NMR structural studies on antifreeze proteins

1998 ◽  
Vol 76 (2-3) ◽  
pp. 284-293 ◽  
Author(s):  
Frank D Sönnichsen ◽  
Peter L Davies ◽  
Brian D Sykes
Keyword(s):  
Freezing Point ◽  
Antifreeze Proteins ◽  
Isotopic Labeling ◽  
Inhibition Mechanism ◽  
Structural Studies ◽  
Nmr Analysis ◽  
Ice Surface ◽  
Nmr Data ◽  
Ice Binding ◽  
Nmr Techniques

Antifreeze proteins (AFPs) are a structurally diverse class of proteins that bind to ice and inhibit its growth in a noncolligative manner. This adsorption-inhibition mechanism operating at the ice surface results in a lowering of the (nonequilibrium) freezing point below the melting point. A lowering of ~1°C, which is sufficient to prevent fish from freezing in ice-laden seawater, requires millimolar AFP levels in the blood. The solubility of AFPs at these millimolar concentrations and the small size of the AFPs (typically 3-15 kDa) make them ideal subjects for NMR analysis. Although fish AFPs are naturally abundant, seasonal expression, restricted access to polar fishes, and difficulties in separating numerous similar isoforms have made protein expression the method of choice for producing AFPs for structural studies. Expression of recombinant AFPs has also facilitated NMR analysis by permitting isotopic labeling with 15N and 13C and has permitted mutations to be made to help with the interpretation of NMR data. NMR analysis has recently solved two AFP structures and provided valuable information about the disposition of ice-binding side chains in a third. The potential exists to solve other AFP structures, including the newly described insect AFPs, and to use solid-state NMR techniques to address fundamental questions about the nature of the interaction between AFPs and ice.Key words: NMR spectroscopy, antifreeze, ice-binding affinity, review.

Three-dimensional simulation of ice growth in the presence of antifreeze proteins

2003 ◽  
Vol 81 (1-2) ◽  
pp. 39-45 ◽  
Author(s):  
B Wathen ◽  
M J Kuiper ◽  
V K Walker ◽  
Z Jia
Keyword(s):  
Crystal Growth ◽  
Growth Inhibition ◽  
Antifreeze Proteins ◽  
Three Dimensional ◽  
Computational Method ◽  
Inhibition Mechanism ◽  
Ice Crystal ◽  
Ice Growth ◽  
Ice Binding ◽  
Dimensional Simulation

A Monte Carlo computational method for simulating the growth of entire ice crystals from the liquid phase has been developed specifically to study the inhibition of ice-crystal growth by antifreeze proteins (AFPs). AFPs are found in the fluids of certain organisms that inhabit freezing environments and constrain ice-crystal growth by adsorbtion to the ice surface, but their inhibition mechanism is still poorly understood. Thus, it was of interest to incorporate these molecules into the dynamic ice simulations to examine the inhibition phenomenon on a whole-crystal basis. We have undertaken simulations with AFPs from two different organisms that differ in activity; the insect AFP has up to 100 times the activity of the fish AFP on a molar basis. Simulations involving insect and fish AFPs have achieved ice-growth inhibition at simulation temperatures within reported activity ranges for both fish and insect AFPs, accompanied by resulting ice morphologies similar to those observed experimentally. These results, as well as other studies on ice-etching patterns and ice burst growth at temperatures below known AFP ice-growth inhibition abilities suggest that AFP activity is dominated by the AFP ice-binding position rather than AFP ice-binding strength. PACS No.: 07.05T

scholarly journals Preordering of water is not needed for ice recognition by hyperactive antifreeze proteins

2018 ◽  
Vol 115 (33) ◽  
pp. 8266-8271 ◽  
Author(s):  
Arpa Hudait ◽  
Daniel R. Moberg ◽  
Yuqing Qiu ◽  
Nathan Odendahl ◽  
Francesco Paesani ◽  
...  
Keyword(s):  
Binding Site ◽  
Raman Spectra ◽  
Antifreeze Proteins ◽  
Antifreeze Protein ◽  
Bulk Liquid ◽  
Cold Environments ◽  
Ice Surface ◽  
Ice Binding ◽  
Binding Surface ◽  
Optimal Candidate

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 proteinTmAFP 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 whichTmAFP 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.

