1
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Liu M, Li J, Ma H, Qin G, Niu M, Zhang X, Zhang J, Wei Y, Han J, Liang Y, Zhang S, Yin L, Zhu H, Huang Y, Li L, Zheng X, Liu C. Structural and physicochemical characteristics of wheat starch as influenced by freeze-thawed cycles and antifreeze protein from Sabina chinensis (Linn.) Ant. cv. Kaizuca leaves. Food Chem X 2023; 20:100927. [PMID: 38144810 PMCID: PMC10740099 DOI: 10.1016/j.fochx.2023.100927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 09/28/2023] [Accepted: 10/03/2023] [Indexed: 12/26/2023] Open
Abstract
The effects of freeze-thawed cycles (FTs) and a new antifreeze protein from Sabina chinensis (Linn.) Ant. cv. Kaizuca leaves (ScAFP) on the structure and physicochemical characteristics of wheat starch were studied. The mechanical breaking exerted by ice crystals on starch granules during FTs gradually deepened, sequentially squeezing the surface (2-6 FTs), amorphous region (8 FTs) and crystalline region (10 FTs) of starch granules. These changes led to reduced thermal stability, increased retrogradation tendency, and weakened gel network structure. The addition of ScAFP retarded the damage of ice crystals on starch granule structure and crystal structure during FTs, and significantly reduced the retrogradation tendency. Compared with native starch, the hardness of freeze-thawed starch without and with added ScAFP after 10 FTs decreased by 17.85% and 9.22%, respectively, indicating ScAFP improved the gel texture properties of freeze-thawed starch. This study provides new strategies for improving the quality of frozen starch-based foods.
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Affiliation(s)
- Mei Liu
- National Engineering Laboratory/Key Laboratory of Henan Province, Henan University of Technology, Zhengzhou 450001, China
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Jie Li
- National Engineering Laboratory/Key Laboratory of Henan Province, Henan University of Technology, Zhengzhou 450001, China
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Hao Ma
- National Engineering Laboratory/Key Laboratory of Henan Province, Henan University of Technology, Zhengzhou 450001, China
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Guolan Qin
- National Engineering Laboratory/Key Laboratory of Henan Province, Henan University of Technology, Zhengzhou 450001, China
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Mengge Niu
- National Engineering Laboratory/Key Laboratory of Henan Province, Henan University of Technology, Zhengzhou 450001, China
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Xiaoyin Zhang
- National Engineering Laboratory/Key Laboratory of Henan Province, Henan University of Technology, Zhengzhou 450001, China
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Jin Zhang
- National Engineering Laboratory/Key Laboratory of Henan Province, Henan University of Technology, Zhengzhou 450001, China
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Yangkun Wei
- National Engineering Laboratory/Key Laboratory of Henan Province, Henan University of Technology, Zhengzhou 450001, China
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Jiajing Han
- National Engineering Laboratory/Key Laboratory of Henan Province, Henan University of Technology, Zhengzhou 450001, China
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Ying Liang
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Shenying Zhang
- National Engineering Laboratory/Key Laboratory of Henan Province, Henan University of Technology, Zhengzhou 450001, China
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Lulu Yin
- National Engineering Laboratory/Key Laboratory of Henan Province, Henan University of Technology, Zhengzhou 450001, China
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Haojia Zhu
- National Engineering Laboratory/Key Laboratory of Henan Province, Henan University of Technology, Zhengzhou 450001, China
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Ying Huang
- National Engineering Laboratory/Key Laboratory of Henan Province, Henan University of Technology, Zhengzhou 450001, China
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Limin Li
- National Engineering Laboratory/Key Laboratory of Henan Province, Henan University of Technology, Zhengzhou 450001, China
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Xueling Zheng
- National Engineering Laboratory/Key Laboratory of Henan Province, Henan University of Technology, Zhengzhou 450001, China
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Chong Liu
- National Engineering Laboratory/Key Laboratory of Henan Province, Henan University of Technology, Zhengzhou 450001, China
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001, China
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Yang F, Jiang W, Chen X, Chen X, Wu J, Huang J, Cai X, Wang S. Identification of Novel Antifreeze Peptides from Takifugu obscurus Skin and Molecular Mechanism in Inhibiting Ice Crystal Growth. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:14148-14156. [PMID: 36314886 DOI: 10.1021/acs.jafc.2c04393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Foodborne hydrolyzed antifreeze peptides have been widely used in the food industry and the biomedical field. However, the components of hydrolyzed peptides are complex and the molecular mechanism remains unclear. This study focused on identification and mechanism analysis of novel antifreeze peptides from Takifugu obscurus skin by traditional methods and computer-assisted techniques. Results showed that three peptides (EGPRAGGAPG, GDAGPSGPAGPTG, and GEAGPAGPAG) possessed cryoprotection via reducing the freezing point and inhibiting ice crystal growth. Molecular docking confirmed that the cryoprotective property was related to peptide structure, especially α-helix, and hydrogen bond sites. Moreover, the antifreeze peptides were double-faces, which controlled ice crystals while affecting the arrangement of surrounding water molecules, thus exhibiting a strong antifreeze activity. This investigation deepens the comprehension of the mechanism of antifreeze peptides at molecular scale, and the novel efficient antifreeze peptides can be developed in antifreeze materials design and applied in food industry.
