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Hernández‐Sánchez I, Rindfleisch T, Alpers J, Dulle M, Garvey CJ, Knox‐Brown P, Miettinen MS, Nagy G, Pusterla JM, Rekas A, Shou K, Stadler AM, Walther D, Wolff M, Zuther E, Thalhammer A. Functional in vitro diversity of an intrinsically disordered plant protein during freeze-thawing is encoded by its structural plasticity. Protein Sci 2024; 33:e4989. [PMID: 38659213 PMCID: PMC11043620 DOI: 10.1002/pro.4989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 03/09/2024] [Accepted: 03/31/2024] [Indexed: 04/26/2024]
Abstract
Intrinsically disordered late embryogenesis abundant (LEA) proteins play a central role in the tolerance of plants and other organisms to dehydration brought upon, for example, by freezing temperatures, high salt concentration, drought or desiccation, and many LEA proteins have been found to stabilize dehydration-sensitive cellular structures. Their conformational ensembles are highly sensitive to the environment, allowing them to undergo conformational changes and adopt ordered secondary and quaternary structures and to participate in formation of membraneless organelles. In an interdisciplinary approach, we discovered how the functional diversity of the Arabidopsis thaliana LEA protein COR15A found in vitro is encoded in its structural repertoire, with the stabilization of membranes being achieved at the level of secondary structure and the stabilization of enzymes accomplished by the formation of oligomeric complexes. We provide molecular details on intra- and inter-monomeric helix-helix interactions, demonstrate how oligomerization is driven by an α-helical molecular recognition feature (α-MoRF) and provide a rationale that the formation of noncanonical, loosely packed, right-handed coiled-coils might be a recurring theme for homo- and hetero-oligomerization of LEA proteins.
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Affiliation(s)
- Itzell Hernández‐Sánchez
- Max‐Planck Institute of Molecular Plant PhysiologyPotsdamGermany
- Present address:
Center for Desert Agriculture, Biological and Environmental Science and Engineering DivisionKing Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - Tobias Rindfleisch
- Max‐Planck Institute of Molecular Plant PhysiologyPotsdamGermany
- Physical BiochemistryUniversity of PotsdamPotsdamGermany
- Department of ChemistryUniversity of BergenBergenNorway
- Computational Biology Unit, Department of InformaticsUniversity of BergenBergenNorway
| | - Jessica Alpers
- Max‐Planck Institute of Molecular Plant PhysiologyPotsdamGermany
| | - Martin Dulle
- Jülich Centre for Neutron Science (JCNS‐1) and Institute of Biological Information Processing (IBI‐8: Neutron Scattering and Biological Matter)Forschungszentrum Jülich GmbHJülichGermany
| | | | - Patrick Knox‐Brown
- Physical BiochemistryUniversity of PotsdamPotsdamGermany
- Present address:
Department of Discovery Pharmaceutical SciencesMerck & Co., Inc.South San FranciscoCaliforniaUSA
| | - Markus S. Miettinen
- Department of ChemistryUniversity of BergenBergenNorway
- Computational Biology Unit, Department of InformaticsUniversity of BergenBergenNorway
- Department of Theory and Bio‐SystemsMax Planck Institute of Colloids and InterfacesPotsdamGermany
| | - Gergely Nagy
- Neutron Scattering DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Julio M. Pusterla
- Jülich Centre for Neutron Science (JCNS‐1) and Institute of Biological Information Processing (IBI‐8: Neutron Scattering and Biological Matter)Forschungszentrum Jülich GmbHJülichGermany
| | - Agata Rekas
- Australian Nuclear Science and Technology Organization (ANSTO)KirraweeNew South WalesAustralia
| | - Keyun Shou
- Jülich Centre for Neutron Science (JCNS‐1) and Institute of Biological Information Processing (IBI‐8: Neutron Scattering and Biological Matter)Forschungszentrum Jülich GmbHJülichGermany
- Australian Nuclear Science and Technology Organization (ANSTO)KirraweeNew South WalesAustralia
- Institute of Physical Chemistry, RWTH Aachen UniversityAachenGermany
| | - Andreas M. Stadler
- Jülich Centre for Neutron Science (JCNS‐1) and Institute of Biological Information Processing (IBI‐8: Neutron Scattering and Biological Matter)Forschungszentrum Jülich GmbHJülichGermany
- Institute of Physical Chemistry, RWTH Aachen UniversityAachenGermany
| | - Dirk Walther
- Max‐Planck Institute of Molecular Plant PhysiologyPotsdamGermany
| | - Martin Wolff
- Physical BiochemistryUniversity of PotsdamPotsdamGermany
| | - Ellen Zuther
- Max‐Planck Institute of Molecular Plant PhysiologyPotsdamGermany
- Present address:
Center of Artificial Intelligence in Public Health Research (ZKI‐PH)Robert Koch InstituteBerlinGermany
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2
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Xie Y, Zhou K, Tan L, Ma Y, Li C, Zhou H, Wang Z, Xu B. Coexisting with Ice Crystals: Cryogenic Preservation of Muscle Food─Mechanisms, Challenges, and Cutting-Edge Strategies. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:19221-19239. [PMID: 37947813 DOI: 10.1021/acs.jafc.3c06155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Cryopreservation, one of the most effective preservation methods, is essential for maintaining the safety and quality of food. However, there is no denying the fact that the quality of muscle food deteriorates as a result of the unavoidable production of ice. Advancements in cryoregulatory materials and techniques have effectively mitigated the adverse impacts of ice, thereby enhancing the standard of freezing preservation. The first part of this overview explains how ice forms, including the theoretical foundations of nucleation, growth, and recrystallization as well as the key influencing factors that affect each process. Subsequently, the impact of ice formation on the eating quality and nutritional value of muscle food is delineated. A systematic explanation of cutting-edge strategies based on nucleation intervention, growth control, and recrystallization inhibition is offered. These methods include antifreeze proteins, ice-nucleating proteins, antifreeze peptides, natural deep eutectic solvents, polysaccharides, amino acids, and their derivatives. Furthermore, advanced physical techniques such as electrostatic fields, magnetic fields, acoustic fields, liquid nitrogen, and supercooling preservation techniques are expounded upon, which effectively hinder the formation of ice crystals during cryopreservation. The paper outlines the difficulties and potential directions in ice inhibition for effective cryopreservation.
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Affiliation(s)
- Yong Xie
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China
| | - Kai Zhou
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China
- Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230601, China
| | - Lijun Tan
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China
| | - Yunhao Ma
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China
| | - Cong Li
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China
- Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230601, China
| | - Hui Zhou
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China
- Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230601, China
| | - Zhaoming Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China
- Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230601, China
| | - Baocai Xu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China
- Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230601, China
- Food Laboratory of Zhongyuan, Luohe 462300, Henan, China
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3
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Zielkiewicz J. Mechanism of antifreeze protein functioning and the "anchored clathrate water" concept. J Chem Phys 2023; 159:085101. [PMID: 37622597 DOI: 10.1063/5.0158590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/04/2023] [Indexed: 08/26/2023] Open
Abstract
In liquid water, there is a natural tendency to form aggregates that consist of water molecules linked by hydrogen bonds. Such spontaneously formed aggregates are surrounded by a "sea" of disordered water molecules, with both forms remaining in equilibrium. The process of creating water aggregates also takes place in the solvation water of proteins, but in this case, the interactions of water molecules with the protein surface shift the equilibrium of the process. In this paper, we analyze the structural properties of the solvation water in antifreeze proteins (AFPs). The results of molecular dynamics analysis with the use of various parameters related to the structure of solvation water on the protein surface are presented. We found that in the vicinity of the active region responsible for the binding of AFPs to ice, the equilibrium is clearly shifted toward the formation of "ice-like aggregates," and the solvation water has a more ordered ice-like structure. We have demonstrated that a reduction in the tendency to create "ice-like aggregates" results in a significant reduction in the antifreeze activity of the protein. We conclude that shifting the equilibrium in favor of the formation of "ice-like aggregates" in the solvation water in the active region is a prerequisite for the biological functionality of AFPs, at least for AFPs having a well-defined ice binding area. In addition, our results fully confirm the validity of the "anchored clathrate water" concept, formulated by Garnham et al. [Proc. Natl. Acad. Sci. U. S. A. 108, 7363 (2011)].
