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Muraoka M. Measurement of Ice-Binding Protein Inhibition of Non-ice Crystal Growth. Methods Mol Biol 2024; 2730:155-167. [PMID: 37943457 DOI: 10.1007/978-1-0716-3503-2_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
The kinetic hydrate inhibitor (KHI) was developed to prevent the formation of undesirable gas hydrate crystals in natural gas pipelines. Studies of antifreeze proteins (AFPs) are gaining attention in the natural gas research field due to their performance in crystal growth inhibition, excellent biodegradation, and low toxicity. Studies of AFPs may provide clues for developing future commercial KHIs used offshore. This chapter presents a simple method of evaluating AFP inhibitory performance as a KHI on tetrahydrofuran (THF) hydrate growth with a unidirectional growth apparatus.
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Affiliation(s)
- Michihiro Muraoka
- Energy Process Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan.
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2
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Melnik BS, Glukhova KA, Sokolova (Voronova) EA, Balalaeva IV, Garbuzynskiy SO, Finkelstein AV. Physics of Ice Nucleation and Antinucleation: Action of Ice-Binding Proteins. Biomolecules 2023; 14:54. [PMID: 38254654 PMCID: PMC10813080 DOI: 10.3390/biom14010054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/09/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
Ice-binding proteins are crucial for the adaptation of various organisms to low temperatures. Some of these, called antifreeze proteins, are usually thought to inhibit growth and/or recrystallization of ice crystals. However, prior to these events, ice must somehow appear in the organism, either coming from outside or forming inside it through the nucleation process. Unlike most other works, our paper is focused on ice nucleation and not on the behavior of the already-nucleated ice, its growth, etc. The nucleation kinetics is studied both theoretically and experimentally. In the theoretical section, special attention is paid to surfaces that bind ice stronger than water and thus can be "ice nucleators", potent or relatively weak; but without them, ice cannot be nucleated in any way in calm water at temperatures above -30 °C. For experimental studies, we used: (i) the ice-binding protein mIBP83, which is a previously constructed mutant of a spruce budworm Choristoneura fumiferana antifreeze protein, and (ii) a hyperactive ice-binding antifreeze protein, RmAFP1, from a longhorn beetle Rhagium mordax. We have shown that RmAFP1 (but not mIBP83) definitely decreased the ice nucleation temperature of water in test tubes (where ice originates at much higher temperatures than in bulk water and thus the process is affected by some ice-nucleating surfaces) and, most importantly, that both of the studied ice-binding proteins significantly decreased the ice nucleation temperature that had been significantly raised in the presence of potent ice nucleators (CuO powder and ice-nucleating bacteria Pseudomonas syringae). Additional experiments on human cells have shown that mIBP83 is concentrated in some cell regions of the cooled cells. Thus, the ice-binding protein interacts not only with ice, but also with other sites that act or potentially may act as ice nucleators. Such ice-preventing interaction may be the crucial biological task of ice-binding proteins.
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Affiliation(s)
- Bogdan S. Melnik
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (K.A.G.); (S.O.G.)
| | - Ksenia A. Glukhova
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (K.A.G.); (S.O.G.)
| | - Evgeniya A. Sokolova (Voronova)
- Institute of Biology and Biomedicine, Lobachevsky State University of Nizhny Novgorod, 603022 Nizhny Novgorod, Russia (I.V.B.)
| | - Irina V. Balalaeva
- Institute of Biology and Biomedicine, Lobachevsky State University of Nizhny Novgorod, 603022 Nizhny Novgorod, Russia (I.V.B.)
| | - Sergiy O. Garbuzynskiy
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (K.A.G.); (S.O.G.)
| | - Alexei V. Finkelstein
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (K.A.G.); (S.O.G.)
- Faculty of Biotechnology, Lomonosov Moscow State University, 142290 Pushchino, Russia
- Faculty of Biology, Lomonosov Moscow State University, 119192 Moscow, Russia
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3
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Masuda Y, Kheawkanha T, Nagahama A, Kawasaki K, Konno T, Yamanaka K, Tatemoto H. Antifreeze protein type III addition to freezing extender comprehensively improves post-thaw sperm properties in Okinawan native Agu pig. Anim Reprod Sci 2023; 252:107232. [PMID: 37075564 DOI: 10.1016/j.anireprosci.2023.107232] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/28/2023] [Accepted: 04/12/2023] [Indexed: 04/21/2023]
Abstract
Sperm cryopreservation often leads to physical cell damage through ice crystal formation. This study evaluates the improvements to freezing extender cryoprotective activity due to antifreeze protein (AFP) addition, which primarily acts on ice crystal formation, through investigating the post-thaw sperm properties of Okinawan native Agu pig. Six individual boar sperm samples were diluted with the freezing extender supplemented with 1 μg/mL of AFP I or AFP III and then subjected to cryopreservation. Treatment with AFP I during the freezing procedure had no improvement for any characteristics after thawing compared to untreated sperm. In contrast, the addition of AFP III to the freezing extender strongly increased sperm motility, mitochondria and cell membrane integrity, and the acrosomal proteolytic activity of frozen-thawed sperm in 5 of 6 individuals (P < 0.05). Furthermore, cryoinjury prevention by AFP III significantly enhanced sperm viability (by ATP content), and maintained DNA quality and in vitro sperm penetrability compared with AFP I treatment (P < 0.05). These findings demonstrate that AFP III addition to the freezing extender of boar sperm is more effective in maintaining sperm characteristics than the extender without AFP III or AFP I, despite individual differences in response.
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Affiliation(s)
- Yusuke Masuda
- Faculty of Agriculture, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan
| | - Theerapat Kheawkanha
- Faculty of Agriculture, Khon Kaen University, Muang Khon Kaen District, Khon Kaen 40002, Thailand
| | - Ayari Nagahama
- Faculty of Agriculture, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan
| | - Kokoro Kawasaki
- Faculty of Agriculture, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan
| | - Toshihiro Konno
- Faculty of Agriculture, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan
| | - Kenichi Yamanaka
- Faculty of Agriculture, Saga University, Saga city, Saga 840-8502, Japan
| | - Hideki Tatemoto
- Faculty of Agriculture, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan.
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4
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Midya US, Bandyopadhyay S. Elucidating the Sluggish Water Dynamics at the Ice-Binding Surface of the Hyperactive Tenebrio molitor Antifreeze Protein. J Phys Chem B 2023; 127:121-132. [PMID: 36594578 DOI: 10.1021/acs.jpcb.2c06478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Quasi-ice-like hydration waters on the ice-binding surface (IBS) of an antifreeze protein (AFP) commonly exhibit sluggish dynamics especially at low temperatures. In this work, we have analyzed molecular dynamics (MD) simulation trajectories at two different temperatures for Tenebrio molitor antifreeze protein (TmAFP) to explore whether the unique quasi-ice-like structuring of hydration water has any impact on making their dynamics slower on the IBS of the protein. Our calculation reveals that, as translational dynamics is coupled with the conformational fluctuations, hydration water on the IBS exhibits sluggish translational motion due to reduced flexibility of the IBS compared to that on the non-ice-binding surface (NIBS) of the protein. Interestingly, it is noticed that rotational motion of hydration water is not coupled with the conformational fluctuations of the surfaces. In that case, structural relaxations of the protein-water (PW) and water-water (WW) hydrogen bonds compete with each other to make the rotational dynamics of hydration water around the IBS either faster or slower with respect to those around the NIBS. At low temperature, the slower structural relaxation of water-water hydrogen bonds dominates and imparts sluggish rotational motion of the hydration water on the IBS of the protein. The slower structural relaxation of water-water hydrogen bonds and hence the retarded rotational dynamics, despite the weak short-lived PW hydrogen bonds on the IBS, is clearly a manifestation of the rigid quasi-ice-like structure of the hydration shell on that surface.
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Affiliation(s)
- Uday Sankar Midya
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
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5
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Monteiro MM, de Mello Seal DC, de Souza JH, Trevisan M, Arruda LCP, Silva SV, Guerra MMP. Effect of antifreeze protein type III on frozen/thawed of spermatozoa recover from goat epididymis. Res Vet Sci 2023; 154:108-112. [PMID: 36571888 DOI: 10.1016/j.rvsc.2022.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/31/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022]
Abstract
The objective of this study was to evaluate the effect of antifreeze protein type III (AFP III) on the freezing of epididymal spermatozoa of goats. A total of 16 pairs of testicles were collected in a slaughterhouse and transported at approximately 5 °C in a thermal box. Epididymal spermatozoa were recovered by retrograde lavage and evaluated using a phase contrast microscope. Then, they were cryopreserved in extender based on Tris-egg yolk, supplemented with AFP III (0, 1, 10, 100 μg/mL), using an automated system. After thawing (37 °C/30 s), the spermatozoa kinetics were evaluated using the CASA automated system; and plasma and acrosome membrane integrity, mitochondrial membrane potential, and intracellular ROS production, by flow cytometry. There was no difference (P ≥ 0.05) between the experimental groups for the parameters of spermatozoa kinetics, mitochondrial membrane potential, and ROS production. However, the integrity of plasma and acrosome membranes of frozen spermatozoa with 100 μg/mL of AFP III was lower (P < 0.05) than the control group. It was concluded that the addition of AFP III to the Tris-egg yolk extender, used in the freezing of sperm obtained from the epididymis of goats, did not improve the preservation of these cells.
