1
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Thosar AU, Cai Y, Marks SM, Vicars Z, Choi J, Pallath A, Patel AJ. On the engulfment of antifreeze proteins by ice. Proc Natl Acad Sci U S A 2024; 121:e2320205121. [PMID: 38833468 DOI: 10.1073/pnas.2320205121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 04/16/2024] [Indexed: 06/06/2024] Open
Abstract
Antifreeze proteins (AFPs) are remarkable biomolecules that suppress ice formation at trace concentrations. To inhibit ice growth, AFPs must not only bind to ice crystals, but also resist engulfment by ice. The highest supercooling, [Formula: see text], for which AFPs are able to resist engulfment is widely believed to scale as the inverse of the separation, [Formula: see text], between bound AFPs, whereas its dependence on the molecular characteristics of the AFP remains poorly understood. By using specialized molecular simulations and interfacial thermodynamics, here, we show that in contrast with conventional wisdom, [Formula: see text] scales as [Formula: see text] and not as [Formula: see text]. We further show that [Formula: see text] is proportional to AFP size and that diverse naturally occurring AFPs are optimal at resisting engulfment by ice. By facilitating the development of AFP structure-function relationships, we hope that our findings will pave the way for the rational design of AFPs.
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Affiliation(s)
- Aniket U Thosar
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104
| | - Yusheng Cai
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104
| | - Sean M Marks
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104
| | - Zachariah Vicars
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104
| | - Jeongmoon Choi
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104
| | - Akash Pallath
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104
| | - Amish J Patel
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104
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2
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Hudait A. Multiscale Molecular Dynamics Simulations of Ice-Binding Proteins. Methods Mol Biol 2024; 2730:185-202. [PMID: 37943459 DOI: 10.1007/978-1-0716-3503-2_13] [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
Ice-binding proteins (IBPs) are a diverse class of proteins that are essential for the survival of organisms in cold conditions. IBPs are diverse in their function and can prevent or promote ice growth and selectively bind to specific crystallographic planes of the growing ice lattice. Moreover, IBPs are widely utilized to modulate ice crystal growth and recrystallization in the food industry and as cryoprotectants to preserve biological matter. A key unresolved aspect of the mode of action is how the ice-binding sites of these proteins distinguish between ice and water and interact with multiple crystal facets of the ice. The use of molecular dynamics (MD) simulation allows us to thoroughly investigate the binding mechanism and energetics of ice-binding proteins, to complement and expand on the mechanistic understandings gained from experiments. In this chapter, we describe a series of molecular dynamics simulation methodologies to investigate the mechanism of action of ice-binding proteins. Specifically, we provide detailed instructions to set up MD simulations to study the binding and interaction of ice-binding proteins using atomistic and coarse-grained simulations.
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Affiliation(s)
- Arpa Hudait
- Department of Chemistry, Chicago Center for Theoretical Chemistry, The University of Chicago, Chicago, IL, USA.
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3
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Farag H, Peters B. Engulfment Avalanches and Thermal Hysteresis for Antifreeze Proteins on Supercooled Ice. J Phys Chem B 2023. [PMID: 37294871 DOI: 10.1021/acs.jpcb.3c01089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Antifreeze proteins (AFPs) bind to the ice-water surface and prevent ice growth at temperatures below 0 °C through a Gibbs-Thomson effect. Each adsorbed AFP creates a metastable depression on the surface that locally resists ice growth, until ice engulfs the AFP. We recently predicted the susceptibility to engulfment as a function of AFP size, distance between AFPs, and supercooling [ J. Chem. Phys. 2023, 158, 094501]. For an ensemble of AFPs adsorbed on the ice surface, the most isolated AFPs are the most susceptible, and when an isolated AFP gets engulfed, its former neighbors become more isolated and more susceptible to engulfment. Thus, an initial engulfment event can trigger an avalanche of subsequent engulfment events, leading to a sudden surge of unrestrained ice growth. This work develops a model to predict the supercooling at which the first engulfment event will occur for an ensemble of randomly distributed AFP pinning sites on an ice surface. Specifically, we formulate an inhomogeneous survival probability that accounts for the AFP coverage, the distribution of AFP neighbor distances, the resulting ensemble of engulfment rates, the ice surface area, and the cooling rate. We use the model to predict thermal hysteresis trends and compare with experimental data.
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Affiliation(s)
- Hossam Farag
- Nuclear, Plasma, and Radiological Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Baron Peters
- Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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4
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Water-organizing motif continuity is critical for potent ice nucleation protein activity. Nat Commun 2022; 13:5019. [PMID: 36028506 PMCID: PMC9418140 DOI: 10.1038/s41467-022-32469-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 07/29/2022] [Indexed: 12/02/2022] Open
Abstract
Bacterial ice nucleation proteins (INPs) can cause frost damage to plants by nucleating ice formation at high sub-zero temperatures. Modeling of Pseudomonas borealis INP by AlphaFold suggests that the central domain of 65 tandem sixteen-residue repeats forms a beta-solenoid with arrays of outward-pointing threonines and tyrosines, which may organize water molecules into an ice-like pattern. Here we report that mutating some of these residues in a central segment of P. borealis INP, expressed in Escherichia coli, decreases ice nucleation activity more than the section’s deletion. Insertion of a bulky domain has the same effect, indicating that the continuity of the water-organizing repeats is critical for optimal activity. The ~10 C-terminal coils differ from the other 55 coils in being more basic and lacking water-organizing motifs; deletion of this region eliminates INP activity. We show through sequence modifications how arrays of conserved motifs form the large ice-nucleating surface required for potency. Ice nucleation proteins have the same tandemly arrayed water-organizing motifs seen in some antifreeze proteins, but on a larger scale. The authors show that mutation, interruption, and truncation of these arrays reduce ice nucleation activity indicating that the two protein types share a common mechanism.
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5
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Wu X, Yao F, Zhang H, Li J. Antifreeze proteins and their biomimetics for cell cryopreservation: Mechanism, function and application-A review. Int J Biol Macromol 2021; 192:1276-1291. [PMID: 34634336 DOI: 10.1016/j.ijbiomac.2021.09.211] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/30/2021] [Accepted: 09/30/2021] [Indexed: 12/26/2022]
Abstract
Cell-based therapy is a promising technology for intractable diseases and health care applications, in which cryopreservation has become an essential procedure to realize the production of therapeutic cells. Ice recrystallization is the major factor that affects the post-thaw viability of cells. As a typical series of biomacromolecules with ice recrystallization inhibition (IRI) activity, antifreeze proteins (AFPs) have been employed in cell cryopreservation. Meanwhile, synthesized materials with IRI activity have emerged in the name of biomimetics of AFPs to expand their availability and practicality. However, fabrication of AFPs mimetics is in a chaotic period. There remains little commonality among different AFPs mimetics, then it is difficult to set guidelines on their design. With no doubt, a comprehensive understanding on the antifreezing mechanism of AFPs in molecular level will enable us to rebuild the function of AFPs, and provide convenience to clarify the relationship between structure and function of these early stage biomimetics. In this review, we would discuss those previously reported biomimetics to summarize their structure characteristics concerning the IRI activity and attempt to develop a roadmap for guiding the design of novel AFPs mimetics.