Experimental correlation between thermal hysteresis activity and the distance between antifreeze proteins on an ice surface

RSC Advances ◽  
2015 ◽  
Vol 5 (11) ◽  
pp. 7848-7853 ◽  
Author(s):  
Ran Drori ◽  
Peter L. Davies ◽  
Ido Braslavsky
Keyword(s):  
Fluorescence Microscopy ◽  
Thermal Hysteresis ◽  
Freezing Point ◽  
Antifreeze Proteins ◽  
Microfluidic Devices ◽  
Freezing Point Depression ◽  
Thermal Hysteresis Activity ◽  
Ice Surface ◽  
Experimental Correlation ◽  
Temperature Controlled

Temperature-controlled microfluidic devices and fluorescence microscopy illustrate the correlation between freezing-point depression and the distance between antifreeze proteins on an ice surface.

scholarly journals Structure and function of antifreeze proteins

2002 ◽  
Vol 357 (1423) ◽  
pp. 927-935 ◽  
Author(s):  
Peter L. Davies ◽  
Jason Baardsnes ◽  
Michael J. Kuiper ◽  
Virginia K. Walker
Keyword(s):  
Binding Sites ◽  
Antifreeze Proteins ◽  
Tight Binding ◽  
Three Dimensional ◽  
Structure And Function ◽  
Site Directed Mutagenesis ◽  
Ice Surface ◽  
Ice Binding ◽  
And Function ◽  
Van Der Waals Contacts

High–resolution three–dimensional structures are now available for four of seven non–homologous fish and insect antifreeze proteins (AFPs). For each of these structures, the ice–binding site of the AFP has been defined by site–directed mutagenesis, and ice etching has indicated that the ice surface is bound by the AFP. A comparison of these extremely diverse ice–binding proteins shows that they have the following attributes in common. The binding sites are relatively flat and engage a substantial proportion of the protein's surface area in ice binding. They are also somewhat hydrophobic—more so than that portion of the protein exposed to the solvent. Surface–surface complementarity appears to be the key to tight binding in which the contribution of hydrogen bonding seems to be secondary to van der Waals contacts.

Rarely Occurring Natural Products Isolated from Vincetoxicum stocksii

2019 ◽  
Vol 41 (4) ◽  
pp. 695-695
Author(s):  
Saima Khan Saima Khan ◽  
Muhammad Imran Tousif Muhammad Imran Tousif ◽  
Naheed Raiz Naheed Raiz ◽  
Mamona Nazir Mamona Nazir ◽  
Mahreen Mukhtar Mahreen Mukhtar ◽  
...  
Keyword(s):  
Natural Products ◽  
Methanol Extract ◽  
High Resolution Mass Spectrometry ◽  
Ethyl Acetate Fraction ◽  
2D Nmr ◽  
Ethyl Carbamate ◽  
Carbamic Acid ◽  
Nmr Analysis ◽  
Nmr Techniques ◽  
Resolution Mass

Silica gel column chromatography of the ethyl acetate fraction of methanol extract of Vincetoxicum stocksii resulted in the separation of three new rarely occurring natural products; [4-(4-(methoxycarbonyl)benzyl)phenyl] carbamic acid (1), bis[di-p-phenylmethane]ethyl carbamate (2), methyl 2-hydroxy-3-(2-hydroxy-5-(3-methylbut-2-enyl)phenyl)-2-(4-hydroxyphenyl) propanoate, stocksiloate(3), along with five known compounds; 1-(4-hydroxy-3-methoxyphenyl)-1,2,3,-propanetriol (4), feruloyl-6-O-β-D-glucopyranoside (5), 4-hydroxy-3,5-dimethoxybenzoic acid (6), apocynin (7) and vincetomine (8). The structures of compounds 1 and 2 were established with help of 1D, 2D-NMR techniques and high resolution mass spectrometry, whereas, compound 3 could only be characterized tentatively by 1D, 2D-NMR techniques. Compounds 1 is new compound while 2 is synthetically known but never been reported from natural source. The known compounds were identified due to 1D NMR analysis and in comparison with the literature values. Compounds 1-3 were found inactive in an anti-urease assay.

scholarly journals Five sesquiterpenes from the root Aucklandia lappa Decne.

2019 ◽  
pp. 5-11
Author(s):  
Chjuo Fuguan ◽  
Seesregdorj S ◽  
Gerelt-Od Ya
Keyword(s):  
Phenolic Compounds ◽  
Nmr Spectra ◽  
Previous Literature ◽  
Two Dimensional ◽  
Nmr Data ◽  
Nmr Techniques ◽  
The One ◽  
Dehydrocostus Lactone ◽  
First Time

