1
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Zhang M, Qiu Z, Yang K, Zhou W, Liu W, Lu J, Guo L. Design, synthesis and antifreeze properties of biomimetic peptoid oligomers. Chem Commun (Camb) 2023. [PMID: 37128894 DOI: 10.1039/d3cc01062g] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Ice crystals can cause great damage. The utilization of antifreeze agents is an efficient method to prevent or reduce ice crystal formation and growth. Synthetic antifreeze agents are toxic and have low efficiency, and natural antifreeze proteins suffer from high cost and low stability. Here, we have designed and synthesized a series of peptoid oligomers by mimicking the antifreeze protein structure, and the structure-property relationship was also studied. The reported peptoids here have excellent antifreeze properties and are nontoxic to cells. These novel peptoid materials have great potential to replace current commonly used antifreeze agents, such as dimethyl sulfoxide, and become a new generation of antifreeze agents applied in cryopreservation.
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Affiliation(s)
- Min Zhang
- Research School of Polymeric Materials, School of Materials Sciences & Engineering, Jiangsu University, Zhenjiang, 212013, P. R. China.
| | - Zhifeng Qiu
- Research School of Polymeric Materials, School of Materials Sciences & Engineering, Jiangsu University, Zhenjiang, 212013, P. R. China.
| | - Kang Yang
- Research School of Polymeric Materials, School of Materials Sciences & Engineering, Jiangsu University, Zhenjiang, 212013, P. R. China.
| | - Wencheng Zhou
- Research School of Polymeric Materials, School of Materials Sciences & Engineering, Jiangsu University, Zhenjiang, 212013, P. R. China.
| | - Wenqi Liu
- Research School of Polymeric Materials, School of Materials Sciences & Engineering, Jiangsu University, Zhenjiang, 212013, P. R. China.
| | - Jianwei Lu
- Research School of Polymeric Materials, School of Materials Sciences & Engineering, Jiangsu University, Zhenjiang, 212013, P. R. China.
| | - Li Guo
- Research School of Polymeric Materials, School of Materials Sciences & Engineering, Jiangsu University, Zhenjiang, 212013, P. R. China.
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2
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Cui M, Li J, Li J, Wang F, Li X, Yu J, Huang Y, Liu Y. Screening and characterization of a novel antifreeze peptide from silver carp muscle hydrolysate. Food Chem 2023; 403:134480. [DOI: 10.1016/j.foodchem.2022.134480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/28/2022] [Accepted: 09/28/2022] [Indexed: 11/28/2022]
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3
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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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4
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Tirado-Kulieva VA, Miranda-Zamora WR, Hernández-Martínez E, Pantoja-Tirado LR, Bazán-Tantaleán DL, Camacho-Orbegoso EW. Effect of antifreeze proteins on the freeze-thaw cycle of foods: fundamentals, mechanisms of action, current challenges and recommendations for future work. Heliyon 2022; 8:e10973. [PMID: 36262292 PMCID: PMC9573917 DOI: 10.1016/j.heliyon.2022.e10973] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 06/13/2022] [Accepted: 09/30/2022] [Indexed: 11/19/2022] Open
Abstract
Freezing is widely used in food preservation, but if not carried out properly, ice crystals can multiply (nucleation) or grow (recrystallization) rapidly. This also affects thawing, causing structural damage and affecting overall quality. The objective of this review is to comprehensively study the cryoprotective effect of antifreeze proteins (AFPs), highlighting their role in the freeze-thaw process of food. The properties of AFPs are based on their thermal hysteresis capacity (THC), on the modification of crystal morphology and on the inhibition of ice recrystallization. The mechanism of action of AFPs is based on the adsorption-inhibition theory, but the specific role of hydrogen and hydrophobic bonds/residues and structural characteristics is also detailed. Because of the properties of AFPs, they have been successfully used to preserve the quality of a wide variety of refrigerated and frozen foods. Among the limitations of the use of AFPs, the high cost of production stands out, but currently there are solutions such as the use the production of recombinant proteins, cloning and chemical synthesis. Although in vitro, in vivo and human studies have shown that AFPs are non-toxic, their safety remains a matter of debate. Further studies are recommended to expand knowledge about AFPs, to reduce costs in their large-scale production, to understand their interaction with other food compounds and their possible effects on the consumer.
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Affiliation(s)
| | | | | | - Lucia Ruth Pantoja-Tirado
- Carrera Profesional de Ingeniería en Industrias Alimentarias, Universidad Nacional Autónoma de Tayacaja Daniel Hernández Morillo, Peru
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5
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Water-organizing motif continuity is critical for potent ice nucleation protein activity. Nat Commun 2022; 13:5019. [PMID: 36028506 PMCID: PMC9418140 DOI: 10.1038/s41467-022-32469-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 07/29/2022] [Indexed: 12/02/2022] Open
Abstract
Bacterial ice nucleation proteins (INPs) can cause frost damage to plants by nucleating ice formation at high sub-zero temperatures. Modeling of Pseudomonas borealis INP by AlphaFold suggests that the central domain of 65 tandem sixteen-residue repeats forms a beta-solenoid with arrays of outward-pointing threonines and tyrosines, which may organize water molecules into an ice-like pattern. Here we report that mutating some of these residues in a central segment of P. borealis INP, expressed in Escherichia coli, decreases ice nucleation activity more than the section’s deletion. Insertion of a bulky domain has the same effect, indicating that the continuity of the water-organizing repeats is critical for optimal activity. The ~10 C-terminal coils differ from the other 55 coils in being more basic and lacking water-organizing motifs; deletion of this region eliminates INP activity. We show through sequence modifications how arrays of conserved motifs form the large ice-nucleating surface required for potency. Ice nucleation proteins have the same tandemly arrayed water-organizing motifs seen in some antifreeze proteins, but on a larger scale. The authors show that mutation, interruption, and truncation of these arrays reduce ice nucleation activity indicating that the two protein types share a common mechanism.
