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China.
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8
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Sirotinskaya V, Bar Dolev M, Yashunsky V, Bahari L, Braslavsky I. Extended Temperature Range of the Ice-Binding Protein Activity. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:7395-7404. [PMID: 38527127 PMCID: PMC11008235 DOI: 10.1021/acs.langmuir.3c03710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 03/07/2024] [Accepted: 03/08/2024] [Indexed: 03/27/2024]
Abstract
Ice-binding proteins (IBPs) are expressed in various organisms for several functions, such as protecting them from freezing and freeze injuries. Via adsorption on ice surfaces, IBPs depress ice growth and recrystallization and affect nucleation and ice shaping. IBPs have shown promise in mitigating ice growth under moderate supercooling conditions, but their functionality under cryogenic conditions has been less explored. In this study, we investigate the impact of two types of antifreeze proteins (AFPs): type III AFP from fish and a hyperactive AFP from an insect, the Tenebrio molitor AFP, in vitrified dimethylsulfoxide (DMSO) solutions. We report that these AFPs depress devitrification at -80 °C. Furthermore, in cases where devitrification does occur, AFPs depress ice recrystallization during the warming stage. The data directly demonstrate that AFPs are active at temperatures below the regime of homogeneous nucleation. This research paves the way for exploring AFPs as potential enhancers of cryopreservation techniques, minimizing ice-growth-related damage, and promoting advancements in this vital field.
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Affiliation(s)
- Vera Sirotinskaya
- Institute
of Biochemistry, Food Science, and Nutrition, Robert H. Smith Faculty
of Agriculture, Food and Environment, The
Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Maya Bar Dolev
- Institute
of Biochemistry, Food Science, and Nutrition, Robert H. Smith Faculty
of Agriculture, Food and Environment, The
Hebrew University of Jerusalem, Rehovot 7610001, Israel
- Faculty
of Biotechnology and Food Engineering, Technion, Haifa 3200003, Israel
| | - Victor Yashunsky
- Institute
of Biochemistry, Food Science, and Nutrition, Robert H. Smith Faculty
of Agriculture, Food and Environment, The
Hebrew University of Jerusalem, Rehovot 7610001, Israel
- The
Swiss Institute for Dryland Environmental and Energy Research, Ben Gurion University, Beer-Sheva 84105, Israel
| | - Liat Bahari
- Institute
of Biochemistry, Food Science, and Nutrition, Robert H. Smith Faculty
of Agriculture, Food and Environment, The
Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Ido Braslavsky
- Institute
of Biochemistry, Food Science, and Nutrition, Robert H. Smith Faculty
of Agriculture, Food and Environment, The
Hebrew University of Jerusalem, Rehovot 7610001, Israel
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9
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Grabowska J, Kuffel A, Zielkiewicz J. Long-range, water-mediated interaction between a moderately active antifreeze protein molecule and the surface of ice. J Chem Phys 2024; 160:095101. [PMID: 38445741 DOI: 10.1063/5.0187663] [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: 11/15/2023] [Accepted: 02/16/2024] [Indexed: 03/07/2024] Open
Abstract
Using molecular dynamics simulations, we show that a molecule of moderately active antifreeze protein (type III AFP, QAE HPLC-12 isoform) is able to interact with ice in an indirect manner. This interaction occurs between the ice binding site (IBS) of the AFP III molecule and the surface of ice, and it is mediated by liquid water, which separates these surfaces. As a result, the AFP III molecule positions itself at a specific orientation and distance relative to the surface of ice, which enables the effective binding (via hydrogen bonds) of the molecule with the nascent ice surface. Our results show that the final adsorption of the AFP III molecule on the surface of ice is not achieved by chaotic diffusion movements, but it is preceded by a remote, water-mediated interaction between the IBS and the surface of ice. The key factor that determines the existence of this interaction is the ability of water molecules to spontaneously form large, high-volume aggregates that can be anchored to both the IBS of the AFP molecule and the surface of ice. The results presented in this work for AFP III are in full agreement with the ones obtained by us previously for hyperactive CfAFP, which indicates that the mechanism of the remote interaction of these molecules with ice remains unchanged despite significant differences in the molecular structure of their ice binding sites. For that reason, we can expect that also other types of AFPs interact with the ice surface according to an analogous mechanism.