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Affiliation(s)
- Millena Maria Monteiro
- Laboratory of Andrology, Department of Veterinary Medicine, University Federal Rural of Pernambuco (UFRPE), Recife, Pernambuco, Brazil.
| | - Desirée Coelho de Mello Seal
- Laboratory of Andrology, Department of Veterinary Medicine, University Federal Rural of Pernambuco (UFRPE), Recife, Pernambuco, Brazil
| | - Jerônimo Hugo de Souza
- Laboratory of Andrology, Department of Veterinary Medicine, University Federal Rural of Pernambuco (UFRPE), Recife, Pernambuco, Brazil
| | - Mariana Trevisan
- Laboratory of Andrology, Department of Veterinary Medicine, University Federal Rural of Pernambuco (UFRPE), Recife, Pernambuco, Brazil
| | - Lúcia Cristina Pereira Arruda
- Laboratory of Andrology, Department of Veterinary Medicine, University Federal Rural of Pernambuco (UFRPE), Recife, Pernambuco, Brazil
| | - Sildivane Valcácia Silva
- Department of Biotechnology, Biotechnology Center, University Federal of Paraíba (UFPB), João Pessoa, Paraíba, Brazil
| | - Maria Madalena Pessoa Guerra
- Laboratory of Andrology, Department of Veterinary Medicine, University Federal Rural of Pernambuco (UFRPE), Recife, Pernambuco, Brazil
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6
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Guo HB, Perminov A, Bekele S, Kedziora G, Farajollahi S, Varaljay V, Hinkle K, Molinero V, Meister K, Hung C, Dennis P, Kelley-Loughnane N, Berry R. AlphaFold2 models indicate that protein sequence determines both structure and dynamics. Sci Rep 2022; 12:10696. [PMID: 35739160 PMCID: PMC9226352 DOI: 10.1038/s41598-022-14382-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 06/06/2022] [Indexed: 12/29/2022] Open
Abstract
AlphaFold 2 (AF2) has placed Molecular Biology in a new era where we can visualize, analyze and interpret the structures and functions of all proteins solely from their primary sequences. We performed AF2 structure predictions for various protein systems, including globular proteins, a multi-domain protein, an intrinsically disordered protein (IDP), a randomized protein, two larger proteins (> 1000 AA), a heterodimer and a homodimer protein complex. Our results show that along with the three dimensional (3D) structures, AF2 also decodes protein sequences into residue flexibilities via both the predicted local distance difference test (pLDDT) scores of the models, and the predicted aligned error (PAE) maps. We show that PAE maps from AF2 are correlated with the distance variation (DV) matrices from molecular dynamics (MD) simulations, which reveals that the PAE maps can predict the dynamical nature of protein residues. Here, we introduce the AF2-scores, which are simply derived from pLDDT scores and are in the range of [0, 1]. We found that for most protein models, including large proteins and protein complexes, the AF2-scores are highly correlated with the root mean square fluctuations (RMSF) calculated from MD simulations. However, for an IDP and a randomized protein, the AF2-scores do not correlate with the RMSF from MD, especially for the IDP. Our results indicate that the protein structures predicted by AF2 also convey information of the residue flexibility, i.e., protein dynamics.
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Affiliation(s)
- Hao-Bo Guo
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, 45433, OH, USA
- UES Inc., Dayton, OH, USA
| | - Alexander Perminov
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, 45433, OH, USA
- Computer Science Department, Miami University, Oxford, OH, USA
| | - Selemon Bekele
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, 45433, OH, USA
- UES Inc., Dayton, OH, USA
| | - Gary Kedziora
- General Dynamics Information Technology, Inc., Wright-Patterson Air Force Base, 45433, OH, USA
| | - Sanaz Farajollahi
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, 45433, OH, USA
- UES Inc., Dayton, OH, USA
| | - Vanessa Varaljay
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, 45433, OH, USA
| | - Kevin Hinkle
- Department of Chemical and Materials Engineering, Dayton University, Dayton, OH, USA
| | - Valeria Molinero
- Department of Chemistry, The University of Utah, Salt Lake City, UT, USA
| | - Konrad Meister
- Department of Natural Sciences, University of Alaska Southeast, Juneau, AK, USA
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Chia Hung
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, 45433, OH, USA
| | - Patrick Dennis
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, 45433, OH, USA
| | - Nancy Kelley-Loughnane
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, 45433, OH, USA.
| | - Rajiv Berry
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, 45433, OH, USA.
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7
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Ghalamara S, Silva S, Brazinha C, Pintado M. Structural diversity of marine anti-freezing proteins, properties and potential applications: a review. BIORESOUR BIOPROCESS 2022; 9:5. [PMID: 38647561 PMCID: PMC10992025 DOI: 10.1186/s40643-022-00494-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/08/2022] [Indexed: 11/10/2022] Open
Abstract
Cold-adapted organisms, such as fishes, insects, plants and bacteria produce a group of proteins known as antifreeze proteins (AFPs). The specific functions of AFPs, including thermal hysteresis (TH), ice recrystallization inhibition (IRI), dynamic ice shaping (DIS) and interaction with membranes, attracted significant interest for their incorporation into commercial products. AFPs represent their effects by lowering the water freezing point as well as preventing the growth of ice crystals and recrystallization during frozen storage. The potential of AFPs to modify ice growth results in ice crystal stabilizing over a defined temperature range and inhibiting ice recrystallization, which could minimize drip loss during thawing, improve the quality and increase the shelf-life of frozen products. Most cryopreservation studies using marine-derived AFPs have shown that the addition of AFPs can increase post-thaw viability. Nevertheless, the reduced availability of bulk proteins and the need of biotechnological techniques for industrial production, limit the possible usage in foods. Despite all these drawbacks, relatively small concentrations are enough to show activity, which suggests AFPs as potential food additives in the future. The present work aims to review the results of numerous investigations on marine-derived AFPs and discuss their structure, function, physicochemical properties, purification and potential applications.
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Affiliation(s)
- Soudabeh Ghalamara
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal
| | - Sara Silva
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal
| | - Carla Brazinha
- LAQV/Requimte, Faculdade de Ciências E Tecnologia, Universidade Nova de Lisboa, Campus de Caparica, 2829-516, Caparica, Portugal
| | - Manuela Pintado
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal.
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8
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Baskaran A, Kaari M, Venugopal G, Manikkam R, Joseph J, Bhaskar PV. Anti freeze proteins (Afp): Properties, sources and applications - A review. Int J Biol Macromol 2021; 189:292-305. [PMID: 34419548 DOI: 10.1016/j.ijbiomac.2021.08.105] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 11/17/2022]
Abstract
Extreme cold marine and freshwater temperatures (below 4 °C) induce massive deterioration to the cell membranes of organisms resulting in the formation of ice crystals, consequently causing organelle damage or cell death. One of the adaptive mechanisms organisms have evolved to thrive in cold environments is the production of antifreeze proteins with the functional capabilities to withstand frigid temperatures. Antifreeze proteins are extensively identified in different cold-tolerant species and they facilitate the persistence of cold-adapted organisms by decreasing the freezing point of their body fluids. Various structurally diverse types of antifreeze proteins detected possess the ability to modify ice crystal growth by thermal hysteresis and ice recrystallization inhibition. The unique properties of antifreeze proteins have made them a promising resource in industry, biomedicine, food storage and cryobiology. This review collates the findings of the various studies carried out in the past and the recent developments observed in the properties, functional mechanisms, classification, distinct sources and the ever-increasing applications of antifreeze proteins. This review also summarizes the possibilities of the way forward to identify new avenues of research on anti-freeze proteins.
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Affiliation(s)
- Abirami Baskaran
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600 119, Tamil Nadu, India
| | - Manigundan Kaari
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600 119, Tamil Nadu, India
| | - Gopikrishnan Venugopal
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600 119, Tamil Nadu, India
| | - Radhakrishnan Manikkam
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600 119, Tamil Nadu, India.
| | - Jerrine Joseph
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600 119, Tamil Nadu, India
| | - Parli V Bhaskar
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Vasco-da-Gama 403804, Goa, India
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9
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Biswas A, Barone V, Daidone I. High Water Density at Non-Ice-Binding Surfaces Contributes to the Hyperactivity of Antifreeze Proteins. J Phys Chem Lett 2021; 12:8777-8783. [PMID: 34491750 PMCID: PMC8450935 DOI: 10.1021/acs.jpclett.1c01855] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/16/2021] [Indexed: 05/30/2023]
Abstract
Antifreeze proteins (AFPs) can bind to ice nuclei thereby inhibiting their growth and their hydration shell is believed to play a fundamental role. Here, we use molecular dynamics simulations to characterize the hydration shell of four moderately-active and four hyperactive AFPs. The local water density around the ice-binding-surface (IBS) is found to be lower than that around the non-ice-binding surface (NIBS) and this difference correlates with the higher hydrophobicity of the former. While the water-density increase (with respect to bulk) around the IBS is similar between moderately-active and hyperactive AFPs, it differs around the NIBS, being higher for the hyperactive AFPs. We hypothesize that while the lower water density at the IBS can pave the way to protein binding to ice nuclei, irrespective of the antifreeze activity, the higher density at the NIBS of the hyperactive AFPs contribute to their enhanced ability in inhibiting ice growth around the bound AFPs.
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Affiliation(s)
- Akash
Deep Biswas
- Scuola
Normale Superiore di Pisa, Piazza dei Cavalieri 7, Pisa 56126, Italy
- Department
of Physical and Chemical Sciences, University
of L’Aquila, via
Vetoio (Coppito 1), 67010 L’Aquila, Italy
| | - Vincenzo Barone
- Scuola
Normale Superiore di Pisa, Piazza dei Cavalieri 7, Pisa 56126, Italy
- National
Institute for Nuclear Physics (INFN) Pisa Section, Largo Bruno Pontecorvo 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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10
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Mehdipour M, Daghigh-Kia H, Najafi A, Martínez-Pastor F. Type III antifreeze protein (AFP) improves the post-thaw quality and in vivo fertility of rooster spermatozoa. Poult Sci 2021; 100:101291. [PMID: 34217904 PMCID: PMC8260870 DOI: 10.1016/j.psj.2021.101291] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 05/18/2021] [Accepted: 05/21/2021] [Indexed: 01/08/2023] Open
Abstract
Antifreeze proteins (AFP) have the potential for improving sperm cryopreservation. We have applied Type III antifreeze protein (AFP3) on the cryopreservation of spermatozoa from broiler breeder roosters, aiming to enhance post-thawing quality and fertility. Semen was extended at 37°C in Lake's extender containing AFP3 at 0.01, 0.1, 1, 5, and 10 µg/mL (no AFP3 as control). Post-thawing sperm assessment included sperm motility (CASA), morphology, membrane functionality by hypoosmotic swelling test (HOST), lipoperoxidation as malondialdehyde (MDA) production, and sperm viability, early apoptosis (phosphatidylserine exposure as annexin V-positive staining in viable spermatozoa), and mitochondrial activity by flow cytometry. Fertility was assessed after artificial insemination (30 hens/treatment). Total and progressive motility, membrane functionality, and mitochondrial activity increased in 0.1 and 1 µg/mL AFP, compared to control and other concentrations, whereas apoptosis was significantly lower. VAP, VSL, and viability were significantly higher for 1 µg/mL AFP3 than with the other treatments except for 0.1 µg/mL (which was not always significantly different from the control or other concentrations), and with abnormal forms being significantly lower. The proportion of fertilized and hatched eggs was also higher for 1 µg/mL AFP3, with 0.1 µg/mL also showing significantly higher results than the control, and no differences with other concentrations). In conclusion, 1 µg/mL AFP3 could improve the post-thawing results of rooster spermatozoa frozen in Lake's extender. According to our results, concentrations between 1 and 0.1 µg/mL could be similarly efficient.
