1
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Okamoto R, Orii R, Shibata H, Maki Y, Tsuda S, Kajihara Y. Regulating Antifreeze Activity through Water: Latent Functions of the Sugars of Antifreeze Glycoprotein Revealed by Total Chemical Synthesis. Chemistry 2023; 29:e202203553. [PMID: 36722034 DOI: 10.1002/chem.202203553] [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: 11/15/2022] [Revised: 01/27/2023] [Accepted: 01/27/2023] [Indexed: 02/02/2023]
Abstract
Antifreeze glycoprotein (AFGP), which inhibits the freezing of water, is highly O-glycosylated with a disaccharide, d-Galβ1-3-d-GalNAcα (GalGalNAc). To elucidate the function of the sugar residues for antifreeze activity at the molecular level, we conducted a total chemical synthesis of partially sugar deleted AFGP derivatives, and unnatural forms of AFGPs incorporating glucose (Glc)-type sugars instead of galactose (Gal)-type sugars. These elaborated AFGP derivatives demonstrated that the stereochemistry of each sugar residue on AFGPs precisely correlates with the antifreeze activity. A hydrogen-deuterium exchange experiment using synthetic AFGPs revealed a different dynamic behavior of water around sugar residues depending on the sugar structures. These results indicate that sugar residues on AFGP form a unique dynamic water phase that disturbs the absorbance of water molecules onto the ice surface, thereby inhibiting freezing.
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Affiliation(s)
- Ryo Okamoto
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan.,Forefront Research Center Department, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Ryo Orii
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Hiroyuki Shibata
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Yuta Maki
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan.,Forefront Research Center Department, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Sakae Tsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) 2-17-2-1 Tsukisamu-Higashi, Toyohira, Sapporo, Hokkaido, 0628517, Japan
| | - Yasuhiro Kajihara
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan.,Forefront Research Center Department, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
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2
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Zhang W, Liu H, Fu H, Shao X, Cai W. Revealing the Mechanism of Irreversible Binding of Antifreeze Glycoproteins to Ice. J Phys Chem B 2022; 126:10637-10645. [PMID: 36513495 DOI: 10.1021/acs.jpcb.2c06183] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Antifreeze glycoproteins (AFGPs) are a special kind of antifreeze proteins with strong flexibility. Whether their antifreeze activity is achieved by reversibly or irreversibly binding to ice is widely debated, and the molecular mechanism of irreversible binding remains unclear. In this work, the antifreeze mechanism of the smallest AFGP isoform, AFGP8, is investigated at the atomic level. The results indicate that AFGP8 can bind to ice both reversibly through its hydrophobic methyl groups (peptide binding) and irreversibly through its hydrophilic disaccharide moieties (saccharide binding). Although peptide binding occurs faster than saccharide binding, free-energy calculations indicate that the latter is energetically more favorable. In saccharide binding, at least one disaccharide moiety is frozen in the grown ice, resulting in irreversible binding, while the other moieties significantly perturb the water hydrogen-bonding network, thus inhibiting ice growth more effectively. The present study reveals the coexistence of reversible and irreversible bindings of AFGP8, both contributing to the inhibition of ice growth and further provides molecular mechanism of irreversible binding.
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Affiliation(s)
- Weijia Zhang
- Research Center for Analytical Sciences, Haihe Laboratory of Sustainable Chemical Transformations, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, College of Chemistry, Nankai University, Tianjin300071, China
| | - Han Liu
- Research Center for Analytical Sciences, Haihe Laboratory of Sustainable Chemical Transformations, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, College of Chemistry, Nankai University, Tianjin300071, China
| | - Haohao Fu
- Research Center for Analytical Sciences, Haihe Laboratory of Sustainable Chemical Transformations, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, College of Chemistry, Nankai University, Tianjin300071, China
| | - Xueguang Shao
- Research Center for Analytical Sciences, Haihe Laboratory of Sustainable Chemical Transformations, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, College of Chemistry, Nankai University, Tianjin300071, China
| | - Wensheng Cai
- Research Center for Analytical Sciences, Haihe Laboratory of Sustainable Chemical Transformations, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, College of Chemistry, Nankai University, Tianjin300071, China
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3
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Long FQ, Jin T, Han KL, Zhuang W. Impact of borate on structure of antifreeze glycoproteins. CHINESE J CHEM PHYS 2021. [DOI: 10.1063/1674-0068/cjcp2107120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Feng-qin Long
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tan Jin
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
| | - Ke-li Han
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Wei Zhuang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
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4
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Sun Y, Giubertoni G, Bakker HJ, Liu J, Wagner M, Ng DYW, Devries AL, Meister K. Disaccharide Residues are Required for Native Antifreeze Glycoprotein Activity. Biomacromolecules 2021; 22:2595-2603. [PMID: 33957041 PMCID: PMC8207503 DOI: 10.1021/acs.biomac.1c00313] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Antifreeze glycoproteins
(AFGPs) are able to bind to ice, halt
its growth, and are the most potent inhibitors of ice recrystallization
known. The structural basis for AFGP’s unique properties remains
largely elusive. Here we determined the antifreeze activities of AFGP
variants that we constructed by chemically modifying the hydroxyl
groups of the disaccharide of natural AFGPs. Using nuclear magnetic
resonance, two-dimensional infrared spectroscopy, and circular dichroism,
the expected modifications were confirmed as well as their effect
on AFGPs solution structure. We find that the presence of all the
hydroxyls on the disaccharides is a requirement for the native AFGP
hysteresis as well as the maximal inhibition of ice recrystallization.
The saccharide hydroxyls are apparently as important as the acetyl
group on the galactosamine, the α-linkage between the disaccharide
and threonine, and the methyl groups on the threonine and alanine.
We conclude that the use of hydrogen-bonding through the hydroxyl
groups of the disaccharide and hydrophobic interactions through the
polypeptide backbone are equally important in promoting the antifreeze
activities observed in the native AFGPs. These important criteria
should be considered when designing synthetic mimics.