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Affiliation(s)
- Jan Zielkiewicz
- Faculty of Chemistry, Department of Physical Chemistry, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
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4
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de Haas RJ, Tas RP, van den Broek D, Zheng C, Nguyen H, Kang A, Bera AK, King NP, Voets IK, de Vries R. De novo designed ice-binding proteins from twist-constrained helices. Proc Natl Acad Sci U S A 2023; 120:e2220380120. [PMID: 37364125 PMCID: PMC10319034 DOI: 10.1073/pnas.2220380120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 05/02/2023] [Indexed: 06/28/2023] Open
Abstract
Attaining molecular-level control over solidification processes is a crucial aspect of materials science. To control ice formation, organisms have evolved bewildering arrays of ice-binding proteins (IBPs), but these have poorly understood structure-activity relationships. We propose that reverse engineering using de novo computational protein design can shed light on structure-activity relationships of IBPs. We hypothesized that the model alpha-helical winter flounder antifreeze protein uses an unusual undertwisting of its alpha-helix to align its putative ice-binding threonine residues in exactly the same direction. We test this hypothesis by designing a series of straight three-helix bundles with an ice-binding helix projecting threonines and two supporting helices constraining the twist of the ice-binding helix. Our findings show that ice-recrystallization inhibition by the designed proteins increases with the degree of designed undertwisting, thus validating our hypothesis, and opening up avenues for the computational design of IBPs.
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Affiliation(s)
- Robbert J. de Haas
- Department of Physical Chemistry and Soft Matter, Wageningen University and Research, Wageningen, WE6708, The Netherlands
| | - Roderick P. Tas
- Laboratory of Self-Organizing Soft Matter, Department of Chemical Engineering and Chemistry and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, MB5600, The Netherlands
| | - Daniëlle van den Broek
- Laboratory of Self-Organizing Soft Matter, Department of Chemical Engineering and Chemistry and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, MB5600, The Netherlands
| | - Chuanbao Zheng
- Department of Physical Chemistry and Soft Matter, Wageningen University and Research, Wageningen, WE6708, The Netherlands
| | - Hannah Nguyen
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Alex Kang
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Asim K. Bera
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Neil P. King
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Ilja K. Voets
- Laboratory of Self-Organizing Soft Matter, Department of Chemical Engineering and Chemistry and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, MB5600, The Netherlands
| | - Renko de Vries
- Department of Physical Chemistry and Soft Matter, Wageningen University and Research, Wageningen, WE6708, The Netherlands
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5
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Jeon N, Jeong IH, Cho E, Choi I, Lee J, Han EH, Lee HJ, Lee PC, Lee E. Microcurvature Controllable Metal-Organic Framework Nanoagents Capable of Ice-Lattice Matching for Cellular Cryopreservation. JACS AU 2023; 3:154-164. [PMID: 36711099 PMCID: PMC9875254 DOI: 10.1021/jacsau.2c00562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/06/2022] [Accepted: 12/07/2022] [Indexed: 06/18/2023]
Abstract
Ice-binding proteins (IBPs) produced by psychrophilic organisms to adapt for the survival of psychrophiles in subzero conditions have received illustrious interest as a cryopreservation agent required for cells and tissues to completely recover after freezing/thawing. Depressing water-freezing point and avoiding ice-crystal growth affect their activities which are closely related to the presence of ice crystal well-matched binding moiety. The interaction of IBPs with ice and water is critical in enhancing their freeze avoidance against cell or tissue damage. Metal-organic frameworks (MOFs) with a controllable lattice at the molecular level and a size at the nanometer scale can offer periodically ordered ice-binding sites by modifying organic linkers and controlling microcurvature at the ice surface. Herein, zirconium (Zr)-based MOF-801 nanoparticles (NPs) with good biocompatibility were used as a cryoprotectant that is well dispersed and colloidal-stable in an aqueous solution. The MOF NP size was precisely controlled, and 10, 35, 100, and 250 nm NPs were prepared. The specific IBPs-mimicking pendants (valine and threonine) were simply introduced into the MOF NP-surface through the acrylate-based functionalization to endow with hydrophilic and hydrophobic dualities. When small-sized MOF-801 NPs were attached to ice, they confined ice growth in high curvature between the adsorption sites because of the decreased radius of the convex area of the growth region, leading to highly enhanced ice recrystallization inhibition (IRI). Surface-functionalized MOF NPs could increase the number of anchored clathrate water molecules with hydrophilic/hydrophobic balance of the ice-binding moiety, effectively inhibiting ice growth. The MOF-801 NPs were biocompatible with various cell lines regardless of concentration or NP surface-functionalization, whereas the smaller-sized surface-functionalized NPs showed a good cell recovery rate after freezing/thawing by induction of IRI. This study provides a strategy for the fabrication of low-cost, high-volume antifreeze nanoagents that can extend useful applications to organ transplantation, cord blood storage, and vaccines/drugs.
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Affiliation(s)
- Nayeong Jeon
- School
of Materials Science and Engineering, Gwangju
Institute of Science and Technology (GIST), Gwangju61005, Republic of Korea
| | - In-ho Jeong
- Department
of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul05505, Republic
of Korea
| | - Eunyeong Cho
- Composites
Research Division, Korea Institute of Materials
Science (KIMS), Changwon51508, Republic of Korea
| | - Ilhyung Choi
- School
of Materials Science and Engineering, Gwangju
Institute of Science and Technology (GIST), Gwangju61005, Republic of Korea
| | - Jiyeon Lee
- School
of Materials Science and Engineering, Gwangju
Institute of Science and Technology (GIST), Gwangju61005, Republic of Korea
| | - Eun Hee Han
- Research
Center for Bioconvergence Analysis, Korea
Basic Science Institute (KBSI), Cheongju28119, Republic of Korea
| | - Hee Jung Lee
- Composites
Research Division, Korea Institute of Materials
Science (KIMS), Changwon51508, Republic of Korea
| | - Peter C.W. Lee
- Department
of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul05505, Republic
of Korea
| | - Eunji Lee
- School
of Materials Science and Engineering, Gwangju
Institute of Science and Technology (GIST), Gwangju61005, Republic of Korea
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Lin M, Cao H, Li J. Control strategies of ice nucleation, growth, and recrystallization for cryopreservation. Acta Biomater 2023; 155:35-56. [PMID: 36323355 DOI: 10.1016/j.actbio.2022.10.056] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/20/2022] [Accepted: 10/26/2022] [Indexed: 02/02/2023]
Abstract
The cryopreservation of biomaterials is fundamental to modern biotechnology and biomedicine, but the biggest challenge is the formation of ice, resulting in fatal cryoinjury to biomaterials. To date, abundant ice control strategies have been utilized to inhibit ice formation and thus improve cryopreservation efficiency. This review focuses on the mechanisms of existing control strategies regulating ice formation and the corresponding applications to biomaterial cryopreservation, which are of guiding significance for the development of ice control strategies. Herein, basics related to biomaterial cryopreservation are introduced first. Then, the theoretical bases of ice nucleation, growth, and recrystallization are presented, from which the key factors affecting each process are analyzed, respectively. Ice nucleation is mainly affected by melting temperature, interfacial tension, shape factor, and kinetic prefactor, and ice growth is mainly affected by solution viscosity and cooling/warming rate, while ice recrystallization is inhibited by adsorption or diffusion mechanisms. Furthermore, the corresponding research methods and specific control strategies for each process are summarized. The review ends with an outlook of the current challenges and future perspectives in cryopreservation. STATEMENT OF SIGNIFICANCE: Ice formation is the major limitation of cryopreservation, which causes fatal cryoinjury to cryopreserved biomaterials. This review focuses on the three processes related to ice formation, called nucleation, growth, and recrystallization. The theoretical models, key influencing factors, research methods and corresponding ice control strategies of each process are summarized and discussed, respectively. The systematic introduction on mechanisms and control strategies of ice formation is instructive for the cryopreservation development.