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Affiliation(s)
- Mahdieh Mehdipour
- Department of Animal Science, College of Agriculture, University of Tabriz, Tabriz, Iran
| | - Hossein Daghigh-Kia
- Department of Animal Science, College of Agriculture, University of Tabriz, Tabriz, Iran.
| | - Abouzar Najafi
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran
| | - Felipe Martínez-Pastor
- Institute of Animal Health and Cattle Development (INDEGSAL) and Department of Molecular Biology (Cell Biology), University of León, León 24071, Spain
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11
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Pal P, Chakraborty S, Jana B. Differential Hydration of Ice‐Binding Surface of Globular and Hyperactive Antifreeze Proteins. ADVANCED THEORY AND SIMULATIONS 2021. [DOI: 10.1002/adts.202100090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Prasun Pal
- School of Chemical Sciences Indian Association for the Cultivation of Science, Jadavpur Kolkata 700032 India
| | | | - Biman Jana
- School of Chemical Sciences Indian Association for the Cultivation of Science, Jadavpur Kolkata 700032 India
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12
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Gruneberg AK, Graham LA, Eves R, Agrawal P, Oleschuk RD, Davies PL. Ice recrystallization inhibition activity varies with ice-binding protein type and does not correlate with thermal hysteresis. Cryobiology 2021; 99:28-39. [PMID: 33529683 DOI: 10.1016/j.cryobiol.2021.01.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 01/07/2021] [Accepted: 01/23/2021] [Indexed: 01/06/2023]
Abstract
Ice-binding proteins (IBPs) inhibit the growth of ice through surface adsorption. In some freeze-resistant fishes and insects, circulating IBPs serve as antifreeze proteins to stop ice growth by lowering the freezing point. Plants are less able to avoid freezing and some use IBPs to minimize the damage caused in the frozen state by ice recrystallization, which is the growth of large ice grains at the expense of small ones. Here we have accurately and reproducibly measured the ice recrystallization inhibition (IRI) activity of over a dozen naturally occurring IBPs from fishes, insects, plants, and microorganisms using a modified 'splat' method on serial dilutions of IBPs whose concentrations were determined by amino acid analysis. The endpoint of IRI, which was scored as the lowest protein concentration at which no recrystallization was observed, varied for the different IBPs over two orders of magnitude from 1000 nM to 5 nM. Moreover, there was no apparent correlation between their IRI levels and reported antifreeze activities. IBPs from insects and fishes had similar IRI activity, even though the insect IBPs are typically 10x more active in freezing point depression. Plant IBPs had weak antifreeze activity but were more effective at IRI. Bacterial IBPs involved in ice adhesion showed both strong freezing point depression and IRI. Two trends did emerge, including that basal plane binding IBPs correlated with stronger IRI activity and larger IBPs had higher IRI activity.
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Affiliation(s)
- Audrey K Gruneberg
- Department of Biomedical and Molecular Sciences, Queen's University. 18 Stuart Street, Kingston, Ontario, K7L3N6, Canada
| | - Laurie A Graham
- Department of Biomedical and Molecular Sciences, Queen's University. 18 Stuart Street, Kingston, Ontario, K7L3N6, Canada
| | - Robert Eves
- Department of Biomedical and Molecular Sciences, Queen's University. 18 Stuart Street, Kingston, Ontario, K7L3N6, Canada
| | - Prashant Agrawal
- Department of Chemistry, Queen's University. 90 Bader Lane, Kingston, Ontario, K7L2S8, Canada
| | - Richard D Oleschuk
- Department of Chemistry, Queen's University. 90 Bader Lane, Kingston, Ontario, K7L2S8, Canada
| | - Peter L Davies
- Department of Biomedical and Molecular Sciences, Queen's University. 18 Stuart Street, Kingston, Ontario, K7L3N6, Canada.
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13
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Choi SR, Lee J, Seo YJ, Kong HS, Kim M, Jin E, Lee JR, Lee JH. Molecular basis of ice-binding and cryopreservation activities of type III antifreeze proteins. Comput Struct Biotechnol J 2021; 19:897-909. [PMID: 33598104 PMCID: PMC7851773 DOI: 10.1016/j.csbj.2021.01.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 01/13/2021] [Accepted: 01/14/2021] [Indexed: 01/08/2023] Open
Abstract
The QAE2ACT and SP ACT mutants showed full TH and IRI activities. Active AFPs effectively preserved intact follicle and prevented DSB damage. Active AFPs exhibited unique structural feature in the first 310 helix of the IBS. Unique structure of the IBS determines TH, IRI, and cryopreservation activities.
Antifreeze proteins (AFPs) can inhibit the freezing of body fluid at subzero temperatures to promote the survival of various organisms living in polar regions. Type III AFPs are categorized into three subgroups, QAE1, QAE2, and SP isoforms, based on differences in their isoelectric points. We determined the thermal hysteresis (TH), ice recrystallization inhibition (IRI), and cryopreservation activity of three isoforms of the notched-fin eelpout AFP and their mutant constructs and characterized their structural and dynamic features using NMR. The QAE1 isoform is the most active among the three classes of III AFP isoforms, and the mutants of inactive QAE2 and SP isoforms, QAE2ACT and SPACT, displayed the full TH and IRI activities with resepect to QAE1 isoform. Cryopreservation studies using mouse ovarian tissue revealed that the QAE1 isoform and the active mutants, QAE2ACT and SPACT, more effectively preserved intact follicle morphology and prevented DNA double-strand break damage more efficiently than the inactive isoforms. It was also found that all active AFPs, QAE1, QAE2ACT, and SPACT, formed unique H-bonds with the first 310 helix, an interaction that plays an important role in the formation of anchored clathrate water networks for efficient binding to the primary prism and pyramidal planes of ice crystals, which was disrupted in the inactive isoforms. Our studies provide valuable insights into the molecular mechanism of the TH and IRI activity, as well as the cryopreservation efficiency, of type III AFPs.
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Key Words
- AFP, Antifreeze protein
- Antifreeze protein
- CPA, cryoprotective agent
- Cryopreservation
- D-PBS, Dulbecco’s phosphate-buffered saline
- DMSO, dimethyl sulfoxide
- DSB, double-strand break
- EG, ethylene glycol
- H-bond, hydrogen bond
- IBP, ice-binding protein
- IBS, ice-binding surface
- IRI, ice recrystallization inhibition
- Ice crystallization inhibition
- NMR
- OT, ovarian tissue
- QAE, quaternary-amino-ethyl
- RT, room temperature
- SP, sulfopropyl
- TH, thermal hysteresis
- TUNEL, terminal deoxynucleotidyl transferase dUTP nick end labelling
- Thermal hysteresis
- nfeAFP, notched-fin eelpout AFP
- wt, wild-type
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Affiliation(s)
- Seo-Ree Choi
- Department of Chemistry and Research Institute of Natural Science, Gyeongsang National University, Gyeongnam 52828, Republic of Korea
| | - Jaewang Lee
- Department of Obstetrics and Gynecology, Seoul National University Bundang Hospital, Gyeonggi 13620, Republic of Korea.,Department of Biomedical Laboratory Science, Eulji University, Gyeonggi 13135, Republic of Korea
| | - Yeo-Jin Seo
- Department of Chemistry and Research Institute of Natural Science, Gyeongsang National University, Gyeongnam 52828, Republic of Korea
| | - Hyun Sun Kong
- Department of Obstetrics and Gynecology, Seoul National University Bundang Hospital, Gyeonggi 13620, Republic of Korea
| | - Minjae Kim
- Department of Life Science, Hanyang University, Seoul 04763, Republic of Korea
| | - EonSeon Jin
- Department of Life Science, Hanyang University, Seoul 04763, Republic of Korea
| | - Jung Ryeol Lee
- Department of Obstetrics and Gynecology, Seoul National University Bundang Hospital, Gyeonggi 13620, Republic of Korea.,Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Joon-Hwa Lee
- Department of Chemistry and Research Institute of Natural Science, Gyeongsang National University, Gyeongnam 52828, Republic of Korea
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14
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Hobbs RS, Hall JR, Graham LA, Davies PL, Fletcher GL. Antifreeze protein dispersion in eelpouts and related fishes reveals migration and climate alteration within the last 20 Ma. PLoS One 2020; 15:e0243273. [PMID: 33320906 PMCID: PMC7737890 DOI: 10.1371/journal.pone.0243273] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 11/18/2020] [Indexed: 12/31/2022] Open
Abstract
Antifreeze proteins inhibit ice growth and are crucial for the survival of supercooled fish living in icy seawater. Of the four antifreeze protein types found in fishes, the globular type III from eelpouts is the one restricted to a single infraorder (Zoarcales), which is the only clade know to have antifreeze protein-producing species at both poles. Our analysis of over 60 unique antifreeze protein gene sequences from several Zoarcales species indicates this gene family arose around 18 Ma ago, in the Northern Hemisphere, supporting recent data suggesting that the Arctic Seas were ice-laden earlier than originally thought. The Antarctic was subject to widespread glaciation over 30 Ma and the Notothenioid fishes that produce an unrelated antifreeze glycoprotein extensively exploited the adjoining seas. We show that species from one Zoarcales family only encroached on this niche in the last few Ma, entering an environment already dominated by ice-resistant fishes, long after the onset of glaciation. As eelpouts are one of the dominant benthic fish groups of the deep ocean, they likely migrated from the north to Antarctica via the cold depths, losing all but the fully active isoform gene along the way. In contrast, northern species have retained both the fully active (QAE) and partially active (SP) isoforms for at least 15 Ma, which suggests that the combination of isoforms is functionally advantageous.