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Affiliation(s)
- Xiaojun Wu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
| | - Fanglian Yao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300350, China
| | - Hong Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300350, China.
| | - Junjie Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300350, China.
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6
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Beetle and mussel-inspired chimeric protein for fabricating anti-icing coating. Colloids Surf B Biointerfaces 2021; 210:112252. [PMID: 34902712 DOI: 10.1016/j.colsurfb.2021.112252] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 11/24/2021] [Accepted: 11/25/2021] [Indexed: 11/23/2022]
Abstract
Ice accretion on surfaces can cause serious damages and economic losses in industries and civilian facilities. Antifreeze proteins (AFPs) as evolutionary adaptation products of organisms to cold climates, provide solutions for alleviating icing problems. In this work, a chimeric protein Mfp-AFP was rationally designed combining mussel-inspired adhesive domain with Tenebrio molitor-derived antifreeze protein domain. Expectedly, the multifunctional Mfp-AFP can lower the freezing point of water and inhibit ice recrystallization. The chimeric protein could also readily modify diverse solid surfaces due to the adhesive domain containing Dopa, and resist frosting and delay ice formation due to the beetle-derived antifreeze fragment. Moreover, Mfp-AFP coatings display excellent biocompatibility proved by cytocompatibility and hemolysis assays. Here, the designed multifunctional protein coatings provide an alternative strategy for fabricating anti-icing surfaces.
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7
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Schmüser L, Trefz M, Roeters SJ, Beckner W, Pfaendtner J, Otzen D, Woutersen S, Bonn M, Schneider D, Weidner T. Membrane Structure of Aquaporin Observed with Combined Experimental and Theoretical Sum Frequency Generation Spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:13452-13459. [PMID: 34729987 DOI: 10.1021/acs.langmuir.1c02206] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
High-resolution structural information on membrane proteins is essential for understanding cell biology and for the structure-based design of new medical drugs and drug delivery strategies. X-ray diffraction (XRD) can provide angstrom-level information about the structure of membrane proteins, yet for XRD experiments, proteins are removed from their native membrane environment, chemically stabilized, and crystallized, all of which can compromise the conformation. Here, we describe how a combination of surface-sensitive vibrational spectroscopy and molecular dynamics simulations can account for the native membrane environment. We observe the structure of a glycerol facilitator channel (GlpF), an aquaporin membrane channel finely tuned to selectively transport water and glycerol molecules across the membrane barrier. We find subtle but significant differences between the XRD structure and the inferred in situ structure of GlpF.
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Affiliation(s)
- L Schmüser
- Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - M Trefz
- Department of Chemistry-Biochemistry, University of Mainz, Johann-Joachim-Becher-Weg 30, 55128 Mainz, Germany
| | - S J Roeters
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - W Beckner
- Department of Chemical Engineering, University of Washington, 105 Benson Hall, Seattle, Washington 98195-1750, United States
| | - J Pfaendtner
- Department of Chemical Engineering, University of Washington, 105 Benson Hall, Seattle, Washington 98195-1750, United States
| | - D Otzen
- iNANO, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - S Woutersen
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - M Bonn
- Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
| | - D Schneider
- Department of Chemistry-Biochemistry, University of Mainz, Johann-Joachim-Becher-Weg 30, 55128 Mainz, Germany
| | - T Weidner
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
- Department of Chemical Engineering, University of Washington, 105 Benson Hall, Seattle, Washington 98195-1750, United States
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8
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Cui S, Zhang W, Shao X, Cai W. Hyperactive Antifreeze Proteins Promote Ice Growth before Binding to It. J Chem Inf Model 2021; 62:5165-5174. [PMID: 34711054 DOI: 10.1021/acs.jcim.1c00915] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The antifreeze mechanism of antifreeze proteins (AFPs) evolved by organisms has been widely studied. However, detailed knowledge of the synergy between AFPs and ice crystals still remains fragmentary. In the present contribution, the cooperative effect of the hyperactive insect antifreeze protein TmAFP and ice crystals on the interfacial water during the entire process of inhibiting ice growth is systematically investigated at the atomic level and compared with its low activity mutant and a nonantifreeze protein. The results indicate a significant synergy between TmAFP and ice crystals, which enables the TmAFP to promote the ice growth before adsorbing on the surfaces of the ice crystals, while the mutant and the nonantifreeze protein cannot promote the ice growth due to the lack of this synergy. When TmAFP approaches the ice surface, the interfacial water is induced by both the AFP and the ice crystals to form the anchored clathrate motif, which binds TmAFP to the ice surface, resulting in a local increase in the curvature of the ice surface, thereby inhibiting the growth of ice. In this study, three stages, namely, promotion, adsorption, and inhibition, are observed in the complete process of TmAFP inhibiting ice growth, and the synergistic mechanism between protein and ice crystals is revealed. The results are helpful for the design of antifreeze proteins and bioinspired antifreeze materials with superior performance.
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Affiliation(s)
- Shaoli Cui
- Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Tianjin 300071, China
| | - Weijia Zhang
- Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Tianjin 300071, China
| | - Xueguang Shao
- Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Tianjin 300071, China
| | - Wensheng Cai
- Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Tianjin 300071, China
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9
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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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10
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Analysis of the Sequence Characteristics of Antifreeze Protein. Life (Basel) 2021; 11:life11060520. [PMID: 34204983 PMCID: PMC8226703 DOI: 10.3390/life11060520] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/27/2021] [Accepted: 05/31/2021] [Indexed: 12/31/2022] Open
Abstract
Antifreeze protein (AFP) is a proteinaceous compound with improved antifreeze ability and binding ability to ice to prevent its growth. As a surface-active material, a small number of AFPs have a tremendous influence on the growth of ice. Therefore, identifying novel AFPs is important to understand protein–ice interactions and create novel ice-binding domains. To date, predicting AFPs is difficult due to their low sequence similarity for the ice-binding domain and the lack of common features among different AFPs. Here, a computational engine was developed to predict the features of AFPs and reveal the most important 39 features for AFP identification, such as antifreeze-like/N-acetylneuraminic acid synthase C-terminal, insect AFP motif, C-type lectin-like, and EGF-like domain. With this newly presented computational method, a group of previously confirmed functional AFP motifs was screened out. This study has identified some potential new AFP motifs and contributes to understanding biological antifreeze mechanisms.