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Affiliation(s)
- Fujia Yang
- College of Chemical Engineering, Fuzhou University, Fuzhou350108, P.R. China
- College of Biological Science and Engineering, Fuzhou University, Fuzhou350108, P.R. China
| | - Wenting Jiang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou350108, P.R. China
| | - Xu Chen
- College of Biological Science and Engineering, Fuzhou University, Fuzhou350108, P.R. China
| | - Xuan Chen
- College of Chemical Engineering, Fuzhou University, Fuzhou350108, P.R. China
- College of Biological Science and Engineering, Fuzhou University, Fuzhou350108, P.R. China
| | - Jinhong Wu
- Department of Food Science and Engineering, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai200240, P.R. China
| | - Jianlian Huang
- Key Laboratory of Refrigeration and Conditioning Aquatic Products Processing of Ministry of Agriculture and Rural Affairs, Xiamen361022, P.R. China
- Fujian Anjoy Foods Co. Ltd., Xiamen361022, P.R. China
| | - Xixi Cai
- College of Biological Science and Engineering, Fuzhou University, Fuzhou350108, P.R. China
| | - Shaoyun Wang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou350108, P.R. China
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3
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Eskandari A, Leow TC, Rahman MBA, Oslan SN. Antifreeze Proteins and Their Practical Utilization in Industry, Medicine, and Agriculture. Biomolecules 2020; 10:biom10121649. [PMID: 33317024 PMCID: PMC7764015 DOI: 10.3390/biom10121649] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/28/2020] [Accepted: 11/30/2020] [Indexed: 12/15/2022] Open
Abstract
Antifreeze proteins (AFPs) are specific proteins, glycopeptides, and peptides made by different organisms to allow cells to survive in sub-zero conditions. AFPs function by reducing the water’s freezing point and avoiding ice crystals’ growth in the frozen stage. Their capability in modifying ice growth leads to the stabilization of ice crystals within a given temperature range and the inhibition of ice recrystallization that decreases the drip loss during thawing. This review presents the potential applications of AFPs from different sources and types. AFPs can be found in diverse sources such as fish, yeast, plants, bacteria, and insects. Various sources reveal different α-helices and β-sheets structures. Recently, analysis of AFPs has been conducted through bioinformatics tools to analyze their functions within proper time. AFPs can be used widely in various aspects of application and have significant industrial functions, encompassing the enhancement of foods’ freezing and liquefying properties, protection of frost plants, enhancement of ice cream’s texture, cryosurgery, and cryopreservation of cells and tissues. In conclusion, these applications and physical properties of AFPs can be further explored to meet other industrial players. Designing the peptide-based AFP can also be done to subsequently improve its function.
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Affiliation(s)
- Azadeh Eskandari
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, UPM, Serdang 43400, Selangor, Malaysia; (A.E.); (T.C.L.)
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM, Serdang 43400, Selangor, Malaysia
| | - Thean Chor Leow
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, UPM, Serdang 43400, Selangor, Malaysia; (A.E.); (T.C.L.)
