1
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Wang Z, Ye X, Chen Y, Liu Y, Xie S, Tao Y, Zhang J, Wan X. Stereoselective Crystallization of Chiral Pharmaceuticals Aided by Cellulose Derivatives through Helical Pattern Matching. Chemistry 2024; 30:e202401550. [PMID: 38925570 DOI: 10.1002/chem.202401550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 06/21/2024] [Accepted: 06/25/2024] [Indexed: 06/28/2024]
Abstract
Stereoselective inhibition aided by "tailor-made" polymeric additives is an efficient approach to obtain enantiopure compounds through conglomerate crystallization. The chemical and configurational match between the side groups of polymers and the molecules of undesired enantiomer is considered to be a necessary condition for successful stereoseparation. Whereas in this contribution, we present an effective resolution of chiral pharmaceuticals by using cellulose acetates as the additives, which stereoselectively reside on the specific crystal faces of one enantiomer and inhibit its crystal nucleation and growth through helical pattern and supramolecular interaction complementarity. An investigation of nimodipine serves as a case study to highlight the novelty of this strategy wherein R-crystals exhibiting an impressive enantiomeric excess value of 97 % can be attained by employing a mere 0.01 wt % cellulose acetate. Guaifenesin and phenyl lactic acid are also well-resolved by utilizing this methodology. Our work not only brings about a brand-new design strategy for "tailor-made" additives, but will also promote the further exploration of the endless potential for utilizing natural biomolecules in chiral recognition and resolution.
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Affiliation(s)
- Zhaoxu Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
- Shanxi-Zheda Institute of Advanced Materials and Chemical Engineering, Taiyuan, 030032, China
| | - Xichong Ye
- Shaanxi International Research Center for Soft Matter, State Key Laboratory for Mechanical Behavior of Materials, School of Materials Science and Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Yifu Chen
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Yingze Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Siyu Xie
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Yi Tao
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Jie Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Xinhua Wan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
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2
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Graham LA, Davies PL. Fish antifreeze protein origin in sculpins by frameshifting within a duplicated housekeeping gene. FEBS J 2024. [PMID: 38923815 DOI: 10.1111/febs.17205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 03/25/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024]
Abstract
Antifreeze proteins (AFPs) are found in a variety of marine cold-water fishes where they prevent freezing by binding to nascent ice crystals. Their diversity (types I, II, III and antifreeze glycoproteins), as well as their scattered taxonomic distribution hint at their complex evolutionary history. In particular, type I AFPs appear to have arisen in response to the Late Cenozoic Ice Age that began ~ 34 million years ago via convergence in four different groups of fish that diverged from lineages lacking this AFP. The progenitor of the alanine-rich α-helical type I AFPs of sculpins has now been identified as lunapark, an integral membrane protein of the endoplasmic reticulum. Following gene duplication and loss of all but three of the 15 exons, the final exon, which encoded a glutamate- and glutamine-rich segment, was converted to an alanine-rich sequence by a combination of frameshifting and mutation. Subsequent gene duplications produced numerous isoforms falling into four distinct groups. The origin of the flounder type I AFP is quite different. Here, a small segment from the original antiviral protein gene was amplified and the rest of the coding sequence was lost, while the gene structure was largely retained. The independent origins of type I AFPs with up to 83% sequence identity in flounder and sculpin demonstrate strong convergent selection at the level of protein sequence for alanine-rich single alpha helices that bind to ice. Recent acquisition of these AFPs has allowed sculpins to occupy icy seawater niches with reduced competition and predation from other teleost species.
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Affiliation(s)
- Laurie A Graham
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Canada
| | - Peter L Davies
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Canada
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3
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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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4
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Zhang N, Du YT, Yao PQ, Huang HY, Zhang LR, Zhang FS, Liu JJ. Synergistic Effect of Hyperactive Antifreeze Protein on Inhibition of Gas-Hydrate Growth by Hydrophobic and Hydrophilic Groups. J Phys Chem B 2023; 127:10469-10477. [PMID: 38018897 DOI: 10.1021/acs.jpcb.3c04009] [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: 11/30/2023]
Abstract
Antifreeze proteins (AFPs) are biodegradable inhibitors that effectively prevent the formation of natural gas hydrates that block pipelines. In this study, molecular dynamics simulations were employed to establish a kinetic model of the hyperactive insect antifreeze protein (Tenebrio molitor, TmAFP) and its mutants to inhibit the growth of sI natural methane hydrate. Simulations revealed that the hydrophobic and hydrophilic groups of threonine (Thr) residues at hydrate-binding sites played a synergistic role in binding hydrates. The hydrophobic groups anchored TmAFP to the hydrate surface through residues Thr39-Thr65 by migrating pendant hydrophobic methyl groups to the hydrate semicages. The hydrophilic groups stabilized TmAFP by hydrogen bonding with water molecules and integrating them into a quasi-hydrate structure, which more effectively inhibited hydrate growth. The results suggest that the hydrate growth inhibition is attributed to both the shape complementarity and the flexibility of binding residues. The synergy between hydrophobic and hydrophilic groups provides guidance for the design of more effective hydrate inhibitors.
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Affiliation(s)
- Nan Zhang
- School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| | - Yue-Ting Du
- School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| | - Pei-Qi Yao
- School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| | - Hui-Yi Huang
- School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| | - Li-Rong Zhang
- School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| | - Feng-Shou Zhang
- The Key Laboratory of Beam Technology and Material Modification of Ministry of Education, Beijing Normal University, Beijing 100875, China
| | - Jun-Jie Liu
- School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
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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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6
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Delesky EA, Garcia LF, Lobo AJ, Mikofsky RA, Dowdy ND, Wallat JD, Miyake GM, Srubar WV. Bioinspired Threonine-Based Polymers with Potent Ice Recrystallization Inhibition Activity. ACS APPLIED POLYMER MATERIALS 2022; 4:7934-7942. [PMID: 36714526 PMCID: PMC9881732 DOI: 10.1021/acsapm.2c01496] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Ice growth mitigation is a pervasive challenge for multiple industries. In nature, ice-binding proteins (IBPs) demonstrate potent ice growth prevention through ice recrystallization inhibition (IRI). However, IBPs are expensive, difficult to produce in large quantities, and exhibit minimal resilience to nonphysiological environmental stressors, such as pH. For these reasons, researchers have turned to bioinspired polymeric materials that mimic IBP behavior. To date, however, no synthetic polymer has rivaled the ability of native IBPs to display IRI activity at ultralow nanomolar concentrations. In this work, we study the IRI activity of peptides and polypeptides inspired by common ice-binding residues of IBPs to inform the synthesis and characterization of a potent bioinspired polymer that mimics IBP behavior. We show first that the threonine polypeptide (pThr) displays the best IRI activity in phosphate-buffered saline (PBS). Second, we use pThr as a molecular model to synthesize and test a bioinspired polymer, poly(2-hydroxypropyl methacrylamide) (pHPMA). We show that pHPMA exhibits potent IRI activity in neutral PBS at ultralow concentrations (0.01 mg/mL). pHPMA demonstrates potent IRI activity at low molecular weights (2.3 kDa), with improved activity at higher molecular weights (32.8 kDa). These results substantiate that pHPMA is a robust molecule that mitigates ice crystal growth at concentrations similar to native IBPs.