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6
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Wu X, Yao F, Zhang H, Li J. Antifreeze proteins and their biomimetics for cell cryopreservation: Mechanism, function and application-A review. Int J Biol Macromol 2021; 192:1276-1291. [PMID: 34634336 DOI: 10.1016/j.ijbiomac.2021.09.211] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/30/2021] [Accepted: 09/30/2021] [Indexed: 12/26/2022]
Abstract
Cell-based therapy is a promising technology for intractable diseases and health care applications, in which cryopreservation has become an essential procedure to realize the production of therapeutic cells. Ice recrystallization is the major factor that affects the post-thaw viability of cells. As a typical series of biomacromolecules with ice recrystallization inhibition (IRI) activity, antifreeze proteins (AFPs) have been employed in cell cryopreservation. Meanwhile, synthesized materials with IRI activity have emerged in the name of biomimetics of AFPs to expand their availability and practicality. However, fabrication of AFPs mimetics is in a chaotic period. There remains little commonality among different AFPs mimetics, then it is difficult to set guidelines on their design. With no doubt, a comprehensive understanding on the antifreezing mechanism of AFPs in molecular level will enable us to rebuild the function of AFPs, and provide convenience to clarify the relationship between structure and function of these early stage biomimetics. In this review, we would discuss those previously reported biomimetics to summarize their structure characteristics concerning the IRI activity and attempt to develop a roadmap for guiding the design of novel AFPs mimetics.
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Affiliation(s)
- Xiaojun Wu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
| | - Fanglian Yao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300350, China
| | - Hong Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300350, China.
| | - Junjie Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300350, China.
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7
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Analysis of the Sequence Characteristics of Antifreeze Protein. Life (Basel) 2021; 11:life11060520. [PMID: 34204983 PMCID: PMC8226703 DOI: 10.3390/life11060520] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/27/2021] [Accepted: 05/31/2021] [Indexed: 12/31/2022] Open
Abstract
Antifreeze protein (AFP) is a proteinaceous compound with improved antifreeze ability and binding ability to ice to prevent its growth. As a surface-active material, a small number of AFPs have a tremendous influence on the growth of ice. Therefore, identifying novel AFPs is important to understand protein–ice interactions and create novel ice-binding domains. To date, predicting AFPs is difficult due to their low sequence similarity for the ice-binding domain and the lack of common features among different AFPs. Here, a computational engine was developed to predict the features of AFPs and reveal the most important 39 features for AFP identification, such as antifreeze-like/N-acetylneuraminic acid synthase C-terminal, insect AFP motif, C-type lectin-like, and EGF-like domain. With this newly presented computational method, a group of previously confirmed functional AFP motifs was screened out. This study has identified some potential new AFP motifs and contributes to understanding biological antifreeze mechanisms.
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8
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Ice Growth Suppression in the Solution Flows of Antifreeze Protein and Sodium Chloride in a Mini-Channel. Processes (Basel) 2021. [DOI: 10.3390/pr9020306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The control of ice growth inside channels of aqueous solution flows is important in numerous fields, including (a) cold-energy transportation plants and (b) the preservation of supercooled human organs for transplantation. A promising method for this control is to add a substance that influences ice growth in the flows. However, limited results have been reported on the effects of such additives. Using a microscope, we measured the growth of ice from one sidewall toward the opposite sidewall of a mini-channel, where aqueous solutions of sodium chloride and antifreeze protein flowed. Our aim was to considerably suppress ice growth by mixing the two solutes. Inclined interfaces, the overlapping of serrated interfaces, and interfaces with sharp and flat tips were observed in the cases of the protein-solution, salt-solution, and mixed-solution flows, respectively. In addition, it was found that the average interface velocity in the case of the mixed-solution flow was the lowest and decreased by 64% compared with that of pure water. This significant suppression of the ice-layer growth can be attributed to the synergistic effects of the ions and antifreeze protein on the diffusion of protein.
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9
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10
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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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11
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Carrot ‘antifreeze’ protein has an irregular ice-binding site that confers weak freezing point depression but strong inhibition of ice recrystallization. Biochem J 2020; 477:2179-2192. [DOI: 10.1042/bcj20200238] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/21/2020] [Accepted: 05/27/2020] [Indexed: 11/17/2022]
Abstract
Ice-binding proteins (IBPs) are found in many biological kingdoms where they protect organisms from freezing damage as antifreeze agents or inhibitors of ice recrystallization. Here, the crystal structure of recombinant IBP from carrot (Daucus carota) has been solved to a resolution of 2.3 Å. As predicted, the protein is a structural homologue of a plant polygalacturonase-inhibiting protein forming a curved solenoid structure with a leucine-rich repeat motif. Unexpectedly, close examination of its surface did not reveal any large regions of flat, regularly spaced hydrophobic residues that characterize the ice-binding sites (IBSs) of potent antifreeze proteins from freeze-resistant fish and insects. An IBS was defined by site-directed mutagenesis of residues on the convex surface of the carrot solenoid. This imperfect site is reminiscent of the irregular IBS of grass ‘antifreeze’ protein. Like the grass protein, the carrot IBP has weak freezing point depression activity but is extremely active at nanomolar concentrations in inhibiting ice recrystallization. Ice crystals formed in the presence of both plant proteins grow slowly and evenly in all directions. We suggest that this slow, controlled ice growth is desirable for freeze tolerance. The fact that two plant IBPs have evolved very different protein structures to affect ice in a similar manner suggests this pattern of weak freezing point depression and strong ice recrystallization inhibition helps their host to tolerate freezing rather than to resist it.