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM, Serdang 43400, Selangor, Malaysia
- Enzyme Technology Laboratory, Institute of Bioscience, Universiti Putra Malaysia, UPM, Serdang 43400, Selangor, Malaysia
| | | | - Siti Nurbaya Oslan
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, UPM, Serdang 43400, Selangor, Malaysia; (A.E.); (T.C.L.)
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM, Serdang 43400, Selangor, Malaysia
- Enzyme Technology Laboratory, Institute of Bioscience, Universiti Putra Malaysia, UPM, Serdang 43400, Selangor, Malaysia
- Correspondence: ; Tel.: +60-39769-6710; Fax: +60-39769-7590
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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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5
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Xiang H, Yang X, Ke L, Hu Y. The properties, biotechnologies, and applications of antifreeze proteins. Int J Biol Macromol 2020; 153:661-675. [PMID: 32156540 DOI: 10.1016/j.ijbiomac.2020.03.040] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/04/2020] [Accepted: 03/06/2020] [Indexed: 01/30/2023]
Abstract
By natural selection, organisms evolve different solutions to cope with extremely cold weather. The emergence of an antifreeze protein gene is one of the most momentous solutions. Antifreeze proteins possess an importantly functional ability for organisms to survive in cold environments and are widely found in various cold-tolerant species. In this review, we summarize the origin of antifreeze proteins, describe the diversity of their species-specific properties and functions, and highlight the related biotechnology on the basis of both laboratory tests and bioinformatics analysis. The most recent advances in the applications of antifreeze proteins are also discussed. We expect that this systematic review will contribute to the comprehensive knowledge of antifreeze proteins to readers.
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Affiliation(s)
- Hong Xiang
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China.; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institutes of Advanced Technology
| | - Xiaohu Yang
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China.; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institutes of Advanced Technology
| | - Lei Ke
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China.; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institutes of Advanced Technology
| | - Yong Hu
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China.; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institutes of Advanced Technology.
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6
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Di Natale A, Jarau M, Russell SK, Horricks RA, Lillie BN, Dixon B, Lumsden JS. Rainbow trout Oncorhynchus mykiss (Walbaum) type IV ice-structuring protein LS-12 in the acute-phase response to Flavobacterium psychrophilum infection. JOURNAL OF FISH DISEASES 2019; 42:975-984. [PMID: 31066066 DOI: 10.1111/jfd.13002] [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: 07/09/2018] [Revised: 02/27/2019] [Accepted: 02/27/2019] [Indexed: 06/09/2023]
Abstract
A previous proteomic study examining the plasma acute-phase response of rainbow trout to sterile inflammation highlighted an unidentified 9.5-kDa spot using 2D-PAGE, which was dramatically increased. The 15 amino acid sequence obtained from this protein spot allowed rapid amplification of cDNA ends PCR to generate a 443-bp nucleotide sequence that was 98.6% similar to type-4 ice-structuring protein LS-12 from Atlantic salmon Salmo salar Linnaeus. Quantitative reverse translation PCR and an ELISA were used to measure gene expression and plasma concentrations of LS-12 following experimental intraperitoneal injection of rainbow trout with either 106 or 108 colony-forming units (CFU) of Flavobacterium psychrophilum. There was no significant change in the plasma concentration of LS-12 up to 15 days post-infection in any group. Hepatic LS-12 gene expression was significantly reduced at 3 and 6 days (p < 0.001) post-infection in fish injected with 108 CFU of F. psychrophilum relative to control fish, while branchial or head kidney expression was unchanged. Infected fish had significantly increased hepatic gene expression of serum amyloid A, confirming an acute-phase response. Under the conditions used, LS-12 is not a positive acute-phase protein in rainbow trout.