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Affiliation(s)
- Rod S. Hobbs
- Department of Ocean Sciences, Memorial University of Newfoundland, St John’s, Newfoundland, Canada
| | - Jennifer R. Hall
- Aquatic Research Cluster, CREAIT Network, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Laurie A. Graham
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
- * E-mail:
| | - Peter L. Davies
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
| | - Garth L. Fletcher
- Department of Ocean Sciences, Memorial University of Newfoundland, St John’s, Newfoundland, Canada
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15
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Kozuch DJ, Stillinger FH, Debenedetti PG. Genetic Algorithm Approach for the Optimization of Protein Antifreeze Activity Using Molecular Simulations. J Chem Theory Comput 2020; 16:7866-7873. [PMID: 33201707 DOI: 10.1021/acs.jctc.0c00773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Antifreeze proteins (AFPs) are of much interest for their ability to inhibit ice growth at low concentrations. In this work, we present a genetic algorithm for the in silico design of AFP mutants with improved antifreeze activity, measured as the predicted thermal hysteresis at a fixed concentration, ΔTC. Central to the algorithm is our recently developed neural network method for predicting ΔTC from molecular simulations [Kozuch et al., PNAS, 115, 13252 (2018)]. Applying the algorithm to three structurally diverse AFPs, wfAFP, rQAE, and RiAFP, we find that significantly improved mutants are discovered for rQAE and RiAFP. Testing of the optimized mutants shows an increase in ΔTC of 0.572 ± 0.11 K (262 ± 50.6%) and 1.33 ± 0.14 K (39.9 ± 4.19%) over the native structures for rQAE and RiAFP, respectively. Structural analysis of the optimized mutants reveals that the algorithm is able to exploit two pathways for enhancing the predicted antifreeze activity of the mutants: (1) increasing the local order of surface waters by encouraging the formation of internal water channels in the protein and (2) increasing the total ice-binding area by improving the planar structure of the ice-binding surface. Additionally, analysis of all mutants explored by the algorithm reveals that a subset of residues, mainly nonpolar, are particularly helpful in improving antifreeze activity at the ice-binding surface.
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Affiliation(s)
- Daniel J Kozuch
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Frank H Stillinger
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Pablo G Debenedetti
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
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16
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Jang H, Kwon HJ, Sun WS, Hwang S, Hwang IS, Kim S, Lee JH, Lee SG, Lee JW. Effects of Leucosporidium-derived ice-binding protein (LeIBP) on bull semen cryopreservation. Vet Med Sci 2020; 6:447-453. [PMID: 32323490 PMCID: PMC7397894 DOI: 10.1002/vms3.269] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 03/11/2020] [Accepted: 03/23/2020] [Indexed: 12/02/2022] Open
Abstract
We examined the effect of ice‐binding protein derived from Leucosporidium (LeIBP) on the cryopreservation of bull semen and compared it with that derived from previously reported Antifreeze Protein III (AFPIII). Six concentrations of LeIBP (10–1 ~ 104 μg/ml) and AFPIII (10–1 ~ 104 μg/ml) were added to the bull semen extender, respectively. Sperm kinematic parameters were measured to examine sperm toxicity and cryopreserved sperm quality. Measures of antioxidant activity such as superoxide dismutase (SOD), reduced glutathione/oxidative glutathione (GSH/GSSG), and total antioxidant capacity (TAC) were analysed to identify the effect of LeIBP on sperm quality. In addition, sperm viability was analysed using a flow cytometer and fluorescence microscope by SYBR14/PI staining. The results showed that the LeIBP groups (0.1, 1 and 10 μg/ml) were less toxic, and the quality of the sperm were dramatically improved in the extenders containing 0.1 μg/ml LeIBP among concentrations of LeIBP and AFPIII. The SOD activity of LeIBP was greater than that of AFPIII and control. In addition, sperm viability was enhanced in the LeIBP‐treated group. In summary, LeIBP is a useful cryoprotective adjuvant for bull sperm cryopreservation, and the most efficient concentration of LeIBP is 0.1 μg/ml.
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Affiliation(s)
- Hoon Jang
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Hyo J Kwon
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Wu S Sun
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Seongsoo Hwang
- Animal Biotechnology Division, National Institute of Animal Science, Wanju, Korea
| | - In S Hwang
- Animal Biotechnology Division, National Institute of Animal Science, Wanju, Korea
| | - Sungwoo Kim
- Animal Genetic Resources Station, National Institute of Animal Science, Namwon, Korea
| | - Jun H Lee
- Department of Polar Bioconvergence Research, Division of life Science, Korea Polar Research Institute, Incheon, Korea
| | - Sung G Lee
- Department of Polar Bioconvergence Research, Division of life Science, Korea Polar Research Institute, Incheon, Korea
| | - Jeong W Lee
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
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17
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Kumari S, Muthachikavil AV, Tiwari JK, Punnathanam SN. Computational Study of Differences between Antifreeze Activity of Type-III Antifreeze Protein from Ocean Pout and Its Mutant. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:2439-2448. [PMID: 32069407 DOI: 10.1021/acs.langmuir.0c00065] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The antifreeze activity of a type-III antifreeze protein (AFP) expressed in ocean pout (Zoarces americanus) is compared with that of a specific mutant (T18N) using all-atom molecular dynamics simulations. The antifreeze activity of the mutant is only 10% of the wild-type AFP. The results from this simulation study revealed the following insights into the mechanism of antifreeze action by type-III AFPs. The AFP gets adsorbed to the advancing ice front due to its hydrophobic nature. A part of the hydrophobicity is caused by the presence of clathrate structure of water molecules near the ice-binding surface (IBS). The mutation in the AFP disrupts this structure and thereby reduces the ability of the mutant to adsorb to the ice-water interface leading to the loss of antifreeze activity. The mutation, however, has no effect on the ability of the adsorbed protein to bind to the growing ice phase. Simulations also revealed that all surfaces of the protein can bind to the ice phase, although the IBS is the preferred surface.
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Affiliation(s)
- Surbhi Kumari
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru 560012, India
| | - Aswin V Muthachikavil
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru 560012, India
| | - Jyoti Kumar Tiwari
- Hindustan Unilever R&D, 64 Whitefield Main Road, Bengaluru 560066, India
| | - Sudeep N Punnathanam
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru 560012, India
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18
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Surís-Valls R, Voets IK. Peptidic Antifreeze Materials: Prospects and Challenges. Int J Mol Sci 2019; 20:E5149. [PMID: 31627404 PMCID: PMC6834126 DOI: 10.3390/ijms20205149] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 10/05/2019] [Accepted: 10/10/2019] [Indexed: 12/28/2022] Open
Abstract
Necessitated by the subzero temperatures and seasonal exposure to ice, various organisms have developed a remarkably effective means to survive the harsh climate of their natural habitats. Their ice-binding (glyco)proteins keep the nucleation and growth of ice crystals in check by recognizing and binding to specific ice crystal faces, which arrests further ice growth and inhibits ice recrystallization (IRI). Inspired by the success of this adaptive strategy, various approaches have been proposed over the past decades to engineer materials that harness these cryoprotective features. In this review we discuss the prospects and challenges associated with these advances focusing in particular on peptidic antifreeze materials both identical and akin to natural ice-binding proteins (IBPs). We address the latest advances in their design, synthesis, characterization and application in preservation of biologics and foods. Particular attention is devoted to insights in structure-activity relations culminating in the synthesis of de novo peptide analogues. These are sequences that resemble but are not identical to naturally occurring IBPs. We also draw attention to impactful developments in solid-phase peptide synthesis and 'greener' synthesis routes, which may aid to overcome one of the major bottlenecks in the translation of this technology: unavailability of large quantities of low-cost antifreeze materials with excellent IRI activity at (sub)micromolar concentrations.
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Affiliation(s)
- Romà Surís-Valls
- Laboratory of Self-Organizing Soft Matter, Laboratory of Macro-Organic Chemistry, Department of Chemical Engineering and Chemistry & Institute for Complex Molecular Systems, Eindhoven University of Technology, Post Office Box 513, 5600 MD Eindhoven, The Netherlands.
| | - Ilja K Voets
- Laboratory of Self-Organizing Soft Matter, Laboratory of Macro-Organic Chemistry, Department of Chemical Engineering and Chemistry & Institute for Complex Molecular Systems, Eindhoven University of Technology, Post Office Box 513, 5600 MD Eindhoven, The Netherlands.
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19
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Chakraborty S, Jana B. Ordered hydration layer mediated ice adsorption of a globular antifreeze protein: mechanistic insight. Phys Chem Chem Phys 2019; 21:19298-19310. [DOI: 10.1039/c9cp03135a] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The ice binding surface of a type III AFP induces water ordering at lower temperature, which mediates its adsorption on the ice surface.
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Affiliation(s)
- Sandipan Chakraborty
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata-700032
- India
| | - Biman Jana
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata-700032
- India
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20
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Muraoka M, Ohtake M, Yamamoto Y. Kinetic inhibition effect of Type I and III antifreeze proteins on unidirectional tetrahydrofuran hydrate crystal growth. RSC Adv 2019; 9:11530-11537. [PMID: 35520232 PMCID: PMC9063353 DOI: 10.1039/c9ra00627c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 04/01/2019] [Indexed: 11/21/2022] Open
Abstract
Experiments were performed to evaluate the kinetic inhibition effect of Type I and Type III antifreeze proteins (AFPs) on the growth of tetrahydrofuran (THF) clathrate hydrate crystals using the unidirectional growth technique.