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12
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Kumari S, Muthachikavil AV, Tiwari JK, Punnathanam SN. Computational Study of Differences between Antifreeze Activity of Type-III Antifreeze Protein from Ocean Pout and Its Mutant. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:2439-2448. [PMID: 32069407 DOI: 10.1021/acs.langmuir.0c00065] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The antifreeze activity of a type-III antifreeze protein (AFP) expressed in ocean pout (Zoarces americanus) is compared with that of a specific mutant (T18N) using all-atom molecular dynamics simulations. The antifreeze activity of the mutant is only 10% of the wild-type AFP. The results from this simulation study revealed the following insights into the mechanism of antifreeze action by type-III AFPs. The AFP gets adsorbed to the advancing ice front due to its hydrophobic nature. A part of the hydrophobicity is caused by the presence of clathrate structure of water molecules near the ice-binding surface (IBS). The mutation in the AFP disrupts this structure and thereby reduces the ability of the mutant to adsorb to the ice-water interface leading to the loss of antifreeze activity. The mutation, however, has no effect on the ability of the adsorbed protein to bind to the growing ice phase. Simulations also revealed that all surfaces of the protein can bind to the ice phase, although the IBS is the preferred surface.
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Affiliation(s)
- Surbhi Kumari
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru 560012, India
| | - Aswin V Muthachikavil
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru 560012, India
| | - Jyoti Kumar Tiwari
- Hindustan Unilever R&D, 64 Whitefield Main Road, Bengaluru 560066, India
| | - Sudeep N Punnathanam
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru 560012, India
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13
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14
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Zanetti-Polzi L, Biswas AD, Del Galdo S, Barone V, Daidone I. Hydration Shell of Antifreeze Proteins: Unveiling the Role of Non-Ice-Binding Surfaces. J Phys Chem B 2019; 123:6474-6480. [PMID: 31280567 DOI: 10.1021/acs.jpcb.9b06375] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Antifreeze proteins (AFPs) have the ability to inhibit ice growth by binding to ice nuclei. Their ice-binding mechanism is still unclear, yet the hydration layer is thought to play a fundamental role. Here, we use molecular dynamics simulations to characterize the hydration shell of two AFPs and two non-AFPs. The calculated shell thickness and density of the AFPs do not feature any relevant difference with respect to the non-AFPs. Moreover, the hydration shell density is always higher than the bulk density and, thus, no low-density, ice-like layer is detected at the ice-binding surface (IBS) of AFPs. Instead, we observe local water-density differences in AFPs between the IBS (lower density) and the non-IBS (higher density). The lower solvent density at the ice-binding site can pave the way to the protein binding to ice nuclei, while the higher solvent density at the non-ice-binding surfaces might provide protection against ice growth.
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Affiliation(s)
- Laura Zanetti-Polzi
- Department of Physical and Chemical Sciences , University of L'Aquila , via Vetoio (Coppito 1) , 67010 L'Aquila , Italy
| | - Akash Deep Biswas
- Department of Physical and Chemical Sciences , University of L'Aquila , via Vetoio (Coppito 1) , 67010 L'Aquila , Italy.,Scuola Normale Superiore di Pisa , Piazza dei Cavalieri 7 , I-56126 Pisa , Italy
| | - Sara Del Galdo
- Scuola Normale Superiore di Pisa , Piazza dei Cavalieri 7 , I-56126 Pisa , Italy.,Institute for the Chemistry of Organometallic Compounds , Italian National Council for Research (ICCOMCNR) , Via G. Moruzzi 1 , I-6124 Pisa , Italy
| | - Vincenzo Barone
- Scuola Normale Superiore di Pisa , Piazza dei Cavalieri 7 , I-56126 Pisa , Italy.,National Institute for Nuclear Physics (INFN) Pisa Section , Largo BrunoPontecorvo 3 , 56127 Pisa , Italy
| | - Isabella Daidone
- Department of Physical and Chemical Sciences , University of L'Aquila , via Vetoio (Coppito 1) , 67010 L'Aquila , Italy
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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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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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19
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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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20
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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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21
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Yagasaki T, Matsumoto M, Tanaka H. Adsorption of Kinetic Hydrate Inhibitors on Growing Surfaces: A Molecular Dynamics Study. J Phys Chem B 2018; 122:3396-3406. [PMID: 29278335 DOI: 10.1021/acs.jpcb.7b10356] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We investigate the mechanism of a typical kinetic hydrate inhibitor (KHI), polyvinylcaprolactam (PVCap), which has been applied to prevent hydrate plugs from forming in gas pipe lines, using molecular dynamics simulations of crystal growth of ethylene oxide hydrate. Water-soluble ethylene oxide is chosen as a guest species to avoid problems associated with the presence of the gas phase in the simulation cell such as slow crystal growth. A PVCap dodecamer adsorbs irreversibly on the hydrate surface which grows at supercooling of 3 K when the hydrophobic part of two pendent groups are trapped in open cages at the surface. The amide hydrogen bonds make no contribution to the adsorption. PVCap can adsorb on various crystallographic planes of sI hydrate. This is in contrast to antifreeze proteins, each of which prefers a specific plane of ice. The trapped PVCap gives rise to necessarily the concave surface of the hydrate. The crystal growth rate decreases with increasing surface curvature, indicating that the inhibition by PVCap is explained by the Gibbs-Thomson effect.
