Deciphering the Role of the Non-ice-binding Surface in the Antifreeze Activity of Hyperactive Antifreeze Proteins

2020 ◽  
Vol 124 (23) ◽  
pp. 4686-4696
Author(s):  
Prasun Pal ◽  
Sandipan Chakraborty ◽  
Biman Jana
Keyword(s):  
Antifreeze Proteins ◽  
Ice Binding ◽  
Binding Surface ◽  
Antifreeze Activity

Hydration Shell of Antifreeze Proteins: Unveiling the Role of Non-Ice-Binding Surfaces

2019 ◽  
Vol 123 (30) ◽  
pp. 6474-6480 ◽  
Author(s):  
Laura Zanetti-Polzi ◽  
Akash Deep Biswas ◽  
Sara Del Galdo ◽  
Vincenzo Barone ◽  
Isabella Daidone
Keyword(s):  
Antifreeze Proteins ◽  
Hydration Shell ◽  
Ice Binding

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.

A Ca2+-dependent bacterial antifreeze protein domain has a novel β-helical ice-binding fold

2008 ◽  
Vol 411 (1) ◽  
pp. 171-180 ◽  
Author(s):  
Christopher P. Garnham ◽  
Jack A. Gilbert ◽  
Christopher P. Hartman ◽  
Robert L. Campbell ◽  
Johanna Laybourn-Parry ◽  
...  
Keyword(s):  
Freezing Point ◽  
Protein Domain ◽  
Site Directed Mutagenesis ◽  
Hydrophobic Core ◽  
Amino Acid Region ◽  
Ice Binding ◽  
Binding Surface ◽  
The Antarctic ◽  
Antifreeze Activity ◽  
Acid Region

AFPs (antifreeze proteins) are produced by many organisms that inhabit ice-laden environments. They facilitate survival at sub-zero temperatures by binding to, and inhibiting, the growth of ice crystals in solution. The Antarctic bacterium Marinomonas primoryensis produces an exceptionally large (>1 MDa) hyperactive Ca2+-dependent AFP. We have cloned, expressed and characterized a 322-amino-acid region of the protein where the antifreeze activity is localized that shows similarity to the RTX (repeats-in-toxin) family of proteins. The recombinant protein requires Ca2+ for structure and activity, and it is capable of depressing the freezing point of a solution in excess of 2 °C at a concentration of 0.5 mg/ml, therefore classifying it as a hyperactive AFP. We have developed a homology-guided model of the antifreeze region based partly on the Ca2+-bound β-roll from alkaline protease. The model has identified both a novel β-helical fold and an ice-binding site. The interior of the β-helix contains a single row of bound Ca2+ ions down one side of the structure and a hydrophobic core down the opposite side. The ice-binding surface consists of parallel repetitive arrays of threonine and aspartic acid/asparagine residues located down the Ca2+-bound side of the structure. The model was tested and validated by site-directed mutagenesis. It explains the Ca2+-dependency of the region, as well its hyperactive antifreeze activity. This is the first bacterial AFP to be structurally characterized and is one of only five hyperactive AFPs identified to date.

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.

scholarly journals Structure-function analysis of microRNA 3′-end trimming by Nibbler

2020 ◽  
Vol 117 (48) ◽  
pp. 30370-30379
Author(s):  
Wei Xie ◽  
Ivica Sowemimo ◽  
Rippei Hayashi ◽  
Juncheng Wang ◽  
Thomas R. Burkard ◽  
...  
Keyword(s):  
Rna Binding ◽  
Function Analysis ◽  
Principal Role ◽  
Functional Studies ◽  
Surface Patches ◽  
Activity Modeling ◽  
Binding Surface ◽  
Catalytic Cleavage ◽  
Cleavage Motif

Nibbler (Nbr) is a 3′-to-5′ exoribonuclease whose catalytic 3′-end trimming activity impacts microRNA (miRNA) and PIWI-interacting RNA (piRNA) biogenesis. Here, we report on structural and functional studies to decipher the contributions of Nbr’s N-terminal domain (NTD) and exonucleolytic domain (EXO) in miRNA 3′-end trimming. We have solved the crystal structures of the NTD core and EXO domains of Nbr, both in the apo-state. The NTD-core domain ofAedes aegyptiNbr adopts a HEAT-like repeat scaffold with basic patches constituting an RNA-binding surface exhibiting a preference for binding double-strand RNA (dsRNA) over single-strand RNA (ssRNA). Structure-guided functional assays inDrosophilaS2 cells confirmed a principal role of the NTD in exonucleolytic miRNA trimming, which depends on basic surface patches. Gain-of-function experiments revealed a potential role of the NTD in recruiting Nbr to Argonaute-bound small RNA substrates. The EXO domain ofA. aegyptiandDrosophila melanogasterNbr adopt a mixed α/β-scaffold with a deep pocket lined by a DEDDy catalytic cleavage motif. We demonstrate that Nbr’s EXO domain exhibits Mn2+-dependent ssRNA-specific 3′-to-5′ exoribonuclease activity. Modeling of a 3′ terminal Uridine into the catalytic pocket of Nbr EXO indicates that 2′-O-methylation of the 3′-U would result in a steric clash with a tryptophan side chain, suggesting that 2′-O-methylation protects small RNAs from Nbr-mediated trimming. Overall, our data establish that Nbr requires its NTD as a substrate recruitment platform to execute exonucleolytic miRNA maturation, catalyzed by the ribonuclease EXO domain.

Protective role of antifreeze proteins on sterlet (Acipenser ruthenus) sperm during cryopreservation

2018 ◽  
Vol 44 (6) ◽  
pp. 1527-1533 ◽  
Author(s):  
Miaomiao Xin ◽  
Jan Sterba ◽  
Anna Shaliutina-Kolesova ◽  
Borys Dzyuba ◽  
Jaroslava Lieskovska ◽  
...  
Keyword(s):  
Antifreeze Proteins ◽  
Protective Role ◽  
Acipenser Ruthenus ◽  
Sterlet Acipenser Ruthenus
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