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Affiliation(s)
- Adrian Di Natale
- Fish Pathology Laboratory, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Maureen Jarau
- Fish Pathology Laboratory, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Spencer K Russell
- Fish Pathology Laboratory, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Ryan A Horricks
- Fish Pathology Laboratory, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Brandon N Lillie
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Brian Dixon
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - John S Lumsden
- Fish Pathology Laboratory, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
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7
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Gong S, Yang D, Wu Q, Wang S, Fang Z, Li Y, Xu F, Wang Z, Wu J. Evaluation of the antifreeze effects and its related mechanism of sericin peptides on the frozen dough of steamed potato bread. J FOOD PROCESS PRES 2019. [DOI: 10.1111/jfpp.14053] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shengxiang Gong
- The Key Laboratory of Synthetic and Biological Colloids, Ministry of Education Jiangnan University Wuxi China
- Department of Food Science and Engineering, School of Agriculture and Biology Shanghai Jiao Tong University Shanghai China
| | - Danlu Yang
- Department of Food Science and Engineering, School of Agriculture and Biology Shanghai Jiao Tong University Shanghai China
| | - Qiaoyu Wu
- Department of Food Science and Engineering, School of Agriculture and Biology Shanghai Jiao Tong University Shanghai China
| | - Shaoyun Wang
- Institute of Food and Marine Bioresources, College of Biological Science and Technology Fuzhou University Fuzhou China
| | - Zhong Fang
- The Key Laboratory of Synthetic and Biological Colloids, Ministry of Education Jiangnan University Wuxi China
| | - Yue Li
- The Key Laboratory of Synthetic and Biological Colloids, Ministry of Education Jiangnan University Wuxi China
| | - Feifei Xu
- The Key Laboratory of Synthetic and Biological Colloids, Ministry of Education Jiangnan University Wuxi China
| | - Zhengwu Wang
- Department of Food Science and Engineering, School of Agriculture and Biology Shanghai Jiao Tong University Shanghai China
| | - Jinhong Wu
- The Key Laboratory of Synthetic and Biological Colloids, Ministry of Education Jiangnan University Wuxi China
- Department of Food Science and Engineering, School of Agriculture and Biology Shanghai Jiao Tong University Shanghai China
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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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9
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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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10
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Midya US, Bandyopadhyay S. Interfacial Water Arrangement in the Ice-Bound State of an Antifreeze Protein: A Molecular Dynamics Simulation Study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:5499-5510. [PMID: 28505449 DOI: 10.1021/acs.langmuir.7b01206] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Molecular dynamics (MD) simulations have been carried out to study the heterogeneous ice nucleation on modeled peptide surfaces. Simulations show that large peptide surfaces made by TxT (threonine-x-threonine) motifs with the arrangements of threonine (Thr) residues identical to the periodic arrangements of waters on either the basal or prism plane of ice are capable of ice nucleation. Nucleated ice plane is the (0001) basal plane of hexagonal ice (Ih) or (111) plane of cubic ice (Ic). However, due to predefined simulation cell dimensions, the ice growth is only observed on the surface where the Thr residues are arranged like the water arrangement on the basal plane of ice Ih. The γ-methyl and γ-hydroxyl groups of Thr residue are necessary for such ice formation. From this ice nucleation and growth simulation, the interfacial water arrangement in the ice-bound state of Tenebrio molitor antifreeze protein (TmAFP) has been determined. The interfacial water arrangement in the ice-bound state of TmAFP is characterized by five-membered hydrogen bonded rings, where each of the hydroxyl groups of the Thr residues on the ice-binding surface (IBS) of the protein is a ring member. It is found that the water arrangement at the protein-ice interface is distorted from that in bulk ice. Our analysis further reveals that the hydroxyl groups of Thr residues on the IBS of TmAFP form maximum three hydrogen bonds each with the waters in the bound state and methyl groups of Thr residues occupy wider spaces than the normal grooves on the (111) plane of ice Ic. Methyl groups are also located above and along the 3-fold rotational axes of the chair-formed hexagonal hydrogen bonded water rings on the (111) plane.