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Affiliation(s)
- Takuma Yagasaki
- Research Institute for Interdisciplinary Science , Okayama University , Okayama 700-8530 , Japan
| | - Masakazu Matsumoto
- Research Institute for Interdisciplinary Science , Okayama University , Okayama 700-8530 , Japan
| | - Hideki Tanaka
- Research Institute for Interdisciplinary Science , Okayama University , Okayama 700-8530 , Japan
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22
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Peramo A. Molecular dynamics studies show solvation structure of type III antifreeze protein is disrupted at low pH. Comput Biol Chem 2018; 73:13-24. [PMID: 29413812 DOI: 10.1016/j.compbiolchem.2018.01.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 01/10/2018] [Accepted: 01/17/2018] [Indexed: 02/02/2023]
Abstract
Antifreeze proteins are a class of biological molecules of interest in many research and industrial applications due to their highly specialized function, but there is little information of their stability and properties under varied pH derived from computational studies. To gain novel insights in this area, we conducted molecular dynamics (MD) simulations with the antifreeze protein 1KDF at varied temperatures and pH. Water solvation and H-bond formation around specific residues - ASN14, THR18 and GLN44 - involved in its antifreeze activity were extensively studied. We found that at pH1 there was a disruption in water solvation around the basal and the ice binding surfaces of the molecule. This was induced by a small change in the secondary structure propensities of some titrable residues, particularly GLU35. This change explains the experimentally observed reduction in antifreeze activity previously reported for this protein at pH1. We also found that THR18 showed extremely low H-bond formation, and that the three antifreeze residues all had very low average H-bond lifetimes. Our results confirm long-standing assumptions that these small, compact molecules can maintain their antifreeze activity in a wide range of pH, while demonstrating the mechanism that may reduce antifreeze activity at low pH. This aspect is useful when considering industrial and commercial use of antifreeze proteins subject to extreme pH environments, in particular in food industrial applications.
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Affiliation(s)
- Antonio Peramo
- Escuela de Física y Matematicas, Facultad de Ciencias, Escuela Politécnica Superior del Chimborazo, Riobamba, Ecuador.
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23
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Nguyen CT, Yuan M, Yu JS, Ye T, Cao H, Xu F. Isolation of ice structuring collagen peptide by ice affinity adsorption, its ice-binding mechanism and breadmaking performance in frozen dough. J Food Biochem 2018. [DOI: 10.1111/jfbc.12506] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Cong Thanh Nguyen
- School of Medical Instrument and Food Engineering; University of Shanghai for Science and Technology; Shanghai People's Republic of China
| | - Min Yuan
- School of Medical Instrument and Food Engineering; University of Shanghai for Science and Technology; Shanghai People's Republic of China
| | - Jing Song Yu
- School of Medical Instrument and Food Engineering; University of Shanghai for Science and Technology; Shanghai People's Republic of China
| | - Tai Ye
- School of Medical Instrument and Food Engineering; University of Shanghai for Science and Technology; Shanghai People's Republic of China
| | - Hui Cao
- School of Medical Instrument and Food Engineering; University of Shanghai for Science and Technology; Shanghai People's Republic of China
| | - Fei Xu
- School of Medical Instrument and Food Engineering; University of Shanghai for Science and Technology; Shanghai People's Republic of China
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24
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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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25
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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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26
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Balance between hydration enthalpy and entropy is important for ice binding surfaces in Antifreeze Proteins. Sci Rep 2017; 7:11901. [PMID: 28928396 PMCID: PMC5605524 DOI: 10.1038/s41598-017-11982-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 08/29/2017] [Indexed: 11/21/2022] Open
Abstract
Antifreeze Proteins (AFPs) inhibit the growth of an ice crystal by binding to it. The detailed binding mechanism is, however, still not fully understood. We investigated three AFPs using Molecular Dynamics simulations in combination with Grid Inhomogeneous Solvation Theory, exploring their hydration thermodynamics. The observed enthalpic and entropic differences between the ice-binding sites and the inactive surface reveal key properties essential for proteins in order to bind ice: While entropic contributions are similar for all sites, the enthalpic gain for all ice-binding sites is lower than for the rest of the protein surface. In contrast to most of the recently published studies, our analyses show that enthalpic interactions are as important as an ice-like pre-ordering. Based on these observations, we propose a new, thermodynamically more refined mechanism of the ice recognition process showing that the appropriate balance between entropy and enthalpy facilitates ice-binding of proteins. Especially, high enthalpic interactions between the protein surface and water can hinder the ice-binding activity.