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Affiliation(s)
- Michihiro Muraoka
- Research Institute of Energy Frontier
- National Institute of Advanced Industrial Science and Technology (AIST)
- Tsukuba
- Japan
| | - Michika Ohtake
- Research Institute of Energy Frontier
- National Institute of Advanced Industrial Science and Technology (AIST)
- Tsukuba
- Japan
| | - Yoshitaka Yamamoto
- Research Institute of Energy Frontier
- National Institute of Advanced Industrial Science and Technology (AIST)
- Tsukuba
- Japan
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21
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Brotzakis ZF, Voets IK, Bakker HJ, Bolhuis PG. Water structure and dynamics in the hydration layer of a type III anti-freeze protein. Phys Chem Chem Phys 2018; 20:6996-7006. [PMID: 29468240 DOI: 10.1039/c8cp00170g] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report on a molecular dynamics study on the relation between the structure and the orientational (and hydrogen bond) dynamics of hydration water around the ocean pout AFP III anti-freeze protein. We find evidence for an increasing tetrahedral structure from the area opposite to the ice binding site (IBS) towards the protein IBS, with the strongest signal of tetrahedral structure around the THR-18 residue of the IBS. The tetrahedral structural parameter mostly positively correlates with increased reorientation decay times. Interestingly, for several key (polar) residues that are not part of the IBS but are in its vicinity, we observe a decrease of the reorientation time with increasing tetrahedral structure. A similar anti-correlation is observed for the hydrogen-bonded water molecules. These effects are enhanced at a lower temperature. We interpret these results in terms of the structure-making and structure-breaking residues. Moreover, we investigate the tetrahedral structure and dynamics of waters at a partially dehydrated IBS, and for the protein adsorbed at the air-water interface. We find that the mutation changes the preferred protein orientation upon adsorption at an air-water interface. These results are in agreement with the water-air Vibration Sum Frequency Generation spectroscopic experiments showing a strongly reduced tetrahedral signal upon mutation at the IBS.
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Affiliation(s)
- Z Faidon Brotzakis
- Van't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
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22
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Polypentagonal ice-like water networks emerge solely in an activity-improved variant of ice-binding protein. Proc Natl Acad Sci U S A 2018; 115:5456-5461. [PMID: 29735675 PMCID: PMC6003529 DOI: 10.1073/pnas.1800635115] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Polypentagonal water networks were recently observed in a protein capable of binding to ice crystals, or ice-binding protein (IBP). To examine such water networks and clarify their role in ice-binding, we determined X-ray crystal structures of a 65-residue defective isoform of a Zoarcidae-derived IBP (wild type, WT) and its five single mutants (A20L, A20G, A20T, A20V, and A20I). Polypentagonal water networks composed of ∼50 semiclathrate waters were observed solely on the strongest A20I mutant, which appeared to include a tetrahedral water cluster exhibiting a perfect position match to the [Formula: see text] first prism plane of a single ice crystal. Inclusion of another symmetrical water cluster in the polypentagonal network showed a perfect complementarity to the waters constructing the [Formula: see text] pyramidal ice plane. The order of ice-binding strength was A20L < A20G < WT < A20T < A20V < A20I, where the top three mutants capable of binding to the first prism and the pyramidal ice planes commonly contained a bifurcated γ-CH3 group. These results suggest that a fine-tuning of the surface of Zoarcidae-derived IBP assisted by a side-chain group regulates the holding property of its polypentagonal water network, the function of which is to freeze the host protein to specific ice planes.
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23
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Ice cream structure modification by ice-binding proteins. Food Chem 2018; 246:164-171. [DOI: 10.1016/j.foodchem.2017.10.152] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Revised: 10/26/2017] [Accepted: 10/31/2017] [Indexed: 11/22/2022]
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24
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Mahatabuddin S, Tsuda S. Applications of Antifreeze Proteins: Practical Use of the Quality Products from Japanese Fishes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1081:321-337. [PMID: 30288717 DOI: 10.1007/978-981-13-1244-1_17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Numerous embryonic ice crystals are generated in water at the moment of freezing. These crystals grow and merge together to form an ice block that can be generally observed. Antifreeze protein (AFP) is capable of binding to the embryonic ice crystals, inhibiting such an ice block formation. Fish-derived AFP additionally binds to membrane lipid bilayers to prolong the lifetime of cells. These unique abilities of AFP have been studied extensively for the development of advanced techniques, such as ice recrystallization inhibitors, freeze-tolerant gels, cell preservation fluids, and high-porosity ceramics, for which mass-preparation method of the quality product of AFP utilizing fish muscle homogenates made a significant contribution. In this chapter, we present both fundamental and advanced information of fish AFPs that have been especially discovered from mid-latitude sea area, which will provide a hint to develop more advanced techniques applicable in both medical and industrial fields.
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Affiliation(s)
- Sheikh Mahatabuddin
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
| | - Sakae Tsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan.
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25
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Verreault D, Alamdari S, Roeters SJ, Pandey R, Pfaendtner J, Weidner T. Ice-binding site of surface-bound type III antifreeze protein partially decoupled from water. Phys Chem Chem Phys 2018; 20:26926-26933. [DOI: 10.1039/c8cp03382j] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Combined SFG/MD analysis together with spectral calculations revealed that type III antifreeze proteins adsorbed at the air–water interface maintains a native state and adopts an orientation that leads to a partial decoupling of its ice-binding site from water.
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Affiliation(s)
| | - Sarah Alamdari
- Department of Chemical Engineering
- University of Washington
- Seattle
- USA
| | | | - Ravindra Pandey
- Department of Chemistry
- Indian Institute of Technology
- Roorkee 247667
- India
| | - Jim Pfaendtner
- Department of Chemical Engineering
- University of Washington
- Seattle
- USA
| | - Tobias Weidner
- Department of Chemistry
- Aarhus University
- 8000 Aarhus C
- Denmark
- Department of Chemical Engineering
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26
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Affiliation(s)
- Alexander G. Shtukenberg
- Department of Chemistry and Molecular
Design Institute, New York University, 100 Washington Square East, New York City, New York 10003, United States
| | - Michael D. Ward
- Department of Chemistry and Molecular
Design Institute, New York University, 100 Washington Square East, New York City, New York 10003, United States
| | - Bart Kahr
- Department of Chemistry and Molecular
Design Institute, New York University, 100 Washington Square East, New York City, New York 10003, United States
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27
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28
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Zhou H, Infante Ferreira C. Effect of type-III Anti-Freeze Proteins (AFPs) on CO2 hydrate formation rate. Chem Eng Sci 2017. [DOI: 10.1016/j.ces.2017.03.060] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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29
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Stevens CA, Semrau J, Chiriac D, Litschko M, Campbell RL, Langelaan DN, Smith SP, Davies PL, Allingham JS. Peptide backbone circularization enhances antifreeze protein thermostability. Protein Sci 2017; 26:1932-1941. [PMID: 28691252 DOI: 10.1002/pro.3228] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 06/22/2017] [Accepted: 07/03/2017] [Indexed: 11/09/2022]
Abstract
Antifreeze proteins (AFPs) are a class of ice-binding proteins that promote survival of a variety of cold-adapted organisms by decreasing the freezing temperature of bodily fluids. A growing number of biomedical, agricultural, and commercial products, such as organs, foods, and industrial fluids, have benefited from the ability of AFPs to control ice crystal growth and prevent ice recrystallization at subzero temperatures. One limitation of AFP use in these latter contexts is their tendency to denature and irreversibly lose activity at the elevated temperatures of certain industrial processing or large-scale AFP production. Using the small, thermolabile type III AFP as a model system, we demonstrate that AFP thermostability is dramatically enhanced via split intein-mediated N- and C-terminal end ligation. To engineer this circular protein, computational modeling and molecular dynamics simulations were applied to identify an extein sequence that would fill the 20-Å gap separating the free ends of the AFP, yet impose little impact on the structure and entropic properties of its ice-binding surface. The top candidate was then expressed in bacteria, and the circularized protein was isolated from the intein domains by ice-affinity purification. This circularized AFP induced bipyramidal ice crystals during ice growth in the hysteresis gap and retained 40% of this activity even after incubation at 100°C for 30 min. NMR analysis implicated enhanced thermostability or refolding capacity of this protein compared to the noncyclized wild-type AFP. These studies support protein backbone circularization as a means to expand the thermostability and practical applications of AFPs.
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Affiliation(s)
- Corey A Stevens
- Protein Function Discovery Group and the Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - Joanna Semrau
- Protein Function Discovery Group and the Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - Dragos Chiriac
- Protein Function Discovery Group and the Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - Morgan Litschko
- Protein Function Discovery Group and the Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - Robert L Campbell
- Protein Function Discovery Group and the Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - David N Langelaan
- Protein Function Discovery Group and the Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - Steven P Smith
- Protein Function Discovery Group and the Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - Peter L Davies
- Protein Function Discovery Group and the Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - John S Allingham
- Protein Function Discovery Group and the Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, K7L 3N6, Canada
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Kim HJ, Lee JH, Hur YB, Lee CW, Park SH, Koo BW. Marine Antifreeze Proteins: Structure, Function, and Application to Cryopreservation as a Potential Cryoprotectant. Mar Drugs 2017; 15:md15020027. [PMID: 28134801 PMCID: PMC5334608 DOI: 10.3390/md15020027] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 01/20/2017] [Indexed: 11/16/2022] Open
Abstract
Antifreeze proteins (AFPs) are biological antifreezes with unique properties, including thermal hysteresis(TH),ice recrystallization inhibition(IRI),and interaction with membranes and/or membrane proteins. These properties have been utilized in the preservation of biological samples at low temperatures. Here, we review the structure and function of marine-derived AFPs, including moderately active fish AFPs and hyperactive polar AFPs. We also survey previous and current reports of cryopreservation using AFPs. Cryopreserved biological samples are relatively diverse ranging from diatoms and reproductive cells to embryos and organs. Cryopreserved biological samples mainly originate from mammals. Most cryopreservation trials using marine-derived AFPs have demonstrated that addition of AFPs can improve post-thaw viability regardless of freezing method (slow-freezing or vitrification), storage temperature, and types of biological sample type.
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Affiliation(s)
- Hak Jun Kim
- Department of Chemistry, Pukyong National University, Busan 48513, Korea.
| | - Jun Hyuck Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon 21990, Korea.
| | - Young Baek Hur
- Tidal Flat Research Institute, National Fisheries Research and Development Institute, Gunsan, Jeonbuk 54014, Korea.
| | - Chang Woo Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon 21990, Korea.
| | - Sun-Ha Park
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon 21990, Korea.
| | - Bon-Won Koo
- Department of Chemistry, Pukyong National University, Busan 48513, Korea.