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Affiliation(s)
- Elizabeth A Delesky
- Materials Science and Engineering Program, University of Colorado Boulder, Boulder, Colorado 80309-0428, United States
| | - Luis F Garcia
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Aparna J Lobo
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309-0428, United States
| | - Rebecca A Mikofsky
- Materials Science and Engineering Program, University of Colorado Boulder, Boulder, Colorado 80309-0428, United States
| | - Nicolas D Dowdy
- Materials Science and Engineering Program, University of Colorado Boulder, Boulder, Colorado 80309-0428, United States
| | - Jaqueline D Wallat
- Department of Civil, Environmental, and Architectural Engineering, University of Colorado Boulder, Boulder, Colorado 80309-0428, United States
| | - Garret M Miyake
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Wil V Srubar
- Materials Science and Engineering Program and Department of Civil, Environmental, and Architectural Engineering, University of Colorado Boulder, Boulder, Colorado 80309-0428, United States
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7
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Delesky EA, Srubar WV. Ice-binding proteins and bioinspired synthetic mimics in non-physiological environments. iScience 2022; 25:104286. [PMID: 35573196 PMCID: PMC9097698 DOI: 10.1016/j.isci.2022.104286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Elizabeth A. Delesky
- Materials Science and Engineering Program, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Wil V. Srubar
- Materials Science and Engineering Program, University of Colorado Boulder, Boulder, CO 80309, USA
- Department of Civil, Environmental and Architectural Engineering, University of Colorado Boulder, ECOT 441 UCB 428, Boulder, CO 80309, USA
- Corresponding author
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8
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Fu D, Sun Y, Gao H, Liu B, Kang X, Chen H. Identification and Functional Characterization of Antifreeze Protein and Its Mutants in Dendroctonus armandi (Coleoptera: Curculionidae: Scolytinae) Larvae Under Cold Stress. ENVIRONMENTAL ENTOMOLOGY 2022; 51:167-181. [PMID: 34897398 DOI: 10.1093/ee/nvab134] [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] [Received: 07/22/2021] [Indexed: 06/14/2023]
Abstract
Dendroctonus armandi (Tsai and Li) (Coleoptera: Curculionidae: Scolytinae) is considered to be the most destructive forest pest in the Qinling and Bashan Mountains of China. Low winter temperatures limit insect's populations, distribution, activity, and development. Insects have developed different strategies such as freeze-tolerance and freeze-avoidance to survive in low temperature conditions. In the present study, we used gene cloning, real-time polymerase chain reaction (PCR), RNA interference (RNAi), and heterologous expression to study the function of the D. armandi antifreeze protein gene (DaAFP). We cloned the 800 bp full-length cDNA encoding 228 amino acids of DaAFP and analyzed its structure using bioinformatics analysis. The DaAFP amino acid sequence exhibited 24-86% similarity with other insect species. The expression of DaAFP was high in January and in the larvae, head, and midgut of D. armandi. In addition, the expression of DaAFP increased with decreasing temperature and increasing exposure time. RNAi analysis also demonstrated that AFP plays an important role in the cold tolerance of overwintering larvae. The thermal hysteresis and antifreeze activity assay of DaAFP and its mutants indicated that the more regular the DaAFP threonine-cystine-threonine (TXT) motif, the stronger the antifreeze activity. These results suggest that DaAFP plays an essential role as a biological cryoprotectant in overwintering D. armandi larvae and provides a theoretical basis for new pest control methods.
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Affiliation(s)
- Danyang Fu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
| | - Yaya Sun
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
| | - Haiming Gao
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
| | - Bin Liu
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaotong Kang
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
| | - Hui Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
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9
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Gharib G, Saeidiharzand S, Sadaghiani AK, Koşar A. Antifreeze Proteins: A Tale of Evolution From Origin to Energy Applications. Front Bioeng Biotechnol 2022; 9:770588. [PMID: 35186912 PMCID: PMC8851421 DOI: 10.3389/fbioe.2021.770588] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 12/31/2021] [Indexed: 11/19/2022] Open
Abstract
Icing and formation of ice crystals is a major obstacle against applications ranging from energy systems to transportation and aviation. Icing not only introduces excess thermal resistance, but it also reduces the safety in operating systems. Many organisms living under harsh climate and subzero temperature conditions have developed extraordinary survival strategies to avoid or delay ice crystal formation. There are several types of antifreeze glycoproteins with ice-binding ability to hamper ice growth, ice nucleation, and recrystallization. Scientists adopted similar approaches to utilize a new generation of engineered antifreeze and ice-binding proteins as bio cryoprotective agents for preservation and industrial applications. There are numerous types of antifreeze proteins (AFPs) categorized according to their structures and functions. The main challenge in employing such biomolecules on industrial surfaces is the stabilization/coating with high efficiency. In this review, we discuss various classes of antifreeze proteins. Our particular focus is on the elaboration of potential industrial applications of anti-freeze polypeptides.
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Affiliation(s)
- Ghazaleh Gharib
- Faculty of Engineering and Natural Sciences (FENS), Sabanci University, Istanbul, Turkey
- Sabanci University Nanotechnology and Application Center (SUNUM), Sabanci University, Istanbul, Turkey
- Center of Excellence for Functional Surfaces and Interfaces for Nano-Diagnostics (EFSUN), Sabanci University, Istanbul, Turkey
| | - Shaghayegh Saeidiharzand
- Faculty of Engineering and Natural Sciences (FENS), Sabanci University, Istanbul, Turkey
- Sabanci University Nanotechnology and Application Center (SUNUM), Sabanci University, Istanbul, Turkey
| | - Abdolali K. Sadaghiani
- Faculty of Engineering and Natural Sciences (FENS), Sabanci University, Istanbul, Turkey
- Sabanci University Nanotechnology and Application Center (SUNUM), Sabanci University, Istanbul, Turkey
- Center of Excellence for Functional Surfaces and Interfaces for Nano-Diagnostics (EFSUN), Sabanci University, Istanbul, Turkey
- *Correspondence: Abdolali K. Sadaghiani, ; Ali Koşar,
| | - Ali Koşar
- Faculty of Engineering and Natural Sciences (FENS), Sabanci University, Istanbul, Turkey
- Sabanci University Nanotechnology and Application Center (SUNUM), Sabanci University, Istanbul, Turkey
- Center of Excellence for Functional Surfaces and Interfaces for Nano-Diagnostics (EFSUN), Sabanci University, Istanbul, Turkey
- *Correspondence: Abdolali K. Sadaghiani, ; Ali Koşar,
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10
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Prediction and analysis of antifreeze proteins. Heliyon 2021; 7:e07953. [PMID: 34604556 PMCID: PMC8473546 DOI: 10.1016/j.heliyon.2021.e07953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/28/2021] [Accepted: 09/03/2021] [Indexed: 11/20/2022] Open
Abstract
Antifreeze proteins (AFPs) are proteins that protect cellular fluids and body fluids from freezing by inhibiting the nucleation and growth of ice crystals and preventing ice recrystallization, thereby contributing to the maintenance of life in living organisms. They exist in fish, insects, microorganisms, and fungi. However, the number of known AFPs is currently limited, and it is essential to construct a reliable dataset of AFPs and develop a bioinformatics tool to predict AFPs. In this work, we first collected AFPs sequences from UniProtKB considering the reliability of annotations and, based on these datasets, developed a prediction system using random forest. We achieved accuracies of 0.961 and 0.947 for non-redundant sequences with less than 90% and 30% identities and achieved the accuracy of 0.953 for representative sequences for each species. Using the ability of random forest, we identified the sequence features that contributed to the prediction. Some sequence features were common to AFPs from different species. These features include the Cys content, Ala-Ala content, Trp-Gly content, and the amino acids' distribution related to the disorder propensity. The computer program and the dataset developed in this work are available from the GitHub site: https://github.com/ryomiya/Prediction-and-analysis-of-antifreeze-proteins.
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11
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Pal P, Chakraborty S, Jana B. Differential Hydration of Ice‐Binding Surface of Globular and Hyperactive Antifreeze Proteins. ADVANCED THEORY AND SIMULATIONS 2021. [DOI: 10.1002/adts.202100090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Prasun Pal
- School of Chemical Sciences Indian Association for the Cultivation of Science, Jadavpur Kolkata 700032 India
| | | | - Biman Jana
- School of Chemical Sciences Indian Association for the Cultivation of Science, Jadavpur Kolkata 700032 India
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12
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Crystal structure of an insect antifreeze protein reveals ordered waters on the ice-binding surface. Biochem J 2021; 477:3271-3286. [PMID: 32794579 DOI: 10.1042/bcj20200539] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/10/2020] [Accepted: 08/14/2020] [Indexed: 11/17/2022]
Abstract
Antifreeze proteins (AFPs) are characterized by their ability to adsorb to the surface of ice crystals and prevent any further crystal growth. AFPs have independently evolved for this purpose in a variety of organisms that encounter the threat of freezing, including many species of polar fish, insects, plants and microorganisms. Despite their diverse origins and structures, it has been suggested that all AFPs can organize ice-like water patterns on one side of the protein (the ice-binding site) that helps bind the AFP to ice. Here, to test this hypothesis, we have solved the crystal structure at 2.05 Å resolution of an AFP from the longhorn beetle, Rhagium mordax with five molecules in the unit cell. This AFP is hyperactive, and its crystal structure resembles that of the R. inquisitor ortholog in having a β-solenoid fold with a wide, flat ice-binding surface formed by four parallel rows of mainly Thr residues. The key difference between these structures is that the R. inquisitor AFP crystallized with its ice-binding site (IBS) making protein-protein contacts that limited the surface water patterns. Whereas the R. mordax AFP crystallized with the IBSs exposed to solvent enabling two layers of unrestricted ordered surface waters to be seen. These crystal waters make close matches to ice lattice waters on the basal and primary prism planes.