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27
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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: 96] [Impact Index Per Article: 13.7] [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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28
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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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29
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Urbańczyk M, Góra J, Latajka R, Sewald N. Antifreeze glycopeptides: from structure and activity studies to current approaches in chemical synthesis. Amino Acids 2016; 49:209-222. [PMID: 27913993 PMCID: PMC5274654 DOI: 10.1007/s00726-016-2368-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 11/18/2016] [Indexed: 01/02/2023]
Abstract
Antifreeze glycopeptides (AFGPs) are a class of biological antifreeze agents found predominantly in Arctic and Antarctic species of fish. They possess the ability to regulate ice nucleation and ice crystal growth, thus creating viable life conditions at temperatures below the freezing point of body fluids. AFGPs usually consist of 4–55 repetitions of the tripeptide unit Ala–Ala–Thr that is O-glycosylated at the threonine side chains with β-d-galactosyl-(1 → 3)-α-N-acetyl-d-galactosamine. Due to their interesting properties and high antifreeze activity, they have many potential applications, e.g., in food industry and medicine. Current research is focused towards understanding the relationship between the structural preferences and the activity of the AFGPs, as well as developing time and cost efficient ways of synthesis of this class of molecules. Recent computational studies in conjunction with experimental results from NMR and THz spectroscopies were a possible breakthrough in understanding the mechanism of action of AFGPs. At the moment, as a result of these findings, the focus of research is shifted towards the analysis of behaviour of the hydration shell around AFGPs and the impact of water-dynamics retardation caused by AFGPs on ice crystal growth. In the field of organic synthesis of AFGP analogues, most of the novel protocols are centered around solid-phase peptide synthesis and multiple efforts are made to optimize this approach. In this review, we present the current state of knowledge regarding the structure and activity of AFGPs, as well as approaches to organic synthesis of these molecules with focus on the most recent developments.
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Affiliation(s)
- Małgorzata Urbańczyk
- Department of Organic and Pharmaceutical Technology, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże St. Wyspiańskiego 29, 50-370, Wrocław, Poland
| | - Jerzy Góra
- Department of Organic and Pharmaceutical Technology, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże St. Wyspiańskiego 29, 50-370, Wrocław, Poland
| | - Rafał Latajka
- Department of Organic and Pharmaceutical Technology, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże St. Wyspiańskiego 29, 50-370, Wrocław, Poland.
| | - Norbert Sewald
- Organic Chemistry III, Department of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615, Bielefeld, Germany.
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30
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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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31
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Ice Growth Inhibition in Antifreeze Polypeptide Solution by Short-Time Solution Preheating. PLoS One 2016; 11:e0154782. [PMID: 27152720 PMCID: PMC4859470 DOI: 10.1371/journal.pone.0154782] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 04/19/2016] [Indexed: 11/24/2022] Open
Abstract
The objective of this study is to enhance the inhibition of ice growth in the aqueous solution of a polypeptide, which is inspired by winter flounder antifreeze protein. We carried out measurements on unidirectional freezing of the polypeptide solution. The thickness of the solution was 0.02 mm, and the concentration of polypeptide was varied from 0 to 2 mg/mL. We captured successive microscopic images of ice/solution interfaces, and measured the interface velocity from the locations of tips of the pectinate interface in the images. We also simultaneously measured the temperature by using a small thermocouple. The ice/solution interface temperature was defined by the temperature at the tips. It was found that the interface temperature was decreased with an increasing concentration of polypeptide. To try varying the activity of the polypeptide, we preheated the polypeptide solution and cooled it before carrying out the measurements. Preheating for 1–5 hours was found to cause a further decrease in the interface temperature. Furthermore, wider regions of solution and ice with inclined interfaces in the pectinate interface structure were observed, compared with the case where the solution was not preheated. Thus, the ice growth inhibition was enhanced by this preheating. To investigate the reason for this enhancement, we measured the conformation and aggregates of polypeptide in the solution. We also measured the local concentration of polypeptide. It was found that the polypeptide aggregates became larger as a result of preheating, although the polypeptide conformation was unchanged. These large aggregates caused both adsorption to the interface and the wide regions of supercooled solution in the pectinate interface structure.
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32
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Blocking rapid ice crystal growth through nonbasal plane adsorption of antifreeze proteins. Proc Natl Acad Sci U S A 2016; 113:3740-5. [PMID: 26936953 DOI: 10.1073/pnas.1524109113] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Antifreeze proteins (AFPs) are a unique class of proteins that bind to growing ice crystal surfaces and arrest further ice growth. AFPs have gained a large interest for their use in antifreeze formulations for water-based materials, such as foods, waterborne paints, and organ transplants. Instead of commonly used colligative antifreezes such as salts and alcohols, the advantage of using AFPs as an additive is that they do not alter the physicochemical properties of the water-based material. Here, we report the first comprehensive evaluation of thermal hysteresis (TH) and ice recrystallization inhibition (IRI) activity of all major classes of AFPs using cryoscopy, sonocrystallization, and recrystallization assays. The results show that TH activities determined by cryoscopy and sonocrystallization differ markedly, and that TH and IRI activities are not correlated. The absence of a distinct correlation in antifreeze activity points to a mechanistic difference in ice growth inhibition by the different classes of AFPs: blocking fast ice growth requires rapid nonbasal plane adsorption, whereas basal plane adsorption is only relevant at long annealing times and at small undercooling. These findings clearly demonstrate that biomimetic analogs of antifreeze (glyco)proteins should be tailored to the specific requirements of the targeted application.