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11
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Mousazadehkasin M, Tsavalas JG. Insights into Design of Biomimetic Glycerol-Grafted Polyol-Based Polymers for Ice Nucleation/Recrystallization Inhibition and Thermal Hysteresis Activity. Biomacromolecules 2020; 21:4626-4637. [DOI: 10.1021/acs.biomac.0c00907] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Mohammad Mousazadehkasin
- Department of Chemistry, University of New Hampshire, Durham, New Hampshire 03824, United States
| | - John G. Tsavalas
- Department of Chemistry, University of New Hampshire, Durham, New Hampshire 03824, United States
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12
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Pal P, Chakraborty S, Jana B. Deciphering the Role of the Non-ice-binding Surface in the Antifreeze Activity of Hyperactive Antifreeze Proteins. J Phys Chem B 2020; 124:4686-4696. [PMID: 32425044 DOI: 10.1021/acs.jpcb.0c01206] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Antifreeze proteins (AFPs) show thermal hysteresis through specific interaction with the ice crystal. Hyperactive AFPs interact with the ice surface through a threonine-rich motif present at their ice-binding surface (IBS). Ordering of water around the IBS was extensively investigated. However, the role of non-IBS in ice growth inhibition is yet to be understood completely. The present study explores the nature of hydration and its length-scale evaluation around the non-IBS for hyperactive AFPs. We observed that the hydration layer of non-IBS is liquid-like, even in highly supercooled conditions, and the nature of hydration is drastically different from the hydration pattern of non-AFP surfaces. In similar conditions, the hydration layer around the IBS is ice-like ordered. Non-IBS of the hyperactive AFP exposes toward the bulk and is able to maintain the liquid-like character of its hydration water up to 15 Å. We also find that the amino acid compositions and their spatial distribution on the non-IBS are markedly different from those of the IBS and non-AFP surfaces. These results elucidate the combined role of IBS and non-IBS in ice-growth inhibition. While IBS is required to adsorb on ice efficiently, the exposed non-IBS may prevent ice nucleation/growth on top of the bound AFPs.
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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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13
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Antifreeze protein from Anatolia polita (ApAFP914) improved outcome of vitrified in vitro sheep embryos. Cryobiology 2020; 93:109-114. [PMID: 32032586 DOI: 10.1016/j.cryobiol.2020.02.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 02/02/2020] [Accepted: 02/03/2020] [Indexed: 01/25/2023]
Abstract
Embryo cryopreservation is an important tool to preserve endangered species. As a cryoprotectant for mouse oocytes, antifreeze protein from Anatolica polita (ApAFP914) has demonstrated utility. In the present study, the effects of controlled slow freezing and vitrification methods on the survival rate of sheep oocytes fertilized in vitro after freezing-thawing were compared. Different ApAFP914 concentrations were added to the vitrification liquid for exploring the effect of antifreeze protein on the warmed embryos. The results showed that the survival and hatching rates of in vitro derived embryos were significantly higher than that of the slow freezing method. Furthermore, among the cryopreserved embryos at different developmental stages, the survival and hatching rates of the expanded blastocyst were significantly higher than those of the blastocysts, early blastocysts and morula. The survival and the hatching rates of the fast-growing embryos were both significantly higher than that of the slow-growing embryos. Additionally, treatment of ApAFP914 (5-30 μg/mL) did not increase the freezing efficiency of the 6-6.5 d embryos. However, addition of 10 μg/mL of ApAFP914 significantly increased the hatching rate of slow-growing embryos. In conclusion, our study suggests that the vitrification is better than the slow freezing method for the conservation of in vitro sheep embryos, and supplementation of ApAFP914 (10 μg/mL) significantly increased the hatching rate of slow-growing embryos after cryopreservation.
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14
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Hosseinpour S, Roeters SJ, Bonn M, Peukert W, Woutersen S, Weidner T. Structure and Dynamics of Interfacial Peptides and Proteins from Vibrational Sum-Frequency Generation Spectroscopy. Chem Rev 2020; 120:3420-3465. [DOI: 10.1021/acs.chemrev.9b00410] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Saman Hosseinpour
- Institute of Particle Technology (LFG), Friedrich-Alexander-University Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany
| | | | - Mischa Bonn
- Molecular Spectroscopy Department, Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Wolfgang Peukert
- Institute of Particle Technology (LFG), Friedrich-Alexander-University Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany
| | - Sander Woutersen
- Van’t Hoff Institute for Molecular Sciences, University of Amsterdam, 1098 EP Amsterdam, The Netherlands
| | - Tobias Weidner
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
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15
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Tian Y, Zhu Z, Sun DW. Naturally sourced biosubstances for regulating freezing points in food researches: Fundamentals, current applications and future trends. Trends Food Sci Technol 2020. [DOI: 10.1016/j.tifs.2019.11.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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16
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Wang Y, Du J, Ma X, Wang H, Chou KC, Li Q. Chirality discrimination at the carvone air/liquid interfaces detected by heterodyne-detected sum frequency generation. Heliyon 2019; 5:e03061. [PMID: 31890974 PMCID: PMC6928311 DOI: 10.1016/j.heliyon.2019.e03061] [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: 11/14/2018] [Revised: 03/23/2019] [Accepted: 12/12/2019] [Indexed: 11/29/2022] Open
Abstract
The chiral signal of the carvone air/liquid interface is probed by heterodyne-detected sum frequency generation (HD-SFG) without the electronic resonance. The chiral SFG spectra exhibit two distinguishable spectral signatures. Four chiral vibrational peaks of the R- and S-carvone molecules are with opposite signs, which can directly determine the surface molecular chirality. Two achiral vibrational peaks are also observed with the same sign. The different spectral signatures can provide a detailed chirality characterization at the molecular interface.