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13
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Arsiccio A, Pisano R. The Ice-Water Interface and Protein Stability: A Review. J Pharm Sci 2020; 109:2116-2130. [DOI: 10.1016/j.xphs.2020.03.022] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 03/09/2020] [Accepted: 03/23/2020] [Indexed: 11/25/2022]
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14
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Surís-Valls R, Voets IK. Peptidic Antifreeze Materials: Prospects and Challenges. Int J Mol Sci 2019; 20:E5149. [PMID: 31627404 PMCID: PMC6834126 DOI: 10.3390/ijms20205149] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 10/05/2019] [Accepted: 10/10/2019] [Indexed: 12/28/2022] Open
Abstract
Necessitated by the subzero temperatures and seasonal exposure to ice, various organisms have developed a remarkably effective means to survive the harsh climate of their natural habitats. Their ice-binding (glyco)proteins keep the nucleation and growth of ice crystals in check by recognizing and binding to specific ice crystal faces, which arrests further ice growth and inhibits ice recrystallization (IRI). Inspired by the success of this adaptive strategy, various approaches have been proposed over the past decades to engineer materials that harness these cryoprotective features. In this review we discuss the prospects and challenges associated with these advances focusing in particular on peptidic antifreeze materials both identical and akin to natural ice-binding proteins (IBPs). We address the latest advances in their design, synthesis, characterization and application in preservation of biologics and foods. Particular attention is devoted to insights in structure-activity relations culminating in the synthesis of de novo peptide analogues. These are sequences that resemble but are not identical to naturally occurring IBPs. We also draw attention to impactful developments in solid-phase peptide synthesis and 'greener' synthesis routes, which may aid to overcome one of the major bottlenecks in the translation of this technology: unavailability of large quantities of low-cost antifreeze materials with excellent IRI activity at (sub)micromolar concentrations.
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Affiliation(s)
- Romà Surís-Valls
- Laboratory of Self-Organizing Soft Matter, Laboratory of Macro-Organic Chemistry, Department of Chemical Engineering and Chemistry & Institute for Complex Molecular Systems, Eindhoven University of Technology, Post Office Box 513, 5600 MD Eindhoven, The Netherlands.
| | - Ilja K Voets
- Laboratory of Self-Organizing Soft Matter, Laboratory of Macro-Organic Chemistry, Department of Chemical Engineering and Chemistry & Institute for Complex Molecular Systems, Eindhoven University of Technology, Post Office Box 513, 5600 MD Eindhoven, The Netherlands.
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15
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Perez AF, Taing KR, Quon JC, Flores A, Ba Y. Effect of Type I Antifreeze Proteins on the Freezing and Melting Processes of Cryoprotective Solutions Studied by Site-Directed Spin Labeling Technique. CRYSTALS 2019; 9. [PMID: 33224522 PMCID: PMC7678753 DOI: 10.3390/cryst9070352] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Antifreeze proteins (AFPs) protect organisms living in subzero environments from freezing injury, which render them potential applications for cryopreservation of living cells, organs, and tissues. Cryoprotective agents (CPAs), such as glycerol and propylene glycol, have been used as ingredients to treat cellular tissues and organs to prevent ice crystal’s formation at low temperatures. To assess AFP’s function in CPA solutions, we have the applied site-directed spin labeling technique to a Type I AFP. A two-step process to prevent bulk freezing of the CPA solutions was observed by the cryo-photo microscopy, i.e., (1) thermodynamic freezing point depression by the CPAs; and (2) inhibition to the growth of seed ice crystals by the AFP. Electron paramagnetic resonance (EPR) experiments were also carried out from room temperature to 97 K, and vice versa. The EPR results indicate that the spin labeled AFP bound to ice surfaces, and inhibit the growths of ice through the bulk freezing processes in the CPA solutions. The ice-surface bound AFP in the frozen matrices could also prevent the formation of large ice crystals during the melting processes of the solutions. Our study illustrates that AFPs can play an active role in CPA solutions for cryopreservation applications.
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Affiliation(s)
- Adiel F Perez
- Department of Chemistry and Biochemistry, California State University, Los Angeles, 5151 State University Drive, Los Angeles, CA 90032, USA
| | - Kyle R Taing
- Department of Chemistry and Biochemistry, California State University, Los Angeles, 5151 State University Drive, Los Angeles, CA 90032, USA
| | - Justin C Quon
- Department of Chemistry and Biochemistry, California State University, Los Angeles, 5151 State University Drive, Los Angeles, CA 90032, USA
| | - Antonia Flores
- Department of Chemistry and Biochemistry, California State University, Los Angeles, 5151 State University Drive, Los Angeles, CA 90032, USA
| | - Yong Ba
- Department of Chemistry and Biochemistry, California State University, Los Angeles, 5151 State University Drive, Los Angeles, CA 90032, USA
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16
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Bhatnagar B, Zakharov B, Fisyuk A, Wen X, Karim F, Lee K, Seryotkin Y, Mogodi M, Fitch A, Boldyreva E, Kostyuchenko A, Shalaev E. Protein/Ice Interaction: High-Resolution Synchrotron X-ray Diffraction Differentiates Pharmaceutical Proteins from Lysozyme. J Phys Chem B 2019; 123:5690-5699. [DOI: 10.1021/acs.jpcb.9b02443] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Bakul Bhatnagar
- BTx PharmSci Pharmaceutical R&D, Pfizer, Inc., One Burtt Road, Andover 01810, Massachusetts, United States
| | - Boris Zakharov
- Boreskov Institute of Catalysis, Siberian Branch of the RAS, Lavrentieva Avenue, 5, Novosibirsk 630090, Russia
- Novosibirsk State University, Pirogova Street, 2, Novosibirsk 630090, Russia
| | - Alexander Fisyuk
- Laboratory of Organic Synthesis, Chemistry Department, Omsk F.M. Dostoevsky State University, Prospect Mira 55a, Omsk 644053, Russian Federation
- Laboratory of New Organic Materials, Omsk State Technical University, 11 Mira Avenue, Omsk 644050, Russian Federation
| | - Xin Wen
- Department of Chemistry and Biochemistry, California State University, Los Angeles, Los Angeles 90032, California, United States
| | - Fawziya Karim
- BTx PharmSci Pharmaceutical R&D, Pfizer, Inc., One Burtt Road, Andover 01810, Massachusetts, United States
| | - Kimberly Lee
- Department of Chemistry and Biochemistry, California State University, Los Angeles, Los Angeles 90032, California, United States
| | - Yurii Seryotkin
- Novosibirsk State University, Pirogova Street, 2, Novosibirsk 630090, Russia
- Sobolev Institute of Geology and Mineralogy, Siberian Branch of the RAS, Ac.Koptyuga Avenue 3, Novosibirsk 630090, Russian Federation
| | - Mashikoane Mogodi
- The European Synchrotron Radiation Facility (ESRF), 71 Avenue des Martyrs, Grenoble 38043, France
| | - Andy Fitch
- The European Synchrotron Radiation Facility (ESRF), 71 Avenue des Martyrs, Grenoble 38043, France
| | - Elena Boldyreva
- Boreskov Institute of Catalysis, Siberian Branch of the RAS, Lavrentieva Avenue, 5, Novosibirsk 630090, Russia
- Novosibirsk State University, Pirogova Street, 2, Novosibirsk 630090, Russia
| | - Anastasia Kostyuchenko
- Laboratory of New Organic Materials, Omsk State Technical University, 11 Mira Avenue, Omsk 644050, Russian Federation
| | - Evgenyi Shalaev
- Allergan Inc., Pharmaceutical Development, 2525 DuPont Dr, Irvine 92612, California, United States
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17
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Takeshita Y, Waku T, Wilson PW, Hagiwara Y. Effects of Winter Flounder Antifreeze Protein on the Growth of Ice Particles in an Ice Slurry Flow in Mini-Channels. Biomolecules 2019; 9:biom9020070. [PMID: 30781718 PMCID: PMC6407026 DOI: 10.3390/biom9020070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 02/01/2019] [Accepted: 02/05/2019] [Indexed: 11/16/2022] Open
Abstract
The control of ice growth in ice slurry is important for many fields, including (a) the cooling of the brain during cardiac arrest, (b) the storage and transportation of fresh fish and fruits, and (c) the development of distributed air-conditioning systems. One of the promising methods for the control is to use a substance such as antifreeze protein. We have observed and report here growth states of ice particles in both quiescent and flowing aqueous solutions of winter flounder antifreeze proteins in mini-channels with a microscope. We also measured ice growth rates. Our aim was to improve the levels of ice growth inhibition by subjecting the antifreeze protein solution both to preheating and to concentrating by ultrafiltration. We have found that the ice growth inhibition by the antifreeze protein decreased in flowing solutions compared with that in quiescent solutions. In addition, unlike unidirectional freezing experiments, the preheating of the antifreeze protein solution reduced the ice growth inhibition properties. This is because the direction of flow, containing HPLC6 and its aggregates, to the ice particle surfaces can change as the ice particle grows, and thus the probability of interaction between HPLC6 and ice surfaces does not increase. In contrast to this, ultrafiltration after preheating the solution improved the ice growth inhibition. This may be due to the interaction between ice surfaces and many aggregates in the concentrates.
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Affiliation(s)
- Yuki Takeshita
- Division of Mechanophysics, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan.
| | - Tomonori Waku
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan.
| | - Peter W Wilson
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan.
| | - Yoshimichi Hagiwara
- Faculty of Mechanical Engineering, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan.
