scholarly journals Crystal structure of an insect antifreeze protein reveals ordered waters on the ice-binding surface

2020 ◽  
Vol 477 (17) ◽  
pp. 3271-3286 ◽  
Author(s):  
Qilu Ye ◽  
Robert Eves ◽  
Robert L. Campbell ◽  
Peter L. Davies
Keyword(s):  
Crystal Structure ◽  
Crystal Growth ◽  
Binding Site ◽  
Surface Waters ◽  
Ice Crystals ◽  
Ice Binding ◽  
Binding Surface ◽  
Longhorn Beetle ◽  
Polar Fish ◽  
Ice Lattice

Antifreeze proteins (AFPs) are characterized by their ability to adsorb to the surface of ice crystals and prevent any further crystal growth. AFPs have independently evolved for this purpose in a variety of organisms that encounter the threat of freezing, including many species of polar fish, insects, plants and microorganisms. Despite their diverse origins and structures, it has been suggested that all AFPs can organize ice-like water patterns on one side of the protein (the ice-binding site) that helps bind the AFP to ice. Here, to test this hypothesis, we have solved the crystal structure at 2.05 Å resolution of an AFP from the longhorn beetle, Rhagium mordax with five molecules in the unit cell. This AFP is hyperactive, and its crystal structure resembles that of the R. inquisitor ortholog in having a β-solenoid fold with a wide, flat ice-binding surface formed by four parallel rows of mainly Thr residues. The key difference between these structures is that the R. inquisitor AFP crystallized with its ice-binding site (IBS) making protein–protein contacts that limited the surface water patterns. Whereas the R. mordax AFP crystallized with the IBSs exposed to solvent enabling two layers of unrestricted ordered surface waters to be seen. These crystal waters make close matches to ice lattice waters on the basal and primary prism planes.

scholarly journals Growth suppression of ice crystal basal face in the presence of a moderate ice-binding protein does not confer hyperactivity

2018 ◽  
Vol 115 (29) ◽  
pp. 7479-7484 ◽  
Author(s):  
Maddalena Bayer-Giraldi ◽  
Gen Sazaki ◽  
Ken Nagashima ◽  
Sepp Kipfstuhl ◽  
Dmitry A. Vorontsov ◽  
...  
Keyword(s):  
Crystal Growth ◽  
Heat Dissipation ◽  
Freezing Point ◽  
Binding Protein ◽  
Ice Crystals ◽  
Ice Crystal ◽  
Freezing Point Depression ◽  
Basal Face ◽  
Ice Binding ◽  
Ice Binding Protein

Ice-binding proteins (IBPs) affect ice crystal growth by attaching to crystal faces. We present the effects on the growth of an ice single crystal caused by an ice-binding protein from the sea ice microalga Fragilariopsis cylindrus (fcIBP) that is characterized by the widespread domain of unknown function 3494 (DUF3494) and known to cause a moderate freezing point depression (below 1 °C). By the application of interferometry, bright-field microscopy, and fluorescence microscopy, we observed that the fcIBP attaches to the basal faces of ice crystals, thereby inhibiting their growth in the c direction and resulting in an increase in the effective supercooling with increasing fcIBP concentration. In addition, we observed that the fcIBP attaches to prism faces and inhibits their growth. In the event that the effective supercooling is small and crystals are faceted, this process causes an emergence of prism faces and suppresses crystal growth in the a direction. When the effective supercooling is large and ice crystals have developed into a dendritic shape, the suppression of prism face growth results in thinner dendrite branches, and growth in the a direction is accelerated due to enhanced latent heat dissipation. Our observations clearly indicate that the fcIBP occupies a separate position in the classification of IBPs due to the fact that it suppresses the growth of basal faces, despite its moderate freezing point depression.

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.

Single Crystal Growth of High-Pressure Phases of Ice and Salt Hydrate Far Below the Original Melting Point by Mixing Alcohol: Crystal Structure Determination of Magnesium Chloride Heptahydrate

2020 ◽  
Author(s):  
Keishiro Yamashita ◽  
Kazuki Komatsu ◽  
Hiroyuki Kagi
Keyword(s):  
Crystal Structure ◽  
High Pressure ◽  
Crystal Growth ◽  
Single Crystal ◽  
Room Temperature ◽  
Growth Technique ◽  
Salt Hydrate ◽  
X Ray

An crystal-growth technique for single crystal x-ray structure analysis of high-pressure forms of hydrogen-bonded crystals is proposed. We used alcohol mixture (methanol: ethanol = 4:1 in volumetric ratio), which is a widely used pressure transmitting medium, inhibiting the nucleation and growth of unwanted crystals. In this paper, two kinds of single crystals which have not been obtained using a conventional experimental technique were obtained using this technique: ice VI at 1.99 GPa and MgCl<sub>2</sub>·7H<sub>2</sub>O at 2.50 GPa at room temperature. Here we first report the crystal structure of MgCl2·7H2O. This technique simultaneously meets the requirement of hydrostaticity for high-pressure experiments and has feasibility for further in-situ measurements.