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31
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Phippen SW, Stevens CA, Vance TDR, King NP, Baker D, Davies PL. Multivalent Display of Antifreeze Proteins by Fusion to Self-Assembling Protein Cages Enhances Ice-Binding Activities. Biochemistry 2016; 55:6811-6820. [PMID: 27951652 DOI: 10.1021/acs.biochem.6b00864] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Antifreeze proteins (AFPs) are small monomeric proteins that adsorb to the surface of ice to inhibit ice crystal growth and impart freeze resistance to the organisms producing them. Previously, monomeric AFPs have been conjugated to the termini of branched polymers to increase their activity through the simultaneous binding of more than one AFP to ice. Here, we describe a superior approach to increasing AFP activity through oligomerization that eliminates the need for conjugation reactions with varying levels of efficiency. A moderately active AFP from a fish and a hyperactive AFP from an Antarctic bacterium were genetically fused to the C-termini of one component of the 24-subunit protein cage T33-21, resulting in protein nanoparticles that multivalently display exactly 12 AFPs. The resulting nanoparticles exhibited freezing point depression >50-fold greater than that seen with the same concentration of monomeric AFP and a similar increase in the level of ice-recrystallization inhibition. These results support the anchored clathrate mechanism of binding of AFP to ice. The enhanced freezing point depression could be due to the difficulty of overgrowing a larger AFP on the ice surface and the improved ice-recrystallization inhibition to the ability of the nanoparticle to simultaneously bind multiple ice grains. Oligomerization of these proteins using self-assembling protein cages will be useful in a variety of biotechnology and cryobiology applications.
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Affiliation(s)
- Sean W Phippen
- Department of Biomedical and Molecular Sciences, Queen's University , Kingston, Ontario K7L 3N6, Canada
| | - Corey A Stevens
- Department of Biomedical and Molecular Sciences, Queen's University , Kingston, Ontario K7L 3N6, Canada
| | - Tyler D R Vance
- Department of Biomedical and Molecular Sciences, Queen's University , Kingston, Ontario K7L 3N6, Canada
| | - Neil P King
- Department of Biochemistry, University of Washington , Seattle, Washington 98195, United States.,Institute for Protein Design, University of Washington , Seattle, Washington 98195, United States
| | - David Baker
- Department of Biochemistry, University of Washington , Seattle, Washington 98195, United States.,Institute for Protein Design, University of Washington , Seattle, Washington 98195, United States.,Howard Hughes Medical Institute, University of Washington , Seattle, Washington 98195, United States
| | - Peter L Davies
- Department of Biomedical and Molecular Sciences, Queen's University , Kingston, Ontario K7L 3N6, Canada
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32
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Choi SR, Seo YJ, Kim M, Eo Y, Ahn HC, Lee AR, Park CJ, Ryu KS, Cheong HK, Lee SS, Jin E, Lee JH. NMR study of the antifreeze activities of active and inactive isoforms of a type III antifreeze protein. FEBS Lett 2016; 590:4202-4212. [PMID: 27718246 DOI: 10.1002/1873-3468.12451] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 09/23/2016] [Accepted: 09/30/2016] [Indexed: 11/06/2022]
Abstract
The quaternary-amino-ethyl 1 (QAE1) isoforms of type III antifreeze proteins (AFPs) prevent the growth of ice crystals within organisms living in polar regions. We determined the antifreeze activity of wild-type and mutant constructs of the Japanese notched-fin eelpout (Zoarces elongates Kner) AFP8 (nfeAFP8) and characterized the structural and dynamics properties of their ice-binding surface using NMR. We found that the three constructs containing the V20G mutation were incapable of stopping the growth of ice crystals and exhibited structural changes, as well as increased conformational flexibility, in the first 310 helix (residues 18-22) of the sequence. Our results suggest that the inactive nfeAFP8s are incapable of anchoring water molecules due to the unusual and flexible backbone conformation of their primary prism plane-binding surface.
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Affiliation(s)
- Seo-Ree Choi
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam, Korea
| | - Yeo-Jin Seo
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam, Korea
| | - Minjae Kim
- Department of Life Science, Hanyang University, Seoul, Korea
| | - Yumi Eo
- College of Pharmacy, Dongguk University, Gyeonggi, Korea
| | - Hee-Chul Ahn
- College of Pharmacy, Dongguk University, Gyeonggi, Korea
| | - Ae-Ree Lee
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam, Korea
| | | | | | | | - Shim Sung Lee
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam, Korea
| | - EonSeon Jin
- Department of Life Science, Hanyang University, Seoul, Korea
| | - Joon-Hwa Lee
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam, Korea.,Division of Magnetic Resonance, KBSI, Chungbuk, Korea
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33
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Affiliation(s)
- Maya Bar Dolev
- Institute of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty of Agricultural, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel; ,
| | - Ido Braslavsky
- Institute of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty of Agricultural, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel; ,
| | - Peter L. Davies
- Department of Biomedical and Molecular Science, Queen's University, Kingston, Ontario K7L 3N6, Canada;
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34
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Yoshida K, Baron AQR, Uchiyama H, Tsutsui S, Yamaguchi T. Structure and collective dynamics of hydrated anti-freeze protein type III from 180 K to 298 K by X-ray diffraction and inelastic X-ray scattering. J Chem Phys 2016; 144:134505. [PMID: 27059578 DOI: 10.1063/1.4944987] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We investigated hydrated antifreeze protein type III (AFP III) powder with a hydration level h (=mass of water/mass of protein) of 0.4 in the temperature range between 180 K and 298 K using X-ray diffraction and inelastic X-ray scattering (IXS). The X-ray diffraction data showed smooth, largely monotonic changes between 180 K and 298 K without freezing water. Meanwhile, the collective dynamics observed by IXS showed a strong change in the sound velocity at 180 K, after being largely temperature independent at higher temperatures (298-220 K). We interpret this change in terms of the dynamic transition previously discussed using other probes including THz IR absorption spectroscopy and incoherent elastic and quasi-elastic neutron scattering. This finding suggests that the dynamic transition of hydrated proteins is observable on the subpicosecond time scale as well as nano- and pico-second scales, both in collective dynamics from IXS and single particle dynamics from neutron scattering. Moreover, it is most likely that the dynamic transition of hydrated AFP III is not directly correlated with its hydration structure.
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Affiliation(s)
- Koji Yoshida
- Department of Chemistry, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
| | - Alfred Q R Baron
- Materials Dynamics Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Hiroshi Uchiyama
- Research and Utilization Division, Japan Synchrotron Radiation Research Institute, SPring-8, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Satoshi Tsutsui
- Research and Utilization Division, Japan Synchrotron Radiation Research Institute, SPring-8, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Toshio Yamaguchi
- Department of Chemistry, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
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35
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Abstract
Ice binding proteins (IBPs) are produced by various cold-adapted organisms to protect their body tissues against freeze damage. First discovered in Antarctic fish living in shallow waters, IBPs were later found in insects, microorganisms, and plants. Despite great structural diversity, all IBPs adhere to growing ice crystals, which is essential for their extensive repertoire of biological functions. Some IBPs maintain liquid inclusions within ice or inhibit recrystallization of ice, while other types suppress freezing by blocking further ice growth. In contrast, ice nucleating proteins stimulate ice nucleation just below 0 °C. Despite huge commercial interest and major scientific breakthroughs, the precise working mechanism of IBPs has not yet been unraveled. In this review, the authors outline the state-of-the-art in experimental and theoretical IBP research and discuss future scientific challenges. The interaction of IBPs with ice, water and ions is examined, focusing in particular on ice growth inhibition mechanisms.
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37
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Blocking rapid ice crystal growth through nonbasal plane adsorption of antifreeze proteins. Proc Natl Acad Sci U S A 2016; 113:3740-5. [PMID: 26936953 DOI: 10.1073/pnas.1524109113] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Antifreeze proteins (AFPs) are a unique class of proteins that bind to growing ice crystal surfaces and arrest further ice growth. AFPs have gained a large interest for their use in antifreeze formulations for water-based materials, such as foods, waterborne paints, and organ transplants. Instead of commonly used colligative antifreezes such as salts and alcohols, the advantage of using AFPs as an additive is that they do not alter the physicochemical properties of the water-based material. Here, we report the first comprehensive evaluation of thermal hysteresis (TH) and ice recrystallization inhibition (IRI) activity of all major classes of AFPs using cryoscopy, sonocrystallization, and recrystallization assays. The results show that TH activities determined by cryoscopy and sonocrystallization differ markedly, and that TH and IRI activities are not correlated. The absence of a distinct correlation in antifreeze activity points to a mechanistic difference in ice growth inhibition by the different classes of AFPs: blocking fast ice growth requires rapid nonbasal plane adsorption, whereas basal plane adsorption is only relevant at long annealing times and at small undercooling. These findings clearly demonstrate that biomimetic analogs of antifreeze (glyco)proteins should be tailored to the specific requirements of the targeted application.
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38
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Sun T, Gauthier SY, Campbell RL, Davies PL. Revealing Surface Waters on an Antifreeze Protein by Fusion Protein Crystallography Combined with Molecular Dynamic Simulations. J Phys Chem B 2015; 119:12808-15. [PMID: 26371748 DOI: 10.1021/acs.jpcb.5b06474] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Antifreeze proteins (AFPs) adsorb to ice through an extensive, flat, relatively hydrophobic surface. It has been suggested that this ice-binding site (IBS) organizes surface waters into an ice-like clathrate arrangement that matches and fuses to the quasi-liquid layer on the ice surface. On cooling, these waters join the ice lattice and freeze the AFP to its ligand. Evidence for the generality of this binding mechanism is limited because AFPs tend to crystallize with their IBS as a preferred protein-protein contact surface, which displaces some bound waters. Type III AFP is a 7 kDa globular protein with an IBS made up two adjacent surfaces. In the crystal structure of the most active isoform (QAE1), the part of the IBS that docks to the primary prism plane of ice is partially exposed to solvent and has clathrate waters present that match this plane of ice. The adjacent IBS, which matches the pyramidal plane of ice, is involved in protein-protein crystal contacts with few surface waters. Here we have changed the protein-protein contacts in the ice-binding region by crystallizing a fusion of QAE1 to maltose-binding protein. In this 1.9 Å structure, the IBS that fits the pyramidal plane of ice is exposed to solvent. By combining crystallography data with MD simulations, the surface waters on both sides of the IBS were revealed and match well with the target ice planes. The waters on the pyramidal plane IBS were loosely constrained, which might explain why other isoforms of type III AFP that lack the prism plane IBS are less active than QAE1. The AFP fusion crystallization method can potentially be used to force the exposure to solvent of the IBS on other AFPs to reveal the locations of key surface waters.