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18
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Ice recrystallization is strongly inhibited when antifreeze proteins bind to multiple ice planes. Sci Rep 2019; 9:2212. [PMID: 30760774 PMCID: PMC6374469 DOI: 10.1038/s41598-018-36546-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 11/23/2018] [Indexed: 02/07/2023] Open
Abstract
Ice recrystallization is a phenomenon observed as the increase in ice crystal size within an already frozen material. Antifreeze proteins (AFPs), a class of proteins capable of arresting ice crystal growth, are known to inhibit this phenomenon even at sub milli-molar concentrations. A tremendous range in the possible applications of AFPs is hence expected in both medical and industrial fields, while a key determinant of the ice recrystallization inhibition (IRI) is hardly understood. Here, IRI efficiency and ice plane affinity were examined for the wild-type AFPI–III, a defective AFPIII isoform, and a fungal AFP isoform. To simplify the IRI analysis using the formal representation of Ostwald-ripening (r3 = r03 + kt), we monitored specific ice grains exhibiting only uniform growth, for which maximum Feret diameter was measured. The cube of an ice grain’s radius (r3) increased proportionately with time (t), and its slope gave the recrystallization rate (k). There was a significant difference in the IRI efficiency between the samples, and the fungal AFP possessing the activity with the smallest amount (0.27 μM) exhibited an affinity to multiple ice planes. These results suggest that the IRI efficiency is maximized when AFPs bind to a whole set of ice planes.
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19
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Brotzakis ZF, Voets IK, Bakker HJ, Bolhuis PG. Water structure and dynamics in the hydration layer of a type III anti-freeze protein. Phys Chem Chem Phys 2018; 20:6996-7006. [PMID: 29468240 DOI: 10.1039/c8cp00170g] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report on a molecular dynamics study on the relation between the structure and the orientational (and hydrogen bond) dynamics of hydration water around the ocean pout AFP III anti-freeze protein. We find evidence for an increasing tetrahedral structure from the area opposite to the ice binding site (IBS) towards the protein IBS, with the strongest signal of tetrahedral structure around the THR-18 residue of the IBS. The tetrahedral structural parameter mostly positively correlates with increased reorientation decay times. Interestingly, for several key (polar) residues that are not part of the IBS but are in its vicinity, we observe a decrease of the reorientation time with increasing tetrahedral structure. A similar anti-correlation is observed for the hydrogen-bonded water molecules. These effects are enhanced at a lower temperature. We interpret these results in terms of the structure-making and structure-breaking residues. Moreover, we investigate the tetrahedral structure and dynamics of waters at a partially dehydrated IBS, and for the protein adsorbed at the air-water interface. We find that the mutation changes the preferred protein orientation upon adsorption at an air-water interface. These results are in agreement with the water-air Vibration Sum Frequency Generation spectroscopic experiments showing a strongly reduced tetrahedral signal upon mutation at the IBS.
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Affiliation(s)
- Z Faidon Brotzakis
- Van't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
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20
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Lee H. Effects of hydrophobic and hydrogen-bond interactions on the binding affinity of antifreeze proteins to specific ice planes. J Mol Graph Model 2018; 87:48-55. [PMID: 30502671 DOI: 10.1016/j.jmgm.2018.11.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 11/17/2018] [Accepted: 11/19/2018] [Indexed: 11/26/2022]
Abstract
Tenebrio molitor antifreeze protein (TmAFP) was simulated with growing ice surfaces such as primary prism, secondary prism, basal, and pyramidal planes. The ice-binding site of TmAFP, which is full of threonine (Thr), binds to the primary-prism plane but does not bind to other ice planes, in agreement with experiments showing the fast adsorption of TmAFP to the primary-prism plane. To mimic the ice-binding site of shorthorn sculpin AFP (ssAFP; type I) that predominantly consists of alanine (Ala) and has the binding affinity to the secondary-prism plane, the ice-binding site of TmAFP was mutated by replacing a few Thr residues with Ala residues, showing that mutated TmAFP binds to the secondary-prism plane, similar to the ice-binding affinity of ssAFP. Ala residues are located at the cavity of ice, while Thr residues form hydrogen bonds with water molecules. When the mutated TmAFP is further modified by removing Thr, it does not bind to the secondary-prism plane. These findings indicate that simulations can successfully capture the experimentally observed binding affinity of AFP to specific ice planes, to an extent dependent on hydrophobicity of the ice-binding site. In particular, the addition of hydrophobic residues influences the ice-binding affinity of TmAFP, while a certain amount of hydrophilic residue is still required for hydrogen-bond interactions, which supports experimental observations regarding the key roles of hydrophobic and hydrophilic interactions on the AFP-ice binding.
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Affiliation(s)
- Hwankyu Lee
- Department of Chemical Engineering, Dankook University, Yongin-si, Gyeonggi-do, 16890, South Korea.
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21
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Midya US, Bandyopadhyay S. Role of Polar and Nonpolar Groups in the Activity of Antifreeze Proteins: A Molecular Dynamics Simulation Study. J Phys Chem B 2018; 122:9389-9398. [DOI: 10.1021/acs.jpcb.8b08506] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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22
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Abstract
Antifreeze proteins (AFPs) protect marine fishes from freezing in icy seawater. They evolved relatively recently, most likely in response to the formation of sea ice and Cenozoic glaciations that occurred less than 50 million years ago, following a greenhouse Earth event. Based on their diversity, AFPs have independently evolved on many occasions to serve the same function, with some remarkable examples of convergent evolution at the structural level, and even instances of lateral gene transfer. For some AFPs, the progenitor gene is recognizable. The intense selection pressure exerted by icy seawater, which can rapidly kill unprotected fish, has led to massive AFP gene amplification, as well as some partial gene duplications that have increased the size and activity of the antifreeze. The many protein evolutionary processes described in Gordon H. Dixon's Essays in Biochemistry article will be illustrated here by examples from studies on AFPs. Abbreviations: AFGP: antifreeze glycoproteins; AFP: antifreeze proteins; GHD: Gordon H. Dixon; SAS: sialic acid synthase; TH: thermal hysteresis.
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Affiliation(s)
- Peter L Davies
- a Department of Biomedical and Molecular Sciences , Queen's University , Kingston , Canada
| | - Laurie A Graham
- a Department of Biomedical and Molecular Sciences , Queen's University , Kingston , Canada
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23
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Molecular Dynamics Analysis of Synergistic Effects of Ions and Winter Flounder Antifreeze Protein Adjacent to Ice-Solution Surfaces. CRYSTALS 2018. [DOI: 10.3390/cryst8070302] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The control of freezing saline water at the micrometer level has become very important in cryosurgery and cryopreservation of stem cells and foods. Adding antifreeze protein to saline water is a promising method for controlling the freezing because the protein produces a gap between the melting point and the freezing point. Furthermore, a synergistic effect of the solutes occurs in which the freezing point depression of a mixed solution is more noticeable than the sum of two freezing point depressions of single-solute solutions. However, the mechanism of this effect has not yet been clarified. Thus, we have carried out a molecular dynamics simulation on aqueous solutions of winter flounder antifreeze protein and sodium chloride or calcium chloride with an ice layer. The results show that the cations inhibit the hydrogen bond among water molecules not only in the salt solutions but also in the mixed solutions. This inhibition depends on the local number of ions and the valence of cations. The space for water molecules to form the hydrogen bonds becomes small in the case of the mixed solution of the protein and calcium chloride. These findings are consistent with the synergistic effect. In addition, it is found that the diffusion of ions near positively-charged residues is attenuated. This attenuation causes an increase in the possibility of water molecules staying near or inside the hydration shells of the ions. Furthermore, the first hydration shells of the cations become weak in the vicinity of the arginine, lysine and glutamic-acid residues. These factors can be considered to be possible mechanisms of the synergistic effect.