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Affiliation(s)
- Min Lin
- Key Laboratory for Thermal Science and Power Engineering of Ministry of Education, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory for CO(2) Utilization and Reduction Technology, Tsinghua University, Beijing 100084, China
| | - Haishan Cao
- Key Laboratory for Thermal Science and Power Engineering of Ministry of Education, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory for CO(2) Utilization and Reduction Technology, Tsinghua University, Beijing 100084, China.
| | - Junming Li
- Key Laboratory for Thermal Science and Power Engineering of Ministry of Education, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory for CO(2) Utilization and Reduction Technology, Tsinghua University, Beijing 100084, China
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7
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Lee C, Lee Y, Jung WH, Kim TY, Kim T, Kim DN, Ahn DJ. Peptide-DNA origami as a cryoprotectant for cell preservation. SCIENCE ADVANCES 2022; 8:eadd0185. [PMID: 36306364 PMCID: PMC9616499 DOI: 10.1126/sciadv.add0185] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 09/12/2022] [Indexed: 05/21/2023]
Abstract
Cryopreservation of cells is essential for the conservation and cold chain of bioproducts and cell-based medicines. Here, we demonstrate that self-assembled DNA origami nanostructures have a substantial ability to protect cells undergoing freeze-thaw cycles; thereby, they can be used as cryoprotectant agents, because their nanoscale morphology and ice-philicity are tailored. In particular, a single-layered DNA origami nanopatch functionalized with antifreezing threonine peptides enabled the viability of HSC-3 cells to reach 56% after 1 month of cryopreservation, surpassing dimethyl sulfoxide, which produced 38% viability. It also exhibited minimal dependence on the cryopreservation period and freezing conditions. We attribute this outcome to the fact that the peptide-functionalized DNA nanopatches exert multisite actions for the retardation of ice growth in both intra- and extracellular regions and the protection of cell membranes during cryopreservation. This discovery is expected to deepen our fundamental understanding of cell survival under freezing environment and affect current cryopreservation technologies.
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Affiliation(s)
- Chanseok Lee
- Institute of Advanced Machines and Design, Seoul National University, Seoul 08826, Korea
- The w:i Interface Augmentation Center, Korea University, Seoul 02841, Korea
| | - Yedam Lee
- The w:i Interface Augmentation Center, Korea University, Seoul 02841, Korea
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Korea
| | - Woo Hyuk Jung
- The w:i Interface Augmentation Center, Korea University, Seoul 02841, Korea
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Korea
| | - Tae-Yeon Kim
- Department of Mechanical Engineering, Seoul National University, Seoul 08826, Korea
| | - Taehwi Kim
- Department of Mechanical Engineering, Seoul National University, Seoul 08826, Korea
| | - Do-Nyun Kim
- Institute of Advanced Machines and Design, Seoul National University, Seoul 08826, Korea
- The w:i Interface Augmentation Center, Korea University, Seoul 02841, Korea
- Department of Mechanical Engineering, Seoul National University, Seoul 08826, Korea
- Corresponding author. (D.J.A.); (D.-N.K.)
| | - Dong June Ahn
- The w:i Interface Augmentation Center, Korea University, Seoul 02841, Korea
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Korea
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Korea
- Corresponding author. (D.J.A.); (D.-N.K.)
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8
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Ding Z, Wang C, Zhou B, Su M, Yang S, Li Y, Qu C, Liu H. Antifreezing Hydroxyl Monolayer of Small Molecules on a Nanogold Surface. NANO LETTERS 2022; 22:5307-5315. [PMID: 35695804 DOI: 10.1021/acs.nanolett.2c01267] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The rational design of ice recrystallization inhibition (IRI) materials is challenging due to the poor understanding of the IRI mechanism at the molecular level. Here we report several new findings about IRI. (1) A dense hydroxyl monolayer of small molecules, e.g. 6-aza-2-thiothymine (ATT), adsorbed on a nanogold surface was demonstrated, for the first time, to have IRI activity. Five structural analogues adsorbed on groups nanogold with outward hydroxyl or methyl were created to evidence the origin of IRI activity. (2) Their IRI mechanism is closely related to the density of hydroxyls on a nanogold surface. However, the hydrophobic interaction in our model is not essential for macroscopic IRI activity. (3) A molecular dynamics simulation elucidates the hydroxyl density dependent IRI trajectories underlying the experimental observations, and the radial distribution function reveals that the methyl even slightly hinders the formation of hydrogen bonding due to a hydrophobic interaction. This work sheds more light on the IRI mechanism that should help in the customization of novel IRI materials.
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Affiliation(s)
- Zhongxiang Ding
- China Light Industry Key Laboratory of Meat Microbial Control and Utilization, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, People's Republic of China
| | - Chao Wang
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei 230027, People's Republic of China
| | - Baomei Zhou
- China Light Industry Key Laboratory of Meat Microbial Control and Utilization, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, People's Republic of China
| | - Mengke Su
- China Light Industry Key Laboratory of Meat Microbial Control and Utilization, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, People's Republic of China
| | - Shixuan Yang
- China Light Industry Key Laboratory of Meat Microbial Control and Utilization, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, People's Republic of China
| | - Yuzhu Li
- China Light Industry Key Laboratory of Meat Microbial Control and Utilization, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, People's Republic of China
| | - Cheng Qu
- China Light Industry Key Laboratory of Meat Microbial Control and Utilization, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, People's Republic of China
| | - Honglin Liu
- China Light Industry Key Laboratory of Meat Microbial Control and Utilization, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, People's Republic of China
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9
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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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10
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An LY, Dai Z, Di B, Xu LL. Advances in Cryochemistry: Mechanisms, Reactions and Applications. Molecules 2021; 26:750. [PMID: 33535547 PMCID: PMC7867104 DOI: 10.3390/molecules26030750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 01/28/2021] [Accepted: 01/28/2021] [Indexed: 01/23/2023] Open
Abstract
It is counterintuitive that chemical reactions can be accelerated by freezing, but this amazing phenomenon was discovered as early as the 1960s. In frozen systems, the increase in reaction rate is caused by various mechanisms and the freeze concentration effect is the main reason for the observed acceleration. Some accelerated reactions have great application value in the chemistry synthesis and environmental fields; at the same time, certain reactions accelerated at low temperature during the storage of food, medicine, and biological products should cause concern. The study of reactions accelerated by freezing will overturn common sense and provide a new strategy for researchers in the chemistry field. In this review, we mainly introduce various mechanisms for accelerating reactions induced by freezing and summarize a variety of accelerated cryochemical reactions and their applications.