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33
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Cao H, Zhao Y, Zhu YB, Xu F, Yu JS, Yuan M. Antifreeze and cryoprotective activities of ice-binding collagen peptides from pig skin. Food Chem 2016; 194:1245-53. [DOI: 10.1016/j.foodchem.2015.08.102] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Revised: 07/30/2015] [Accepted: 08/24/2015] [Indexed: 12/01/2022]
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34
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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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35
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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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36
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Kar RK, Bhunia A. Will It Be Beneficial To Simulate the Antifreeze Proteins at Ice Freezing Condition or at Lower Temperature? J Phys Chem B 2015; 119:11485-95. [DOI: 10.1021/acs.jpcb.5b04919] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rajiv K. Kar
- Department
of Biophysics, Bose Institute, P-1/12, CIT Scheme VII M, Kolkata 700054, India
| | - Anirban Bhunia
- Department
of Biophysics, Bose Institute, P-1/12, CIT Scheme VII M, Kolkata 700054, India
- Biophysics
and Department of Chemistry, University of Michigan, 930 N. University
Avenue, Ann Arbor, Michigan 48109, United States
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37
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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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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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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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Rice CV, Middaugh A, Wickham JR, Friedline A, Thomas KJ, Scull E, Johnson K, Zachariah M, Garimella R. Bacterial lipoteichoic acid enhances cryosurvival. Extremophiles 2014; 19:297-305. [PMID: 25477208 DOI: 10.1007/s00792-014-0714-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 11/16/2014] [Indexed: 11/24/2022]
Abstract
Antifreeze proteins in fish, plants, and insects provide protection to a few degrees below freezing. Microbes have been found to survive at even lower temperatures, and with a few exceptions, antifreeze proteins are missing. We show that lipoteichoic acid (LTA), a biopolymer in the cell wall of Gram-positive bacteria, can be added to B. subtilis cultures and increase freeze tolerance. At 1 % w/v, LTA enables a 50 % survival rate, similar to the results obtained with 1 % w/v glycerol as measured with the resazurin cell viability assay. In the absence of added LTA or glycerol, a very small number of B. subtilis cells survive freezing. This suggests that an innate freeze tolerance mechanism exists. While cryoprotection can be provided by extracellular polymeric substances, our data demonstrate a role for LTA in cryoprotection. Currently, the exact mode of action for LTA cryoprotection is unknown. With a molecular weight of 3-5 kDa, it is unlikely to enter the cell cytoplasm. However, low temperature microscopy data show small ice crystals aligned along channels of liquid water. Our observations suggest that teichoic acids could protect liquid water within biofilms and planktonic bacteria, augmenting the role of brine while also raising the possibility for survival without brine present.
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Affiliation(s)
- Charles V Rice
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA,
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41
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Vorontsov DA, Sazaki G, Hyon SH, Matsumura K, Furukawa Y. Antifreeze Effect of Carboxylated ε-Poly-l-lysine on the Growth Kinetics of Ice Crystals. J Phys Chem B 2014; 118:10240-9. [DOI: 10.1021/jp507697q] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Dmitry A. Vorontsov
- Lobachevsky State University of Nizhny Novgorod, Gagarin Avenue,
23, Nizhny Novgorod, 603950 Russia
- Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060-0819 Japan
| | - Gen Sazaki
- Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060-0819 Japan
| | - Suong-Hyu Hyon
- Center for Fiber and Textile Science, Kyoto Institute of Technology, 105 Jibucho, Kyoto Fushimi-ku, Kyoto, 612-8374 Japan
| | - Kazuaki Matsumura
- Japan Advanced Institute of Science and Technology, Asahidai 1-1, Nomi-shi, Ishikawa, 923-1292 Japan
| | - Yoshinori Furukawa
- Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060-0819 Japan
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42
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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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43
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Bang JK, Lee JH, Murugan RN, Lee SG, Do H, Koh HY, Shim HE, Kim HC, Kim HJ. Antifreeze peptides and glycopeptides, and their derivatives: potential uses in biotechnology. Mar Drugs 2013; 11:2013-41. [PMID: 23752356 PMCID: PMC3721219 DOI: 10.3390/md11062013] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Revised: 04/22/2013] [Accepted: 05/10/2013] [Indexed: 01/14/2023] Open
Abstract
Antifreeze proteins (AFPs) and glycoproteins (AFGPs), collectively called AF(G)Ps, constitute a diverse class of proteins found in various Arctic and Antarctic fish, as well as in amphibians, plants, and insects. These compounds possess the ability to inhibit the formation of ice and are therefore essential to the survival of many marine teleost fishes that routinely encounter sub-zero temperatures. Owing to this property, AF(G)Ps have potential applications in many areas such as storage of cells or tissues at low temperature, ice slurries for refrigeration systems, and food storage. In contrast to AFGPs, which are composed of repeated tripeptide units (Ala-Ala-Thr)n with minor sequence variations, AFPs possess very different primary, secondary, and tertiary structures. The isolation and purification of AFGPs is laborious, costly, and often results in mixtures, making characterization difficult. Recent structural investigations into the mechanism by which linear and cyclic AFGPs inhibit ice crystallization have led to significant progress toward the synthesis and assessment of several synthetic mimics of AFGPs. This review article will summarize synthetic AFGP mimics as well as current challenges in designing compounds capable of mimicking AFGPs. It will also cover our recent efforts in exploring whether peptoid mimics can serve as structural and functional mimics of native AFGPs.
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Affiliation(s)
- Jeong Kyu Bang
- Division of Magnetic Resonance, Korea Basic Scienc Institute, Chungbuk 363-833, Korea; E-Mails: (J.K.B.); (R.N.M.)
| | - Jun Hyuck Lee
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, Korea; E-Mails: (J.H.L.); (S.G.L.); (H.D.); (H.Y.K.); (H.-E.S.)