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24
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He Z, Liu K, Wang J. Bioinspired Materials for Controlling Ice Nucleation, Growth, and Recrystallization. Acc Chem Res 2018; 51:1082-1091. [PMID: 29664599 DOI: 10.1021/acs.accounts.7b00528] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Ice formation, mainly consisting of ice nucleation, ice growth, and ice recrystallization, is ubiquitous and crucial in wide-ranging fields from cryobiology to atmospheric physics. Despite active research for more than a century, the mechanism of ice formation is still far from satisfactory. Meanwhile, nature has unique ways of controlling ice formation and can provide resourceful avenues to unravel the mechanism of ice formation. For instance, antifreeze proteins (AFPs) protect living organisms from freezing damage via controlling ice formation, for example, tuning ice nucleation, shaping ice crystals, and inhibiting ice growth and recrystallization. In addition, AFP mimics can have applications in cryopreservation of cells, tissues, and organs, food storage, and anti-icing materials. Therefore, continuous efforts have been made to understand the mechanism of AFPs and design AFP inspired materials. In this Account, we first review our recent research progress in understanding the mechanism of AFPs in controlling ice formation. A Janus effect of AFPs on ice nucleation was discovered, which was achieved via selectively tethering the ice-binding face (IBF) or the non-ice-binding face (NIBF) of AFPs to solid surfaces and investigating specifically the effect of the other face on ice nucleation. Through molecular dynamics (MD) simulation analysis, we observed ordered hexagonal ice-like water structure atop the IBF and disordered water structure atop the NIBF. Therefore, we conclude that the interfacial water plays a critical role in controlling ice formation. Next, we discuss the design and fabrication of AFP mimics with capabilities in tuning ice nucleation and controlling ice shape and growth, as well as inhibiting ice recrystallization. For example, we tuned ice nucleation via modifying solid surfaces with supercharged unfolded polypeptides (SUPs) and polyelectrolyte brushes (PBs) with different counterions. We found graphene oxide (GO) and oxidized quasi-carbon nitride quantum dots (OQCNs) had profound effects in controlling ice shape and inhibiting ice growth. We also studied the ion-specific effect on ice recrystallization inhibition (IRI) with a large variety of anions and cations. All functionalities are achieved by tuning the properties of interfacial water on these materials, which reinforces the importance of the interfacial water in controlling ice formation. Finally, we review the development of novel application-oriented materials emerging from our enhanced understanding of ice formation, for example, ultralow ice adhesion coatings with aqueous lubricating layer, cryopreservation of cells by inhibiting ice recrystallization, and two-dimensional (2D) and three-dimensional (3D) porous materials with tunable pore sizes through recrystallized ice crystal templates. This Account sheds new light on the molecular mechanism of ice formation and will inspire the design of unprecedented functional materials based on controlled ice formation.
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Affiliation(s)
- Zhiyuan He
- Key Laboratory of Green Printing, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Liu
- Key Laboratory of Green Printing, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianjun Wang
- Key Laboratory of Green Printing, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
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25
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Bredow M, Tomalty HE, Smith L, Walker VK. Ice and anti-nucleating activities of an ice-binding protein from the annual grass, Brachypodium distachyon. PLANT, CELL & ENVIRONMENT 2018; 41:983-992. [PMID: 28035668 DOI: 10.1111/pce.12889] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 12/14/2016] [Accepted: 12/15/2016] [Indexed: 05/15/2023]
Abstract
Plants exposed to sub-zero temperatures face unique challenges that threaten their survival. The growth of ice crystals in the extracellular space can cause cellular dehydration, plasma membrane rupture and eventual cell death. Additionally, some pathogenic bacteria cause tissue damage by initiating ice crystal growth at high sub-zero temperatures through the use of ice-nucleating proteins (INPs), presumably to access nutrients from lysed cells. An annual species of brome grass, Brachypodium distachyon (Bd), produces an ice-binding protein (IBP) that shapes ice with a modest depression of the freezing point (~0.1 °C at 1 mg/mL), but high ice-recrystallization inhibition (IRI) activity, allowing ice crystals to remain small at near melting temperatures. This IBP, known as BdIRI, is unlike other characterized IBPs with a single ice-binding face, as mutational analysis indicates that BdIRI adsorbs to ice on two faces. BdIRI also dramatically attenuates the nucleation of ice by bacterial INPs (up to -2.26 °C). This 'anti-nucleating' activity is significantly higher than previously documented for any IBP.
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Affiliation(s)
- Melissa Bredow
- Department of Biology, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - Heather E Tomalty
- Department of Biology, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - Lindsay Smith
- Department of Biology, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - Virginia K Walker
- Department of Biology, Queen's University, Kingston, Ontario, K7L 3N6, Canada
- Department of Biomedical and Molecular Sciences, and School of Environmental Studies, Queen's University, Kingston, Ontario, K7L 3N6, Canada
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26
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Affiliation(s)
- Alexander G. Shtukenberg
- Department of Chemistry and Molecular
Design Institute, New York University, 100 Washington Square East, New York City, New York 10003, United States
| | - Michael D. Ward
- Department of Chemistry and Molecular
Design Institute, New York University, 100 Washington Square East, New York City, New York 10003, United States
| | - Bart Kahr
- Department of Chemistry and Molecular
Design Institute, New York University, 100 Washington Square East, New York City, New York 10003, United States
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27
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Wang C, Pakhomova S, Newcomer ME, Christner BC, Luo BH. Structural basis of antifreeze activity of a bacterial multi-domain antifreeze protein. PLoS One 2017; 12:e0187169. [PMID: 29108002 PMCID: PMC5673226 DOI: 10.1371/journal.pone.0187169] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 10/13/2017] [Indexed: 01/05/2023] Open
Abstract
Antifreeze proteins (AFPs) enhance the survival of organisms inhabiting cold environments by affecting the formation and/or structure of ice. We report the crystal structure of the first multi-domain AFP that has been characterized. The two ice binding domains are structurally similar. Each consists of an irregular β-helix with a triangular cross-section and a long α-helix that runs parallel on one side of the β-helix. Both domains are stabilized by hydrophobic interactions. A flat plane on the same face of each domain’s β-helix was identified as the ice binding site. Mutating any of the smaller residues on the ice binding site to bulkier ones decreased the antifreeze activity. The bulky side chain of Leu174 in domain A sterically hinders the binding of water molecules to the protein backbone, partially explaining why antifreeze activity by domain A is inferior to that of domain B. Our data provide a molecular basis for understanding differences in antifreeze activity between the two domains of this protein and general insight on how structural differences in the ice-binding sites affect the activity of AFPs.
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Affiliation(s)
- Chen Wang
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Svetlana Pakhomova
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Marcia E. Newcomer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Brent C. Christner
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
- Department of Microbiology and Cell Science, Biodiversity Institute, University of Florida, Gainesville, Florida, United States of America
| | - Bing-Hao Luo
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
- * E-mail:
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28
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Li LF, Liang XX. Influence of Adsorption Orientation on the Statistical Mechanics Model of Type I Antifreeze Protein: The Thermal Hysteresis Temperature. J Phys Chem B 2017; 121:9513-9517. [PMID: 28956610 DOI: 10.1021/acs.jpcb.7b06619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The antifreeze activity of type I antifreeze proteins (AFPIs) is studied on the basis of the statistical mechanics theory, by taking the AFP's adsorption orientation into account. The thermal hysteresis temperatures are calculated by determining the system Gibbs function as well as the AFP molecule coverage rate on the ice-crystal surface. The numerical results for the thermal hysteresis temperatures of AFP9, HPLC-6, and AAAA2kE are obtained for both of the cases with and without inclusion of the adsorption orientation. The results show that the influence of the adsorption orientation on the thermal hysteresis temperature cannot be neglected. The theoretical results are coincidental preferably with the experimental data.
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Affiliation(s)
- Li-Fen Li
- Department of Basic Curriculum, North China Institute of Science and Technology , Beijing 101601, China
| | - Xi-Xia Liang
- Department of Physics, Inner Mongolia University , Hohhot 010021, China
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29
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Voets IK. From ice-binding proteins to bio-inspired antifreeze materials. SOFT MATTER 2017; 13:4808-4823. [PMID: 28657626 PMCID: PMC5708349 DOI: 10.1039/c6sm02867e] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 06/16/2017] [Indexed: 05/07/2023]
Abstract
Ice-binding proteins (IBP) facilitate survival under extreme conditions in diverse life forms. IBPs in polar fishes block further growth of internalized environmental ice and inhibit ice recrystallization of accumulated internal crystals. Algae use IBPs to structure ice, while ice adhesion is critical for the Antarctic bacterium Marinomonas primoryensis. Successful translation of this natural cryoprotective ability into man-made materials holds great promise but is still in its infancy. This review covers recent advances in the field of ice-binding proteins and their synthetic analogues, highlighting fundamental insights into IBP functioning as a foundation for the knowledge-based development of cheap, bio-inspired mimics through scalable production routes. Recent advances in the utilisation of IBPs and their analogues to e.g. improve cryopreservation, ice-templating strategies, gas hydrate inhibition and other technologies are presented.
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Affiliation(s)
- I K Voets
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Post Office Box 513, 5600 MD Eindhoven, The Netherlands. and Laboratory of Macromolecular and Organic Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, Post Office Box 513, 5600 MD Eindhoven, The Netherlands and Laboratory of Physical Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, Post Office Box 513, 5600 MD Eindhoven, The Netherlands
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30
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Mahatabuddin S, Hanada Y, Nishimiya Y, Miura A, Kondo H, Davies PL, Tsuda S. Concentration-dependent oligomerization of an alpha-helical antifreeze polypeptide makes it hyperactive. Sci Rep 2017; 7:42501. [PMID: 28211917 PMCID: PMC5304152 DOI: 10.1038/srep42501] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 01/13/2017] [Indexed: 11/09/2022] Open
Abstract
A supersoluble 40-residue type I antifreeze protein (AFP) was discovered in a righteye flounder, the barfin plaice (bp). Unlike all other AFPs characterized to date, bpAFP transitions from moderately-active to hyperactive with increasing concentration. At sub-mM concentrations, bpAFP bound to pyramidal planes of ice to shape it into a bi-pyramidal hexagonal trapezohedron, similarly to the other moderately-active AFPs. At mM concentrations, bpAFP uniquely underwent further binding to the whole ice crystal surface including the basal planes. The latter caused a bursting ice crystal growth normal to c-axis, 3 °C of high thermal hysteresis, and alteration of an ice crystal into a smaller lemon-shaped morphology, all of which are well-known properties of hyperactive AFPs. Analytical ultracentrifugation showed this activity transition is associated with oligomerization to form tetramer, which might be the forerunner of a naturally occurring four-helix-bundle AFP in other flounders.