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Affiliation(s)
- Lu-Yan An
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; (L.-Y.A.); (Z.D.)
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Zhen Dai
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; (L.-Y.A.); (Z.D.)
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Bin Di
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; (L.-Y.A.); (Z.D.)
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Li-Li Xu
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; (L.-Y.A.); (Z.D.)
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
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11
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Understanding the inhibition performance of polyvinylcaprolactam and interactions with water molecules. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.138070] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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12
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Li T, Li M, Zhong Q, Wu T. Effect of Fibril Length on the Ice Recrystallization Inhibition Activity of Nanocelluloses. Carbohydr Polym 2020; 240:116275. [DOI: 10.1016/j.carbpol.2020.116275] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/07/2020] [Accepted: 04/08/2020] [Indexed: 12/21/2022]
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13
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Knox-Brown P, Rindfleisch T, Günther A, Balow K, Bremer A, Walther D, Miettinen MS, Hincha DK, Thalhammer A. Similar Yet Different-Structural and Functional Diversity among Arabidopsis thaliana LEA_4 Proteins. Int J Mol Sci 2020; 21:E2794. [PMID: 32316452 PMCID: PMC7215670 DOI: 10.3390/ijms21082794] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/15/2020] [Accepted: 04/16/2020] [Indexed: 12/28/2022] Open
Abstract
The importance of intrinsically disordered late embryogenesis abundant (LEA) proteins in the tolerance to abiotic stresses involving cellular dehydration is undisputed. While structural transitions of LEA proteins in response to changes in water availability are commonly observed and several molecular functions have been suggested, a systematic, comprehensive and comparative study of possible underlying sequence-structure-function relationships is still lacking. We performed molecular dynamics (MD) simulations as well as spectroscopic and light scattering experiments to characterize six members of two distinct, lowly homologous clades of LEA_4 family proteins from Arabidopsis thaliana. We compared structural and functional characteristics to elucidate to what degree structure and function are encoded in LEA protein sequences and complemented these findings with physicochemical properties identified in a systematic bioinformatics study of the entire Arabidopsis thaliana LEA_4 family. Our results demonstrate that although the six experimentally characterized LEA_4 proteins have similar structural and functional characteristics, differences concerning their folding propensity and membrane stabilization capacity during a freeze/thaw cycle are obvious. These differences cannot be easily attributed to sequence conservation, simple physicochemical characteristics or the abundance of sequence motifs. Moreover, the folding propensity does not appear to be correlated with membrane stabilization capacity. Therefore, the refinement of LEA_4 structural and functional properties is likely encoded in specific patterns of their physicochemical characteristics.
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Affiliation(s)
- Patrick Knox-Brown
- Physical Biochemistry, University of Potsdam, Karl-Liebknecht-Str. 24–25, D-14476 Potsdam, Germany; (P.K.-B.); (T.R.)
| | - Tobias Rindfleisch
- Physical Biochemistry, University of Potsdam, Karl-Liebknecht-Str. 24–25, D-14476 Potsdam, Germany; (P.K.-B.); (T.R.)
| | - Anne Günther
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam, Germany; (A.G.); (K.B.); (A.B.); (D.W.); (D.K.H.)
| | - Kim Balow
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam, Germany; (A.G.); (K.B.); (A.B.); (D.W.); (D.K.H.)
| | - Anne Bremer
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam, Germany; (A.G.); (K.B.); (A.B.); (D.W.); (D.K.H.)
- Department for Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Dirk Walther
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam, Germany; (A.G.); (K.B.); (A.B.); (D.W.); (D.K.H.)
| | - Markus S. Miettinen
- Max-Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, D-14476 Potsdam, Germany;
| | - Dirk K. Hincha
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam, Germany; (A.G.); (K.B.); (A.B.); (D.W.); (D.K.H.)
| | - Anja Thalhammer
- Physical Biochemistry, University of Potsdam, Karl-Liebknecht-Str. 24–25, D-14476 Potsdam, Germany; (P.K.-B.); (T.R.)
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14
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Li T, Zhong Q, Zhao B, Lenaghan S, Wang S, Wu T. Effect of surface charge density on the ice recrystallization inhibition activity of nanocelluloses. Carbohydr Polym 2020; 234:115863. [PMID: 32070502 DOI: 10.1016/j.carbpol.2020.115863] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 12/26/2019] [Accepted: 01/11/2020] [Indexed: 12/26/2022]
Abstract
Recently nanocelluloses have been found to possess ice recrystallization inhibition (IRI) activity, which have several potential applications. The present study focuses on the relationship between the surface charge density (SCD) of nanocelluloses and IRI activity. Cellulose nanocrystals (CNCs) and 2, 2, 6, 6-tetramethylpiperidine-1-oxyl oxidized cellulose nanofibrils (TEMPO-CNFs) with similar degrees of polymerization (DP) or fibril lengths but with different SCDs were prepared and characterized for IRI activity. When the SCD of CNCs was progressively reduced, an initial increase of IRI activity was observed, followed by a decrease due to fibril aggregation. CNCs with a low SCD became IRI active at increased unfrozen water fractions and higher annealing temperatures. TEMPO-CNFs with a low SCD also had higher IRI activity. Additionally, lowering pH to protonate the carboxylate groups of TEMPO-CNFs enhanced the IRI activity. These research findings are important in producing nanocelluloses with enhanced IRI activity and understanding their structure-activity relationship.
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Affiliation(s)
- Teng Li
- Department of Food Science, University of Tennessee, 2510 River Drive, Knoxville, TN, 37996, USA
| | - Qixin Zhong
- Department of Food Science, University of Tennessee, 2510 River Drive, Knoxville, TN, 37996, USA
| | - Bin Zhao
- Department of Chemistry, University of Tennessee, 1420 Circle Drive, Knoxville, TN, 37996, USA
| | - Scott Lenaghan
- Department of Food Science, University of Tennessee, 2510 River Drive, Knoxville, TN, 37996, USA; Center for Agricultural Synthetic Biology, 2640 Morgan Circle Drive, Knoxville, TN 37996, USA
| | - Siqun Wang
- The Center for Renewable Carbon, University of Tennessee, 2506 Jacob Drive, Knoxville, TN 37996, USA
| | - Tao Wu
- Department of Food Science, University of Tennessee, 2510 River Drive, Knoxville, TN, 37996, USA.
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15
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16
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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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17
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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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18
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Hudait A, Qiu Y, Odendahl N, Molinero V. Hydrogen-Bonding and Hydrophobic Groups Contribute Equally to the Binding of Hyperactive Antifreeze and Ice-Nucleating Proteins to Ice. J Am Chem Soc 2019; 141:7887-7898. [DOI: 10.1021/jacs.9b02248] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Arpa Hudait
- Department of Chemistry, The University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Yuqing Qiu
- Department of Chemistry, The University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Nathan Odendahl
- Department of Chemistry, The University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Valeria Molinero
- Department of Chemistry, The University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
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19
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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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20
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Lee H. Effects of hydrophobic and hydrogen-bond interactions on the binding affinity of antifreeze proteins to specific ice planes. J Mol Graph Model 2018; 87:48-55. [PMID: 30502671 DOI: 10.1016/j.jmgm.2018.11.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 11/17/2018] [Accepted: 11/19/2018] [Indexed: 11/26/2022]
Abstract
Tenebrio molitor antifreeze protein (TmAFP) was simulated with growing ice surfaces such as primary prism, secondary prism, basal, and pyramidal planes. The ice-binding site of TmAFP, which is full of threonine (Thr), binds to the primary-prism plane but does not bind to other ice planes, in agreement with experiments showing the fast adsorption of TmAFP to the primary-prism plane. To mimic the ice-binding site of shorthorn sculpin AFP (ssAFP; type I) that predominantly consists of alanine (Ala) and has the binding affinity to the secondary-prism plane, the ice-binding site of TmAFP was mutated by replacing a few Thr residues with Ala residues, showing that mutated TmAFP binds to the secondary-prism plane, similar to the ice-binding affinity of ssAFP. Ala residues are located at the cavity of ice, while Thr residues form hydrogen bonds with water molecules. When the mutated TmAFP is further modified by removing Thr, it does not bind to the secondary-prism plane. These findings indicate that simulations can successfully capture the experimentally observed binding affinity of AFP to specific ice planes, to an extent dependent on hydrophobicity of the ice-binding site. In particular, the addition of hydrophobic residues influences the ice-binding affinity of TmAFP, while a certain amount of hydrophilic residue is still required for hydrogen-bond interactions, which supports experimental observations regarding the key roles of hydrophobic and hydrophilic interactions on the AFP-ice binding.