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Affiliation(s)
- Uday Sankar Midya
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology , Kharagpur - 721302, India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology , Kharagpur - 721302, India
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11
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CryoProtect: A Web Server for Classifying Antifreeze Proteins from Nonantifreeze Proteins. J CHEM-NY 2017. [DOI: 10.1155/2017/9861752] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Antifreeze protein (AFP) is an ice-binding protein that protects organisms from freezing in extremely cold environments. AFPs are found across a diverse range of species and, therefore, significantly differ in their structures. As there are no consensus sequences available for determining the ice-binding domain of AFPs, thus the prediction and characterization of AFPs from their sequence is a challenging task. This study addresses this issue by predicting AFPs directly from sequence on a large set of 478 AFPs and 9,139 non-AFPs using machine learning (e.g., random forest) as a function of interpretable features (e.g., amino acid composition, dipeptide composition, and physicochemical properties). Furthermore, AFPs were characterized using propensity scores and important physicochemical properties via statistical and principal component analysis. The predictive model afforded high performance with an accuracy of 88.28% and results revealed that AFPs are likely to be composed of hydrophobic amino acids as well as amino acids with hydroxyl and sulfhydryl side chains. The predictive model is provided as a free publicly available web server called CryoProtect for classifying query protein sequence as being either AFP or non-AFP. The data set and source code are for reproducing the results which are provided on GitHub.
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12
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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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13
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Wu J, Rong Y, Wang Z, Zhou Y, Wang S, Zhao B. Isolation and characterisation of sericin antifreeze peptides and molecular dynamics modelling of their ice-binding interaction. Food Chem 2015; 174:621-9. [DOI: 10.1016/j.foodchem.2014.11.100] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 10/21/2014] [Accepted: 11/17/2014] [Indexed: 02/03/2023]
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14
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Kristiansen E, Wilkens C, Vincents B, Friis D, Lorentzen AB, Jenssen H, Løbner-Olesen A, Ramløv H. Hyperactive antifreeze proteins from longhorn beetles: some structural insights. JOURNAL OF INSECT PHYSIOLOGY 2012; 58:1502-1510. [PMID: 23000739 DOI: 10.1016/j.jinsphys.2012.09.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 09/07/2012] [Accepted: 09/10/2012] [Indexed: 06/01/2023]
Abstract
This study reports on structural characteristics of hyperactive antifreeze proteins (AFPs) from two species of longhorn beetles. In Rhagium mordax, eight unique mRNAs coding for five different mature AFPs were identified from cold-hardy individuals. These AFPs are apparently homologues to a previously characterized AFP from the closely related species Rhagium inquisitor, and consist of six identifiable repeats of a putative ice binding motif TxTxTxT spaced irregularly apart by segments varying in length from 13 to 20 residues. Circular dichroism spectra show that the AFPs from both species have a high content of β-sheet and low levels of α-helix and random coil. Theoretical predictions of residue-specific secondary structure locate these β-sheets within the putative ice-binding motifs and the central parts of the segments separating them, consistent with an overall β-helical structure with the ice-binding motifs stacked in a β-sheet on one side of the coil. Molecular dynamics models based on these findings show that these AFPs would be energetically stable in a β-helical conformation.
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Affiliation(s)
- Erlend Kristiansen
- Institute of Science, Systems and Models, Roskilde University Center, DK-4000 Roskilde, Denmark
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15
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Collino S, Evans JS. Molecular specifications of a mineral modulation sequence derived from the aragonite-promoting protein n16. Biomacromolecules 2008; 9:1909-18. [PMID: 18558739 DOI: 10.1021/bm8001599] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
In the nacre layer of the mollusk, proteins play an important role in regulating the morphology and lattice structure of calcium carbonate minerals. However, this process remains elusive due to the fact that we do not understand how protein sequences control the structure and morphology of biominerals. To take us a step further in this direction, we report the molecular structure of a 30 AA N-terminal mineral interactive sequence (n16N) of the aragonite-promoting protein, n16, and contrast these findings to those previously reported for two "calcite-blocker" nacre-associated sequences, AP7N and AP24N. We find that n16N is conformationally labile and adopts a random-coil conformation that possesses short, dispersed extended beta-strand segments that are located at the A1-Y2, K5-Y9, Y11-I14, and D21-N25 sequence blocks. Like AP7N and AP24N, Ca(II) ion interactions with n16N alter chain dynamics and local structure, and n16N is adsorbed onto calcite crystals and cannot easily be displaced via differential washing techniques. Furthermore, all three sequences have planar surface regions that could serve as putative sites for mineral interactions or ion cluster formation. However, what sets n16N apart from AP7N and AP24N are different folding propensities as well as unique molecular surface features and amino acid composition. n16N has a more condensed structure that, in the presence of TFE, folds into a beta-strand. This contrasts with the more open structures of AP7N and AP24N that are induced by TFE to fold into alpha-helices. Mapping of the n16N molecular surface reveals significant cationic regions and diffuse anionic charge, which contrasts with the small anionic "pocket" regions of AP7N/AP24N. Finally, n16N has 50% fewer sites for mineral surface- or ion cluster-associated water interactions compared to AP7N and AP24N. Overall, the structure of n16N is "tuned" to a different function within the in vitro mineralization scheme. The different features found in AP7N, AP24N, and n16N could be exploited for engineering polypeptides that recognize and bind to different surface features of inorganic crystalline solids.