- Department of Polar Sciences, University of Science and Technology, Incheon 406-840, Korea
| | - Ravichandran N. Murugan
- Division of Magnetic Resonance, Korea Basic Scienc Institute, Chungbuk 363-833, Korea; E-Mails: (J.K.B.); (R.N.M.)
| | - Sung Gu Lee
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, Korea; E-Mails: (J.H.L.); (S.G.L.); (H.D.); (H.Y.K.); (H.-E.S.)
- Department of Polar Sciences, University of Science and Technology, Incheon 406-840, Korea
| | - Hackwon Do
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, Korea; E-Mails: (J.H.L.); (S.G.L.); (H.D.); (H.Y.K.); (H.-E.S.)
- Department of Polar Sciences, University of Science and Technology, Incheon 406-840, Korea
| | - Hye Yeon Koh
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, Korea; E-Mails: (J.H.L.); (S.G.L.); (H.D.); (H.Y.K.); (H.-E.S.)
| | - Hye-Eun Shim
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, Korea; E-Mails: (J.H.L.); (S.G.L.); (H.D.); (H.Y.K.); (H.-E.S.)
| | - Hyun-Cheol Kim
- Division of Polar Climate Research, Korea Polar Research Institute, Incheon 406-840, Korea; E-Mail:
| | - Hak Jun Kim
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, Korea; E-Mails: (J.H.L.); (S.G.L.); (H.D.); (H.Y.K.); (H.-E.S.)
- Department of Polar Sciences, University of Science and Technology, Incheon 406-840, Korea
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +82-32-760-5550; Fax: +82-32-760-5598
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44
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Mizrahy O, Bar-Dolev M, Guy S, Braslavsky I. Inhibition of ice growth and recrystallization by zirconium acetate and zirconium acetate hydroxide. PLoS One 2013; 8:e59540. [PMID: 23555701 PMCID: PMC3605400 DOI: 10.1371/journal.pone.0059540] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 02/15/2013] [Indexed: 12/29/2022] Open
Abstract
The control over ice crystal growth, melting, and shaping is important in a variety of fields, including cell and food preservation and ice templating for the production of composite materials. Control over ice growth remains a challenge in industry, and the demand for new cryoprotectants is high. Naturally occurring cryoprotectants, such as antifreeze proteins (AFPs), present one solution for modulating ice crystal growth; however, the production of AFPs is expensive and inefficient. These obstacles can be overcome by identifying synthetic substitutes with similar AFP properties. Zirconium acetate (ZRA) was recently found to induce the formation of hexagonal cavities in materials prepared by ice templating. Here, we continue this line of study and examine the effects of ZRA and a related compound, zirconium acetate hydroxide (ZRAH), on ice growth, shaping, and recrystallization. We found that the growth rate of ice crystals was significantly reduced in the presence of ZRA and ZRAH, and that solutions containing these compounds display a small degree of thermal hysteresis, depending on the solution pH. The compounds were found to inhibit recrystallization in a manner similar to that observed in the presence of AFPs. The favorable properties of ZRA and ZRAH suggest tremendous potential utility in industrial applications.
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Affiliation(s)
- Ortal Mizrahy
- The Institute of Biochemistry, Food Science, and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Maya Bar-Dolev
- The Institute of Biochemistry, Food Science, and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
- * E-mail:
| | - Shlomit Guy
- The Institute of Biochemistry, Food Science, and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Ido Braslavsky
- The Institute of Biochemistry, Food Science, and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
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45
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Haridas V, Naik S. Natural macromolecular antifreeze agents to synthetic antifreeze agents. RSC Adv 2013. [DOI: 10.1039/c3ra00081h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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46
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Wang S, Amornwittawat N, Wen X. Thermodynamic Analysis of Thermal Hysteresis: Mechanistic Insights into Biological Antifreezes. THE JOURNAL OF CHEMICAL THERMODYNAMICS 2012; 53:125-130. [PMID: 22822266 PMCID: PMC3398711 DOI: 10.1016/j.jct.2012.04.028] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Antifreeze proteins (AFPs) bind to ice crystal surfaces and thus inhibit the ice growth. The mechanism for how AFPs suppress freezing is commonly modeled as an adsorption-inhibition process by the Gibbs-Thomson effect. Here we develop an improved adsorption-inhibition model for AFP action based on the thermodynamics of impurity adsorption on the crystal surfaces. We demonstrate the derivation of a realistic relationship between surface protein coverage and the protein concentration. We show that the improved model provides a quantitatively better fit to the experimental antifreeze activities of AFPs from distinct structural classes, including fish and insect AFPs, in a wide range of concentrations. Our theoretical results yielded the adsorption coefficients of the AFPs on ice, suggesting that, despite the distinct difference in their antifreeze activities and structures, the affinities of the AFPs to ice are very close and the mechanism of AFP action is a kinetically controlled, reversible process. The applications of the model to more complex systems along with its potential limitations are also discussed.