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Affiliation(s)
- Hwankyu Lee
- Department of Chemical Engineering, Dankook University, Yongin-si, Gyeonggi-do, 16890, South Korea.
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21
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Midya US, Bandyopadhyay S. Role of Polar and Nonpolar Groups in the Activity of Antifreeze Proteins: A Molecular Dynamics Simulation Study. J Phys Chem B 2018; 122:9389-9398. [DOI: 10.1021/acs.jpcb.8b08506] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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22
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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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23
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Adam MK, Jarrett‐Wilkins C, Beards M, Staykov E, MacFarlane LR, Bell TDM, Matthews JM, Manners I, Faul CFJ, Moens PDJ, Ben RN, Wilkinson BL. 1D Self‐Assembly and Ice Recrystallization Inhibition Activity of Antifreeze Glycopeptide‐Functionalized Perylene Bisimides. Chemistry 2018; 24:7834-7839. [DOI: 10.1002/chem.201800857] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Indexed: 01/18/2023]
Affiliation(s)
- Madeleine K. Adam
- Department of Chemistry and Biomolecular Sciences University of Ottawa Ottawa K1N 6N5 Canada
| | | | - Michael Beards
- School of Chemistry Monash University Melbourne 3800 Australia
| | - Emiliyan Staykov
- Department of Chemistry and Biomolecular Sciences University of Ottawa Ottawa K1N 6N5 Canada
| | | | - Toby D. M. Bell
- School of Chemistry Monash University Melbourne 3800 Australia
| | - Jacqueline M. Matthews
- School of Life and Environmental Sciences The University of Sydney Sydney 2006 Australia
| | - Ian Manners
- School of Chemistry University of Bristol Bristol BS8 1TS UK
| | | | - Pierre D. J. Moens
- School of Science and Technology University of New England Armidale 2351 Australia
| | - Robert N. Ben
- Department of Chemistry and Biomolecular Sciences University of Ottawa Ottawa K1N 6N5 Canada
| | - Brendan L. Wilkinson
- School of Science and Technology University of New England Armidale 2351 Australia
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24
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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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25
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Hudait A, Odendahl N, Qiu Y, Paesani F, Molinero V. Ice-Nucleating and Antifreeze Proteins Recognize Ice through a Diversity of Anchored Clathrate and Ice-like Motifs. J Am Chem Soc 2018; 140:4905-4912. [PMID: 29564892 DOI: 10.1021/jacs.8b01246] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Cold-adapted organisms produce antifreeze and ice-nucleating proteins to prevent and promote ice formation. The crystal structure of hyperactive bacterial antifreeze protein (AFP) MpAFP suggests that this protein binds ice through an anchored clathrate motif. It is not known whether other hyperactive AFPs and ice-nucleating proteins (INPs) use the same motif to recognize or nucleate ice. Here we use molecular simulations to elucidate the ice-binding motifs of hyperactive insect AFPs and a model INP of Pseudomonas syringae. We find that insect AFPs recognize ice through anchored clathrate motifs distinct from that of MpAFP. By performing simulations of ice nucleation by PsINP, we identify two distinct ice-binding sites on opposite sides of the β-helix. The ice-nucleating sequences identified in the simulations agree with those previously proposed for the closely related INP of Pseudomonas borealis based on the structure of the protein. The simulations indicate that these sites have comparable ice-nucleating efficiency, but distinct binding motifs, controlled by the amino acid sequence: one is an anchored clathrate and the other ice-like. We conclude that anchored clathrate and ice-like motifs can be equally effective for binding proteins to ice and promoting ice nucleation.
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Affiliation(s)
- Arpa Hudait
- Department of Chemistry , 315 South 1400 East , The University of Utah , Salt Lake City , Utah 84112-0580 , United States
| | - Nathan Odendahl
- Department of Chemistry , 315 South 1400 East , The University of Utah , Salt Lake City , Utah 84112-0580 , United States
| | - Yuqing Qiu
- Department of Chemistry , 315 South 1400 East , The University of Utah , Salt Lake City , Utah 84112-0580 , United States
| | - Francesco Paesani
- Department of Chemistry and Biochemistry , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92093 , United States
| | - Valeria Molinero
- Department of Chemistry , 315 South 1400 East , The University of Utah , Salt Lake City , Utah 84112-0580 , United States
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26
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Flores A, Quon JC, Perez AF, Ba Y. Mechanisms of antifreeze proteins investigated via the site-directed spin labeling technique. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2018; 47:611-630. [PMID: 29487966 DOI: 10.1007/s00249-018-1285-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 01/28/2018] [Accepted: 02/15/2018] [Indexed: 12/01/2022]
Abstract
The site-directed spin labeling (SDSL) technique was used to examine the antifreeze mechanisms of type-I antifreeze proteins (AFPs). The effects on the growth of seed ice crystals by the spin-label groups attached to different side chains of the AFPs were observed, and the states of water molecules surrounding the spin-label groups were probed via analyses of variable-temperature (VT) dependent electron paramagnetic resonance (EPR) spectra. The first set of experiments revealed the antifreeze activities of the spin-labeled AFPs at the microscopic level, while the second set of experiments displayed those at the molecular level. The experimental results confirmed the putative ice-binding surface (IBS) of type-I AFPs. The VT EPR spectra indicate that type-I AFPs can inhibit the nucleation of seed ice crystals down to ~ - 20 °C in their aqueous solutions. Thus, the present authors believe that AFPs protect organisms from freezing damage in two ways: (1) inhibiting the nucleation of seed ice crystals, and (2) hindering the growth of seed ice crystals once they have formed. The first mechanism should play a more significant role in protecting against freezing damage among organisms living in cold environments. The VT EPR spectra also revealed that liquid-like water molecules existed around the spin-labeled non-ice-binding side chains of the AFPs frozen within the ice matrices, and ice surrounding the spin-label groups melted at subzero temperatures during the heating process. This manuscript concludes with the proposed model of antifreeze mechanisms of AFPs based on the experimental results.