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Affiliation(s)
- Sebastiano Collino
- Laboratory for Chemical Physics, Center for Biomolecular Materials Spectroscopy, New York University, 345 East 24th Street, Room 1007, New York, New York 10010, USA
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16
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Salvay AG, Santos J, Howard EI. Electro-optical properties characterization of fish type III antifreeze protein. J Biol Phys 2008; 33:389-97. [PMID: 19669526 DOI: 10.1007/s10867-008-9080-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2007] [Accepted: 04/15/2008] [Indexed: 10/22/2022] Open
Abstract
Antifreeze proteins (AFPs) are ice-binding proteins that depress the freezing point of water in a non-colligative manner without a significant modification of the melting point. Found in the blood and tissues of some organisms (such as fish, insects, plants, and soil bacteria), AFPs play an important role in subzero temperature survival. Fish Type III AFP is present in members of the subclass Zoarcoidei. AFPIII are small 7-kDa-or 14-kDa tandem-globular proteins. In the present work, we study the behavior of several physical properties, such as the low-frequency dielectric permittivity spectrum, circular dichroism, and electrical conductivity of Fish Type III AFP solutions measured at different concentrations. The combination of the information obtained from these measurements could be explained through the formation of AFP molecular aggregates or, alternatively, by the existence of some other type of interparticle interactions. Thermal stability and electro-optical behavior, when proteins are dissolved in deuterated water, were also investigated.
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Affiliation(s)
- Andrés G Salvay
- Instituto de Física de Líquidos y Sistemas Biológicos (IFLYSIB), Universidad Nacional de La Plata, 1900BTE La Plata, Argentina
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17
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Molecular basis for antifreeze activity difference of two insect antifreeze protein isoforms. ACTA ACUST UNITED AC 2007. [DOI: 10.1007/s11426-007-0027-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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18
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Affiliation(s)
- Ninad Prabhu
- Johnson Research Foundation, Dept. of Biochemistry and Biophysics, University of Pennsylvania
| | - Kim Sharp
- Johnson Research Foundation, Dept. of Biochemistry and Biophysics, University of Pennsylvania
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19
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Liu K, Jia Z, Chen G, Tung C, Liu R. Systematic size study of an insect antifreeze protein and its interaction with ice. Biophys J 2005; 88:953-8. [PMID: 15713600 PMCID: PMC1305167 DOI: 10.1529/biophysj.104.051169] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Because of their remarkable ability to depress the freezing point of aqueous solutions, antifreeze proteins (AFPs) play a critical role in helping many organisms survive subzero temperatures. The beta-helical insect AFP structures solved to date, consisting of multiple repeating circular loops or coils, are perhaps the most regular protein structures discovered thus far. Taking an exceptional advantage of the unusually high structural regularity of insect AFPs, we have employed both semiempirical and quantum mechanics computational approaches to systematically investigate the relationship between the number of AFP coils and the AFP-ice interaction energy, an indicator of antifreeze activity. We generated a series of AFP models with varying numbers of 12-residue coils (sequence TCTxSxxCxxAx) and calculated their interaction energies with ice. Using several independent computational methods, we found that the AFP-ice interaction energy increased as the number of coils increased, until an upper bound was reached. The increase of interaction energy was significant for each of the first five coils, and there was a clear synergism that gradually diminished and even decreased with further increase of the number of coils. Our results are in excellent agreement with the recently reported experimental observations.