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Affiliation(s)
- Joanna Grabowska
- Faculty of Chemistry, Department of Physical Chemistry, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Anna Kuffel
- Faculty of Chemistry, Department of Physical Chemistry, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Jan Zielkiewicz
- Faculty of Chemistry, Department of Physical Chemistry, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
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10
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Drori R, Stevens CA. Divergent Mechanisms of Ice Growth Inhibition by Antifreeze Proteins. Methods Mol Biol 2024; 2730:169-181. [PMID: 37943458 DOI: 10.1007/978-1-0716-3503-2_12] [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
Antifreeze proteins (AFPs) are biomolecules that can bind to ice and hinder its growth, thus holding significant potential for biotechnological and biomedical applications. AFPs are a subset of ice-binding proteins (IBPs) and are found in various organisms across different life kingdoms. This mini-review investigates the underlying mechanisms by which AFPs impede ice growth, emphasizing the disparities between hyperactive and moderate AFPs. Hyperactive AFPs exhibit heightened thermal hysteresis (TH) activity and can bind to both the basal and prism planes of ice crystals, enabling them to endure extremely cold temperatures. In contrast, moderate AFPs predominantly bind to the prism/pyramidal planes and demonstrate lower TH activity. The structural diversity of AFPs and the presence of ordered water molecules on their ice-binding sites (IBS) have been subjects of debate among researchers. Multiple hypotheses have been proposed concerning the significance of ordered water molecules in ice binding. Gaining insights into the binding dynamics and the factors influencing TH activity in AFPs is crucial for the development of efficient synthetic compounds and the establishment of comprehensive models to elucidate ice growth inhibition. Here we emphasize the necessity for further research to unravel the mechanisms of AFPs and presents a pathway for constructing models capable of comprehensively explaining their inhibitory effects on ice growth.
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Affiliation(s)
- Ran Drori
- Department of Chemistry and Biochemistry, Yeshiva University, New York, NY, USA.
| | - Corey A Stevens
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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11
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Chang XJ, Sands DC, Ewart KV. Paradoxical effects on ice nucleation are intrinsic to a small winter flounder antifreeze protein. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:140973. [PMID: 37956730 DOI: 10.1016/j.bbapap.2023.140973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 11/15/2023]
Abstract
Antifreeze proteins (AFPs) bind to ice in solutions, resulting in non-colligative freezing point depression; however, their effects on ice nucleation are not well understood. The predominant plasma AFP of winter flounder (Pseudopleuronectes americanus) is AFP6, which is an amphiphilic alpha helix. In this study, AFP6 and modified constructs were produced as fusion proteins in Escherichia coli, subjected to proteolysis when required and purified prior to use. AFP6 and its recombinant fusion precursor generated similar thermal hysteresis and bipyramidal ice crystals, whereas an inactive mutant AFP6 produced hexagonal crystals and no hysteresis. Circular dichroism spectra of the wild-type and mutant AFP6 were consistent with an alpha helix. The effects of these proteins on ice nucleation were investigated alongside non-AFP proteins using a standard droplet freezing assay. In the presence of nucleating AgI, modest reductions in the nucleation temperature occurred with the addition of mutant AFP6, and several non-AFPs, suggesting non-specific inhibition of AgI-induced ice nucleation. In these experiments, both AFP6 and its recombinant precursor resulted in lower nucleation temperatures, consistent with an additional inhibitory effect. Conversely, in the absence of AgI, AFP6 induced ice nucleation, with no other proteins showing this effect. Nucleation by AFP6 was dose-dependent, reaching a maximum at 1.5 mM protein. Nucleation by AFP6 also required an ice-binding site, as the inactive mutant had no effect. Furthermore, the absence of nucleation by the recombinant precursor protein suggested that the fusion moiety was interfering with the formation of a surface capable of nucleating ice.
