Structure-based characterization and antifreeze properties of a hyperactive ice-binding protein from the Antarctic bacteriumFlavobacterium frigorisPS1

2014 ◽  
Vol 70 (4) ◽  
pp. 1061-1073 ◽  
Author(s):  
Hackwon Do ◽  
Soon-Jong Kim ◽  
Hak Jun Kim ◽  
Jun Hyuck Lee
Keyword(s):  
Amino Acid ◽  
Binding Site ◽  
Disulfide Bond ◽  
Binding Protein ◽  
Size Exclusion ◽  
Sequence Alignments ◽  
Ice Binding ◽  
Ice Binding Protein ◽  
Binding Residues ◽  
The Antarctic

Ice-binding proteins (IBPs) inhibit ice growth through direct interaction with ice crystals to permit the survival of polar organisms in extremely cold environments. FfIBP is an ice-binding protein encoded by the Antarctic bacteriumFlavobacterium frigorisPS1. The X-ray crystal structure of FfIBP was determined to 2.1 Å resolution to gain insight into its ice-binding mechanism. The refined structure of FfIBP shows an intramolecular disulfide bond, and analytical ultracentrifugation and analytical size-exclusion chromatography show that it behaves as a monomer in solution. Sequence alignments and structural comparisons of IBPs allowed two groups of IBPs to be defined, depending on sequence differences between the α2 and α4 loop regions and the presence of the disulfide bond. Although FfIBP closely resemblesLeucosporidium(recently re-classified asGlaciozyma) IBP (LeIBP) in its amino-acid sequence, the thermal hysteresis (TH) activity of FfIBP appears to be tenfold higher than that of LeIBP. A comparison of the FfIBP and LeIBP structures reveals that FfIBP has different ice-binding residues as well as a greater surface area in the ice-binding site. Notably, the ice-binding site of FfIBP is composed of a T-A/G-X-T/N motif, which is similar to the ice-binding residues of hyperactive antifreeze proteins. Thus, it is proposed that the difference in TH activity between FfIBP and LeIBP may arise from the amino-acid composition of the ice-binding site, which correlates with differences in affinity and surface complementarity to the ice crystal. In conclusion, this study provides a molecular basis for understanding the antifreeze mechanism of FfIBP and provides new insights into the reasons for the higher TH activity of FfIBP compared with LeIBP.

scholarly journals Ice-Binding Protein from Shewanella frigidimarinas Inhibits Ice Crystal Growth in Highly Alkaline Solutions

Polymers ◽  
2019 ◽  
Vol 11 (2) ◽  
pp. 299 ◽  
Author(s):  
Elizabeth Delesky ◽  
Shane Frazier ◽  
Jaqueline Wallat ◽  
Kendra Bannister ◽  
Chelsea Heveran ◽  
...  
Keyword(s):  
Crystal Growth ◽  
Ionic Strength ◽  
Binding Protein ◽  
Sodium Dodecyl ◽  
Size Exclusion ◽  
Alkaline Solutions ◽  
Ice Crystal ◽  
Ice Binding ◽  
Sds Page ◽  
Ice Binding Protein

The ability of a natural ice-binding protein from Shewanella frigidimarina (SfIBP) to inhibit ice crystal growth in highly alkaline solutions with increasing pH and ionic strength was investigated in this work. The purity of isolated SfIBP was first confirmed via sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and size-exclusion chromatography with an ultraviolet detector (SEC-UV). Protein stability was evaluated in the alkaline solutions using circular dichroism spectroscopy, SEC-UV, and SDS-PAGE. SfIBP ice recrystallization inhibition (IRI) activity, a measure of ice crystal growth inhibition, was assessed using a modified splat assay. Statistical analysis of results substantiated that, despite partial denaturation and misfolding, SfIBP limited ice crystal growth in alkaline solutions (pH ≤ 12.7) with ionic strength I ≤ 0.05 mol/L, but did not exhibit IRI activity in alkaline solutions where pH ≥ 13.2 and I ≥ 0.16 mol/L. IRI activity of SfIBP in solutions with pH ≤ 12.7 and I ≤ 0.05 mol/L demonstrated up to ≈ 66% reduction in ice crystal size compared to neat solutions.

scholarly journals Whole-genome sequencing of the endemic Antarctic fungus Antarctomyces pellizariae reveals an ice-binding protein, a scarce set of secondary metabolites gene clusters and provides insights on Thelebolales phylogeny

Genomics ◽  
2020 ◽  
Vol 112 (5) ◽  
pp. 2915-2921 ◽  
Author(s):  
Thiago Mafra Batista ◽  
Heron Oliveira Hilario ◽  
Gabriel Antônio Mendes de Brito ◽  
Rennan Garcias Moreira ◽  
Carolina Furtado ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Binding Protein ◽  
Protein A ◽  
Gene Clusters ◽  
Whole Genome ◽  
Ice Binding ◽  
Ice Binding Protein