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Affiliation(s)
- Antonia Flores
- 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
| | - Adiel F Perez
- 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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27
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Mochizuki K, Molinero V. Antifreeze Glycoproteins Bind Reversibly to Ice via Hydrophobic Groups. J Am Chem Soc 2018; 140:4803-4811. [PMID: 29392937 DOI: 10.1021/jacs.7b13630] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Antifreeze molecules allow organisms to survive in subzero environments. Antifreeze glycoproteins (AFGPs), produced by polar fish, are the most potent inhibitors of ice recrystallization. To date, the molecular mechanism by which AFGPs bind to ice has not yet been elucidated. Mutation experiments cannot resolve whether the binding occurs through the peptide, the saccharides, or both. Here, we use molecular simulations to determine the mechanism and driving forces for binding of AFGP8 to ice, its selectivity for the primary prismatic plane, and the molecular origin of its exceptional ice recrystallization activity. Consistent with experiments, AFGP8 in simulations preferentially adopts the PPII helix secondary structure in solution. We show that the segregation of hydrophilic and hydrophobic groups in the PPII helix is vital for ice binding. Binding occurs through adsorption of methyl groups of the peptide and disaccharides to ice, driven by the entropy of dehydration of the hydrophobic groups as they nest in the cavities at the ice surface. The selectivity to the primary prismatic plane originates in the deeper cavities it has compared to the basal plane. We estimate the free energy of binding of AFGP8 and the longer AFGPs4-6, and find them to be consistent with the reversible binding demonstrated in experiments. The simulations reveal that AFGP8 binds to ice through a myriad of conformations that it uses to diffuse through the ice surface and find ice steps, to which it strongly adsorbs. We interpret that the existence of multiple, weak binding sites is the key for the exceptional ice recrystallization inhibition activity of AFGPs.
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Affiliation(s)
- Kenji Mochizuki
- Department of Chemistry , The University of Utah , Salt Lake City , Utah 84112-0580 , United States.,Institute for Fiber Engineering , Shinshu University , Ueda , Nagano 386-8567 , Japan
| | - Valeria Molinero
- Department of Chemistry , The University of Utah , Salt Lake City , Utah 84112-0580 , United States
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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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29
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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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30
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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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Li LF, Liang XX. Influence of Adsorption Orientation on the Statistical Mechanics Model of Type I Antifreeze Protein: The Thermal Hysteresis Temperature. J Phys Chem B 2017; 121:9513-9517. [PMID: 28956610 DOI: 10.1021/acs.jpcb.7b06619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The antifreeze activity of type I antifreeze proteins (AFPIs) is studied on the basis of the statistical mechanics theory, by taking the AFP's adsorption orientation into account. The thermal hysteresis temperatures are calculated by determining the system Gibbs function as well as the AFP molecule coverage rate on the ice-crystal surface. The numerical results for the thermal hysteresis temperatures of AFP9, HPLC-6, and AAAA2kE are obtained for both of the cases with and without inclusion of the adsorption orientation. The results show that the influence of the adsorption orientation on the thermal hysteresis temperature cannot be neglected. The theoretical results are coincidental preferably with the experimental data.
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Affiliation(s)
- Li-Fen Li
- Department of Basic Curriculum, North China Institute of Science and Technology , Beijing 101601, China
| | - Xi-Xia Liang
- Department of Physics, Inner Mongolia University , Hohhot 010021, China
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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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Voets IK. From ice-binding proteins to bio-inspired antifreeze materials. SOFT MATTER 2017; 13:4808-4823. [PMID: 28657626 PMCID: PMC5708349 DOI: 10.1039/c6sm02867e] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 06/16/2017] [Indexed: 05/07/2023]
Abstract
Ice-binding proteins (IBP) facilitate survival under extreme conditions in diverse life forms. IBPs in polar fishes block further growth of internalized environmental ice and inhibit ice recrystallization of accumulated internal crystals. Algae use IBPs to structure ice, while ice adhesion is critical for the Antarctic bacterium Marinomonas primoryensis. Successful translation of this natural cryoprotective ability into man-made materials holds great promise but is still in its infancy. This review covers recent advances in the field of ice-binding proteins and their synthetic analogues, highlighting fundamental insights into IBP functioning as a foundation for the knowledge-based development of cheap, bio-inspired mimics through scalable production routes. Recent advances in the utilisation of IBPs and their analogues to e.g. improve cryopreservation, ice-templating strategies, gas hydrate inhibition and other technologies are presented.
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Affiliation(s)
- I K Voets
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Post Office Box 513, 5600 MD Eindhoven, The Netherlands. and Laboratory of Macromolecular and Organic Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, Post Office Box 513, 5600 MD Eindhoven, The Netherlands and Laboratory of Physical Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, Post Office Box 513, 5600 MD Eindhoven, The Netherlands
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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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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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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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Mitchell DE, Congdon T, Rodger A, Gibson MI. Gold Nanoparticle Aggregation as a Probe of Antifreeze (Glyco) Protein-Inspired Ice Recrystallization Inhibition and Identification of New IRI Active Macromolecules. Sci Rep 2015; 5:15716. [PMID: 26499135 PMCID: PMC4620503 DOI: 10.1038/srep15716] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 10/02/2015] [Indexed: 11/09/2022] Open
Abstract
Antifreeze (glyco)proteins are found in polar fish species and act to slow the rate of growth of ice crystals; a property known as ice recrystallization inhibition. The ability to slow ice growth is of huge technological importance especially in the cryopreservation of donor cells and tissue, but native antifreeze proteins are often not suitable, nor easily available. Therefore, the search for new materials that mimic this function is important, but currently limited by the low-throughout assays associated with the antifreeze properties. Here 30 nm gold nanoparticles are demonstrated to be useful colorimetric probes for ice recrystallization inhibition, giving a visible optical response and is compatible with 96 well plates for high-throughout studies. This method is faster, requires less infrastructure, and has easier interpretation than the currently used 'splat' methods. Using this method, a series of serum proteins were identified to have weak, but specific ice recrystallization inhibition activity, which was removed upon denaturation. It is hoped that high-throughput tools such as this will accelerate the discovery of new antifreeze mimics.
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Affiliation(s)
- Daniel E. Mitchell
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
- MOAC DTC, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Thomas Congdon
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Alison Rodger
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Matthew I. Gibson
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
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38
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Yang R, Zhang C, Gao R, Zhang L. An Effective Antifreeze Protein Predictor with Ensemble Classifiers and Comprehensive Sequence Descriptors. Int J Mol Sci 2015; 16:21191-214. [PMID: 26370959 PMCID: PMC4613249 DOI: 10.3390/ijms160921191] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 08/18/2015] [Accepted: 08/26/2015] [Indexed: 12/03/2022] Open
Abstract
Antifreeze proteins (AFPs) play a pivotal role in the antifreeze effect of overwintering organisms. They have a wide range of applications in numerous fields, such as improving the production of crops and the quality of frozen foods. Accurate identification of AFPs may provide important clues to decipher the underlying mechanisms of AFPs in ice-binding and to facilitate the selection of the most appropriate AFPs for several applications. Based on an ensemble learning technique, this study proposes an AFP identification system called AFP-Ensemble. In this system, random forest classifiers are trained by different training subsets and then aggregated into a consensus classifier by majority voting. The resulting predictor yields a sensitivity of 0.892, a specificity of 0.940, an accuracy of 0.938 and a balanced accuracy of 0.916 on an independent dataset, which are far better than the results obtained by previous methods. These results reveal that AFP-Ensemble is an effective and promising predictor for large-scale determination of AFPs. The detailed feature analysis in this study may give useful insights into the molecular mechanisms of AFP-ice interactions and provide guidance for the related experimental validation. A web server has been designed to implement the proposed method.
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Affiliation(s)
- Runtao Yang
- School of Control Science and Engineering, Shandong University, Jinan 250061, China.
| | - Chengjin Zhang
- School of Control Science and Engineering, Shandong University, Jinan 250061, China.
- School of Mechanical, Electrical and Information Engineering, Shandong University, Weihai 264209, China.
| | - Rui Gao
- School of Control Science and Engineering, Shandong University, Jinan 250061, China.
| | - Lina Zhang
- School of Control Science and Engineering, Shandong University, Jinan 250061, China.