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Affiliation(s)
- Kai Liu
- Department of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
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20
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21
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Yang Z, Zhou Y, Liu K, Cheng Y, Liu R, Chen G, Jia Z. Computational study on the function of water within a beta-helix antifreeze protein dimer and in the process of ice-protein binding. Biophys J 2004; 85:2599-605. [PMID: 14507722 PMCID: PMC1303483 DOI: 10.1016/s0006-3495(03)74682-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Antifreeze proteins (AFPs) help many organisms protect themselves from freezing in subzero temperatures. The most active AFPs found to date are those from insects, which possess exceptionally regular beta-helical structures. On the ice-binding surface of these proteins, regularly arrayed water molecules are observed within the repeating Thr-Xxx-Thr motif, but the exact role of these water molecules remains unknown. In this work, we have employed a number of computational methods to examine the role of these water molecules in an AFP from Tenebrio molitor (TmAFP). Our investigation involved a combination of molecular and quantum mechanical approaches. Properties such as stability, interaction energy, orbital overlap, and conformational analysis of various systems, including TmAFP-water, TmAFP-water-ice, and TmAFP-ice, were systematically evaluated and compared. The regularly arrayed water molecules were found to remain associated with TmAFP before ice binding, demonstrating that they are an intrinsic part of the protein. These water molecules may assist TmAFP in the process of ice recognition and binding. However, after facilitating the initial stages of ice recognition and binding, these water molecules are excluded in the final formation of the AFP-ice complex. The departure of these water molecules enables a better two-dimensional match between TmAFP and ice. These results agree with experimental observations showing that although these water molecules are aligned with the ice-binding hydroxyl groups of Thr residues in one dimension, they are in fact positioned slightly off in the second dimension, making a good two-dimensional match impossible.
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Affiliation(s)
- Zuoyin Yang
- Department of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
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22
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Zhang DQ, Liu B, Feng DR, He YM, Wang SQ, Wang HB, Wang JF. Significance of conservative asparagine residues in the thermal hysteresis activity of carrot antifreeze protein. Biochem J 2004; 377:589-95. [PMID: 14531728 PMCID: PMC1223888 DOI: 10.1042/bj20031249] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2003] [Revised: 10/06/2003] [Accepted: 10/08/2003] [Indexed: 11/17/2022]
Abstract
The approximately 24-amino-acid leucine-rich tandem repeat motif (PXXXXXLXXLXXLXLSXNXLXGXI) of carrot antifreeze protein comprises most of the processed protein and should contribute at least partly to the ice-binding site. Structural predictions using publicly available online sources indicated that the theoretical three-dimensional model of this plant protein includes a 10-loop beta-helix containing the approximately 24-amino-acid tandem repeat. This theoretical model indicated that conservative asparagine residues create putative ice-binding sites with surface complementarity to the 1010 prism plane of ice. We used site-specific mutagenesis to test the importance of these residues, and observed a distinct loss of thermal hysteresis activity when conservative asparagines were replaced with valine or glutamine, whereas a large increase in thermal hysteresis was observed when phenylalanine or threonine residues were replaced with asparagine, putatively resulting in the formation of an ice-binding site. These results confirmed that the ice-binding site of carrot antifreeze protein consists of conservative asparagine residues in each beta-loop. We also found that its thermal hysteresis activity is directly correlated with the length of its asparagine-rich binding site, and hence with the size of its ice-binding face.