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Affiliation(s)
- Xing Jian Chang
- Department of Biochemistry & Molecular Biology, Dalhousie University, PO Box 15000, Halifax, NS B3H 4R2, Canada
| | - Dane C Sands
- Department of Biochemistry & Molecular Biology, Dalhousie University, PO Box 15000, Halifax, NS B3H 4R2, Canada
| | - Kathryn Vanya Ewart
- Department of Biochemistry & Molecular Biology, Dalhousie University, PO Box 15000, Halifax, NS B3H 4R2, Canada; Department of Biology, Dalhousie University, PO Box 15000, Halifax, NS B3H 4R2, Canada.
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12
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Melnik BS, Glukhova KA, Sokolova (Voronova) EA, Balalaeva IV, Garbuzynskiy SO, Finkelstein AV. Physics of Ice Nucleation and Antinucleation: Action of Ice-Binding Proteins. Biomolecules 2023; 14:54. [PMID: 38254654 PMCID: PMC10813080 DOI: 10.3390/biom14010054] [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: 10/27/2023] [Revised: 12/09/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
Ice-binding proteins are crucial for the adaptation of various organisms to low temperatures. Some of these, called antifreeze proteins, are usually thought to inhibit growth and/or recrystallization of ice crystals. However, prior to these events, ice must somehow appear in the organism, either coming from outside or forming inside it through the nucleation process. Unlike most other works, our paper is focused on ice nucleation and not on the behavior of the already-nucleated ice, its growth, etc. The nucleation kinetics is studied both theoretically and experimentally. In the theoretical section, special attention is paid to surfaces that bind ice stronger than water and thus can be "ice nucleators", potent or relatively weak; but without them, ice cannot be nucleated in any way in calm water at temperatures above -30 °C. For experimental studies, we used: (i) the ice-binding protein mIBP83, which is a previously constructed mutant of a spruce budworm Choristoneura fumiferana antifreeze protein, and (ii) a hyperactive ice-binding antifreeze protein, RmAFP1, from a longhorn beetle Rhagium mordax. We have shown that RmAFP1 (but not mIBP83) definitely decreased the ice nucleation temperature of water in test tubes (where ice originates at much higher temperatures than in bulk water and thus the process is affected by some ice-nucleating surfaces) and, most importantly, that both of the studied ice-binding proteins significantly decreased the ice nucleation temperature that had been significantly raised in the presence of potent ice nucleators (CuO powder and ice-nucleating bacteria Pseudomonas syringae). Additional experiments on human cells have shown that mIBP83 is concentrated in some cell regions of the cooled cells. Thus, the ice-binding protein interacts not only with ice, but also with other sites that act or potentially may act as ice nucleators. Such ice-preventing interaction may be the crucial biological task of ice-binding proteins.
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Affiliation(s)
- Bogdan S. Melnik
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (K.A.G.); (S.O.G.)
| | - Ksenia A. Glukhova
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (K.A.G.); (S.O.G.)
| | - Evgeniya A. Sokolova (Voronova)
- Institute of Biology and Biomedicine, Lobachevsky State University of Nizhny Novgorod, 603022 Nizhny Novgorod, Russia (I.V.B.)
| | - Irina V. Balalaeva
- Institute of Biology and Biomedicine, Lobachevsky State University of Nizhny Novgorod, 603022 Nizhny Novgorod, Russia (I.V.B.)
| | - Sergiy O. Garbuzynskiy
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (K.A.G.); (S.O.G.)
| | - Alexei V. Finkelstein
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (K.A.G.); (S.O.G.)