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39
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Duboué-Dijon E, Laage D. Comparative study of hydration shell dynamics around a hyperactive antifreeze protein and around ubiquitin. J Chem Phys 2015; 141:22D529. [PMID: 25494800 DOI: 10.1063/1.4902822] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The hydration layer surrounding a protein plays an essential role in its biochemical function and consists of a heterogeneous ensemble of water molecules with different local environments and different dynamics. What determines the degree of dynamical heterogeneity within the hydration shell and how this changes with temperature remains unclear. Here, we combine molecular dynamics simulations and analytic modeling to study the hydration shell structure and dynamics of a typical globular protein, ubiquitin, and of the spruce budworm hyperactive antifreeze protein over the 230-300 K temperature range. Our results show that the average perturbation induced by both proteins on the reorientation dynamics of water remains moderate and changes weakly with temperature. The dynamical heterogeneity arises mostly from the distribution of protein surface topographies and is little affected by temperature. The ice-binding face of the antifreeze protein induces a short-ranged enhancement of water structure and a greater slowdown of water reorientation dynamics than the non-ice-binding faces whose effect is similar to that of ubiquitin. However, the hydration shell of the ice-binding face remains less tetrahedral than the bulk and is not "ice-like". We finally show that the hydrogen bonds between water and the ice-binding threonine residues are particularly strong due to a steric confinement effect, thereby contributing to the strong binding of the antifreeze protein on ice crystals.
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Affiliation(s)
- Elise Duboué-Dijon
- Département de Chimie, École Normale Supérieure-PSL Research University, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, 24, rue Lhomond, 75005 Paris, France
| | - Damien Laage
- Département de Chimie, École Normale Supérieure-PSL Research University, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, 24, rue Lhomond, 75005 Paris, France
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40
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Sharp KA. The remarkable hydration of the antifreeze protein Maxi: a computational study. J Chem Phys 2015; 141:22D510. [PMID: 25494781 DOI: 10.1063/1.4896693] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The long four-helix bundle antifreeze protein Maxi contains an unusual core for a globular protein. More than 400 ordered waters between the helices form a nano-pore of internal water about 150 Å long. Molecular dynamics simulations of hydrated Maxi were carried out using the CHARMM27 protein forcefield and the TIP3P water model. Solvation in the core and non-core first hydration shell was analyzed in terms of water-water H-bond distance-angle distributions. The core had an increased population of low-angle H-bonds between water pairs relative to bulk water. Enhancement of low angle H-bonds was particularly pronounced for water pairs at the interfaces between apolar and polar regions inside the protein core, characteristic of the anchored clathrate solvation structure seen previously in the ice-nuclei binding surfaces of type I, type III, and beta-helical antifreeze proteins. Anchored clathrate type solvation structure was not seen in the exterior solvation shell except around residues implicated in ice binding. Analysis of solvation dynamics using water residence times and diffusion constants showed that exterior solvation shell waters exchanged rapidly with bulk water, with no difference between ice-binding and non-binding residues. Core waters had about ten-fold slower diffusion than bulk water. Water residence times around core residues averaged about 8 ps, similar to those on the exterior surface, but they tended to exchange primarily with other core water, resulting in longer, >40 ps residence times within the core. Preferential exchange or diffusion of the water along the long axis of the water core of Maxi was not detected.
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Affiliation(s)
- Kim A Sharp
- Department of Biochemistry and Biophysics, E. R. Johnson Foundation, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059, USA
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41
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Kuiper MJ, Morton CJ, Abraham SE, Gray-Weale A. The biological function of an insect antifreeze protein simulated by molecular dynamics. eLife 2015; 4. [PMID: 25951514 PMCID: PMC4442126 DOI: 10.7554/elife.05142] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 05/06/2015] [Indexed: 11/16/2022] Open
Abstract
Antifreeze proteins (AFPs) protect certain cold-adapted organisms from freezing to death by selectively adsorbing to internal ice crystals and inhibiting ice propagation. The molecular details of AFP adsorption-inhibition is uncertain but is proposed to involve the Gibbs–Thomson effect. Here we show by using unbiased molecular dynamics simulations a protein structure-function mechanism for the spruce budworm Choristoneura fumiferana AFP, including stereo-specific binding and consequential melting and freezing inhibition. The protein binds indirectly to the prism ice face through a linear array of ordered water molecules that are structurally distinct from the ice. Mutation of the ice binding surface disrupts water-ordering and abolishes activity. The adsorption is virtually irreversible, and we confirm the ice growth inhibition is consistent with the Gibbs–Thomson law. DOI:http://dx.doi.org/10.7554/eLife.05142.001 Water expands as it freezes. If this happens to the water inside plants and animals, the resulting ice crystals can rupture cells. To prevent this, many plants and animals that live in cold climates have evolved ‘antifreeze proteins’. When a small particle of ice first starts to form, the antifreeze proteins bind to it and prevent the water around it freezing, hence preventing the growth of an ice crystal. There are many different types of antifreeze protein, and some are more active than others. For example, some insects including the spruce budworm are exposed to extremely cold temperatures—sometimes below −30°C—and these insects have antifreeze proteins that are highly active. It is not fully understood how different antifreeze proteins interact with ice and prevent the growth of ice crystals. This is largely because, as yet, there are no experimental techniques that make it possible to see how antifreeze proteins and water molecules arrange themselves at the surface of a growing particle of ice. Instead, scientists have developed computer simulations to investigate this process. While many of these studies have provided valuable information, the computational methods used have only recently become powerful enough to analyze how the antifreeze proteins approach the surface of the ice particle. Kuiper et al. carried out simulations involving a highly active antifreeze protein from the spruce budworm. The results of these simulations revealed that this antifreeze protein does not bind directly to ice; instead, water molecules at the surface of the protein act as a bridge between the protein and the ice. These water molecules are highly ordered and though they have similarities with how water is structured in the ice, they are distinct from the ice lattice itself. Furthermore, this arrangement appears to be important for allowing the spruce budworm antifreeze protein to interact with the ice. This study provides detailed insights as to how a highly active antifreeze protein helps to prevent ice crystals forming. In the future, the computational simulations used here may be extended to study the dynamics of other antifreeze proteins, and also how crystals of other materials form. DOI:http://dx.doi.org/10.7554/eLife.05142.002
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Affiliation(s)
- Michael J Kuiper
- Victorian Life Sciences Computation Initiative, The University of Melbourne, Carlton, Australia
| | - Craig J Morton
- ACRF Rational Drug Discovery Centre, St Vincent's Institute of Medical Research, Fitzroy, Australia
| | - Sneha E Abraham
- School of Chemistry, The University of Melbourne, Melbourne, Australia
| | - Angus Gray-Weale
- School of Chemistry, The University of Melbourne, Melbourne, Australia
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42
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Wu J, Rong Y, Wang Z, Zhou Y, Wang S, Zhao B. Isolation and characterisation of sericin antifreeze peptides and molecular dynamics modelling of their ice-binding interaction. Food Chem 2015; 174:621-9. [DOI: 10.1016/j.foodchem.2014.11.100] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 10/21/2014] [Accepted: 11/17/2014] [Indexed: 02/03/2023]
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43
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Todde G, Hovmöller S, Laaksonen A. Influence of antifreeze proteins on the ice/water interface. J Phys Chem B 2015; 119:3407-13. [PMID: 25611783 DOI: 10.1021/jp5119713] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Antifreeze proteins (AFP) are responsible for the survival of several species, ranging from bacteria to fish, that encounter subzero temperatures in their living environment. AFPs have been divided into two main families, moderately and hyperactive, depending on their thermal hysteresis activity. We have studied one protein from both families, the AFP from the snow flea (sfAFP) and from the winter flounder (wfAFP), which belong to the hyperactive and moderately active family, respectively. On the basis of molecular dynamics simulations, we have estimated the thickness of the water/ice interface for systems both with and without the AFPs attached onto the ice surface. The calculation of the diffusion profiles along the simulation box allowed us to measure the interface width for different ice planes. The obtained widths clearly show a different influence of the two AFPs on the ice/water interface. The different impact of the AFPs here studied on the interface thickness can be related to two AFPs properties: the protein hydrophobic surface and the number of hydrogen bonds that the two AFPs faces form with water molecules.