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Affiliation(s)
- Sen Wang
- Department of Chemistry and Biochemistry, California State University Los Angeles, Los Angeles, California 90032
- Visiting scholar from the Molecular Imaging Program, Stanford University, Stanford, California 94305
| | - Natapol Amornwittawat
- Department of Chemistry and Biochemistry, California State University Los Angeles, Los Angeles, California 90032
| | - Xin Wen
- Department of Chemistry and Biochemistry, California State University Los Angeles, Los Angeles, California 90032
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47
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Ebbinghaus S, Meister K, Prigozhin MB, Devries AL, Havenith M, Dzubiella J, Gruebele M. Functional importance of short-range binding and long-range solvent interactions in helical antifreeze peptides. Biophys J 2012; 103:L20-2. [PMID: 22853917 DOI: 10.1016/j.bpj.2012.06.013] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Revised: 06/08/2012] [Accepted: 06/12/2012] [Indexed: 11/18/2022] Open
Abstract
Short-range ice binding and long-range solvent perturbation both have been implicated in the activity of antifreeze proteins and antifreeze glycoproteins. We study these two mechanisms for activity of winter flounder antifreeze peptide. Four mutants are characterized by freezing point hysteresis (activity), circular dichroism (secondary structure), Förster resonance energy transfer (end-to-end rigidity), molecular dynamics simulation (structure), and terahertz spectroscopy (long-range solvent perturbation). Our results show that the short-range model is sufficient to explain the activity of our mutants, but the long-range model provides a necessary condition for activity: the most active peptides in our data set all have an extended dynamical hydration shell. It appears that antifreeze proteins and antifreeze glycoproteins have reached different evolutionary solutions to the antifreeze problem, utilizing either a few precisely positioned OH groups or a large quantity of OH groups for ice binding, assisted by long-range solvent perturbation.
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Affiliation(s)
- Simon Ebbinghaus
- Department of Physical Chemistry II, Ruhr-Universität Bochum, Bochum, Germany
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48
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Bar-Dolev M, Celik Y, Wettlaufer JS, Davies PL, Braslavsky I. New insights into ice growth and melting modifications by antifreeze proteins. J R Soc Interface 2012; 9:3249-59. [PMID: 22787007 PMCID: PMC3481565 DOI: 10.1098/rsif.2012.0388] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Antifreeze proteins (AFPs) evolved in many organisms, allowing them to survive in cold climates by controlling ice crystal growth. The specific interactions of AFPs with ice determine their potential applications in agriculture, food preservation and medicine. AFPs control the shapes of ice crystals in a manner characteristic of the particular AFP type. Moderately active AFPs cause the formation of elongated bipyramidal crystals, often with seemingly defined facets, while hyperactive AFPs produce more varied crystal shapes. These different morphologies are generally considered to be growth shapes. In a series of bright light and fluorescent microscopy observations of ice crystals in solutions containing different AFPs, we show that crystal shaping also occurs during melting. In particular, the characteristic ice shapes observed in solutions of most hyperactive AFPs are formed during melting. We relate these findings to the affinities of the hyperactive AFPs for the basal plane of ice. Our results demonstrate the relation between basal plane affinity and hyperactivity and show a clear difference in the ice-shaping mechanisms of most moderate and hyperactive AFPs. This study provides key aspects associated with the identification of hyperactive AFPs.
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Affiliation(s)
- Maya Bar-Dolev
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
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49
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Calvaresi M, Höfinger S, Zerbetto F. Local Ice Melting by an Antifreeze Protein. Biomacromolecules 2012; 13:2046-52. [DOI: 10.1021/bm300366f] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Matteo Calvaresi
- Dipartimento di
Chimica “G. Ciamician”, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Siegfried Höfinger
- Dipartimento di
Chimica “G. Ciamician”, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
- Department of Physics, Michigan Technological University, 1400
Townsend Drive, 49931 Houghton, Michigan, United States
| | - Francesco Zerbetto
- Dipartimento di
Chimica “G. Ciamician”, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
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50
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Middleton AJ, Marshall CB, Faucher F, Bar-Dolev M, Braslavsky I, Campbell RL, Walker VK, Davies PL. Antifreeze protein from freeze-tolerant grass has a beta-roll fold with an irregularly structured ice-binding site. J Mol Biol 2012; 416:713-24. [PMID: 22306740 DOI: 10.1016/j.jmb.2012.01.032] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 01/18/2012] [Indexed: 11/16/2022]
Abstract
The grass Lolium perenne produces an ice-binding protein (LpIBP) that helps this perennial tolerate freezing by inhibiting the recrystallization of ice. Ice-binding proteins (IBPs) are also produced by freeze-avoiding organisms to halt the growth of ice and are better known as antifreeze proteins (AFPs). To examine the structural basis for the different roles of these two IBP types, we have solved the first crystal structure of a plant IBP. The 118-residue LpIBP folds as a novel left-handed beta-roll with eight 14- or 15-residue coils and is stabilized by a small hydrophobic core and two internal Asn ladders. The ice-binding site (IBS) is formed by a flat beta-sheet on one surface of the beta-roll. We show that LpIBP binds to both the basal and primary-prism planes of ice, which is the hallmark of hyperactive AFPs. However, the antifreeze activity of LpIBP is less than 10% of that measured for those hyperactive AFPs with convergently evolved beta-solenoid structures. Whereas these hyperactive AFPs have two rows of aligned Thr residues on their IBS, the equivalent arrays in LpIBP are populated by a mixture of Thr, Ser and Val with several side-chain conformations. Substitution of Ser or Val for Thr on the IBS of a hyperactive AFP reduced its antifreeze activity. LpIBP may have evolved an IBS that has low antifreeze activity to avoid damage from rapid ice growth that occurs when temperatures exceed the capacity of AFPs to block ice growth while retaining the ability to inhibit ice recrystallization.
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Affiliation(s)
- Adam J Middleton
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada K7L 3N6
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