- Faculty of Biotechnology, Lomonosov Moscow State University, 142290 Pushchino, Russia
- Faculty of Biology, Lomonosov Moscow State University, 119192 Moscow, Russia
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13
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Xie Y, Zhou K, Tan L, Ma Y, Li C, Zhou H, Wang Z, Xu B. Coexisting with Ice Crystals: Cryogenic Preservation of Muscle Food─Mechanisms, Challenges, and Cutting-Edge Strategies. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:19221-19239. [PMID: 37947813 DOI: 10.1021/acs.jafc.3c06155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Cryopreservation, one of the most effective preservation methods, is essential for maintaining the safety and quality of food. However, there is no denying the fact that the quality of muscle food deteriorates as a result of the unavoidable production of ice. Advancements in cryoregulatory materials and techniques have effectively mitigated the adverse impacts of ice, thereby enhancing the standard of freezing preservation. The first part of this overview explains how ice forms, including the theoretical foundations of nucleation, growth, and recrystallization as well as the key influencing factors that affect each process. Subsequently, the impact of ice formation on the eating quality and nutritional value of muscle food is delineated. A systematic explanation of cutting-edge strategies based on nucleation intervention, growth control, and recrystallization inhibition is offered. These methods include antifreeze proteins, ice-nucleating proteins, antifreeze peptides, natural deep eutectic solvents, polysaccharides, amino acids, and their derivatives. Furthermore, advanced physical techniques such as electrostatic fields, magnetic fields, acoustic fields, liquid nitrogen, and supercooling preservation techniques are expounded upon, which effectively hinder the formation of ice crystals during cryopreservation. The paper outlines the difficulties and potential directions in ice inhibition for effective cryopreservation.
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Affiliation(s)
- Yong Xie
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China
| | - Kai Zhou
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China
- Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230601, China
| | - Lijun Tan
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China
| | - Yunhao Ma
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China
| | - Cong Li
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China
- Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230601, China
| | - Hui Zhou
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China
- Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230601, China
| | - Zhaoming Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China
- Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230601, China
| | - Baocai Xu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China
- Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230601, China
- Food Laboratory of Zhongyuan, Luohe 462300, Henan, China
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14
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Thosar AU, Shalom Y, Braslavsky I, Drori R, Patel AJ. Accumulation of Antifreeze Proteins on Ice Is Determined by Adsorption. J Am Chem Soc 2023; 145:17597-17602. [PMID: 37527507 DOI: 10.1021/jacs.3c02705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
Antifreeze proteins (AFPs) facilitate the survival of diverse organisms in frigid environments by adsorbing to ice crystals and suppressing their growth. The rate of AFP accumulation on ice is determined by an interplay between AFP diffusion from the bulk solution to the ice-water interface and the subsequent adsorption of AFPs to the interface. To interrogate the relative importance of these two processes, here, we combine nonequilibrium fluorescence experiments with a reaction-diffusion model. We find that as diverse AFPs accumulate on ice, their concentration in the aqueous solution does not develop a gradient but remains equal to its bulk concentration throughout our experiments. These findings lead us to conclude that AFP accumulation on ice crystals, which are smaller than 100 μm in radius, is not limited by the diffusion of AFPs, but by the kinetics of AFP adsorption. Our results imply that mass transport limitations do not hinder AFPs from performing their biological function.
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Affiliation(s)
- Aniket U Thosar
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Yitzhar Shalom
- Department of Chemistry and Biochemistry, Yeshiva University, New York, New York 10016, United States
- Department of Physics, Katz School of Science and Health, Yeshiva University, New York, New York 10016, United States
| | - Ido Braslavsky
- The Robert H. Smith Faculty of Agriculture, Food and Environment, Institute of Biochemistry, Food Science and Nutrition, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Ran Drori
- Department of Chemistry and Biochemistry, Yeshiva University, New York, New York 10016, United States
- Department of Physics, Katz School of Science and Health, Yeshiva University, New York, New York 10016, United States
| | - Amish J Patel
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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15
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de Haas RJ, Tas RP, van den Broek D, Zheng C, Nguyen H, Kang A, Bera AK, King NP, Voets IK, de Vries R. De novo designed ice-binding proteins from twist-constrained helices. Proc Natl Acad Sci U S A 2023; 120:e2220380120. [PMID: 37364125 PMCID: PMC10319034 DOI: 10.1073/pnas.2220380120] [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: 12/09/2022] [Accepted: 05/02/2023] [Indexed: 06/28/2023] Open
Abstract
Attaining molecular-level control over solidification processes is a crucial aspect of materials science. To control ice formation, organisms have evolved bewildering arrays of ice-binding proteins (IBPs), but these have poorly understood structure-activity relationships. We propose that reverse engineering using de novo computational protein design can shed light on structure-activity relationships of IBPs. We hypothesized that the model alpha-helical winter flounder antifreeze protein uses an unusual undertwisting of its alpha-helix to align its putative ice-binding threonine residues in exactly the same direction. We test this hypothesis by designing a series of straight three-helix bundles with an ice-binding helix projecting threonines and two supporting helices constraining the twist of the ice-binding helix. Our findings show that ice-recrystallization inhibition by the designed proteins increases with the degree of designed undertwisting, thus validating our hypothesis, and opening up avenues for the computational design of IBPs.