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Affiliation(s)
- Sheikh Mahatabuddin
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Yuichi Hanada
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Yoshiyuki Nishimiya
- Bioproduction Research Institute, ioproduction Research Institute and OPERANDO Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo 062-8517, Japan
| | - Ai Miura
- Bioproduction Research Institute, ioproduction Research Institute and OPERANDO Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo 062-8517, Japan
| | - Hidemasa Kondo
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
- Bioproduction Research Institute, ioproduction Research Institute and OPERANDO Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo 062-8517, Japan
| | - Peter L. Davies
- Protein Function Discovery Group and Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON, K7L 3N6, Canada
| | - Sakae Tsuda
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
- Bioproduction Research Institute, ioproduction Research Institute and OPERANDO Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo 062-8517, Japan
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31
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Kim HJ, Lee JH, Hur YB, Lee CW, Park SH, Koo BW. Marine Antifreeze Proteins: Structure, Function, and Application to Cryopreservation as a Potential Cryoprotectant. Mar Drugs 2017; 15:md15020027. [PMID: 28134801 PMCID: PMC5334608 DOI: 10.3390/md15020027] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 01/20/2017] [Indexed: 11/16/2022] Open
Abstract
Antifreeze proteins (AFPs) are biological antifreezes with unique properties, including thermal hysteresis(TH),ice recrystallization inhibition(IRI),and interaction with membranes and/or membrane proteins. These properties have been utilized in the preservation of biological samples at low temperatures. Here, we review the structure and function of marine-derived AFPs, including moderately active fish AFPs and hyperactive polar AFPs. We also survey previous and current reports of cryopreservation using AFPs. Cryopreserved biological samples are relatively diverse ranging from diatoms and reproductive cells to embryos and organs. Cryopreserved biological samples mainly originate from mammals. Most cryopreservation trials using marine-derived AFPs have demonstrated that addition of AFPs can improve post-thaw viability regardless of freezing method (slow-freezing or vitrification), storage temperature, and types of biological sample type.
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Affiliation(s)
- Hak Jun Kim
- Department of Chemistry, Pukyong National University, Busan 48513, Korea.
| | - Jun Hyuck Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon 21990, Korea.
| | - Young Baek Hur
- Tidal Flat Research Institute, National Fisheries Research and Development Institute, Gunsan, Jeonbuk 54014, Korea.
| | - Chang Woo Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon 21990, Korea.
| | - Sun-Ha Park
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon 21990, Korea.
| | - Bon-Won Koo
- Department of Chemistry, Pukyong National University, Busan 48513, Korea.
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32
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Nguyen H, Le L. Investigation of changes in structure and thermodynamic of spruce budworm antifreeze protein under subfreezing temperature. Sci Rep 2017; 7:40032. [PMID: 28106056 PMCID: PMC5247755 DOI: 10.1038/srep40032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 11/30/2016] [Indexed: 11/29/2022] Open
Abstract
The aim of this theoretical work is to investigate of the changes in structure and thermodynamics of spruce budworm antifreeze protein (sbAFP) at low temperatures by using molecular dynamics simulation. The aqueous solution will form ice crystal network under the vaguely hexagonal shape at low temperature and fully represented the characteristics of hydrophobic interaction. Like ice crystal network, the cyclohexane region (including cyclohexane molecules) have enough of the characteristics of hydrophobic interaction. Therefore, in this research the cyclohexane region will be used as a representation of ice crystal network to investigate the interactions of sbAFP and ice crystal network at low temperature. The activity of sbAFP in subfreezing environment, therefore, can be clearly observed via the changes of the hydrophobic (cyclohexane region) and hydrophilic (water region) interactions. The obtained results from total energies, hydrogen bond lifetime correlation C(t), radial distribution function, mean square deviation and snapshots of sbAFP complexes indicated that sbAFP has some special changes in structure and interaction with water and cyclohexane regions at 278 K, as being transition temperature point of water molecules in sbAFP complex at low temperatures, which is more structured and support the experimental observation that the sbAFP complex becomes more rigid as the temperature is lowered.
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Affiliation(s)
- Hung Nguyen
- Open Lab, Institute for Computational Sciences and Technology at Ho Chi Minh City, Vietnam
| | - Ly Le
- Open Lab, Institute for Computational Sciences and Technology at Ho Chi Minh City, Vietnam.,School of Biotechnology, International University, Vietnam National University at Ho Chi Minh, Vietnam
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33
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Sun T, Davies PL, Walker VK. Structural Basis for the Inhibition of Gas Hydrates by α-Helical Antifreeze Proteins. Biophys J 2016; 109:1698-705. [PMID: 26488661 DOI: 10.1016/j.bpj.2015.08.041] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 08/10/2015] [Accepted: 08/31/2015] [Indexed: 10/22/2022] Open
Abstract
Kinetic hydrate inhibitors (KHIs) are used commercially to inhibit gas hydrate formation and growth in pipelines. However, improvement of these polymers has been constrained by the lack of verified molecular models. Since antifreeze proteins (AFPs) act as KHIs, we have used their solved x-ray crystallographic structures in molecular modeling to explore gas hydrate inhibition. The internal clathrate water network of the fish AFP Maxi, which extends to the protein's outer surface, is remarkably similar to the {100} planes of structure type II (sII) gas hydrate. The crystal structure of this water web has facilitated the construction of in silico models for Maxi and type I AFP binding to sII hydrates. Here, we have substantiated our models with experimental evidence of Maxi binding to the tetrahydrofuran sII model hydrate. Both in silico and experimental evidence support the absorbance-inhibition mechanism proposed for KHI binding to gas hydrates. Based on the Maxi crystal structure we suggest that the inhibitor adsorbs to the gas hydrate lattice through the same anchored clathrate water mechanism used to bind ice. These results will facilitate the rational design of a next generation of effective green KHIs for the petroleum industry to ensure safe and efficient hydrocarbon flow.
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Affiliation(s)
- Tianjun Sun
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Peter L Davies
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada; Department of Biology, Queen's University, Kingston, Ontario, Canada
| | - Virginia K Walker
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada; Department of Biology, Queen's University, Kingston, Ontario, Canada.
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34
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Ramya L, Ramakrishnan V. Interaction ofTenebrio MolitorAntifreeze Protein with Ice Crystal: Insights from Molecular Dynamics Simulations. Mol Inform 2016; 35:268-77. [DOI: 10.1002/minf.201600034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 05/10/2016] [Indexed: 11/09/2022]
Affiliation(s)
- L. Ramya
- Centre for Nanotechnology & Advanced Biomaterials; SASTRA University; Thanjavur-613401 Tamilnadu India
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35
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Abstract
Ice binding proteins (IBPs) are produced by various cold-adapted organisms to protect their body tissues against freeze damage. First discovered in Antarctic fish living in shallow waters, IBPs were later found in insects, microorganisms, and plants. Despite great structural diversity, all IBPs adhere to growing ice crystals, which is essential for their extensive repertoire of biological functions. Some IBPs maintain liquid inclusions within ice or inhibit recrystallization of ice, while other types suppress freezing by blocking further ice growth. In contrast, ice nucleating proteins stimulate ice nucleation just below 0 °C. Despite huge commercial interest and major scientific breakthroughs, the precise working mechanism of IBPs has not yet been unraveled. In this review, the authors outline the state-of-the-art in experimental and theoretical IBP research and discuss future scientific challenges. The interaction of IBPs with ice, water and ions is examined, focusing in particular on ice growth inhibition mechanisms.
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36
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Basu K, Campbell RL, Guo S, Sun T, Davies PL. Modeling repetitive, non-globular proteins. Protein Sci 2016; 25:946-58. [PMID: 26914323 DOI: 10.1002/pro.2907] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 02/10/2016] [Accepted: 02/19/2016] [Indexed: 11/07/2022]
Abstract
While ab initio modeling of protein structures is not routine, certain types of proteins are more straightforward to model than others. Proteins with short repetitive sequences typically exhibit repetitive structures. These repetitive sequences can be more amenable to modeling if some information is known about the predominant secondary structure or other key features of the protein sequence. We have successfully built models of a number of repetitive structures with novel folds using knowledge of the consensus sequence within the sequence repeat and an understanding of the likely secondary structures that these may adopt. Our methods for achieving this success are reviewed here.