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Affiliation(s)
- Yang Wang
- School of Precision Instrument and Opto-electronics Engineering, Tianjin University, Tianjin, China
| | - Jianbin Du
- School of Precision Instrument and Opto-electronics Engineering, Tianjin University, Tianjin, China
| | - Xiangyun Ma
- School of Precision Instrument and Opto-electronics Engineering, Tianjin University, Tianjin, China
| | - Huijie Wang
- School of Precision Instrument and Opto-electronics Engineering, Tianjin University, Tianjin, China
| | - Keng C. Chou
- Department of Chemistry, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
| | - Qifeng Li
- School of Precision Instrument and Opto-electronics Engineering, Tianjin University, Tianjin, China
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17
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18
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Hudait A, Qiu Y, Odendahl N, Molinero V. Hydrogen-Bonding and Hydrophobic Groups Contribute Equally to the Binding of Hyperactive Antifreeze and Ice-Nucleating Proteins to Ice. J Am Chem Soc 2019; 141:7887-7898. [DOI: 10.1021/jacs.9b02248] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Arpa Hudait
- Department of Chemistry, The University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Yuqing Qiu
- Department of Chemistry, The University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Nathan Odendahl
- Department of Chemistry, The University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Valeria Molinero
- Department of Chemistry, The University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
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19
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Meister K, Moll CJ, Chakraborty S, Jana B, DeVries AL, Ramløv H, Bakker HJ. Molecular structure of a hyperactive antifreeze protein adsorbed to ice. J Chem Phys 2019; 150:131101. [DOI: 10.1063/1.5090589] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- K. Meister
- Max Planck Institute for Polymer Science, 55128 Mainz, Germany
| | - C. J. Moll
- AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - S. Chakraborty
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Kolkata, India
| | - B. Jana
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Kolkata, India
| | - A. L. DeVries
- Department of Animal Biology, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, USA
| | - H. Ramløv
- Department of Science and Environment, Roskilde University, 4000 Roskilde, Denmark
| | - H. J. Bakker
- AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
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20
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Lee H. Effects of hydrophobic and hydrogen-bond interactions on the binding affinity of antifreeze proteins to specific ice planes. J Mol Graph Model 2018; 87:48-55. [PMID: 30502671 DOI: 10.1016/j.jmgm.2018.11.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 11/17/2018] [Accepted: 11/19/2018] [Indexed: 11/26/2022]
Abstract
Tenebrio molitor antifreeze protein (TmAFP) was simulated with growing ice surfaces such as primary prism, secondary prism, basal, and pyramidal planes. The ice-binding site of TmAFP, which is full of threonine (Thr), binds to the primary-prism plane but does not bind to other ice planes, in agreement with experiments showing the fast adsorption of TmAFP to the primary-prism plane. To mimic the ice-binding site of shorthorn sculpin AFP (ssAFP; type I) that predominantly consists of alanine (Ala) and has the binding affinity to the secondary-prism plane, the ice-binding site of TmAFP was mutated by replacing a few Thr residues with Ala residues, showing that mutated TmAFP binds to the secondary-prism plane, similar to the ice-binding affinity of ssAFP. Ala residues are located at the cavity of ice, while Thr residues form hydrogen bonds with water molecules. When the mutated TmAFP is further modified by removing Thr, it does not bind to the secondary-prism plane. These findings indicate that simulations can successfully capture the experimentally observed binding affinity of AFP to specific ice planes, to an extent dependent on hydrophobicity of the ice-binding site. In particular, the addition of hydrophobic residues influences the ice-binding affinity of TmAFP, while a certain amount of hydrophilic residue is still required for hydrogen-bond interactions, which supports experimental observations regarding the key roles of hydrophobic and hydrophilic interactions on the AFP-ice binding.
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Affiliation(s)
- Hwankyu Lee
- Department of Chemical Engineering, Dankook University, Yongin-si, Gyeonggi-do, 16890, South Korea.
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21
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Preordering of water is not needed for ice recognition by hyperactive antifreeze proteins. Proc Natl Acad Sci U S A 2018; 115:8266-8271. [PMID: 29987018 DOI: 10.1073/pnas.1806996115] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Antifreeze proteins (AFPs) inhibit ice growth in organisms living in cold environments. Hyperactive insect AFPs are particularly effective, binding ice through "anchored clathrate" motifs. It has been hypothesized that the binding of hyperactive AFPs to ice is facilitated by preordering of water at the ice-binding site (IBS) of the protein in solution. The antifreeze protein TmAFP displays the best matching of its binding site to ice, making it the optimal candidate to develop ice-like order in solution. Here we use multiresolution simulations to unravel the mechanism by which TmAFP recognizes and binds ice. We find that water at the IBS of the antifreeze protein in solution does not acquire ice-like or anchored clathrate-like order. Ice recognition occurs by slow diffusion of the protein to achieve the proper orientation with respect to the ice surface, followed by fast collective organization of the hydration water at the IBS to form an anchored clathrate motif that latches the protein to the ice surface. The simulations suggest that anchored clathrate order could develop on the large ice-binding surfaces of aggregates of ice-nucleating proteins (INP). We compute the infrared and Raman spectra of water in the anchored clathrate motif. The signatures of the OH stretch of water in the anchored clathrate motif can be distinguished from those of bulk liquid in the Raman spectra, but not in the infrared spectra. We thus suggest that Raman spectroscopy may be used to probe the anchored clathrate order at the ice-binding surface of INP aggregates.
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22
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Wellig S, Hamm P. Solvation Layer of Antifreeze Proteins Analyzed with a Markov State Model. J Phys Chem B 2018; 122:11014-11022. [PMID: 29889528 DOI: 10.1021/acs.jpcb.8b04491] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Three structurally very different antifreeze proteins (AFPs) are studied, addressing the question as to what extent the hypothesized preordering-binding mechanism is still relevant in the second solvation layer of the protein and beyond. Assuming a two-state model of water, the solvation layers are analyzed with the help of molecular dynamics simulations together with a Markov state model, which investigates the local tedrahedrality of the water hydrogen-bond network around a given water molecule. It has been shown previously that this analysis can discriminate the high-entropy, high-density state of the liquid (HDL) from its more structured low-density state (LDL). All investigated proteins, regardless of whether they are an AFP or not, have a tendency to increase the amount of HDL in their second solvation layer. The ice binding site (IBS) of the antifreeze proteins counteracts that trend, with either a hole in the HDL layer or a true excess of LDL. The results correlate to a certain extent with recent experiments, which have observed ice-like vibrational (VSFG) spectra for the water atop the IBS of only a subset of antifreeze proteins. It is concluded that the preordering-binding mechanism indeed seems to play a role but is only part of the overall picture.
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Affiliation(s)
- Sebastian Wellig
- Department of Chemistry , University of Zurich , 8057 Zurich , Switzerland
| | - Peter Hamm
- Department of Chemistry , University of Zurich , 8057 Zurich , Switzerland
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23
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Lee H. Structures, dynamics, and hydrogen-bond interactions of antifreeze proteins in TIP4P/Ice water and their dependence on force fields. PLoS One 2018; 13:e0198887. [PMID: 29879205 PMCID: PMC5991737 DOI: 10.1371/journal.pone.0198887] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 05/27/2018] [Indexed: 12/13/2022] Open
Abstract
Tenebrio molitor antifreeze protein (TmAFP) was simulated with growing ice-water interfaces at a realistic melting temperature using TIP4P/Ice water model. To test compatibility of protein force fields (FFs) with TIP4P/Ice water, CHARMM, AMBER, and OPLS FFs were applied. CHARMM and AMBER FFs predict more β-sheet structure and lower diffusivity of TmAFP at the ice-water interface than does OPLS FF, indicating that β-sheet structure is important for the TmAFP-interface binding and antifreeze activity. In particular, CHARMM FF more clearly distinguishes the strengths of hydrogen bonds in the ice-binding and non-ice-binding sites of TmAFP than do other FFs, in agreement with experiments, implying that CHARMM FF can be a reasonable choice to simulate proteins with TIP4P/Ice water. Simulations of mutated TmAFPs show that for the same density of Thr residues, continuous arrangement of Thr with the distance of 0.4~0.6 nm induces the higher extent of antifreeze activity than does intermittent arrangement of Thr with larger distances. These findings suggest the choice of CHARMM FF for AFP-TIP4P/Ice simulations and help explain the relationship between Thr-residue arrangement and antifreeze activity.