Identification and analysis of two sequences encoding ice-binding proteins obtained from a putative bacterial symbiont of the psychrophilic Antarctic ciliate Euplotes focardii

2014 ◽  
Vol 26 (5) ◽  
pp. 491-501 ◽  
Author(s):  
Sandra Pucciarelli ◽  
Federica Chiappori ◽  
Raghul Rajan Devaraj ◽  
Guang Yang ◽  
Ting Yu ◽  
...  
Keyword(s):  
Amino Acid Level ◽  
Bacterial Symbiont ◽  
The Arctic ◽  
Glacial Ice ◽  
Mould Fungus ◽  
Lake Vostok ◽  
Ice Binding ◽  
Stigmatella Aurantiaca ◽  
Ice Binding Protein ◽  
The Antarctic

AbstractWe identified two ice-binding protein (IBP) sequences, named EFsymbAFP and EFsymbIBP, from a putative bacterial symbiont of the Antarctic psychrophilic ciliate Euplotes focardii. EFsymbAFP is 57.43% identical to the antifreeze protein (AFP) from the Stigmatella aurantiaca strain DW4/3-1, which was isolated from the Victoria Valley lower glacier. EFsymbIBP is 53.38% identical to the IBP from the Flavobacteriaceae bacterium strain 3519-10, isolated from the glacial ice of Lake Vostok. EFsymbAFP and EFsymbIBP are 31.73% identical at the amino acid level and are organized in tandem on the bacterial chromosome. The relatively low sequence identity and the tandem organization, which appears unique to this symbiont, suggest an occurrence of horizontal gene transfer (HGT). Structurally, EFsymbAFP and EFsymbIBP are similar to the AFPs from the snow mould fungus Typhula ishikariensis and from the Arctic yeast Leucosporidium sp. AY30. A phylogenetic analysis showed that EFsymbAFP and EFsymbIBP cluster principally with the IBP sequences from other Antarctic bacteria, supporting the view that these sequences belong to an Antarctic symbiontic bacterium of E. focardii. These results confirm that IBPs have a complex evolutionary history, which includes HGT events, most probably due to the demands of the environment and the need for rapid adaptation.

scholarly journals Structure-based classification of ice-binding proteins

2014 ◽  
Vol 70 (a1) ◽  
pp. C1054-C1054
Author(s):  
Hackwon Do ◽  
Chang Woo Lee ◽  
Jun Hyuck Lee
Keyword(s):  
Disulfide Bond ◽  
Binding Proteins ◽  
Structure Refinement ◽  
Head Region ◽  
Sequence Alignments ◽  
Range Interaction ◽  
Loop Region ◽  
Ice Binding ◽  
Structural Identity ◽  
Eukaryotic Microorganisms

Since the antifreeze protein (AFP) super family has low structural identity, classification standard of the AFPs is presently ambiguous. Newly identified ice-binding proteins (IBPs), named so after the function of the AFPs, have similar structural identity and function that interact to the ice. Identification and characterization of IBPs from the eukaryotic microorganisms Typhulaishikariensis (TisAFP) and Leucosporidium sp. (LeIBP) revealed that both are glycosylated and have irregular motif on the ice-binding site (IBS). The IBPs share a unique right-handed β-helix, which provides an advantage of broad-range interaction surface. The other IBP encoded by the Antarctic bacterium Flavobacterium frigoris PSI was determined at 2.1-Å resolution to gain insight into its ice-binding mechanism. The structure of FfIBP shows the presence of an intra-molecular disulfide bond in the loop region between α2 and α4 (capping region), unlike that of LeIBP and TisAFP. Electron density for this disulfide bond was seen between Cys107 and Cys124 during the structure refinement process and the Cβ–Cβ distance between Cys107 and Cys124 was 3.9 Å. By sequence alignments and structural comparisons of IBPs, we defined two groups within IBPs, depending on the sequence differences between the α2 and α4 loop regions and the presence of the disulfide bond. In addition, to investigate the effects of the capping region on the activity and stability of FfIBP, we determined the crystal structure and measured the thermal stability of mutants that swapped the capping region of FfIBP and LeIBP (mFfIBP and mLeIBP). In thermal denaturation experiments, it is clear that the capping-head region of FfIBP is more stable than that of LeIBP and is important for the overall stability of IBP, although it is not directly involved in the antifreeze activity.

The protective effect of Leucosporidium-derived ice-binding protein (LeIBP) on bovine oocytes and embryos during vitrification

2020 ◽  
Vol 151 ◽  
pp. 137-143
Author(s):  
Wu-Sheng Sun ◽  
Hoon Jang ◽  
Hyo Jin Kwon ◽  
Ki Young Kim ◽  
Soo Bin Ahn ◽  
...  
Keyword(s):  
Protective Effect ◽  
Binding Protein ◽  
Ice Binding ◽  
Ice Binding Protein ◽  
Bovine Oocytes

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.

Sign in / Sign up

Export Citation Format

Share Document