The four sesquiterpenes calameone (1), dehydrocostus lactone (2), aristolone (3), alantolactone (4) and one triterpenoid α-amyrine (5), simple phenolic compounds such as 4-hydroxybenzaldehyde, (6), piceol (7), apocynin (8), dihydroconiferyl (9) and coniferyl (10) have been identified by using the proton and carbon NMR spectra which were isolated from a dichloromethane extract of the roots of Aucklandia lappa Decne. Their structures were established by the one‐and two‐dimensional NMR techniques including DEPT, COSY and HMBC spectroscopy. This work examined proton and carbon NMR data of calameone (1) and aristolone (3) for the first time, which had not yet been fully studied in previous literature. Рүда ургамлын (Aucklandia lappa Decne.) терпент нэгдлийн судалгаа Хураангуй: Рүда ургамлын үндэсний дихлорметаны ханднаас хроматографийн аргуудаар эвдесман хэлбэрийн сесквитерпен каламеон (1), аристолон (3), алантолактон (4), гвяан хэлбэрийн сесквитерпен дегидрокостасын лактон (2), тритерпеноид α-амурин (5) болон энгийн фенолт нэгдэл 4-гидроксибензальдегид (6), пицелол (7), апоцинин (8), дегидрокониферол (9), кониферол (10) зэрэг бодисыг химийн цэвэр байдалтай ялгав. Эдгээр бодисын бүтэц байгуулалтыг нэг болон хоёр хэмжээст ЦСР-ын DEPT, COSY, HMBC спектроскопийн аргаар таньж тодорхойлов. Урьд өмнө каламеон (1), аристолон (3) бодисуудын устөрөгч ба нүүрстөрөгчийн атомуудын химийн шилжилтийн утгуудад оноолт бүрэн хийгдээгүй байсан ба энэ хоёр бодисын оноолтыг гүйцээж хийв. Түлхүүр үг: Терпеноид, сесквитерпент лактон, дегидрокостасын лактон, ЦСР.

scholarly journals Janus effect of antifreeze proteins on ice nucleation

2016 ◽  
Vol 113 (51) ◽  
pp. 14739-14744 ◽  
Author(s):  
Kai Liu ◽  
Chunlei Wang ◽  
Ji Ma ◽  
Guosheng Shi ◽  
Xi Yao ◽  
...  
Keyword(s):  
Liquid Water ◽  
Molecular Level ◽  
Simulation Analysis ◽  
Antifreeze Proteins ◽  
Freezing Temperature ◽  
Ice Nucleation ◽  
Dynamics Simulation ◽  
Ice Binding ◽  
Solid Substrates ◽  
Unique Capability

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.

Physical processes behind interactions of microplastic particles with ice

2021 ◽  
Author(s):  
Irina Chubarenko
Keyword(s):  
Laboratory Tests ◽  
Freezing Point ◽  
Ice Cores ◽  
Russian Science ◽  
Density Maximum ◽  
Freshwater Ice ◽  
Ice Surface ◽  
Strong Convection ◽  
The Difference ◽  
Negatively Buoyant

<p>Microplastic particles (MPs) are found in marine ice in larger quantities than in seawater, indicating that the ice is an important link in the chain of spreading of this contaminant. Some studies indicate larger MPs abundance near the ice surface, while others did not find any consistent pattern in the vertical distribution of MPs within sea ice cores. We discuss physical mechanisms of incorporation of MPs in the ice and present the results of laboratory tests, underpinning our conclusions.</p><p>First, plastic hydrophobicity is shown to cause the effect of pushing the floating MPs further up of the newly-forming ice. This leads to a concentration of MPs at the ice surface in the laboratory, while in the field the particles at the surface may by covered by snow and become a part of the upper ice layer. Under open-air test conditions, the bubbles of foamed polystyrene (density 0.04 g/cm<sup>3</sup>), initially floating at the water surface, were gone by weak wind when the firm ice was formed.</p><p>Second, the difference between freshwater and marine ice is considered. Since fresh water has its temperature of the density maximum (Tmd=3.98 C) well above the freezing point (Tfr=0 C), the freshwater ice is formed when the water column is stably stratified for a relatively long period of cooling from the Tmd down to the Tfr. Under such steady conditions, even just slightly positively/negatively buoyant MPs have enough time to rise to the surface / to settle to the bottom. In contrast, the ice in the ocean freezes when thermal convection is at work, further enhanced by the brine release. Thus, strong convection beneath the forming marine ice keeps slightly positively/negatively buoyant MPs in suspension and maintains the contact between the MPs and the forming ice. Laboratory tests show both the difference between the solid-and-transparent freshwater ice and the layered, filled with brine marine ice, and the difference in the level of their contamination.</p><p>Lastly, it is demonstrated that MPs tend to be incorporated in the ice together with air bubbles and in-between the ice plates (in brine channels). This is most probably due t plastics’ hydrophobicity.</p><p>Investigations are supported by the Russian Science Foundation, grant No 19-17-00041.</p>

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