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Affiliation(s)
- Yuling Sun
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Giulia Giubertoni
- NWO Institute AMOLF, 1098 XG Amsterdam, The Netherlands.,University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Huib J Bakker
- NWO Institute AMOLF, 1098 XG Amsterdam, The Netherlands
| | - Jie Liu
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Manfred Wagner
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - David Y W Ng
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Arthur L Devries
- University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Konrad Meister
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany.,University of Alaska Southeast, Juneau, Alaska 99801, United States
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5
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Urbańczyk M, Jewgiński M, Krzciuk-Gula J, Góra J, Latajka R, Sewald N. Synthesis and conformational preferences of short analogues of antifreeze glycopeptides (AFGP). Beilstein J Org Chem 2019; 15:1581-1591. [PMID: 31435440 PMCID: PMC6664394 DOI: 10.3762/bjoc.15.162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 06/12/2019] [Indexed: 01/01/2023] Open
Abstract
Antifreeze glycoproteins are a class of biological agents which enable living at temperatures below the freezing point of the body fluids. Antifreeze glycopeptides usually consist of repeating tripeptide unit (-Ala-Ala-Thr*-), glycosylated at the threonine side chain. However, on the microscopic level, the mechanism of action of these compounds remains unclear. As previous research has shown, antifreeze activity of antifreeze glycopeptides strongly relies on the overall conformation of the molecule as well an on the stereochemistry of amino acid residues. The desired monoglycosylated analogues with acetylated amino termini and the carboxy termini in form of N-methylamide have been synthesized. Conformational nuclear magnetic resonance (NMR) studies of the designed analogues have shown a strong influence of the stereochemistry of amino acid residues on the peptide chain stability, which could be connected to the antifreeze activity of these compounds. A better understanding of the mechanism of action of antifreeze glycopeptides would allow applying these materials, e.g., in food industry and biomedicine.
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Affiliation(s)
- Małgorzata Urbańczyk
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspianskiego 27, Wroclaw, PL-50-370, Poland
| | - Michał Jewgiński
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspianskiego 27, Wroclaw, PL-50-370, Poland
| | - Joanna Krzciuk-Gula
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspianskiego 27, Wroclaw, PL-50-370, Poland
| | - Jerzy Góra
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspianskiego 27, Wroclaw, PL-50-370, Poland
| | - Rafał Latajka
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspianskiego 27, Wroclaw, PL-50-370, Poland
| | - Norbert Sewald
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, Bielefeld, D-33615, Germany
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6
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Her C, Yeh Y, Krishnan VV. The Ensemble of Conformations of Antifreeze Glycoproteins (AFGP8): A Study Using Nuclear Magnetic Resonance Spectroscopy. Biomolecules 2019; 9:biom9060235. [PMID: 31213033 PMCID: PMC6628104 DOI: 10.3390/biom9060235] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/28/2019] [Accepted: 05/30/2019] [Indexed: 12/13/2022] Open
Abstract
The primary sequence of antifreeze glycoproteins (AFGPs) is highly degenerate, consisting of multiple repeats of the same tripeptide, Ala–Ala–Thr*, in which Thr* is a glycosylated threonine with the disaccharide beta-d-galactosyl-(1,3)-alpha-N-acetyl-d-galactosamine. AFGPs seem to function as intrinsically disordered proteins, presenting challenges in determining their native structure. In this work, a different approach was used to elucidate the three-dimensional structure of AFGP8 from the Arctic cod Boreogadussaida and the Antarctic notothenioid Trematomusborchgrevinki. Dimethyl sulfoxide (DMSO), a non-native solvent, was used to make AFGP8 less dynamic in solution. Interestingly, DMSO induced a non-native structure, which could be determined via nuclear magnetic resonance (NMR) spectroscopy. The overall three-dimensional structures of the two AFGP8s from two different natural sources were different from a random coil ensemble, but their “compactness” was very similar, as deduced from NMR measurements. In addition to their similar compactness, the conserved motifs, Ala–Thr*–Pro–Ala and Ala–Thr*–Ala–Ala, present in both AFGP8s, seemed to have very similar three-dimensional structures, leading to a refined definition of local structural motifs. These local structural motifs allowed AFGPs to be considered functioning as effectors, making a transition from disordered to ordered upon binding to the ice surface. In addition, AFGPs could act as dynamic linkers, whereby a short segment folds into a structural motif, while the rest of the AFGPs could still be disordered, thus simultaneously interacting with bulk water molecules and the ice surface, preventing ice crystal growth.
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Affiliation(s)
- Cheenou Her
- Department of Chemistry, California State University, Fresno, CA 93740, USA.
| | - Yin Yeh
- Department of Applied Science, University of California, Davis, CA 95616, USA.
| | - Viswanathan V Krishnan
- Department of Chemistry, California State University, Fresno, CA 93740, USA.
- Department Medical Pathology and Laboratory Medicine, Davis School of Medicine, University of California, Davis, CA 95616, USA.
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7
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Nesmelova IV, Melnikova DL, Ranjan V, Skirda VD. Translational diffusion of unfolded and intrinsically disordered proteins. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2019; 166:85-108. [PMID: 31521238 DOI: 10.1016/bs.pmbts.2019.05.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Translational (or self-diffusion) coefficient in dilute solution is inversely proportional to the size of a diffusing molecule, and hence self-diffusion coefficient measurements have been applied to determine the effective hydrodynamic radii for a range of native and nonnative protein conformations. In particular, translational diffusion coefficient measurements are useful to estimate the hydrodynamic radius of natively (or intrinsically) disordered proteins in solution, and, thereby, probe the compactness of a protein as well as its change when environmental parameters such as temperature, solution pH, or protein concentration are varied. The situation becomes more complicated in concentrated solutions. In this review, we discuss the translational diffusion of disordered proteins in dilute and crowded solutions, focusing primarily on the information provided by pulsed-field gradient NMR technique, and draw analogies to well-structured globular proteins and synthetic polymers.