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Affiliation(s)
- Hwankyu Lee
- Department of Chemical Engineering, Dankook University, Yongin-si, Gyeonggi-do, South Korea
- * E-mail:
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24
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Hygroscopic compounds in spider aggregate glue remove interfacial water to maintain adhesion in humid conditions. Nat Commun 2018; 9:1890. [PMID: 29789602 PMCID: PMC5964112 DOI: 10.1038/s41467-018-04263-z] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Accepted: 04/17/2018] [Indexed: 11/28/2022] Open
Abstract
Adhesion in humid environments is fundamentally challenging because of the presence of interfacial bound water. Spiders often hunt in wet habitats and overcome this challenge using sticky aggregate glue droplets whose adhesion is resistant to interfacial failure under humid conditions. The mechanism by which spider aggregate glue avoids interfacial failure in humid environments is still unknown. Here, we investigate the mechanism of aggregate glue adhesion by using interface-sensitive spectroscopy in conjunction with infrared spectroscopy. We demonstrate that glycoproteins act as primary binding agents at the interface. As humidity increases, we observe reversible changes in the interfacial secondary structure of glycoproteins. Surprisingly, we do not observe liquid-like water at the interface, even though liquid-like water increases inside the bulk with increasing humidity. We hypothesize that the hygroscopic compounds in aggregate glue sequester interfacial water. Using hygroscopic compounds to sequester interfacial water provides a novel design principle for developing water-resistant synthetic adhesives. Spider aggregate glue avoids failure in humid environments but the fundamental mechanism behind it is still unknown. Here, the authors demonstrate that humidity-dependent structural changes of glycoproteins and sequestering of liquid water by low molecular mass compounds prevents adhesion failure of the glue in humid environments.
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25
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Hudait A, Odendahl N, Qiu Y, Paesani F, Molinero V. Ice-Nucleating and Antifreeze Proteins Recognize Ice through a Diversity of Anchored Clathrate and Ice-like Motifs. J Am Chem Soc 2018; 140:4905-4912. [PMID: 29564892 DOI: 10.1021/jacs.8b01246] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Cold-adapted organisms produce antifreeze and ice-nucleating proteins to prevent and promote ice formation. The crystal structure of hyperactive bacterial antifreeze protein (AFP) MpAFP suggests that this protein binds ice through an anchored clathrate motif. It is not known whether other hyperactive AFPs and ice-nucleating proteins (INPs) use the same motif to recognize or nucleate ice. Here we use molecular simulations to elucidate the ice-binding motifs of hyperactive insect AFPs and a model INP of Pseudomonas syringae. We find that insect AFPs recognize ice through anchored clathrate motifs distinct from that of MpAFP. By performing simulations of ice nucleation by PsINP, we identify two distinct ice-binding sites on opposite sides of the β-helix. The ice-nucleating sequences identified in the simulations agree with those previously proposed for the closely related INP of Pseudomonas borealis based on the structure of the protein. The simulations indicate that these sites have comparable ice-nucleating efficiency, but distinct binding motifs, controlled by the amino acid sequence: one is an anchored clathrate and the other ice-like. We conclude that anchored clathrate and ice-like motifs can be equally effective for binding proteins to ice and promoting ice nucleation.
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Affiliation(s)
- Arpa Hudait
- Department of Chemistry , 315 South 1400 East , The University of Utah , Salt Lake City , Utah 84112-0580 , United States
| | - Nathan Odendahl
- Department of Chemistry , 315 South 1400 East , The University of Utah , Salt Lake City , Utah 84112-0580 , United States
| | - Yuqing Qiu
- Department of Chemistry , 315 South 1400 East , The University of Utah , Salt Lake City , Utah 84112-0580 , United States
| | - Francesco Paesani
- Department of Chemistry and Biochemistry , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92093 , United States
| | - Valeria Molinero
- Department of Chemistry , 315 South 1400 East , The University of Utah , Salt Lake City , Utah 84112-0580 , United States
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26
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Sanders SE, Vanselous H, Petersen PB. Water at surfaces with tunable surface chemistries. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:113001. [PMID: 29393860 DOI: 10.1088/1361-648x/aaacb5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Aqueous interfaces are ubiquitous in natural environments, spanning atmospheric, geological, oceanographic, and biological systems, as well as in technical applications, such as fuel cells and membrane filtration. Where liquid water terminates at a surface, an interfacial region is formed, which exhibits distinct properties from the bulk aqueous phase. The unique properties of water are governed by the hydrogen-bonded network. The chemical and physical properties of the surface dictate the boundary conditions of the bulk hydrogen-bonded network and thus the interfacial properties of the water and any molecules in that region. Understanding the properties of interfacial water requires systematically characterizing the structure and dynamics of interfacial water as a function of the surface chemistry. In this review, we focus on the use of experimental surface-specific spectroscopic methods to understand the properties of interfacial water as a function of surface chemistry. Investigations of the air-water interface, as well as efforts in tuning the properties of the air-water interface by adding solutes or surfactants, are briefly discussed. Buried aqueous interfaces can be accessed with careful selection of spectroscopic technique and sample configuration, further expanding the range of chemical environments that can be probed, including solid inorganic materials, polymers, and water immiscible liquids. Solid substrates can be finely tuned by functionalization with self-assembled monolayers, polymers, or biomolecules. These variables provide a platform for systematically tuning the chemical nature of the interface and examining the resulting water structure. Finally, time-resolved methods to probe the dynamics of interfacial water are briefly summarized before discussing the current status and future directions in studying the structure and dynamics of interfacial water.