Alkyl-chain disorder in tetraisohexylammonium bromide

2012 ◽  
Vol 68 (4) ◽  
pp. o152-o155 ◽  
Author(s):  
Malcolm A. Kelland ◽  
Amber L. Thompson
Keyword(s):  
Crystal Structure ◽  
Crystal Growth ◽  
Alkyl Chain ◽  
Growth Inhibitor ◽  
Ammonium Cation ◽  
Asymmetric Unit ◽  
Bromide Anion ◽  
Alkyl Chains ◽  
Hydrate Crystal ◽  
Structure Ii Clathrate Hydrate

Tetraisohexylammonium bromide [systematic name: tetrakis(4-methylpentyl)azanium bromide], C24H52N+·Br−, is a powerful structure II clathrate hydrate crystal-growth inhibitor. The crystal structure, in the space groupP3221, contains one ammonium cation and one bromide anion in the asymmetric unit, both on general positions. At 100 K, the ammonium cation exhibits one ordered isohexyl chain and three disordered isohexyl chains. At 250 K, all four isohexyl chains are disordered. In an effort to reduce the disorder in the alkyl chains, the crystal was thermally cycled, but the disorder remained, indicating that it is dynamic in nature.

scholarly journals Synthesis of magnesium carbonate hydrate from natural talc

2020 ◽  
Vol 18 (1) ◽  
pp. 951-961
Author(s):  
Qiuju Chen ◽  
Tao Hui ◽  
Hongjuan Sun ◽  
Tongjiang Peng ◽  
Wenjin Ding
Keyword(s):  
Crystal Structure ◽  
Particle Size ◽  
Crystal Growth ◽  
Crystal Morphology ◽  
Magnesium Carbonate ◽  
Organic Additives ◽  
X Ray Diffraction ◽  
Morphological Transformation ◽  
X Ray ◽  
Carbonation Process

AbstractVarious morphologies of magnesium carbonate hydrate had been synthesized without using any organic additives by carefully adjusting the reaction temperature and time during the talc carbonation process. At lower temperatures, magnesium carbonate hydrate was prone to display needle-like morphology. With the further increase of the carbonation temperature, the sheet-like crystallites became the preferred morphology, and at higher aging temperatures, these crystallites tended to assemble into layer-like structures with diverse morphologies, such as rose-like particles and nest-like structure. The reaction time had no effect on the crystal morphology, but it affected the particle size and situation of the crystal growth. X-Ray diffraction results showed that these various morphologies were closely related to their crystal structure and compositions. The needle-like magnesium carbonate hydrate had a formula of MgCO3·3H2O, whereas with the morphological transformation from needle-like to sheet-like, rose-like, and nest-like structure, their corresponding compositions also changed from MgCO3·3H2O to 4MgCO3·Mg(OH)2·8H2O, 4MgCO3·Mg(OH)2·5H2O, and 4MgCO3·Mg(OH)2·4H2O.

scholarly journals The crystal structure of poplar apoplastocyanin at 1.8-A resolution. The geometry of the copper-binding site is created by the polypeptide.

1984 ◽  
Vol 259 (5) ◽  
pp. 2822-2825 ◽  
Author(s):  
T P Garrett ◽  
D J Clingeleffer ◽  
J M Guss ◽  
S J Rogers ◽  
H C Freeman
Keyword(s):  
Crystal Structure ◽  
Binding Site ◽  
Copper Binding

scholarly journals Characterization of the Acetate Binding Pocket in the Methanosarcina thermophila Acetate Kinase

2005 ◽  
Vol 187 (7) ◽  
pp. 2386-2394 ◽  
Author(s):  
Cheryl Ingram-Smith ◽  
Andrea Gorrell ◽  
Sarah H. Lawrence ◽  
Prabha Iyer ◽  
Kerry Smith ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Binding Site ◽  
Binding Pocket ◽  
Acetate Kinase ◽  
Phosphoryl Group ◽  
Acetyl Phosphate ◽  
Hydrophobic Pocket ◽  
Methanosarcina Thermophila ◽  
Methyl Group ◽  
Substrate Binding Sites

ABSTRACT Acetate kinase catalyzes the reversible magnesium-dependent synthesis of acetyl phosphate by transfer of the ATP γ-phosphoryl group to acetate. Inspection of the crystal structure of the Methanosarcina thermophila enzyme containing only ADP revealed a solvent-accessible hydrophobic pocket formed by residues Val93, Leu122, Phe179, and Pro232 in the active site cleft, which identified a potential acetate binding site. The hypothesis that this was a binding site was further supported by alignment of all acetate kinase sequences available from databases, which showed strict conservation of all four residues, and the recent crystal structure of the M. thermophila enzyme with acetate bound in this pocket. Replacement of each residue in the pocket produced variants with Km values for acetate that were 7- to 26-fold greater than that of the wild type, and perturbations of this binding pocket also altered the specificity for longer-chain carboxylic acids and acetyl phosphate. The kinetic analyses of variants combined with structural modeling indicated that the pocket has roles in binding the methyl group of acetate, influencing substrate specificity, and orienting the carboxyl group. The kinetic analyses also indicated that binding of acetyl phosphate is more dependent on interactions of the phosphate group with an unidentified residue than on interactions between the methyl group and the hydrophobic pocket. The analyses also indicated that Phe179 is essential for catalysis, possibly for domain closure. Alignments of acetate kinase, propionate kinase, and butyrate kinase sequences obtained from databases suggested that these enzymes have similar catalytic mechanisms and carboxylic acid substrate binding sites.

scholarly journals Synthetic insect antifreeze peptides modify ice crystal growth habit

CrystEngComm ◽  
2017 ◽  
Vol 19 (16) ◽  
pp. 2163-2167 ◽  
Author(s):  
Charles H. Z. Kong ◽  
Ivanhoe K. H. Leung ◽  
Vijayalekshmi Sarojini
Keyword(s):  
Crystal Growth ◽  
Small Molecule ◽  
Growth Habit ◽  
Antifreeze Protein ◽  
Ice Crystals ◽  
Ice Crystal ◽  
Antifreeze Peptides ◽  
Antifreeze Activity

Synthetic antifreeze peptides based on the hyperactive antifreeze protein modify the shape of ice crystals and show enhanced antifreeze activity with the addition of a small molecule.

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