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Affiliation(s)
- Guido Todde
- Department of Material and Environmental Chemistry, Arrhenius Laboratory, Stockholm University , 10691 Stockholm, Sweden
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44
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Todde G, Whitman C, Hovmöller S, Laaksonen A. Induced ice melting by the snow flea antifreeze protein from molecular dynamics simulations. J Phys Chem B 2014; 118:13527-34. [PMID: 25353109 DOI: 10.1021/jp508992e] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Antifreeze proteins (AFP) allow different life forms, insects as well as fish and plants, to survive in subzero environments. AFPs prevent freezing of the physiological fluids. We have studied, through molecular dynamics simulations, the behavior of the small isoform of the AFP found in the snow flea (sfAFP), both in water and at the ice/water interface, of four different ice planes. In water at room temperature, the structure of the sfAFP is found to be slightly unstable. The loop between two polyproline II helices has large fluctuations as well as the C-terminus. Torsional angle analyses show a decrease of the polyproline II helix area in the Ramachandran plots. The protein structure instability, in any case, should not affect its antifreeze activity. At the ice/water interface the sfAFP triggers local melting of the ice surface. Bipyramidal, secondary prism, and prism ice planes melt in the presence of AFP at temperatures below the melting point of ice. Only the basal plane is found to be stable at the same temperatures, indicating an adsorption of the sfAFP on this ice plane as confirmed by experimental evidence.
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Affiliation(s)
- Guido Todde
- Department of Material and Environmental Chemistry, Arrhenius Laboratory, Stockholm University , 10691 Stockholm, Sweden
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45
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Wang S, Wen X, Golen JA, Arifin JF, Rheingold AL. Antifreeze protein-induced selective crystallization of a new thermodynamically and kinetically less preferred molecular crystal. Chemistry 2013; 19:16104-12. [PMID: 24123280 PMCID: PMC3855871 DOI: 10.1002/chem.201302049] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 08/09/2013] [Indexed: 11/12/2022]
Abstract
The formation of a new, dihydrate crystalline form of 5-methyluridine (m(5)U) was selectively induced by a protein additive, antifreeze protein (AFP) in a highly efficient manner (in 10(-6) molar scale, whereas known kinetic additives need 0.1 molar scale). The hemihydrate form (form I, the only previously known crystalline form of m(5)U) and the dihydrate form of m(5)U (form II) obtained herein were characterized using X-ray crystallography and differential scanning calorimetry (DSC). Compared to form I, remarkably, form II is thermodynamically and kinetically less preferred. The presence of AFP can selectively inhibit the appearance of form I and hence allows the growth of form II, the pure form of which cannot grow directly from m(5) U supersaturated solutions under the same conditions. An explanation supported by both experimental and theoretical results is provided for the AFP-induced selection process. Implications on AFP-induced ice shape changes are also discussed. Control of crystallization from supersaturated solutions is of great interest in both fundamental research and practical applications in fields like chemistry, pharmacology and materials science. These findings suggest that crystallization processes with AFPs could be valuable for selective growth of hydrates and polymorphs of important pharmaceutical compounds.
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Affiliation(s)
- Sen Wang
- Molecular Imaging Program, Stanford University, Stanford 94305 (USA), Fax: (+1)650-724-4948
| | - Xin Wen
- Department of Chemistry and Biochemistry, California State University, Los Angeles, 5151 State University Drive, Los Angles 90032 (USA), Fax: (+1)323-343-6490
| | - James A. Golen
- Department of Chemistry and Biochemistry University of California, San Diego, La Jolla, CA 92093 (USA)
| | - Josh F. Arifin
- Department of Chemistry and Biochemistry, California State University, Los Angeles, 5151 State University Drive, Los Angles 90032 (USA), Fax: (+1)323-343-6490
| | - Arnold L. Rheingold
- Department of Chemistry and Biochemistry University of California, San Diego, La Jolla, CA 92093 (USA)
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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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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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Deller RC, Congdon T, Sahid MA, Morgan M, Vatish M, Mitchell DA, Notman R, Gibson MI. Ice recrystallisation inhibition by polyols: comparison of molecular and macromolecular inhibitors and role of hydrophobic units. Biomater Sci 2013; 1:478-485. [DOI: 10.1039/c3bm00194f] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Shah SHH, Kar RK, Asmawi AA, Rahman MBA, Murad AMA, Mahadi NM, Basri M, Rahman RNZA, Salleh AB, Chatterjee S, Tejo BA, Bhunia A. Solution structures, dynamics, and ice growth inhibitory activity of peptide fragments derived from an antarctic yeast protein. PLoS One 2012; 7:e49788. [PMID: 23209600 PMCID: PMC3509122 DOI: 10.1371/journal.pone.0049788] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 10/12/2012] [Indexed: 12/04/2022] Open
Abstract
Exotic functions of antifreeze proteins (AFP) and antifreeze glycopeptides (AFGP) have recently been attracted with much interest to develop them as commercial products. AFPs and AFGPs inhibit ice crystal growth by lowering the water freezing point without changing the water melting point. Our group isolated the Antarctic yeast Glaciozyma antarctica that expresses antifreeze protein to assist it in its survival mechanism at sub-zero temperatures. The protein is unique and novel, indicated by its low sequence homology compared to those of other AFPs. We explore the structure-function relationship of G. antarctica AFP using various approaches ranging from protein structure prediction, peptide design and antifreeze activity assays, nuclear magnetic resonance (NMR) studies and molecular dynamics simulation. The predicted secondary structure of G. antarctica AFP shows several α-helices, assumed to be responsible for its antifreeze activity. We designed several peptide fragments derived from the amino acid sequences of α-helical regions of the parent AFP and they also showed substantial antifreeze activities, below that of the original AFP. The relationship between peptide structure and activity was explored by NMR spectroscopy and molecular dynamics simulation. NMR results show that the antifreeze activity of the peptides correlates with their helicity and geometrical straightforwardness. Furthermore, molecular dynamics simulation also suggests that the activity of the designed peptides can be explained in terms of the structural rigidity/flexibility, i.e., the most active peptide demonstrates higher structural stability, lower flexibility than that of the other peptides with lower activities, and of lower rigidity. This report represents the first detailed report of downsizing a yeast AFP into its peptide fragments with measurable antifreeze activities.
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Affiliation(s)
- Syed Hussinien H. Shah
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
| | - Rajiv K. Kar
- Department of Biophysics, Bose Institute, Kolkata, West Bengal, India
| | - Azren A. Asmawi
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
| | | | | | - Nor M. Mahadi
- Malaysia Genome Institute, UKM Bangi, Selangor, Malaysia
| | - Mahiran Basri
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
| | - Raja Noor Zaliha A. Rahman
- Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
| | - Abu B. Salleh
- Malaysia Genome Institute, UKM Bangi, Selangor, Malaysia
| | | | - Bimo A. Tejo
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute, Kolkata, West Bengal, India
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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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