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Affiliation(s)
- Stephanie E Sanders
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, United States of America
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27
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Brotzakis ZF, Gehre M, Voets IK, Bolhuis PG. Stability and growth mechanism of self-assembling putative antifreeze cyclic peptides. Phys Chem Chem Phys 2018; 19:19032-19042. [PMID: 28702528 DOI: 10.1039/c7cp02465g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Cyclic peptides (CPs) that self-assemble in nanotubes can be candidates for use as antifreeze proteins. Based on the cyclic peptide sequence cyclo-[(l-LYS-d-ALA-l-LEU-d-ALA)2], which can stack into nanotubes, we propose a putative antifreeze cyclic peptide (AFCP) sequence, cyclo-[(l-LYS-d-ALA)2-(l-THR-d-ALA)2], containing THR-ALA-THR ice binding motifs. Using molecular dynamics simulations we investigate the stability of these cyclic peptides and their growth mechanism. Both nanotube sequences get more stable as a function of size. The relative stability of the AFCP sequence CPNT increases at sizes greater than a dimer by forming intermolecular THR side chain H-bonds. We find that, like the naturally occurring AF protein from spruce budworm (Choristoneura fumiferana), the THR distances of the AFCP's ice binding motif match the ice prism plane O-O distances, thus making the AFCP a suitable AF candidate. In addition, we investigated the nanotube growth process, i.e. the association/dissociation of a single CP to an existing AFCP nanotube, by Transition Path Sampling. We found a general dock-lock mechanism, in which a single CP first docks loosely before locking into place. Moreover, we identified several qualitatively different mechanisms for association, involving different metastable intermediates, including a state in which the peptide was misfolded inside the hydrophobic core of the tube. Finally, we find evidence for a mechanism involving non-specific association followed by 1D diffusion. Under most conditions, this will be the dominant pathway. The results yield insights into the mechanisms of peptide assembly, and might lead to an improved design of self-assembling antifreeze proteins.
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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.
| | - Mascha Gehre
- Van't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
| | - Ilja K Voets
- Laboratory of Macromolecular and Organic Chemistry, Laboratory of Physical Chemistry, and Institute for Complex Molecular Systems, Eindhoven University of Technology, Post Office Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Peter G Bolhuis
- Van't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
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28
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Meister K, Paananen A, Speet B, Lienemann M, Bakker HJ. Molecular Structure of Hydrophobins Studied with Site-Directed Mutagenesis and Vibrational Sum-Frequency Generation Spectroscopy. J Phys Chem B 2017; 121:9398-9402. [PMID: 28967753 PMCID: PMC5647563 DOI: 10.1021/acs.jpcb.7b08865] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 09/14/2017] [Indexed: 01/31/2023]
Abstract
Hydrophobins are surface-active fungal proteins that adsorb to the water-air interface and self-assemble into amphiphilic, water-repelling films that have a surface elasticity that is an order of magnitude higher than other molecular films. Here we use surface-specific sum-frequency generation spectroscopy (VSFG) and site-directed mutagenesis to study the properties of class I hydrophobin (HFBI) films from Trichoderma reesei at the molecular level. We identify protein specific HFBI signals in the frequency region 1200-1700 cm-1 that have not been observed in previous VSFG studies on proteins. We find evidence that the aspartic acid residue (D30) next to the hydrophobic patch is involved in lateral intermolecular protein interactions, while the two aspartic acid residues (D40, D43) opposite to the hydrophobic patch are primarily interacting with the water solvent.
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Affiliation(s)
- K. Meister
- AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - A. Paananen
- VTT Technical Research Centre of Finland Ltd, Tietotie, FI-02150 Espoo, Finland
| | - B. Speet
- AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - M. Lienemann
- VTT Technical Research Centre of Finland Ltd, Tietotie, FI-02150 Espoo, Finland
| | - H. J. Bakker
- AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
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29
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Pandey HD, Leitner DM. Thermodynamics of Hydration Water around an Antifreeze Protein: A Molecular Simulation Study. J Phys Chem B 2017; 121:9498-9507. [DOI: 10.1021/acs.jpcb.7b05892] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hari Datt Pandey
- Department of Chemistry and
Chemical Physics Program, University of Nevada, Reno, Nevada 89557, United States
| | - David M. Leitner
- Department of Chemistry and
Chemical Physics Program, University of Nevada, Reno, Nevada 89557, United States
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30
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Takeshita N, Okuno M, Ishibashi TA. Molecular conformation of DPPC phospholipid Langmuir and Langmuir–Blodgett monolayers studied by heterodyne-detected vibrational sum frequency generation spectroscopy. Phys Chem Chem Phys 2017; 19:2060-2066. [DOI: 10.1039/c6cp07800a] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Heterodyne-detected vibrational sum frequency generation spectroscopy was used to investigate molecular structures of DPPC monolayers on water (Langmuir monolayer) and monolayers on a fused silica substrate (Langmuir-Blodgett [LB] monolayer).
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Affiliation(s)
- Naoki Takeshita
- Department of Chemistry
- Graduate School of Pure and Applied Sciences
- University of Tsukuba
- Tsukuba
- Japan
| | - Masanari Okuno
- Department of Chemistry
- Graduate School of Pure and Applied Sciences
- University of Tsukuba
- Tsukuba
- Japan
| | - Taka-aki Ishibashi
- Department of Chemistry
- Graduate School of Pure and Applied Sciences
- University of Tsukuba
- Tsukuba
- Japan
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31
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Devineau S, Inoue KI, Kusaka R, Urashima SH, Nihonyanagi S, Baigl D, Tsuneshige A, Tahara T. Change of the isoelectric point of hemoglobin at the air/water interface probed by the orientational flip-flop of water molecules. Phys Chem Chem Phys 2017; 19:10292-10300. [DOI: 10.1039/c6cp08854f] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Nonlinear vibrational spectroscopy reveals that the isoelectric point of proteins can largely change when the proteins are adsorbed at the air/water interface.
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Affiliation(s)
- Stéphanie Devineau
- Molecular Spectroscopy Laboratory
- RIKEN
- Saitama 351-0198
- Japan
- Ecole Normale Supérieure
| | - Ken-ichi Inoue
- Molecular Spectroscopy Laboratory
- RIKEN
- Saitama 351-0198
- Japan
| | - Ryoji Kusaka
- Molecular Spectroscopy Laboratory
- RIKEN
- Saitama 351-0198
- Japan
| | | | - Satoshi Nihonyanagi
- Molecular Spectroscopy Laboratory
- RIKEN
- Saitama 351-0198
- Japan
- Ultrafast Spectroscopy Research Team
| | - Damien Baigl
- Ecole Normale Supérieure
- PSL Research University
- UPMC Univ Paris 06
- CNRS
- PASTEUR
| | | | - Tahei Tahara
- Molecular Spectroscopy Laboratory
- RIKEN
- Saitama 351-0198
- Japan
- Ultrafast Spectroscopy Research Team
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32
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Liu K, Wang C, Ma J, Shi G, Yao X, Fang H, Song Y, Wang J. Janus effect of antifreeze proteins on ice nucleation. Proc Natl Acad Sci U S A 2016; 113:14739-14744. [PMID: 27930318 PMCID: PMC5187720 DOI: 10.1073/pnas.1614379114] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The mechanism of ice nucleation at the molecular level remains largely unknown. Nature endows antifreeze proteins (AFPs) with the unique capability of controlling ice formation. However, the effect of AFPs on ice nucleation has been under debate. Here we report the observation of both depression and promotion effects of AFPs on ice nucleation via selectively binding the ice-binding face (IBF) and the non-ice-binding face (NIBF) of AFPs to solid substrates. Freezing temperature and delay time assays show that ice nucleation is depressed with the NIBF exposed to liquid water, whereas ice nucleation is facilitated with the IBF exposed to liquid water. The generality of this Janus effect is verified by investigating three representative AFPs. Molecular dynamics simulation analysis shows that the Janus effect can be established by the distinct structures of the hydration layer around IBF and NIBF. Our work greatly enhances the understanding of the mechanism of AFPs at the molecular level and brings insights to the fundamentals of heterogeneous ice nucleation.