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Affiliation(s)
- Tianjun Sun
- Department of Biomedical and Molecular Sciences, Queen's University , Kingston, Ontario, Canada
| | - Sherry Y Gauthier
- Department of Biomedical and Molecular Sciences, Queen's University , Kingston, Ontario, Canada
| | - Robert L Campbell
- Department of Biomedical and Molecular Sciences, Queen's University , Kingston, Ontario, Canada
| | - Peter L Davies
- Department of Biomedical and Molecular Sciences, Queen's University , Kingston, Ontario, Canada
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39
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Ruiz-Arellano RR, Medrano FJ, Moreno A, Romero A. Structure of struthiocalcin-1, an intramineral protein from Struthio camelus eggshell, in two crystal forms. ACTA ACUST UNITED AC 2015; 71:809-18. [PMID: 25849392 DOI: 10.1107/s139900471500125x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 01/20/2015] [Indexed: 11/10/2022]
Abstract
Biomineralization is the process by which living organisms produce minerals. One remarkable example is the formation of eggshells in birds. Struthiocalcins present in the ostrich (Struthio camellus) eggshell matrix act as biosensors of calcite growth during eggshell formation. Here, the crystal structure of struthiocalcin-1 (SCA-1) is reported in two different crystal forms. The structure is a compact single domain with an α/β fold characteristic of the C-type lectin family. In contrast to the related avian ovocleidin OC17, the electrostatic potential on the molecular surface is dominated by an acidic patch. Scanning electron microscopy combined with Raman spectroscopy indicates that these intramineral proteins (SCA-1 and SCA-2) induce calcium carbonate precipitation, leading to the formation of a stable form of calcite in the mature eggshell. Finally, the implications of these two intramineral proteins SCA-1 and SCA-2 in the nucleation of calcite during the formation of eggshells in ratite birds are discussed.
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Affiliation(s)
- Rayana R Ruiz-Arellano
- Instituto de Química, Universidad Nacional Autónoma de México, 04510 Mexico City, Mexico
| | - Francisco J Medrano
- Biología Físico-Química, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Abel Moreno
- Instituto de Química, Universidad Nacional Autónoma de México, 04510 Mexico City, Mexico
| | - Antonio Romero
- Biología Físico-Química, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
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PROVESI JG, AMANTE ER. Revisão: Proteínas anticongelantes – uma tecnologia emergente para o congelamento de alimentos. BRAZILIAN JOURNAL OF FOOD TECHNOLOGY 2015. [DOI: 10.1590/1981-6723.7714] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Um dos métodos mais tradicionais na conservação de alimentos, o congelamento também pode alterar de forma significativa as características do produto. Grandes cristais de gelo provocam alteração na textura e/ou danos a membranas e componentes celulares. As técnicas de congelamento rápido formam cristais de gelo menores do que o processo lento, porém as flutuações de temperatura durante a distribuição e transporte podem promover o crescimento dos cristais. Esse processo é conhecido como recristalização e é uma barreira na utilização do congelamento como método de conservação em muitos casos. O uso de crioprotetores tradicionais, como a sacarose, é uma alternativa limitada, uma vez que concentrações elevadas são requeridas. Na década de 1970, foi descrita em peixes de águas frias uma classe de proteínas que, em baixa concentração, pode interagir e influenciar o crescimento do cristal de gelo. Elas foram chamadas de proteínas anticongelantes (PACs), sendo encontradas também em plantas, animais e micro-organismos ambientados a baixas temperaturas. Essas proteínas podem intervir no processo de formação do núcleo inicial do gelo, reduzir o ponto de congelamento da água, ou, ainda, inibir a recristalização, principalmente para PACs de vegetais. Há diversos trabalhos publicados e algumas patentes registradas para o uso de PACs em diversos alimentos, como lácteos, carnes, massas, frutas e hortaliças, conservando de melhor forma as características originais do alimento. Atualmente, o custo ainda é uma barreira para utilização comercial das PACs. Contudo, a descoberta de novas fontes pode reduzir seu custo e tornar essas proteínas uma ferramenta efetiva na manutenção da textura de alimentos congelados. Baseada em trabalhos que avaliaram aspectos químicos das PACs e exemplos de sua aplicação, esta revisão tem como objetivo principal apresentar as características gerais das PACs e discutir sobre sua utilização.
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41
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Choi YG, Park CJ, Kim HE, Seo YJ, Lee AR, Choi SR, Lee SS, Lee JH. Comparison of backbone dynamics of the type III antifreeze protein and antifreeze-like domain of human sialic acid synthase. JOURNAL OF BIOMOLECULAR NMR 2015; 61:137-150. [PMID: 25575834 DOI: 10.1007/s10858-014-9895-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Accepted: 12/30/2014] [Indexed: 06/04/2023]
Abstract
Antifreeze proteins (AFPs) are found in a variety of cold-adapted (psychrophilic) organisms to promote survival at subzero temperatures by binding to ice crystals and decreasing the freezing temperature of body fluids. The type III AFPs are small globular proteins that consist of one α-helix, three 3(10)-helices, and two β-strands. Sialic acids play important roles in a variety of biological functions, such as development, recognition, and cell adhesion and are synthesized by conserved enzymatic pathways that include sialic acid synthase (SAS). SAS consists of an N-terminal catalytic domain and a C-terminal antifreeze-like (AFL) domain, which is similar to the type III AFPs. Despite having very similar structures, AFL and the type III AFPs exhibit very different temperature-dependent stability and activity. In this study, we have performed backbone dynamics analyses of a type III AFP (HPLC12 isoform) and the AFL domain of human SAS (hAFL) at various temperatures. We also characterized the structural/dynamic properties of the ice-binding surfaces by analyzing the temperature gradient of the amide proton chemical shift and its correlation with chemical shift deviation from random coil. The dynamic properties of the two proteins were very different from each other. While HPLC12 was mostly rigid with a few residues exhibiting slow motions, hAFL showed fast internal motions at low temperature. Our results provide insight into the molecular basis of thermostability and structural flexibility in homologous psychrophilic HPLC12 and mesophilic hAFL proteins.
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Affiliation(s)
- Yong-Geun Choi
- Department of Chemistry and Research Institute of Natural Science, Gyeongsang National University, Jinju, Gyeongnam, 660-701, Republic of Korea
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42
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Abstract
We study the properties of water at the surface of an antifreeze protein with femtosecond surface sum frequency generation spectroscopy. We find clear evidence for the presence of ice-like water layers at the ice-binding site of the protein in aqueous solution at temperatures above the freezing point. Decreasing the temperature to the biological working temperature of the protein (0 °C to -2 °C) increases the amount of ice-like water, while a single point mutation in the ice-binding site is observed to completely disrupt the ice-like character and to eliminate antifreeze activity. Our observations indicate that not the protein itself but ordered ice-like water layers are responsible for the recognition and binding to ice.
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43
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Gaukel V, Leiter A, Spieß WE. Synergism of different fish antifreeze proteins and hydrocolloids on recrystallization inhibition of ice in sucrose solutions. J FOOD ENG 2014. [DOI: 10.1016/j.jfoodeng.2014.05.016] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Banerjee R, Chakraborti P, Bhowmick R, Mukhopadhyay S. Distinct molecular features facilitating ice-binding mechanisms in hyperactive antifreeze proteins closely related to an Antarctic sea ice bacterium. J Biomol Struct Dyn 2014; 33:1424-41. [PMID: 25190099 DOI: 10.1080/07391102.2014.952665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Antifreeze proteins or ice-binding proteins (IBPs) facilitate the survival of certain cellular organisms in freezing environment by inhibiting the growth of ice crystals in solution. Present study identifies orthologs of the IBP of Colwellia sp. SLW05, which were obtained from a wide range of taxa. Phylogenetic analysis on the basis of conserved regions (predicted as the 'ice-binding domain' [IBD]) present in all the orthologs, separates the bacterial and archaeal orthologs from that of the eukaryotes'. Correspondence analysis pointed out that the bacterial and archaeal IBDs have relatively higher average hydrophobicity than the eukaryotic members. IBDs belonging to bacterial as well as archaeal AFPs contain comparatively more strands, and therefore are revealed to be under higher evolutionary selection pressure. Molecular docking studies prove that the ice crystals form more stable complex with the bacterial as well as archaeal proteins than the eukaryotic orthologs. Analysis of the docked structures have traced out the ice-binding sites (IBSs) in all the orthologs which continue to facilitate ice-binding activity even after getting mutated with respect to the well-studied IBSs of Typhula ishikariensis and notably, all these mutations performing ice-binding using 'anchored clathrate mechanism' have been found to prefer polar and hydrophilic amino acids. Horizontal gene transfer studies point toward a strong selection pressure favoring independent evolution of the IBPs in some polar organisms including prokaryotes as well as eukaryotes because these proteins facilitate the polar organisms to acclimatize to the adversities in their niche, thus safeguarding their existence.
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Affiliation(s)
- Rachana Banerjee
- a Department of Biophysics, Molecular Biology and Bioinformatics , University of Calcutta , 92, A.P.C. Road, Kolkata 700009 , India
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45
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Lotze S, Olijve LLC, Voets IK, Bakker HJ. Observation of vibrational energy exchange in a type-III antifreeze protein. J Phys Chem B 2014; 118:8962-71. [PMID: 25051212 DOI: 10.1021/jp503481e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We performed time- and polarization-resolved pump-probe and two-dimensional infrared (2D-IR) experiments to study the dynamics of the amide I vibration of a 7 kDa type-III antifreeze protein. In the pump-probe experiments, we used femtosecond mid-infrared pulses to investigate the vibrational relaxation dynamics of the amide mode. The transient spectra show the presence of two spectral components that decay with different lifetimes, indicative of the presence of two distinct amide subbands. The 2D-IR experiments reveal the coupling between the two bands in the form of cross-peaks. On the basis of previous work by Demirdöven et al. ( J. Am. Chem. Soc. 2004 , 126 , 7981 - 7990 ), we assign the observed bands to the two infrared-active modes α(-) and α(+) found in protein β-sheets. The amplitudes of the cross-peak were found to increase with delay time, indicating that the cross-peaks originate from population transfer between the coupled amide oscillators. The time constant of the energy transfer was found to be 6-7 ps.