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Affiliation(s)
- Irina V Nesmelova
- Department of Physics and Optical Sciences, University of North Carolina, Charlotte, NC, United States; Center for Biomedical Engineering and Science, University of North Carolina, Charlotte, NC, United States.
| | | | - Venkatesh Ranjan
- Department of Chemistry, University of North Carolina, Charlotte, NC, United States
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8
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Pandey P, Mallajosyula SS. Elucidating the role of key structural motifs in antifreeze glycoproteins. Phys Chem Chem Phys 2019; 21:3903-3917. [PMID: 30702099 DOI: 10.1039/c8cp06743k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Antifreeze glycoproteins (AFGPs) are distinctively riveting class of bio-macromolecules, which endows the survival of organisms inhabiting polar and subpolar regions. These proteins are believed to hinder microscopic freezing by interacting with embryonic ice crystals and precluding their further growth. The underlying molecular mechanism by which AFGPs bind to ice has remained elusive due to insufficient structural characterization, with conflicting hypotheses on the possible binding mode of AFGPs - either via the hydrophobic peptide backbone or via the hydrophilic carbohydrate side chains - when interacting with ice. Chemical synthesis has allowed researchers to access synthetic variants of natural AFGPs. These studies revealed that AFGPs exhibit huge variations in their thermal hysteresis and ice shaping behavior with only slight structural variations, especially to the carbohydrate side chains. Four key structural motifs were identified as crucial to AFGP activity: the presence of a threonine γ-methyl group, an α-glycosidic carbohydrate-protein linkage, an acetylamide group (-NHCOCH3) at the C2 position of the carbohydrate linked to the protein, and the presence of carbohydrate hydroxyl groups. In this study, we use molecular dynamics (MD) simulations to probe the microscopic properties of water accompanying these structural variations of AFGPs. We find that these variations primarily influence the conformation space of AFGPs and also crucially control their hydration dynamics. Owing to the disordered nature of AFGPs we use Markov-state modeling to identify the conformational preferences of AFGPs. The simulations reveal the importance of steric bulk, intra-molecular carbohydrate-protein H-bonds and conformational preferences (α- vs. β-linkages) in controlling the spatial segregation of the hydrophilic and hydrophobic regions of AFGPs. We hypothesize that the hydrophobic component of AFGPs is crucial to their binding to ice, which determines the ice shaping ability of AFGPs. However, the hydrophilic carbohydrate hydroxyl groups and their ability to form water bridges control the subsequent hydration dynamics, which is key to the antifreeze properties. Investigating the tetrahedral order parameter of water molecules around the carbohydrates revealed competition between solute- and bulk-influenced solvent structures, with maximum restructuring being observed in the interfacial region 2.5-4.5 Å away from the AFGPs.
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Affiliation(s)
- Poonam Pandey
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Simkheda, Gandhinagar, Gujarat, India.
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9
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Giubertoni G, Meister K, DeVries AL, Bakker HJ. Determination of the Solution Structure of Antifreeze Glycoproteins Using Two-Dimensional Infrared Spectroscopy. J Phys Chem Lett 2019; 10:352-357. [PMID: 30615465 PMCID: PMC6369719 DOI: 10.1021/acs.jpclett.8b03468] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 01/07/2019] [Indexed: 05/20/2023]
Abstract
We study the solution structure of antifreeze glycoproteins (AFGPs) with linear and two-dimensional infrared spectroscopy (2D-IR). With 2D-IR, we study the coupling between the amide I and amide II vibrations of AFGPs. The measured nonlinear spectral response constitutes a much more clearly resolved amide I spectrum than the linear absorption spectrum of the amide I vibrations and allows us to identify the different structural elements of AFGPs in solution. We find clear evidence for the presence of polyproline II (PPII) helical structures already at room temperature, and we find that the fraction of PPII structures increases when the temperature is decreased to the biological working temperature of AFGP. We observe that inhibition of the antifreeze activity of AFGP using borate buffer or enhancing the antifreeze activity using sulfate buffer does not lead to significant changes in the protein conformation. This finding indicates that AFGPs bind to ice with their sugar side chains.
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Affiliation(s)
| | - Konrad Meister
- Max-Planck
Institute for Polymer Research, D-55128 Mainz, Germany
| | - Arthur L. DeVries
- University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Huib J. Bakker
- AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
- E-mail:
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10
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Adam MK, Jarrett‐Wilkins C, Beards M, Staykov E, MacFarlane LR, Bell TDM, Matthews JM, Manners I, Faul CFJ, Moens PDJ, Ben RN, Wilkinson BL. 1D Self‐Assembly and Ice Recrystallization Inhibition Activity of Antifreeze Glycopeptide‐Functionalized Perylene Bisimides. Chemistry 2018; 24:7834-7839. [DOI: 10.1002/chem.201800857] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Indexed: 01/18/2023]
Affiliation(s)
- Madeleine K. Adam
- Department of Chemistry and Biomolecular Sciences University of Ottawa Ottawa K1N 6N5 Canada
| | | | - Michael Beards
- School of Chemistry Monash University Melbourne 3800 Australia
| | - Emiliyan Staykov
- Department of Chemistry and Biomolecular Sciences University of Ottawa Ottawa K1N 6N5 Canada
| | | | - Toby D. M. Bell
- School of Chemistry Monash University Melbourne 3800 Australia
| | - Jacqueline M. Matthews
- School of Life and Environmental Sciences The University of Sydney Sydney 2006 Australia
| | - Ian Manners
- School of Chemistry University of Bristol Bristol BS8 1TS UK
| | | | - Pierre D. J. Moens
- School of Science and Technology University of New England Armidale 2351 Australia
| | - Robert N. Ben
- Department of Chemistry and Biomolecular Sciences University of Ottawa Ottawa K1N 6N5 Canada
| | - Brendan L. Wilkinson
- School of Science and Technology University of New England Armidale 2351 Australia
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11
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Mochizuki K, Molinero V. Antifreeze Glycoproteins Bind Reversibly to Ice via Hydrophobic Groups. J Am Chem Soc 2018; 140:4803-4811. [PMID: 29392937 DOI: 10.1021/jacs.7b13630] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Antifreeze molecules allow organisms to survive in subzero environments. Antifreeze glycoproteins (AFGPs), produced by polar fish, are the most potent inhibitors of ice recrystallization. To date, the molecular mechanism by which AFGPs bind to ice has not yet been elucidated. Mutation experiments cannot resolve whether the binding occurs through the peptide, the saccharides, or both. Here, we use molecular simulations to determine the mechanism and driving forces for binding of AFGP8 to ice, its selectivity for the primary prismatic plane, and the molecular origin of its exceptional ice recrystallization activity. Consistent with experiments, AFGP8 in simulations preferentially adopts the PPII helix secondary structure in solution. We show that the segregation of hydrophilic and hydrophobic groups in the PPII helix is vital for ice binding. Binding occurs through adsorption of methyl groups of the peptide and disaccharides to ice, driven by the entropy of dehydration of the hydrophobic groups as they nest in the cavities at the ice surface. The selectivity to the primary prismatic plane originates in the deeper cavities it has compared to the basal plane. We estimate the free energy of binding of AFGP8 and the longer AFGPs4-6, and find them to be consistent with the reversible binding demonstrated in experiments. The simulations reveal that AFGP8 binds to ice through a myriad of conformations that it uses to diffuse through the ice surface and find ice steps, to which it strongly adsorbs. We interpret that the existence of multiple, weak binding sites is the key for the exceptional ice recrystallization inhibition activity of AFGPs.