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Affiliation(s)
- Kai Liu
- Key Laboratory of Green Printing, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Chunlei Wang
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, People's Republic of China;
| | - Ji Ma
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830046, People's Republic of China
| | - Guosheng Shi
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, People's Republic of China
| | - Xi Yao
- Key Laboratory of Green Printing, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
| | - Haiping Fang
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, People's Republic of China
| | - Yanlin Song
- Key Laboratory of Green Printing, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Jianjun Wang
- Key Laboratory of Green Printing, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China;
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
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33
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Meister K, Bäumer A, Szilvay GR, Paananen A, Bakker HJ. Self-Assembly and Conformational Changes of Hydrophobin Classes at the Air-Water Interface. J Phys Chem Lett 2016; 7:4067-4071. [PMID: 27690211 DOI: 10.1021/acs.jpclett.6b01917] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We use surface-specific vibrational sum-frequency generation spectroscopy (VSFG) to study the structure and self-assembling mechanism of the class I hydrophobin SC3 from Schizophyllum commune and the class II hydrophobin HFBI from Trichoderma reesei. We find that both hydrophobins readily accumulate at the water-air interface and form rigid, highly ordered protein films that give rise to prominent VSFG signals. We identify several resonances that are associated with β-sheet structures and assign them to the central β-barrel core present in both proteins. Differences between the hydrophobin classes are observed in their interfacial self-assembly. For HFBI, we observe no changes in conformation upon adsorption to the water surface. For SC3, we observe an increase in β-sheet-specific signals that supports a surface-driven self-assembly mechanism in which the central β-barrel remains intact and stacks into a larger-scale architecture, amyloid-like rodlets.
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Affiliation(s)
- Konrad Meister
- FOM-Institute for Atomic and Molecular Physics AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Alexander Bäumer
- Physical Chemistry II, Ruhr University Bochum , Universitätsstr. 150, 44801 Bochum, Germany
| | - Geza R Szilvay
- VTT Technical Research Centre of Finland Ltd, Tietotie 2, FI-02150 Espoo, Finland
| | - Arja Paananen
- VTT Technical Research Centre of Finland Ltd, Tietotie 2, FI-02150 Espoo, Finland
| | - Huib J Bakker
- FOM-Institute for Atomic and Molecular Physics AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
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34
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Qadeer S, Khan M, Shahzad Q, Azam A, Ansari M, Rakha B, Ejaz R, Husna A, Duman J, Akhter S. Efficiency of beetle (Dendroides canadensis) recombinant antifreeze protein for buffalo semen freezability and fertility. Theriogenology 2016; 86:1662-9. [DOI: 10.1016/j.theriogenology.2016.05.028] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 05/20/2016] [Accepted: 05/20/2016] [Indexed: 10/21/2022]
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35
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Braunschweig B, Schulze-Zachau F, Nagel E, Engelhardt K, Stoyanov S, Gochev G, Khristov K, Mileva E, Exerowa D, Miller R, Peukert W. Specific effects of Ca(2+) ions and molecular structure of β-lactoglobulin interfacial layers that drive macroscopic foam stability. SOFT MATTER 2016; 12:5995-6004. [PMID: 27337699 PMCID: PMC5048339 DOI: 10.1039/c6sm00636a] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 06/12/2016] [Indexed: 06/01/2023]
Abstract
β-Lactoglobulin (BLG) adsorption layers at air-water interfaces were studied in situ with vibrational sum-frequency generation (SFG), tensiometry, surface dilatational rheology and ellipsometry as a function of bulk Ca(2+) concentration. The relation between the interfacial molecular structure of adsorbed BLG and the interactions with the supporting electrolyte is additionally addressed on higher length scales along the foam hierarchy - from the ubiquitous air-water interface through thin foam films to macroscopic foam. For concentrations <1 mM, a strong decrease in SFG intensity from O-H stretching bands and a slight increase in layer thickness and surface pressure are observed. A further increase in Ca(2+) concentrations above 1 mM causes an apparent change in the polarity of aromatic C-H stretching vibrations from interfacial BLG which we associate to a charge reversal at the interface. Foam film measurements show formation of common black films at Ca(2+) concentrations above 1 mM due to considerable decrease of the stabilizing electrostatic disjoining pressure. These observations also correlate with a minimum in macroscopic foam stability. For concentrations >30 mM Ca(2+), micrographs of foam films show clear signatures of aggregates which tend to increase the stability of foam films. Here, the interfacial layers have a higher surface dilatational elasticity. In fact, macroscopic foams formed from BLG dilutions with high Ca(2+) concentrations where aggregates and interfacial layers with higher elasticity are found, showed the highest stability with much smaller bubble sizes.
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Affiliation(s)
- Björn Braunschweig
- Institute of Particle Technology (LFG), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Cauerstraße 4, 91058 Erlangen, Germany. and Cluster of Excellence Engineering of Advanced Materials (EAM), Nägelsbachstr. 49b, 91052 Erlangen, Germany and Erlangen Graduate School in Advanced Optical Technologies (SAOT), Paul-Gordan-Straße 6, 91052 Erlangen, Germany and Interdisciplinary Center of Functional Particle Systems, Haberstraße 9a, 91058 Erlangen, Germany
| | - Felix Schulze-Zachau
- Institute of Particle Technology (LFG), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Cauerstraße 4, 91058 Erlangen, Germany. and Erlangen Graduate School in Advanced Optical Technologies (SAOT), Paul-Gordan-Straße 6, 91052 Erlangen, Germany and Interdisciplinary Center of Functional Particle Systems, Haberstraße 9a, 91058 Erlangen, Germany
| | - Eva Nagel
- Institute of Particle Technology (LFG), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Cauerstraße 4, 91058 Erlangen, Germany.
| | - Kathrin Engelhardt
- Institute of Particle Technology (LFG), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Cauerstraße 4, 91058 Erlangen, Germany.