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Affiliation(s)
- Dang-Quan Zhang
- The Key Laboratory of Gene Engineering of Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
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23
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Zhao X, Jia MX, Jiang XK, Wu LZ, Li ZT, Chen GJ. Zipper-Featured δ-Peptide Foldamers Driven by Donor−Acceptor Interaction. Design, Synthesis, and Characterization. J Org Chem 2003; 69:270-9. [PMID: 14725438 DOI: 10.1021/jo035149i] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Donor-acceptor interaction between electron-rich 1,5-dioxynaphthalene (DAN) and electron-deficient pyromellitic diimide (PDI) has been utilized to induce the formation of a new kind of zipper-featured delta-peptide foldamers. Seven l-ornithine-based delta-peptides 1a-g, in which one to three DNA and PDI units are incorporated to the two ends of the peptide backbones, respectively, have been designed and prepared by the standard liquid-phase synthetic method. (1)H NMR, UV-vis, and fluorescent quenching studies reveal that all the delta-peptides adopt folding conformations in nonpolar chloroform and polar DMF as a result of intramolecular donor-acceptor interaction between the DAN and PDI units. The folding states become more compact for the peptide skeletons possessing more donor-acceptor interacting sites. Variable-temperature UV-vis experiments indicate that, although the folding is a dynamic process, the folding state can remain even at 150 degrees C in DMF. Circular dichroism (CD) investigations reveal that the new generation of delta-peptides have similar folding patterns. A zipper-featured folding motif has been proposed for the new generation of delta-peptide foldamers. Molecular modeling has generated two most stable folding states for the longest delta-peptide 1g, with an energy difference of 26.80 kcal/mol.
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Affiliation(s)
- Xin Zhao
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 354 Fenglin Lu, Shanghai 200032, China
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24
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Harding MM, Anderberg PI, Haymet ADJ. 'Antifreeze' glycoproteins from polar fish. EUROPEAN JOURNAL OF BIOCHEMISTRY 2003; 270:1381-92. [PMID: 12653993 DOI: 10.1046/j.1432-1033.2003.03488.x] [Citation(s) in RCA: 184] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Antifreeze glycoproteins (AFGPs) constitute the major fraction of protein in the blood serum of Antarctic notothenioids and Arctic cod. Each AFGP consists of a varying number of repeating units of (Ala-Ala-Thr)n, with minor sequence variations, and the disaccharide beta-D-galactosyl-(1-->3)-alpha-N-acetyl-D-galactosamine joined as a glycoside to the hydroxyl oxygen of the Thr residues. These compounds allow the fish to survive in subzero ice-laden polar oceans by kinetically depressing the temperature at which ice grows in a noncolligative manner. In contrast to the more widely studied antifreeze proteins, little is known about the mechanism of ice growth inhibition by AFGPs, and there is no definitive model that explains their properties. This review summarizes the structural and physical properties of AFGPs and advances in the last decade that now provide opportunities for further research in this field. High field NMR spectroscopy and molecular dynamics studies have shown that AFGPs are largely unstructured in aqueous solution. While standard carbohydrate degradation studies confirm the requirement of some of the sugar hydroxyls for antifreeze activity, the importance of following structural elements has not been established: (a) the number of hydroxyls required, (b) the stereochemistry of the sugar hydroxyls (i.e. the requirement of galactose as the sugar), (c) the acetamido group on the first galactose sugar, (d) the stereochemistry of the beta-glycosidic linkage between the two sugars and the alpha-glycosidic linkage to Thr, (e) the requirement of a disaccharide for activity, and (f) the Ala and Thr residues in the polypeptide backbone. The recent successful synthesis of small AFGPs using solution methods and solid-phase chemistry provides the opportunity to perform key structure-activity studies that would clarify the important residues and functional groups required for activity. Genetic studies have shown that the AFGPs present in the two geographically and phylogenetically distinct Antarctic notothenioids and Arctic cod have evolved independently, in a rare example of convergent molecular evolution. The AFGPs exhibit concentration dependent thermal hysteresis with maximum hysteresis (1.2 degrees C at 40 mg x mL-1) observed with the higher molecular mass glycoproteins. The ability to modify the rate and shape of crystal growth and protect cellular membranes during lipid-phase transitions have resulted in identification of a number of potential applications of AFGPs as food additives, and in the cryopreservation and hypothermal storage of cells and tissues.
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Affiliation(s)
- Margaret M Harding
- School of Chemistry, The University of Sydney, New South Wales, Australia.
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25
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Evans JS. ‘Apples’ and ‘oranges’: comparing the structural aspects of biomineral- and ice-interaction proteins. Curr Opin Colloid Interface Sci 2003. [DOI: 10.1016/s1359-0294(03)00009-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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