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Affiliation(s)
- Kenji Mochizuki
- Department of Chemistry , The University of Utah , Salt Lake City , Utah 84112-0580 , United States.,Institute for Fiber Engineering , Shinshu University , Ueda , Nagano 386-8567 , Japan
| | - Valeria Molinero
- Department of Chemistry , The University of Utah , Salt Lake City , Utah 84112-0580 , United States
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12
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Orii R, Sakamoto N, Fukami D, Tsuda S, Izumi M, Kajihara Y, Okamoto R. Total Synthesis of O
-GalNAcylated Antifreeze Glycoprotein using the Switchable Reactivity of Peptidyl-N
-pivaloylguanidine. Chemistry 2017; 23:9253-9257. [DOI: 10.1002/chem.201702243] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Indexed: 01/06/2023]
Affiliation(s)
- Ryo Orii
- Department of Chemistry; Graduate School of Science, Osaka University; 1-1, Toyonaka Osaka 5600043 Japan
| | - Noriko Sakamoto
- Department of Chemistry; Graduate School of Science, Osaka University; 1-1, Toyonaka Osaka 5600043 Japan
| | - Daichi Fukami
- Transdisciplinary Life Science Course; Graduate School of Life Science; Hokkaido University and Bioproduction Research Institute; National Institute of Advanced Industrial Science and Technology (AIST); 2-17-2-1 Tsukisamu-Higashi, Toyohira, Sapporo Hokkaido 0628517 Japan
| | - Sakae Tsuda
- Transdisciplinary Life Science Course; Graduate School of Life Science; Hokkaido University and Bioproduction Research Institute; National Institute of Advanced Industrial Science and Technology (AIST); 2-17-2-1 Tsukisamu-Higashi, Toyohira, Sapporo Hokkaido 0628517 Japan
| | - Masayuki Izumi
- Department of Chemistry; Graduate School of Science, Osaka University; 1-1, Toyonaka Osaka 5600043 Japan
| | - Yasuhiro Kajihara
- Department of Chemistry; Graduate School of Science, Osaka University; 1-1, Toyonaka Osaka 5600043 Japan
| | - Ryo Okamoto
- Department of Chemistry; Graduate School of Science, Osaka University; 1-1, Toyonaka Osaka 5600043 Japan
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13
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Groot CCM, Meister K, DeVries AL, Bakker HJ. Dynamics of the Hydration Water of Antifreeze Glycoproteins. J Phys Chem Lett 2016; 7:4836-4840. [PMID: 27934047 DOI: 10.1021/acs.jpclett.6b02483] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Antifreeze glycoproteins (AFGPs) are unique proteins that inhibit the growth of ice by a mechanism that is still unclear. We study the dynamics of water in aqueous solutions of small and large isoforms of AFGPs using polarization-resolved femtosecond infrared spectroscopy. We find that a fraction of the water molecules is strongly slowed down by the interaction with the antifreeze glycoprotein surface. The fraction of slow water molecules scales with the size and concentration of AFGP, and is similar to the fraction of slow water observed for nonantifreeze proteins, both at room temperature and close to biologically relevant working temperatures. We observe that inhibiting AFGP antifreeze activity using borate buffer induces no changes in the dynamics of water hydrating the AFGP. Our findings support a mechanism in which the sugar unit of AFGP forms the active ice-binding site.
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Affiliation(s)
- Carien C M Groot
- FOM Institute AMOLF , Science Park 104, 1098 XG, Amsterdam, The Netherlands
| | - Konrad Meister
- FOM Institute AMOLF , Science Park 104, 1098 XG, Amsterdam, The Netherlands
| | - Arthur L DeVries
- Department of Animal Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Huib J Bakker
- FOM Institute AMOLF , Science Park 104, 1098 XG, Amsterdam, The Netherlands
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14
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Mallajosyula SS, Vanommeslaeghe K, MacKerell AD. Perturbation of long-range water dynamics as the mechanism for the antifreeze activity of antifreeze glycoprotein. J Phys Chem B 2014; 118:11696-706. [PMID: 25137353 PMCID: PMC4191590 DOI: 10.1021/jp508128d] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Very little is known about the mechanism of antifreeze action of antifreeze glycoproteins (AFGPs) present in Antarctic teleost fish. Recent NMR and CD studies assisted with total synthesis of synthetic AFGP variants have provided insight into the structure of short AFGP glycopeptides, though the observations did not yield information on the antifreeze mechanism of action. In this study, we use Hamiltonian replica exchange (HREX) molecular dynamics simulations to probe the structure and surrounding aqueous environments of both the natural (AFGP8) and synthetic (s-AFGP4) AFGPs. AFGPs can adopt both amphiphilic and pseudoamphiphilic conformations, the preference of which is related to the proline content of the peptide. The arrangement of carbohydrates allows the hydroxyl groups on terminal galactose units to form stable water bridges which in turn influence the hydrogen-bond network, structure, and dynamics of the surrounding solvent. Interestingly, these local effects lead to the perturbation of the tetrahedral environment for water molecules in hydration layers far (10.0-12.0 Å) from the AFGPs. This structure-induced alteration of long-range hydration dynamics is proposed to be the major contributor to antifreeze activity, a conclusion that is in line with terahertz spectroscopy experiments. The detailed structure-mechanism correlation provided in this study could lead to the design of better synthetic AFGP variants.