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Affiliation(s)
- Koli Basu
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - Robert L Campbell
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - Shuaiqi Guo
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - Tianjun Sun
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Peter L Davies
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, K7L 3N6, Canada
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Nguyen H, Dac Van T, Tran N, Le L. Exploring the Effects of Subfreezing Temperature and Salt Concentration on Ice Growth Inhibition of Antarctic Gram-Negative Bacterium Marinomonas Primoryensis Using Coarse-Grained Simulation. Appl Biochem Biotechnol 2016; 178:1534-45. [PMID: 26758589 DOI: 10.1007/s12010-015-1966-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 12/21/2015] [Indexed: 10/22/2022]
Abstract
The aim of this work is to study the freezing process of water molecules surrounding Antarctic Gram-negative bacterium Marinomonas primoryensis antifreeze protein (MpAFP) and the MpAFP interactions to the surface of ice crystals under various marine environments (at different NaCl concentrations of 0.3, 0.6, and 0.8 mol/l). Our result indicates that activating temperature region of MpAFPs reduced as NaCl concentration increased. Specifically, MpAFP was activated and functioned at 0.6 mol/l with temperatures equal or larger 278 K, and at 0.8 mol/l with temperatures equal or larger 270 K. Additionally, MpAFP was inhibited by ice crystal network from 268 to 274 K and solid-liquid hybrid from 276 to 282 K at 0.3 mol/l concentration. Our results shed lights on structural dynamics of MpAFP among different marine environments.
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Affiliation(s)
- Hung Nguyen
- Life Science Laboratory of Institute for Computational Science and Technology, Ho Chi Minh City, Vietnam.
| | - Thanh Dac Van
- Life Science Laboratory of Institute for Computational Science and Technology, Ho Chi Minh City, Vietnam
- School of Biotechnology of Ho Chi Minh International University, Vietnam National University, Ho Chi Minh City, Vietnam
| | - Nhut Tran
- Life Science Laboratory of Institute for Computational Science and Technology, Ho Chi Minh City, Vietnam
| | - Ly Le
- Life Science Laboratory of Institute for Computational Science and Technology, Ho Chi Minh City, Vietnam.
- School of Biotechnology of Ho Chi Minh International University, Vietnam National University, Ho Chi Minh City, Vietnam.
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38
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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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39
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Duboué-Dijon E, Laage D. Comparative study of hydration shell dynamics around a hyperactive antifreeze protein and around ubiquitin. J Chem Phys 2015; 141:22D529. [PMID: 25494800 DOI: 10.1063/1.4902822] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The hydration layer surrounding a protein plays an essential role in its biochemical function and consists of a heterogeneous ensemble of water molecules with different local environments and different dynamics. What determines the degree of dynamical heterogeneity within the hydration shell and how this changes with temperature remains unclear. Here, we combine molecular dynamics simulations and analytic modeling to study the hydration shell structure and dynamics of a typical globular protein, ubiquitin, and of the spruce budworm hyperactive antifreeze protein over the 230-300 K temperature range. Our results show that the average perturbation induced by both proteins on the reorientation dynamics of water remains moderate and changes weakly with temperature. The dynamical heterogeneity arises mostly from the distribution of protein surface topographies and is little affected by temperature. The ice-binding face of the antifreeze protein induces a short-ranged enhancement of water structure and a greater slowdown of water reorientation dynamics than the non-ice-binding faces whose effect is similar to that of ubiquitin. However, the hydration shell of the ice-binding face remains less tetrahedral than the bulk and is not "ice-like". We finally show that the hydrogen bonds between water and the ice-binding threonine residues are particularly strong due to a steric confinement effect, thereby contributing to the strong binding of the antifreeze protein on ice crystals.
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Affiliation(s)
- Elise Duboué-Dijon
- Département de Chimie, École Normale Supérieure-PSL Research University, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, 24, rue Lhomond, 75005 Paris, France
| | - Damien Laage
- Département de Chimie, École Normale Supérieure-PSL Research University, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, 24, rue Lhomond, 75005 Paris, France
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40
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Sharp KA. The remarkable hydration of the antifreeze protein Maxi: a computational study. J Chem Phys 2015; 141:22D510. [PMID: 25494781 DOI: 10.1063/1.4896693] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The long four-helix bundle antifreeze protein Maxi contains an unusual core for a globular protein. More than 400 ordered waters between the helices form a nano-pore of internal water about 150 Å long. Molecular dynamics simulations of hydrated Maxi were carried out using the CHARMM27 protein forcefield and the TIP3P water model. Solvation in the core and non-core first hydration shell was analyzed in terms of water-water H-bond distance-angle distributions. The core had an increased population of low-angle H-bonds between water pairs relative to bulk water. Enhancement of low angle H-bonds was particularly pronounced for water pairs at the interfaces between apolar and polar regions inside the protein core, characteristic of the anchored clathrate solvation structure seen previously in the ice-nuclei binding surfaces of type I, type III, and beta-helical antifreeze proteins. Anchored clathrate type solvation structure was not seen in the exterior solvation shell except around residues implicated in ice binding. Analysis of solvation dynamics using water residence times and diffusion constants showed that exterior solvation shell waters exchanged rapidly with bulk water, with no difference between ice-binding and non-binding residues. Core waters had about ten-fold slower diffusion than bulk water. Water residence times around core residues averaged about 8 ps, similar to those on the exterior surface, but they tended to exchange primarily with other core water, resulting in longer, >40 ps residence times within the core. Preferential exchange or diffusion of the water along the long axis of the water core of Maxi was not detected.
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Affiliation(s)
- Kim A Sharp
- Department of Biochemistry and Biophysics, E. R. Johnson Foundation, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059, USA
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41
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PROVESI JG, AMANTE ER. Revisão: Proteínas anticongelantes – uma tecnologia emergente para o congelamento de alimentos. BRAZILIAN JOURNAL OF FOOD TECHNOLOGY 2015. [DOI: 10.1590/1981-6723.7714] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Um dos métodos mais tradicionais na conservação de alimentos, o congelamento também pode alterar de forma significativa as características do produto. Grandes cristais de gelo provocam alteração na textura e/ou danos a membranas e componentes celulares. As técnicas de congelamento rápido formam cristais de gelo menores do que o processo lento, porém as flutuações de temperatura durante a distribuição e transporte podem promover o crescimento dos cristais. Esse processo é conhecido como recristalização e é uma barreira na utilização do congelamento como método de conservação em muitos casos. O uso de crioprotetores tradicionais, como a sacarose, é uma alternativa limitada, uma vez que concentrações elevadas são requeridas. Na década de 1970, foi descrita em peixes de águas frias uma classe de proteínas que, em baixa concentração, pode interagir e influenciar o crescimento do cristal de gelo. Elas foram chamadas de proteínas anticongelantes (PACs), sendo encontradas também em plantas, animais e micro-organismos ambientados a baixas temperaturas. Essas proteínas podem intervir no processo de formação do núcleo inicial do gelo, reduzir o ponto de congelamento da água, ou, ainda, inibir a recristalização, principalmente para PACs de vegetais. Há diversos trabalhos publicados e algumas patentes registradas para o uso de PACs em diversos alimentos, como lácteos, carnes, massas, frutas e hortaliças, conservando de melhor forma as características originais do alimento. Atualmente, o custo ainda é uma barreira para utilização comercial das PACs. Contudo, a descoberta de novas fontes pode reduzir seu custo e tornar essas proteínas uma ferramenta efetiva na manutenção da textura de alimentos congelados. Baseada em trabalhos que avaliaram aspectos químicos das PACs e exemplos de sua aplicação, esta revisão tem como objetivo principal apresentar as características gerais das PACs e discutir sobre sua utilização.
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42
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Capicciotti CJ, Poisson JS, Boddy CN, Ben RN. Modulation of antifreeze activity and the effect upon post-thaw HepG2 cell viability after cryopreservation. Cryobiology 2015; 70:79-89. [PMID: 25595636 DOI: 10.1016/j.cryobiol.2015.01.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 12/29/2014] [Accepted: 01/06/2015] [Indexed: 01/11/2023]
Abstract
Most antifreeze proteins (AFPs) exhibit two types of "antifreeze activity" - thermal hysteresis (TH) and ice recrystallization inhibition (IRI) activity. The mechanism of TH activity has been studied in depth and is the result of an adsorption of AFPs to the surface of ice with an ice-binding face (IBF). In contrast, the mechanism of ice recrystallization and its inhibition is considerably less understood. In this paper, we examine several different antifreeze proteins, glycoproteins and mutants of the Lolium perenne AFP (LpAFP) to understand how IRI activity is modulated independently of TH activity. This study also examines the ability of the various AF(G)Ps to protect HepG2 cells from cryoinjury. Post-thaw cell viabilities are correlated to TH, IRI activity as well as dynamic ice shaping ability and single ice crystal growth progressions. While these results demonstrate that AF(G)Ps are ineffective as cryoprotectants, they emphasize how ice crystal habit and most importantly, ice growth progression affect HepG2 cell survival during cryopreservation.