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Affiliation(s)
- Robbert J. de Haas
- Department of Physical Chemistry and Soft Matter, Wageningen University and Research, Wageningen, WE6708, The Netherlands
| | - Roderick P. Tas
- Laboratory of Self-Organizing Soft Matter, Department of Chemical Engineering and Chemistry and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, MB5600, The Netherlands
| | - Daniëlle van den Broek
- Laboratory of Self-Organizing Soft Matter, Department of Chemical Engineering and Chemistry and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, MB5600, The Netherlands
| | - Chuanbao Zheng
- Department of Physical Chemistry and Soft Matter, Wageningen University and Research, Wageningen, WE6708, The Netherlands
| | - Hannah Nguyen
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Alex Kang
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Asim K. Bera
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Neil P. King
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Ilja K. Voets
- Laboratory of Self-Organizing Soft Matter, Department of Chemical Engineering and Chemistry and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, MB5600, The Netherlands
| | - Renko de Vries
- Department of Physical Chemistry and Soft Matter, Wageningen University and Research, Wageningen, WE6708, The Netherlands
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16
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Li M, Reeder MW, Wu T. Ice recrystallization inhibition effect of cellulose nanocrystals at constant and cycling temperatures. Int J Biol Macromol 2023:125108. [PMID: 37257528 DOI: 10.1016/j.ijbiomac.2023.125108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/02/2023]
Abstract
Understanding the effects of ice recrystallization inhibitors at varying temperatures is critical for evaluating their applications. We studied the ice recrystallization inhibition (IRI) effects of cellulose nanocrystals (CNCs) at constant and cycling temperatures. A splat assay using a 3.0 % sucrose solution showed that the IRI effect of 0.2 % CNCs decreased with increasing temperatures from -10 °C to -2 °C; the IRI effects of 0.5 % and 1.0 % CNCs remained unchanged for an increase in temperature from -10 °C to -4 °C but decreased at the temperature of -2 °C. A sandwich assay using a 25.0 % sucrose solution revealed that IRI effects increased with increasing temperatures, except in the presence of 0.2 % and 0.5 % CNCs at -5 °C and - 4 °C. A sandwich assay using a 35.0 % sucrose solution revealed that better IRI effects were observed at higher temperatures at all CNCs concentrations. At cycling temperatures, CNCs were inactive for storage times for ≤2 h, regardless of the rate, holding time, and amplitude of temperature fluctuation, but were active for storage times of 2 and 10 days. The IRI effects of CNCs at different temperatures may be related to the coverage of CNCs on ice surface, diffusion rate of CNCs to ice surface, and types of ice recrystallization.
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Affiliation(s)
- Min Li
- Department of Food Science, The University of Tennessee, 2510 River Drive, Knoxville, TN 37996, USA
| | - Matthew Winston Reeder
- Department of Food Science, The University of Tennessee, 2510 River Drive, Knoxville, TN 37996, USA
| | - Tao Wu
- Department of Food Science, The University of Tennessee, 2510 River Drive, Knoxville, TN 37996, USA.
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