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Affiliation(s)
- Sairam S Mallajosyula
- Department of Pharmaceutical Sciences, University of Maryland , 20 Penn Street HSF II, Baltimore, Maryland 21201, United States
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15
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Corcilius L, Santhakumar G, Stone RS, Capicciotti CJ, Joseph S, Matthews JM, Ben RN, Payne RJ. Synthesis of peptides and glycopeptides with polyproline II helical topology as potential antifreeze molecules. Bioorg Med Chem 2013; 21:3569-81. [DOI: 10.1016/j.bmc.2013.02.025] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 02/01/2013] [Accepted: 02/12/2013] [Indexed: 10/27/2022]
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16
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Nagel L, Budke C, Dreyer A, Koop T, Sewald N. Antifreeze glycopeptide diastereomers. Beilstein J Org Chem 2012; 8:1657-67. [PMID: 23209499 PMCID: PMC3510999 DOI: 10.3762/bjoc.8.190] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2012] [Accepted: 08/28/2012] [Indexed: 01/09/2023] Open
Abstract
Antifreeze glycopeptides (AFGPs) are a special class of biological antifreeze agents, which possess the property to inhibit ice growth in the body fluids of arctic and antarctic fish and, thus, enable life under these harsh conditions. AFGPs are composed of 4-55 tripeptide units -Ala-Ala-Thr- glycosylated at the threonine side chains. Despite the structural homology among all the fish species, divergence regarding the composition of the amino acids occurs in peptides from natural sources. Although AFGPs were discovered in the early 1960s, the adsorption mechanism of these macromolecules to the surface of the ice crystals has not yet been fully elucidated. Two AFGP diastereomers containing different amino acid configurations were synthesized to study the influence of amino acid stereochemistry on conformation and antifreeze activity. For this purpose, peptides containing monosaccharide-substituted allo-L- and D-threonine building blocks were assembled by solid-phase peptide synthesis (SPPS). The retro-inverso AFGP analogue contained all amino acids in D-configuration, while the allo-L-diastereomer was composed of L-amino acids, like native AFGPs, with replacement of L-threonine by its allo-L-diastereomer. Both glycopeptides were analyzed regarding their conformational properties, by circular dichroism (CD), and their ability to inhibit ice recrystallization in microphysical experiments.
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Affiliation(s)
- Lilly Nagel
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Carsten Budke
- Physical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Axel Dreyer
- Physical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Thomas Koop
- Physical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Norbert Sewald
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
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17
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Nagel L, Budke C, Erdmann RS, Dreyer A, Wennemers H, Koop T, Sewald N. Influence of Sequential Modifications and Carbohydrate Variations in Synthetic AFGP Analogues on Conformation and Antifreeze Activity. Chemistry 2012; 18:12783-93. [DOI: 10.1002/chem.201202119] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Indexed: 11/08/2022]
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18
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Wilkinson BL, Stone RS, Capicciotti CJ, Thaysen-Andersen M, Matthews JM, Packer NH, Ben RN, Payne RJ. Total Synthesis of Homogeneous Antifreeze Glycopeptides and Glycoproteins. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201108682] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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19
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Wilkinson BL, Stone RS, Capicciotti CJ, Thaysen-Andersen M, Matthews JM, Packer NH, Ben RN, Payne RJ. Total Synthesis of Homogeneous Antifreeze Glycopeptides and Glycoproteins. Angew Chem Int Ed Engl 2012; 51:3606-10. [DOI: 10.1002/anie.201108682] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 01/26/2012] [Indexed: 01/30/2023]
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20
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Nagel L, Plattner C, Budke C, Majer Z, DeVries AL, Berkemeier T, Koop T, Sewald N. Synthesis and characterization of natural and modified antifreeze glycopeptides: glycosylated foldamers. Amino Acids 2011; 41:719-32. [DOI: 10.1007/s00726-011-0937-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Accepted: 04/18/2011] [Indexed: 11/29/2022]
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Abstract
Antifreeze glycoproteins are an important class of biological antifreezes that have potential applications in many areas of medicine, agriculture and industry in which ice crystal growth is damaging. While the synthesis of antifreeze glycoproteins as pure glycoforms has recently been achieved by using ligation and polymerisation strategies, the routine production of large quantities of pure glycoforms remains challenging. A range of C-linked analogues that are readily produced by solid-phase synthesis have delivered novel compounds that are not biological antifreezes, but are potent, non-cytotoxic, ice-recrystallisation inhibitors. Structure-activity studies, the identification of cyclic antifreeze glycoproteins and conformational studies have provided further insight into the requirements for antifreeze activity. These results, coupled with significant advances in approaches to the routine synthesis of different glycoproteins and mimics, present opportunities for the design and synthesis of novel ice-growth-inhibiting and antifreeze compounds.
