scholarly journals Calcium-Binding Generates the Semi-Clathrate Waters on a Type II Antifreeze Protein to Adsorb onto an Ice Crystal Surface

Biomolecules ◽  
2019 ◽  
Vol 9 (5) ◽  
pp. 162 ◽  
Author(s):  
Tatsuya Arai ◽  
Yoshiyuki Nishimiya ◽  
Yasushi Ohyama ◽  
Hidemasa Kondo ◽  
Sakae Tsuda

Hydration is crucial for a function and a ligand recognition of a protein. The hydration shell constructed on an antifreeze protein (AFP) contains many organized waters, through which AFP is thought to bind to specific ice crystal planes. For a Ca2+-dependent species of AFP, however, it has not been clarified how 1 mol of Ca2+-binding is related with the hydration and the ice-binding ability. Here we determined the X-ray crystal structure of a Ca2+-dependent AFP (jsAFP) from Japanese smelt, Hypomesus nipponensis, in both Ca2+-bound and -free states. Their overall structures were closely similar (Root mean square deviation (RMSD) of Cα = 0.31 Å), while they exhibited a significant difference around their Ca2+-binding site. Firstly, the side-chains of four of the five Ca2+-binding residues (Q92, D94 E99, D113, and D114) were oriented to be suitable for ice binding only in the Ca2+-bound state. Second, a Ca2+-binding loop consisting of a segment D94–E99 becomes less flexible by the Ca2+-binding. Third, the Ca2+-binding induces a generation of ice-like clathrate waters around the Ca2+-binding site, which show a perfect position-match to the waters constructing the first prism plane of a single ice crystal. These results suggest that generation of ice-like clathrate waters induced by Ca2+-binding enables the ice-binding of this protein.

2004 ◽  
Vol 377 (3) ◽  
pp. 589-595 ◽  
Author(s):  
Dang-Quan ZHANG ◽  
Bing LIU ◽  
Dong-Ru FENG ◽  
Yan-Ming HE ◽  
Shu-Qi WANG ◽  
...  

The ~24-amino-acid leucine-rich tandem repeat motif (PXXXXXLXXLXXLXLSXNXLXGXI) of carrot antifreeze protein comprises most of the processed protein and should contribute at least partly to the ice-binding site. Structural predictions using publicly available online sources indicated that the theoretical three-dimensional model of this plant protein includes a 10-loop β-helix containing the ~24-amino-acid tandem repeat. This theoretical model indicated that conservative asparagine residues create putative ice-binding sites with surface complementarity to the 1010 prism plane of ice. We used site-specific mutagenesis to test the importance of these residues, and observed a distinct loss of thermal hysteresis activity when conservative asparagines were replaced with valine or glutamine, whereas a large increase in thermal hysteresis was observed when phenylalanine or threonine residues were replaced with asparagine, putatively resulting in the formation of an ice-binding site. These results confirmed that the ice-binding site of carrot antifreeze protein consists of conservative asparagine residues in each β-loop. We also found that its thermal hysteresis activity is directly correlated with the length of its asparagine-rich binding site, and hence with the size of its ice-binding face.


2015 ◽  
Vol 6 (7) ◽  
pp. 1162-1167 ◽  
Author(s):  
Konrad Meister ◽  
Stephan Lotze ◽  
Luuk L. C. Olijve ◽  
Arthur L. DeVries ◽  
John G. Duman ◽  
...  

2012 ◽  
Vol 416 (5) ◽  
pp. 713-724 ◽  
Author(s):  
Adam J. Middleton ◽  
Christopher B. Marshall ◽  
Frédérick Faucher ◽  
Maya Bar-Dolev ◽  
Ido Braslavsky ◽  
...  

Scientifica ◽  
2014 ◽  
Vol 2014 ◽  
pp. 1-20 ◽  
Author(s):  
Janet S. H. Lorv ◽  
David R. Rose ◽  
Bernard R. Glick

Across the world, many ice active bacteria utilize ice crystal controlling proteins for aid in freezing tolerance at subzero temperatures. Ice crystal controlling proteins include both antifreeze and ice nucleation proteins. Antifreeze proteins minimize freezing damage by inhibiting growth of large ice crystals, while ice nucleation proteins induce formation of embryonic ice crystals. Although both protein classes have differing functions, these proteins use the same ice binding mechanisms. Rather than direct binding, it is probable that these protein classes create an ice surface prior to ice crystal surface adsorption. Function is differentiated by molecular size of the protein. This paper reviews the similar and different aspects of bacterial antifreeze and ice nucleation proteins, the role of these proteins in freezing tolerance, prevalence of these proteins in psychrophiles, and current mechanisms of protein-ice interactions.


Biochemistry ◽  
1998 ◽  
Vol 37 (51) ◽  
pp. 17745-17753 ◽  
Author(s):  
Michèle C. Loewen ◽  
Wolfram Gronwald ◽  
Frank D. Sönnichsen ◽  
Brian D. Sykes ◽  
Peter L. Davies

2018 ◽  
Vol 20 (42) ◽  
pp. 26926-26933 ◽  
Author(s):  
Dominique Verreault ◽  
Sarah Alamdari ◽  
Steven J. Roeters ◽  
Ravindra Pandey ◽  
Jim Pfaendtner ◽  
...  

Combined SFG/MD analysis together with spectral calculations revealed that type III antifreeze proteins adsorbed at the air–water interface maintains a native state and adopts an orientation that leads to a partial decoupling of its ice-binding site from water.


Biochemistry ◽  
1998 ◽  
Vol 37 (12) ◽  
pp. 4080-4085 ◽  
Author(s):  
K. Vanya Ewart ◽  
Zhengjun Li ◽  
Daniel S. C. Yang ◽  
Garth L. Fletcher ◽  
Choy L. Hew

2012 ◽  
Vol 109 (24) ◽  
pp. 9360-9365 ◽  
Author(s):  
H. Kondo ◽  
Y. Hanada ◽  
H. Sugimoto ◽  
T. Hoshino ◽  
C. P. Garnham ◽  
...  

FEBS Journal ◽  
2014 ◽  
Vol 281 (16) ◽  
pp. 3576-3590 ◽  
Author(s):  
Yuichi Hanada ◽  
Yoshiyuki Nishimiya ◽  
Ai Miura ◽  
Sakae Tsuda ◽  
Hidemasa Kondo

2018 ◽  
Vol 115 (33) ◽  
pp. 8266-8271 ◽  
Author(s):  
Arpa Hudait ◽  
Daniel R. Moberg ◽  
Yuqing Qiu ◽  
Nathan Odendahl ◽  
Francesco Paesani ◽  
...  

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.


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