| | - Stefan Stoyanov
- Institute of Physical Chemistry, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Georgi Gochev
- Institute of Physical Chemistry, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria and Max-Planck-Institute of Colloids and Interfaces, 14476 Golm/Potsdam, Germany
| | - Khr Khristov
- Institute of Physical Chemistry, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Elena Mileva
- Institute of Physical Chemistry, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Dotchi Exerowa
- Institute of Physical Chemistry, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Reinhard Miller
- Max-Planck-Institute of Colloids and Interfaces, 14476 Golm/Potsdam, Germany
| | - Wolfgang Peukert
- Institute of Particle Technology (LFG), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Cauerstraße 4, 91058 Erlangen, Germany. and Cluster of Excellence Engineering of Advanced Materials (EAM), Nägelsbachstr. 49b, 91052 Erlangen, Germany and Erlangen Graduate School in Advanced Optical Technologies (SAOT), Paul-Gordan-Straße 6, 91052 Erlangen, Germany and Interdisciplinary Center of Functional Particle Systems, Haberstraße 9a, 91058 Erlangen, Germany
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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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Hydration of proteins and nucleic acids: Advances in experiment and theory. A review. Biochim Biophys Acta Gen Subj 2016; 1860:1821-35. [PMID: 27241846 DOI: 10.1016/j.bbagen.2016.05.036] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 05/20/2016] [Accepted: 05/26/2016] [Indexed: 11/21/2022]
Abstract
BACKGROUND Most biological processes involve water, and the interactions of biomolecules with water affect their structure, function and dynamics. SCOPE OF REVIEW This review summarizes the current knowledge of protein and nucleic acid interactions with water, with a special focus on the biomolecular hydration layer. Recent developments in both experimental and computational methods that can be applied to the study of hydration structure and dynamics are reviewed, including software tools for the prediction and characterization of hydration layer properties. MAJOR CONCLUSIONS In the last decade, important advances have been made in our understanding of the factors that determine how biomolecules and their aqueous environment influence each other. Both experimental and computational methods contributed to the gradually emerging consensus picture of biomolecular hydration. GENERAL SIGNIFICANCE An improved knowledge of the structural and thermodynamic properties of the hydration layer will enable a detailed understanding of the various biological processes in which it is involved, with implications for a wide range of applications, including protein-structure prediction and structure-based drug design.
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Pandey R, Usui K, Livingstone RA, Fischer SA, Pfaendtner J, Backus EHG, Nagata Y, Fröhlich-Nowoisky J, Schmüser L, Mauri S, Scheel JF, Knopf DA, Pöschl U, Bonn M, Weidner T. Ice-nucleating bacteria control the order and dynamics of interfacial water. SCIENCE ADVANCES 2016; 2:e1501630. [PMID: 27152346 PMCID: PMC4846457 DOI: 10.1126/sciadv.1501630] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 03/24/2016] [Indexed: 05/22/2023]
Abstract
Ice-nucleating organisms play important roles in the environment. With their ability to induce ice formation at temperatures just below the ice melting point, bacteria such as Pseudomonas syringae attack plants through frost damage using specialized ice-nucleating proteins. Besides the impact on agriculture and microbial ecology, airborne P. syringae can affect atmospheric glaciation processes, with consequences for cloud evolution, precipitation, and climate. Biogenic ice nucleation is also relevant for artificial snow production and for biomimetic materials for controlled interfacial freezing. We use interface-specific sum frequency generation (SFG) spectroscopy to show that hydrogen bonding at the water-bacteria contact imposes structural ordering on the adjacent water network. Experimental SFG data and molecular dynamics simulations demonstrate that ice-active sites within P. syringae feature unique hydrophilic-hydrophobic patterns to enhance ice nucleation. The freezing transition is further facilitated by the highly effective removal of latent heat from the nucleation site, as apparent from time-resolved SFG spectroscopy.
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Affiliation(s)
- Ravindra Pandey
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55218 Mainz, Germany
| | - Kota Usui
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55218 Mainz, Germany
| | - Ruth A. Livingstone
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55218 Mainz, Germany
| | - Sean A. Fischer
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
| | - Jim Pfaendtner
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
| | - Ellen H. G. Backus
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55218 Mainz, Germany
| | - Yuki Nagata
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55218 Mainz, Germany
| | - Janine Fröhlich-Nowoisky
- Multiphase Chemistry Department, Max Planck Institute for Chemistry, Hahn-Meitner-Weg 1, 55128 Mainz, Germany
| | - Lars Schmüser
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55218 Mainz, Germany
| | - Sergio Mauri
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55218 Mainz, Germany
| | - Jan F. Scheel
- Multiphase Chemistry Department, Max Planck Institute for Chemistry, Hahn-Meitner-Weg 1, 55128 Mainz, Germany
| | - Daniel A. Knopf
- Institute for Terrestrial and Planetary Atmospheres/School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Ulrich Pöschl
- Multiphase Chemistry Department, Max Planck Institute for Chemistry, Hahn-Meitner-Weg 1, 55128 Mainz, Germany
| | - Mischa Bonn
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55218 Mainz, Germany
| | - Tobias Weidner
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55218 Mainz, Germany
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
- Corresponding author. E-mail:
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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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40
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Balzerowski P, Meister K, Versluis J, Bakker HJ. Heterodyne-detected sum frequency generation spectroscopy of polyacrylic acid at the air/water-interface. Phys Chem Chem Phys 2016; 18:2481-7. [DOI: 10.1039/c5cp06177f] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A complete picture of the surface affinity and structure of polyacrylic acid at the air–water interface was determined.
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Affiliation(s)
| | - Konrad Meister
- FOM-Institute for Atomic and Molecular Physics AMOLF
- 1098XG Amsterdam
- The Netherlands
| | - Jan Versluis
- FOM-Institute for Atomic and Molecular Physics AMOLF
- 1098XG Amsterdam
- The Netherlands
| | - Huib J. Bakker
- FOM-Institute for Atomic and Molecular Physics AMOLF
- 1098XG Amsterdam
- The Netherlands
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41
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Strazdaite S, Meister K, Bakker HJ. Orientation of polar molecules near charged protein interfaces. Phys Chem Chem Phys 2016; 18:7414-8. [DOI: 10.1039/c5cp06372h] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We study the orientation of water and urea molecules and protein amide vibrations at aqueous α-lactalbumin and α-lactalbumin/urea interfaces using heterodyne-detected vibrational sum frequency generation.
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Affiliation(s)
- Simona Strazdaite
- FOM-Institute for Atomic and Molecular Physics AMOLF
- Amsterdam 1098 XG
- The Netherlands
| | - Konrad Meister
- FOM-Institute for Atomic and Molecular Physics AMOLF
- Amsterdam 1098 XG
- The Netherlands
| | - Huib J. Bakker
- FOM-Institute for Atomic and Molecular Physics AMOLF
- Amsterdam 1098 XG
- The Netherlands
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42
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McDermott ML, Petersen PB. Robust Self-Referencing Method for Chiral Sum Frequency Generation Spectroscopy. J Phys Chem B 2015; 119:12417-23. [DOI: 10.1021/acs.jpcb.5b08176] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- M. Luke McDermott
- Department
of Chemistry and
Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Poul B. Petersen
- Department
of Chemistry and
Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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