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Affiliation(s)
- James Garner
- School of Chemistry, The University of New South Wales, Sydney, NSW 2052, Australia
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22
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Peltier R, Brimble MA, Wojnar JM, Williams DE, Evans CW, DeVries AL. Synthesis and antifreeze activity of fish antifreeze glycoproteins and their analogues. Chem Sci 2010. [DOI: 10.1039/c0sc00194e] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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23
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Tam RY, Rowley CN, Petrov I, Zhang T, Afagh NA, Woo TK, Ben RN. Solution Conformation of C-Linked Antifreeze Glycoprotein Analogues and Modulation of Ice Recrystallization. J Am Chem Soc 2009; 131:15745-53. [DOI: 10.1021/ja904169a] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Roger Y. Tam
- Department of Chemistry, D’Iorio Hall, 10 Marie Curie, University of Ottawa, Ottawa, ON, Canada K1N 6N5
| | - Christopher N. Rowley
- Department of Chemistry, D’Iorio Hall, 10 Marie Curie, University of Ottawa, Ottawa, ON, Canada K1N 6N5
| | - Ivan Petrov
- Department of Chemistry, D’Iorio Hall, 10 Marie Curie, University of Ottawa, Ottawa, ON, Canada K1N 6N5
| | - Tianyi Zhang
- Department of Chemistry, D’Iorio Hall, 10 Marie Curie, University of Ottawa, Ottawa, ON, Canada K1N 6N5
| | - Nicholas A. Afagh
- Department of Chemistry, D’Iorio Hall, 10 Marie Curie, University of Ottawa, Ottawa, ON, Canada K1N 6N5
| | - Tom K. Woo
- Department of Chemistry, D’Iorio Hall, 10 Marie Curie, University of Ottawa, Ottawa, ON, Canada K1N 6N5
| | - Robert N. Ben
- Department of Chemistry, D’Iorio Hall, 10 Marie Curie, University of Ottawa, Ottawa, ON, Canada K1N 6N5
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24
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Uda Y, Zepeda S, Kaneko F, Matsuura Y, Furukawa Y. Adsorption-Induced Conformational Changes of Antifreeze Glycoproteins at the Ice/Water Interface. J Phys Chem B 2007; 111:14355-61. [DOI: 10.1021/jp075429s] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yukihiro Uda
- Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo 060-0819, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka 560-0043, and Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Japan
| | - Salvador Zepeda
- Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo 060-0819, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka 560-0043, and Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Japan
| | - Fumitoshi Kaneko
- Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo 060-0819, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka 560-0043, and Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Japan
| | - Yoshiki Matsuura
- Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo 060-0819, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka 560-0043, and Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Japan
| | - Yoshinori Furukawa
- Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo 060-0819, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka 560-0043, and Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Japan
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25
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Krishnan VV, Fink WH, Feeney RE, Yeh Y. Translational dynamics of antifreeze glycoprotein in supercooled water. Biophys Chem 2005; 110:223-30. [PMID: 15228958 DOI: 10.1016/j.bpc.2004.02.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2004] [Revised: 02/23/2004] [Accepted: 02/23/2004] [Indexed: 11/23/2022]
Abstract
Structure and dynamics of biomolecules in supercooled water assume a particular and distinct importance in the case of antifreeze glycoproteins (AFGPs), which function at sub-zero temperatures. To investigate whether any large-scale structural digressions in the supercooled state are correlated to the function of AFGPs, self-diffusion behavior of the AFGP8, the smallest AFGP is monitored as a function of temperature from 243 to 303 K using nuclear magnetic resonance (NMR) spectroscopy. The experimental results are compared with the hydrodynamic calculations using the viscosity of water at the same temperature range. In order to evaluate results on AFGP8, the smallest AFGP, constituting approximately two-thirds of the total AFGP fraction in fish blood serum, similar experimental and computational calculations were also performed on a set of globular proteins. These results show that even though the general trend of translational dynamics of AFGP is similar to that of the other globular proteins, AFGP8 appears to be more hydrated (approximately 30% increase in the bead radius) than the others over the temperature range studied. These results also suggest that local conformational changes such as segmental librations or hydrogen bond dynamics that are closer to the protein surface are more likely the determining dynamic factors for the function of AFGPs rather than any large-scale structural rearrangements.
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Affiliation(s)
- V V Krishnan
- Molecular Biophysics Group, Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA.
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26
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Michenfelder M, Fu G, Lawrence C, Weaver JC, Wustman BA, Taranto L, Evans JS, Morse DE. Characterization of two molluscan crystal-modulating biomineralization proteins and identification of putative mineral binding domains. Biopolymers 2004; 70:522-33. [PMID: 14648763 DOI: 10.1002/bip.10536] [Citation(s) in RCA: 143] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Ethylenediamine-tetraacetic acid extracted water-soluble matrix proteins in molluscan shells secreted from the mantle epithelia are believed to control crystal nucleation, morphology, orientation, and phase of the deposited mineral. Previously, atomic force microscopy demonstrated that abalone nacre proteins bind to growing step edges and to specific crystallographic faces of calcite, suggesting that inhibition of calcite growth may be one of the molecular processes required for growth of the less thermodynamically stable aragonite phase. Previous experiments were done with protein mixtures. To elucidate the role of single proteins, we have characterized two proteins isolated from the aragonitic component of nacre of the red abalone, Haliotis rufescens. These proteins, purified by hydrophobic interaction chromatography, are designated AP7 and AP24 (aragonitic protein of molecular weight 7 kDa and 24 kDa, respectively). Degenerate oligonucleotide primers corresponding to N-terminal and internal peptide sequences were used to amplify cDNA clones by a polymerase chain reaction from a mantle cDNA library; the deduced primary amino acid sequences are presented. Preliminary crystal growth experiments demonstrate that protein fractions enriched in AP7 and AP24 produced CaCO(3) crystals with morphology distinct from crystals grown in the presence of the total mixture of soluble aragonite-specific proteins. Peptides corresponding to the first 30 residues of the N-terminal sequences of both AP7 and AP24 were generated. The synthetic peptides frustrate the progression of step edges of a growing calcite surface, indicating that sequence features within the N-termini of AP7 and AP24 include domains that interact with CaCO(3). CD analyses demonstrate that the N-terminal peptide sequences do not possess significant percentages of alpha-helix or beta-strand secondary structure in solution. Instead, in both the presence and absence of Ca(II), the peptides retain unfolded conformations that may facilitate protein-mineral interaction.