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Affiliation(s)
- S Lotze
- FOM-Institute for Atomic and Molecular Physics AMOLF , Science Park 104, 1098 XG Amsterdam, The Netherlands
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46
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Hanada Y, Nishimiya Y, Miura A, Tsuda S, Kondo H. Hyperactive antifreeze protein from an Antarctic sea ice bacterium Colwellia sp. has a compound ice-binding site without repetitive sequences. FEBS J 2014; 281:3576-90. [PMID: 24938370 DOI: 10.1111/febs.12878] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 05/22/2014] [Accepted: 06/13/2014] [Indexed: 11/29/2022]
Abstract
UNLABELLED Antifreeze proteins (AFPs) are structurally diverse macromolecules that bind to ice crystals and inhibit their growth to protect the organism from injuries caused by freezing. An AFP identified from the Antarctic bacterium Colwellia sp. strain SLW05 (ColAFP) is homologous to AFPs from a wide variety of psychrophilic microorganisms. To understand the antifreeze function of ColAFP, we have characterized its antifreeze activity and determined the crystal structure of this protein. The recombinant ColAFP exhibited thermal hysteresis activity of approximately 4 °C at a concentration of 0.14 mm, and induced rapid growth of ice crystals in the hexagonal direction. Fluorescence-based ice plane affinity analysis showed that ColAFP binds to multiple planes of ice, including the basal plane. These observations show that ColAFP is a hyperactive AFP. The crystal structure of ColAFP determined at 1.6 Å resolution revealed an irregular β-helical structure, similar to known homologs. Mutational and molecular docking studies showed that ColAFP binds to ice through a compound ice-binding site (IBS) located at a flat surface of the β-helix and the adjoining loop region. The IBS of ColAFP lacks the repetitive sequences that are characteristic of hyperactive AFPs. These results suggest that ColAFP exerts antifreeze activity through a compound IBS that differs from the characteristic IBSs shared by other hyperactive AFPs. This study demonstrates a novel method for protection from freezing by AFPs in psychrophilic microorganisms. DATABASE Structural data for ColAFP have been submitted to the Protein Data Bank (PDB) under accession number 3WP9.
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Affiliation(s)
- Yuichi Hanada
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan; Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Sapporo, Japan
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47
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Do H, Kim SJ, Kim HJ, Lee JH. Structure-based characterization and antifreeze properties of a hyperactive ice-binding protein from the Antarctic bacterium Flavobacterium frigoris PS1. ACTA ACUST UNITED AC 2014; 70:1061-73. [PMID: 24699650 DOI: 10.1107/s1399004714000996] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 01/15/2014] [Indexed: 11/10/2022]
Abstract
Ice-binding proteins (IBPs) inhibit ice growth through direct interaction with ice crystals to permit the survival of polar organisms in extremely cold environments. FfIBP is an ice-binding protein encoded by the Antarctic bacterium Flavobacterium frigoris PS1. The X-ray crystal structure of FfIBP was determined to 2.1 Å resolution to gain insight into its ice-binding mechanism. The refined structure of FfIBP shows an intramolecular disulfide bond, and analytical ultracentrifugation and analytical size-exclusion chromatography show that it behaves as a monomer in solution. Sequence alignments and structural comparisons of IBPs allowed two groups of IBPs to be defined, depending on sequence differences between the α2 and α4 loop regions and the presence of the disulfide bond. Although FfIBP closely resembles Leucosporidium (recently re-classified as Glaciozyma) IBP (LeIBP) in its amino-acid sequence, the thermal hysteresis (TH) activity of FfIBP appears to be tenfold higher than that of LeIBP. A comparison of the FfIBP and LeIBP structures reveals that FfIBP has different ice-binding residues as well as a greater surface area in the ice-binding site. Notably, the ice-binding site of FfIBP is composed of a T-A/G-X-T/N motif, which is similar to the ice-binding residues of hyperactive antifreeze proteins. Thus, it is proposed that the difference in TH activity between FfIBP and LeIBP may arise from the amino-acid composition of the ice-binding site, which correlates with differences in affinity and surface complementarity to the ice crystal. In conclusion, this study provides a molecular basis for understanding the antifreeze mechanism of FfIBP and provides new insights into the reasons for the higher TH activity of FfIBP compared with LeIBP.
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Affiliation(s)
- Hackwon Do
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, Republic of Korea
| | - Soon-Jong Kim
- Department of Chemistry, Mokpo National University, Chonnam 534-729, Republic of Korea
| | - Hak Jun Kim
- Department of Chemistry, Pukyong National University, Busan 608-739, Republic of Korea
| | - Jun Hyuck Lee
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, Republic of Korea
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48
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Basu K, Garnham CP, Nishimiya Y, Tsuda S, Braslavsky I, Davies P. Determining the ice-binding planes of antifreeze proteins by fluorescence-based ice plane affinity. J Vis Exp 2014:e51185. [PMID: 24457629 DOI: 10.3791/51185] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Antifreeze proteins (AFPs) are expressed in a variety of cold-hardy organisms to prevent or slow internal ice growth. AFPs bind to specific planes of ice through their ice-binding surfaces. Fluorescence-based ice plane affinity (FIPA) analysis is a modified technique used to determine the ice planes to which the AFPs bind. FIPA is based on the original ice-etching method for determining AFP-bound ice-planes. It produces clearer images in a shortened experimental time. In FIPA analysis, AFPs are fluorescently labeled with a chimeric tag or a covalent dye then slowly incorporated into a macroscopic single ice crystal, which has been preformed into a hemisphere and oriented to determine the a- and c-axes. The AFP-bound ice hemisphere is imaged under UV light to visualize AFP-bound planes using filters to block out nonspecific light. Fluorescent labeling of the AFPs allows real-time monitoring of AFP adsorption into ice. The labels have been found not to influence the planes to which AFPs bind. FIPA analysis also introduces the option to bind more than one differently tagged AFP on the same single ice crystal to help differentiate their binding planes. These applications of FIPA are helping to advance our understanding of how AFPs bind to ice to halt its growth and why many AFP-producing organisms express multiple AFP isoforms.
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Affiliation(s)
- Koli Basu
- Department of Biomedical and Molecular Sciences, Queen's University
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49
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Mizrahy O, Bar-Dolev M, Guy S, Braslavsky I. Inhibition of ice growth and recrystallization by zirconium acetate and zirconium acetate hydroxide. PLoS One 2013; 8:e59540. [PMID: 23555701 PMCID: PMC3605400 DOI: 10.1371/journal.pone.0059540] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 02/15/2013] [Indexed: 12/29/2022] Open
Abstract
The control over ice crystal growth, melting, and shaping is important in a variety of fields, including cell and food preservation and ice templating for the production of composite materials. Control over ice growth remains a challenge in industry, and the demand for new cryoprotectants is high. Naturally occurring cryoprotectants, such as antifreeze proteins (AFPs), present one solution for modulating ice crystal growth; however, the production of AFPs is expensive and inefficient. These obstacles can be overcome by identifying synthetic substitutes with similar AFP properties. Zirconium acetate (ZRA) was recently found to induce the formation of hexagonal cavities in materials prepared by ice templating. Here, we continue this line of study and examine the effects of ZRA and a related compound, zirconium acetate hydroxide (ZRAH), on ice growth, shaping, and recrystallization. We found that the growth rate of ice crystals was significantly reduced in the presence of ZRA and ZRAH, and that solutions containing these compounds display a small degree of thermal hysteresis, depending on the solution pH. The compounds were found to inhibit recrystallization in a manner similar to that observed in the presence of AFPs. The favorable properties of ZRA and ZRAH suggest tremendous potential utility in industrial applications.
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Affiliation(s)
- Ortal Mizrahy
- The Institute of Biochemistry, Food Science, and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Maya Bar-Dolev
- The Institute of Biochemistry, Food Science, and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
- * E-mail:
| | - Shlomit Guy
- The Institute of Biochemistry, Food Science, and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Ido Braslavsky
- The Institute of Biochemistry, Food Science, and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
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Hakim A, Nguyen JB, Basu K, Zhu DF, Thakral D, Davies PL, Isaacs FJ, Modis Y, Meng W. Crystal structure of an insect antifreeze protein and its implications for ice binding. J Biol Chem 2013; 288:12295-304. [PMID: 23486477 DOI: 10.1074/jbc.m113.450973] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Antifreeze proteins (AFPs) help some organisms resist freezing by binding to ice crystals and inhibiting their growth. The molecular basis for how these proteins recognize and bind ice is not well understood. The longhorn beetle Rhagium inquisitor can supercool to below -25 °C, in part by synthesizing the most potent antifreeze protein studied thus far (RiAFP). We report the crystal structure of the 13-kDa RiAFP, determined at 1.21 Å resolution using direct methods. The structure, which contains 1,914 nonhydrogen protein atoms in the asymmetric unit, is the largest determined ab initio without heavy atoms. It reveals a compressed β-solenoid fold in which the top and bottom sheets are held together by a silk-like interdigitation of short side chains. RiAFP is perhaps the most regular structure yet observed. It is a second independently evolved AFP type in beetles. The two beetle AFPs have in common an extremely flat ice-binding surface comprising regular outward-projecting parallel arrays of threonine residues. The more active, wider RiAFP has four (rather than two) of these arrays between which the crystal structure shows the presence of ice-like waters. Molecular dynamics simulations independently reproduce the locations of these ordered crystallographic waters and predict additional waters that together provide an extensive view of the AFP interaction with ice. By matching several planes of hexagonal ice, these waters may help freeze the AFP to the ice surface, thus providing the molecular basis of ice binding.
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Affiliation(s)
- Aaron Hakim
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
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