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Affiliation(s)
| | - Jessica S Poisson
- Department of Chemistry, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Christopher N Boddy
- Department of Chemistry, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Robert N Ben
- Department of Chemistry, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada.
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Alireza Bagherzadeh S, Alavi S, Ripmeester JA, Englezos P. Why ice-binding type I antifreeze protein acts as a gas hydrate crystal inhibitor. Phys Chem Chem Phys 2015; 17:9984-90. [DOI: 10.1039/c4cp05003g] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The winter flounder antifreeze protein (wf-AFP) acts as a gas hydrate crystal inhibitor by binding to the empty-half cages at the hydrate surfaceviathe cooperative action between methyl groups of threonine and alanine residues.
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Affiliation(s)
- S. Alireza Bagherzadeh
- Department of Chemical and Biological Engineering
- The University of British Columbia
- Vancouver BC
- Canada V6T1Z3
| | - Saman Alavi
- Department of Chemical and Biological Engineering
- The University of British Columbia
- Vancouver BC
- Canada V6T1Z3
- National Research Council of Canada
| | - John A. Ripmeester
- Department of Chemical and Biological Engineering
- The University of British Columbia
- Vancouver BC
- Canada V6T1Z3
- National Research Council of Canada
| | - Peter Englezos
- Department of Chemical and Biological Engineering
- The University of British Columbia
- Vancouver BC
- Canada V6T1Z3
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44
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Davies PL. Ice-binding proteins: a remarkable diversity of structures for stopping and starting ice growth. Trends Biochem Sci 2014; 39:548-55. [DOI: 10.1016/j.tibs.2014.09.005] [Citation(s) in RCA: 268] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 09/24/2014] [Accepted: 09/25/2014] [Indexed: 12/01/2022]
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45
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Jung W, Gwak Y, Davies PL, Kim HJ, Jin E. Isolation and characterization of antifreeze proteins from the antarctic marine microalga Pyramimonas gelidicola. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2014; 16:502-12. [PMID: 24609978 DOI: 10.1007/s10126-014-9567-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 01/21/2014] [Indexed: 05/03/2023]
Abstract
Antifreeze proteins (AFPs) play an important role in the psychrophilic adaptation of polar organisms. AFPs encoded by an Antarctic chlorophyte, identified as Pyramimonas gelidicola, were isolated and characterized. Two AFP isoforms were found from cDNAs and their deduced molecular weights were estimated to be 26.4 kDa (Pg-1-AFP) and 27.1 kDa (Pg-2-AFP). Both AFP cDNAs were cloned and expressed in Escherichia coli. The purified recombinant Pg-1-rAFP and Pg-2-rAFP both showed antifreeze activity based on the measurement of thermal hysteresis (TH) and morphological changes to single ice crystals. Pg-1-rAFP shaped ice crystals into a snowflake pattern with a TH value of 0.6 ± 0.02 °C at ~15 mg/ml. Single ice crystals in Pg-2-rAFP showed a dendritic morphology with a TH value of 0.25 ± 0.02 °C at the same protein concentration. Based on in silico protein structure predictions, the three-dimensional structures of P. gelidicola AFPs match those of their homologs found in fungi and bacteria. They fold as a right-handed β-helix flanked by an α-helix. Unlike the hyperactive insect AFPs, the proposed ice-binding site on one of the flat β-helical surfaces is neither regular nor well-conserved. This might be a characteristic of AFPs used for freeze tolerance as opposed to freeze avoidance. A role for P. gelidicola AFPs in freeze tolerance is also consistent with their relatively low TH values.
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Affiliation(s)
- Woongsic Jung
- Department of Life Science, Division of Natural Sciences, Hanyang University, 133-791, Seoul, South Korea
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46
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Friis DS, Kristiansen E, von Solms N, Ramløv H. Antifreeze activity enhancement by site directed mutagenesis on an antifreeze protein from the beetleRhagium mordax. FEBS Lett 2014; 588:1767-72. [DOI: 10.1016/j.febslet.2014.03.032] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 03/06/2014] [Accepted: 03/15/2014] [Indexed: 10/25/2022]
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47
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Sun T, Lin FH, Campbell RL, Allingham JS, Davies PL. An antifreeze protein folds with an interior network of more than 400 semi-clathrate waters. Science 2014; 343:795-8. [PMID: 24531972 DOI: 10.1126/science.1247407] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
When polypeptide chains fold into a protein, hydrophobic groups are compacted in the center with exclusion of water. We report the crystal structure of an alanine-rich antifreeze protein that retains ~400 waters in its core. The putative ice-binding residues of this dimeric, four-helix bundle protein point inwards and coordinate the interior waters into two intersecting polypentagonal networks. The bundle makes minimal protein contacts between helices, but is stabilized by anchoring to the semi-clathrate water monolayers through backbone carbonyl groups in the protein interior. The ordered waters extend outwards to the protein surface and likely are involved in ice binding. This protein fold supports both the anchored-clathrate water mechanism of antifreeze protein adsorption to ice and the water-expulsion mechanism of protein folding.
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Affiliation(s)
- Tianjun Sun
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
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48
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Kim HE, Jeong M, Lee AR, Park CJ, Lee JH. Temperature-dependent Kinetics Study for Hydrogen Exchange of Type I Antifreeze Protein from Winter Flounder. B KOREAN CHEM SOC 2014. [DOI: 10.5012/bkcs.2014.35.1.286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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49
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Basu K, Garnham CP, Nishimiya Y, Tsuda S, Braslavsky I, Davies P. Determining the ice-binding planes of antifreeze proteins by fluorescence-based ice plane affinity. J Vis Exp 2014:e51185. [PMID: 24457629 DOI: 10.3791/51185] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Antifreeze proteins (AFPs) are expressed in a variety of cold-hardy organisms to prevent or slow internal ice growth. AFPs bind to specific planes of ice through their ice-binding surfaces. Fluorescence-based ice plane affinity (FIPA) analysis is a modified technique used to determine the ice planes to which the AFPs bind. FIPA is based on the original ice-etching method for determining AFP-bound ice-planes. It produces clearer images in a shortened experimental time. In FIPA analysis, AFPs are fluorescently labeled with a chimeric tag or a covalent dye then slowly incorporated into a macroscopic single ice crystal, which has been preformed into a hemisphere and oriented to determine the a- and c-axes. The AFP-bound ice hemisphere is imaged under UV light to visualize AFP-bound planes using filters to block out nonspecific light. Fluorescent labeling of the AFPs allows real-time monitoring of AFP adsorption into ice. The labels have been found not to influence the planes to which AFPs bind. FIPA analysis also introduces the option to bind more than one differently tagged AFP on the same single ice crystal to help differentiate their binding planes. These applications of FIPA are helping to advance our understanding of how AFPs bind to ice to halt its growth and why many AFP-producing organisms express multiple AFP isoforms.
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Affiliation(s)
- Koli Basu
- Department of Biomedical and Molecular Sciences, Queen's University
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Graham LA, Hobbs RS, Fletcher GL, Davies PL. Helical antifreeze proteins have independently evolved in fishes on four occasions. PLoS One 2013; 8:e81285. [PMID: 24324684 PMCID: PMC3855684 DOI: 10.1371/journal.pone.0081285] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 10/21/2013] [Indexed: 12/25/2022] Open
Abstract
Alanine-rich α-helical (type I) antifreeze proteins (AFPs) are produced by a variety of fish species from three different orders to protect against freezing in icy seawater. Interspersed amongst and within these orders are fishes making AFPs that are completely different in both sequence and structure. The origin of this variety of types I, II, III and antifreeze glycoproteins (AFGPs) has been attributed to adaptation following sea-level glaciations that occurred after the divergence of most of the extant families of fish. The presence of similar types of AFPs in distantly related fishes has been ascribed to lateral gene transfer in the case of the structurally complex globular type II lectin-like AFPs and to convergent evolution for the AFGPs, which consist of a well-conserved tripeptide repeat. In this paper, we examine the genesis of the type I AFPs, which are intermediate in complexity. These predominantly α-helical peptides share many features, such as putative capping structures, Ala-richness and amphipathic character. We have added to the type I repertoire by cloning additional sequences from sculpin and have found that the similarities between the type I AFPs of the four distinct groups of fishes are not borne out at the nucleotide level. Both the non-coding sequences and the codon usage patterns are strikingly different. We propose that these AFPs arose via convergence from different progenitor helices with a weak affinity for ice and that their similarity is dictated by the propensity of specific amino acids to form helices and to align water on one side of the helix into an ice-like pattern.
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Affiliation(s)
- Laurie A. Graham
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
| | - Rod S. Hobbs
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Garth L. Fletcher
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Peter L. Davies
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
- * E-mail:
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