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Affiliation(s)
- Martina Michenfelder
- Biomolecular Science and Engineering Program and the Materials Research Laboratory, University of California, Santa Barbara, CA 93106, USA
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27
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Harding MM, Anderberg PI, Haymet ADJ. 'Antifreeze' glycoproteins from polar fish. EUROPEAN JOURNAL OF BIOCHEMISTRY 2003; 270:1381-92. [PMID: 12653993 DOI: 10.1046/j.1432-1033.2003.03488.x] [Citation(s) in RCA: 184] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Antifreeze glycoproteins (AFGPs) constitute the major fraction of protein in the blood serum of Antarctic notothenioids and Arctic cod. Each AFGP consists of a varying number of repeating units of (Ala-Ala-Thr)n, with minor sequence variations, and the disaccharide beta-D-galactosyl-(1-->3)-alpha-N-acetyl-D-galactosamine joined as a glycoside to the hydroxyl oxygen of the Thr residues. These compounds allow the fish to survive in subzero ice-laden polar oceans by kinetically depressing the temperature at which ice grows in a noncolligative manner. In contrast to the more widely studied antifreeze proteins, little is known about the mechanism of ice growth inhibition by AFGPs, and there is no definitive model that explains their properties. This review summarizes the structural and physical properties of AFGPs and advances in the last decade that now provide opportunities for further research in this field. High field NMR spectroscopy and molecular dynamics studies have shown that AFGPs are largely unstructured in aqueous solution. While standard carbohydrate degradation studies confirm the requirement of some of the sugar hydroxyls for antifreeze activity, the importance of following structural elements has not been established: (a) the number of hydroxyls required, (b) the stereochemistry of the sugar hydroxyls (i.e. the requirement of galactose as the sugar), (c) the acetamido group on the first galactose sugar, (d) the stereochemistry of the beta-glycosidic linkage between the two sugars and the alpha-glycosidic linkage to Thr, (e) the requirement of a disaccharide for activity, and (f) the Ala and Thr residues in the polypeptide backbone. The recent successful synthesis of small AFGPs using solution methods and solid-phase chemistry provides the opportunity to perform key structure-activity studies that would clarify the important residues and functional groups required for activity. Genetic studies have shown that the AFGPs present in the two geographically and phylogenetically distinct Antarctic notothenioids and Arctic cod have evolved independently, in a rare example of convergent molecular evolution. The AFGPs exhibit concentration dependent thermal hysteresis with maximum hysteresis (1.2 degrees C at 40 mg x mL-1) observed with the higher molecular mass glycoproteins. The ability to modify the rate and shape of crystal growth and protect cellular membranes during lipid-phase transitions have resulted in identification of a number of potential applications of AFGPs as food additives, and in the cryopreservation and hypothermal storage of cells and tissues.
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Affiliation(s)
- Margaret M Harding
- School of Chemistry, The University of Sydney, New South Wales, Australia.
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28
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Soulages JL, Kim K, Arrese EL, Walters C, Cushman JC. Conformation of a group 2 late embryogenesis abundant protein from soybean. Evidence of poly (L-proline)-type II structure. PLANT PHYSIOLOGY 2003; 131:963-75. [PMID: 12644649 PMCID: PMC166862 DOI: 10.1104/pp.015891] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2002] [Revised: 10/28/2002] [Accepted: 11/15/2002] [Indexed: 05/18/2023]
Abstract
Late embryogenesis abundant (LEA) proteins are members of a large group of hydrophilic, glycine-rich proteins found in plants, algae, fungi, and bacteria known collectively as hydrophilins that are preferentially expressed in response to dehydration or hyperosmotic stress. Group 2 LEA (dehydrins or responsive to abscisic acid) proteins are postulated to stabilize macromolecules against damage by freezing, dehydration, ionic, or osmotic stress. However, the structural and physicochemical properties of group 2 LEA proteins that account for such functions remain unknown. We have analyzed the structural properties of a recombinant form of a soybean (Glycine max) group 2 LEA (rGmDHN1). Differential scanning calorimetry of purified rGmDHN1 demonstrated that the protein does not display a cooperative unfolding transition upon heating. Ultraviolet absorption and circular dichroism spectroscopy revealed that the protein is in a largely hydrated and unstructured conformation in solution. However, ultraviolet absorption and circular dichroism measurements collected at different temperatures showed that the protein exists in equilibrium between two extended conformational states: unordered and left-handed extended helical or poly (L-proline)-type II structures. It is estimated that 27% of the residues of rGmDHN1 adopt or poly (L-proline)-type II-like helical conformation at 12 degrees C. The content of extended helix gradually decreases to 15% as the temperature is increased to 80 degrees C. Studies of the conformation of the protein in solution in the presence of liposomes, trifluoroethanol, and sodium dodecyl sulfate indicated that rGmDHN1 has a very low intrinsic ability to adopt alpha-helical structure and to interact with phospholipid bilayers through amphipathic alpha-helices. The ability of the protein to remain in a highly extended conformation at low temperatures could constitute the basis of the functional role of GmDHN1 in the prevention of freezing, desiccation, ionic, or osmotic stress-related damage to macromolecular structures.
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Affiliation(s)
- Jose L Soulages
- Department of Biochemistry and Molecular Biology, 355 Noble Research Center, Oklahoma State University, Stillwater, Oklahoma 74078-0454, USA
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Tomczak MM, Vígh L, Meyer JD, Manning MC, Hincha DK, Crowe JH. Lipid unsaturation determines the interaction of AFP type I with model membranes during thermotropic phase transitions. Cryobiology 2002; 45:135-42. [PMID: 12482379 DOI: 10.1016/s0011-2240(02)00122-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We have previously shown that antifreeze protein (AFP) type I from winter flounder interacts with the acyl chains of lipids in model membranes containing a mixture of dimyristoylphosphatidylcholine (DMPC) and the plant thylakoid lipid digalactosyldiacylglycerol (DGDG), most likely through hydrophobic interactions. By contrast, in studies with pure phospholipid membranes, no such interaction was seen. DGDG is a highly unsaturated lipid, which renders these studies quite different from the previous studies of AFP-membrane interaction where the lipids were saturated or trans-unsaturated. Therefore, it seemed possible that either the digalactose headgroups or the unsaturated DGDG acyl chains, or both, may be important for interactions of membranes with AFP type I. To distinguish between these possibilities, we catalytically hydrogenated the DGDG to obtain a galactolipid with completely saturated fatty acyl chains. The results with the hydrogenated DGDG were strikingly different from those obtained previously with the unsaturated DGDG; the clear binding of AFPs to the bilayer appeared to be lost. Nevertheless, the temperature-dependent folding of AFP type I was inhibited in the presence of liposomes containing either the unsaturated or the hydrogenated DGDG. The results indicate that the liposomes and protein still interact, even following hydrogenation of the acyl chains, perhaps at the membrane-solution interface.
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Affiliation(s)
- Melanie M Tomczak
- Section of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA.
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Nguyen DH, Colvin ME, Yeh Y, Feeney RE, Fink WH. The dynamics, structure, and conformational free energy of proline-containing antifreeze glycoprotein. Biophys J 2002; 82:2892-905. [PMID: 12023212 PMCID: PMC1302077 DOI: 10.1016/s0006-3495(02)75630-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Recent NMR studies of the solution structure of the 14-amino acid antifreeze glycoprotein AFGP-8 have concluded that the molecule lacks long-range order. The implication that an apparently unstructured molecule can still have a very precise function as a freezing inhibitor seems startling at first consideration. To gain insight into the nature of conformations and motions in AFGP-8, we have undertaken molecular dynamics simulations augmented with free energy calculations using a continuum solvation model. Starting from 10 different NMR structures, 20 ns of dynamics of AFGP were explored. The dynamics show that AFGP structure is composed of four segments, joined by very flexible pivots positioned at alanine 5, 8, and 11. The dynamics also show that the presence of prolines in this small AFGP structure facilitates the adoption of the poly-proline II structure as its overall conformation, although AFGP does adopt other conformations during the course of dynamics as well. The free energies calculated using a continuum solvation model show that the lowest free energy conformations, while being energetically equal, are drastically different in conformations. In other words, this AFGP molecule has many structurally distinct and energetically equal minima in its energy landscape. In addition, conformational, energetic, and hydrogen bond analyses suggest that the intramolecular hydrogen bonds between the N-acetyl group and the protein backbone are an important integral part of the overall stability of the AFGP molecule. The relevance of these findings to the mechanism of freezing inhibition is discussed.
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Affiliation(s)
- Dat H Nguyen
- Department of Chemistry, University of California, Davis, California 95616, USA
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31
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Soulages JL, Kim K, Walters C, Cushman JC. Temperature-induced extended helix/random coil transitions in a group 1 late embryogenesis-abundant protein from soybean. PLANT PHYSIOLOGY 2002; 128:822-32. [PMID: 11891239 PMCID: PMC152196 DOI: 10.1104/pp.010521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2001] [Revised: 09/19/2001] [Accepted: 11/03/2001] [Indexed: 05/09/2023]
Abstract
Group 1 late embryogenesis-abundant (LEA) proteins are a subset of hydrophilins that are postulated to play important roles in protecting plant macromolecules from damage during freezing, desiccation, or osmotic stress. To better understand the putative functional roles of group 1 LEA proteins, we analyzed the structure of a group 1 LEA protein from soybean (Glycine max). Differential scanning calorimetry of the purified, recombinant protein demonstrated that the protein assumed a largely unstructured state in solution. In the presence of trifluoroethanol (50% [w/v]), the protein acquired a 30% alpha-helical content, indicating that the polypeptide is highly restricted to adopt alpha-helical structures. In the presence of sodium dodecyl sulfate (1% [w/v]), 8% of the polypeptide chain adopted an alpha-helical structure. However, incubation with phospholipids showed no effect on the protein structure. Ultraviolet absorption and circular dichroism spectroscopy revealed that the protein existed in equilibrium between two conformational states. Ultraviolet absorption spectroscopy studies also showed that the protein became more hydrated upon heating. Furthermore, circular dichroism spectral measurements indicated that a minimum of 14% of amino acid residues existed in a solvent-exposed, left-handed extended helical or poly (L-proline)-type (PII) conformation at 20 degrees C with the remainder of the protein being unstructured. The content of PII-like structure increased as temperature was lowered. We hypothesize that by favoring the adoption of PII structure, instead of the formation of alpha-helical or beta-sheet structures, group 1 LEA proteins retain a high content of surface area available for interaction with the solvent. This feature could constitute the basis of a potential role of LEA proteins in preventing freezing, desiccation, or osmotic stress damage.
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Affiliation(s)
- Jose L Soulages
- Department of Biochemistry and Molecular Biology, 355 Noble Research Center, Oklahoma State University, Stillwater, Oklahoma 74078-0454, USA
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32
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Tsvetkova NM, Phillips BL, Krishnan VV, Feeney RE, Fink WH, Crowe JH, Risbud SH, Tablin F, Yeh Y. Dynamics of antifreeze glycoproteins in the presence of ice. Biophys J 2002; 82:464-73. [PMID: 11751333 PMCID: PMC1302486 DOI: 10.1016/s0006-3495(02)75411-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Antifreeze glycoproteins from the Greenland cod Boreogadus saida were dimethylated at the N-terminus (m*AFGP) and their dynamics and conformational properties were studied in the presence of ice using (13)C-NMR and FTIR spectroscopy. (13)C-NMR experiments of m*AFGP in D(2)O, in H(2)O, and of freeze-dried m*AFGP were performed as a function of temperature. Dynamic parameters ((1)H T(1 rho) and T(CH)) obtained by varying the contact time revealed notable differences in the motional properties of AFGP between the different states. AFGP/ice dynamics was dominated by fast-scale motions (nanosecond to picosecond time scale), suggesting that the relaxation is markedly affected by the protein hydration. The data suggest that AFGP adopts a similar type of three-dimensional fold both in the presence of ice and in the freeze-dried state. FTIR studies of the amide I band did not show a single prevailing secondary structure in the frozen state. The high number of conformers suggests a high flexibility, and possibly reflects the necessity to expose more ice-binding groups. The data suggest that the effect of hydration on the local mobility of AFGP and the lack of significant change in the backbone conformation in the frozen state may play a role in inhibiting the ice crystal growth.
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Affiliation(s)
- Nelly M Tsvetkova
- Section of Molecular and Cellular Biology, University of California, Davis, California 95616, USA.
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Kindahl L, Sandström C, Norberg T, Kenne L. (1)H NMR studies of hydroxy protons of the V[beta-Gal(1-->3)-alpha-GalNAc(1-->O)]THPGY glycopeptide. Carbohydr Res 2001; 336:319-23. [PMID: 11728401 DOI: 10.1016/s0008-6215(01)00271-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The hydroxy protons of the disaccharide moiety in the glycopeptide Val-[beta-Gal(1-->3)-alpha-GalNAc(1-->O)]-Thr-His-Pro-Gly-Tyr (1) have been investigated in aqueous solution using (1)H NMR spectroscopy. The chemical shifts (delta), coupling constants ((3)J(CH,OH)), temperature coefficients (d delta/dT), exchange rates (k(ex)), and NOEs have been measured. The data show that the O(2')H of Gal has a reduced contact with water due to steric interference caused by the 2-acetamido group of GalNAc. No interaction, in terms of hydrogen bonding exists between the disaccharide and the peptide moieties, but the rotation around the sugar-peptide linkage is restricted.
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Affiliation(s)
- L Kindahl
- Department of Chemistry, Swedish University of Agricultural Sciences, PO Box 7015, SE 750 07 Uppsala, Sweden
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