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D J Bacon - One of the best experts on this subject based on the ideXlab platform.
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dislocation core structure and dynamics in two atomic models of α zirconium
Acta Materialia, 2010Co-Authors: H A Khater, D J BaconAbstract:Abstract Properties of basal and first order Prism Plane dislocations with Burgers vector 1/3 〈 1 1 2 ¯ 0 〉 in α-Zr have been investigated by computer simulation. Results for a recent interatomic potential (MA07) are assessed and compared with an older one (AWB95). The elastic constants have been calculated with the inner relaxations allowed for and the energy and vector of metastable stacking faults have been determined and compared with published ab initio estimates. The core of the screw dislocation spreads principally in the Prism Plane in the MA07 model, in contrast to basal Plane dissociation in the AWB95 model, and the Prism-to-basal ratio of the Peierls stress for the screw is 0.28 with the MA07 model, compared with 3.31 with the AWB95 model. Simulation of the dynamics of dislocation motion under applied stress reveal how the drag coefficient varies with slip system and temperature. The results for the MA07 model are consistent with the known slip geometry of Zr, suggesting that it offers significant advantages for large-scale atomic simulation of dislocation behaviour.
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core structure dislocation energy and peierls stress for 1 3112 0 edge dislocations with 0 0 0 1 and 11 00 slip Planes in α zr
Materials Science and Engineering A-structural Materials Properties Microstructure and Processing, 2005Co-Authors: R E Voskoboinikov, Yu N Osetsky, D J BaconAbstract:Abstract Atomic-scale simulations of edge dislocations of the 1 / 3 1 1 2 ¯ 0 ( 0 0 0 1 ) and 1 / 3 1 1 2 ¯ 0 { 1 1 ¯ 0 0 } slip systems have been carried out using a Finnis-Sinclair-type interatomic potential for α-zirconium. The distribution of atomic displacements in the dislocation core shows that in this model the edge dislocation in the basal Plane dissociates into two Shockley partials whereas the dislocation in the Prism Plane remains undissociated. The effective core radius and core energy are estimated, and dislocation response to increasing applied shear strain is investigated. The core properties and the critical stress for dislocation glide (Peierls stress) depend sensitively on whether the core extends or not.
Peter L Davies - One of the best experts on this subject based on the ideXlab platform.
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experimental correlation between thermal hysteresis activity and the distance between antifreeze proteins on an ice surface
RSC Advances, 2015Co-Authors: Ran Drori, Peter L Davies, Ido BraslavskyAbstract:Antifreeze proteins (AFPs) aid the survival of cold-adapted organisms by inhibiting the growth of ice crystals in the organism. The binding of AFPs to ice separates the melting point from the freezing point of the ice crystal (thermal hysteresis, TH). Although AFPs were discovered more than 40 years ago, the mechanism by which they inhibit ice growth remains unclear. The distance between surface-bound AFPs is thought to correlate directly with the TH activity; however, this correlation has never been experimentally established. A novel microfluidics system was used here to obtain ice crystals covered with GFP-tagged AFPs in an AFP-free solution. This method permits calculation of the surface density of bound AFPs. Fluorescence intensity analysis revealed that the distance between ∼3 nm-long AFPs on the ice surface was 7–35 nm, depending on the AFP solution concentration and time of its exposure to ice. A direct correlation between these distances and the measured TH activity was found for a representative insect AFP, but not for a typical fish AFP. Insect AFPs accumulate over multiple ice crystal Planes, especially the basal Plane. Fish AFPs, which cannot bind to the basal Plane, change the shape of the crystal to minimize the basal Plane area. Thus, we postulate that the surface density of fish AFPs on the Prism Plane is not directly indicative of the TH activity, which ends when ice grows out of the basal Plane and is a function of the basal Plane area. These results significantly contribute to our understanding of the AFP mechanism and will be helpful in applying these proteins in different fields.
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compound ice binding site of an antifreeze protein revealed by mutagenesis and fluorescent tagging
Biochemistry, 2010Co-Authors: Christopher P Garnham, Ido Braslavsky, Adam J Middleton, Aditya Natarajan, Mike J Kuiper, Peter L DaviesAbstract:By binding to the surface of ice crystals, type III antifreeze protein (AFP) can depress the freezing point of fish blood to below that of freezing seawater. This 7-kDa globular protein is encoded by a multigene family that produces two major isoforms, SP and QAE, which are 55% identical. Disruptive mutations on the ice-binding site of type III AFP lower antifreeze activity but can also change ice crystal morphology. By attaching green fluorescent protein to different mutants and isoforms and by examining the binding of these fusion proteins to single-crystal ice hemispheres, we show that type III AFP has a compound ice-binding site. There are two adjacent, flat, ice-binding surfaces at 150° to each other. One binds the primary Prism Plane of ice; the other, a pyramidal Plane. Steric mutations on the latter surface cause elongation of the ice crystal as primary Prism Plane binding becomes dominant. SP isoforms naturally have a greatly reduced ability to bind the Prism Planes of ice. Mutations that make th...
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Direct Visualization of Spruce Budworm Antifreeze Protein Interacting with Ice Crystals: Basal Plane Affinity Confers Hyperactivity
Biophysical journal, 2008Co-Authors: Natalya Pertaya, Peter L Davies, Christopher B. Marshall, Yeliz Celik, Ido BraslavskyAbstract:Antifreeze proteins (AFPs) protect certain organisms from freezing by adhering to ice crystals, thereby preventing their growth. All AFPs depress the nonequilibrium freezing temperature below the melting point; however AFPs from overwintering insects, such as the spruce budworm (sbw) are 10–100 times more effective than most fish AFPs. It has been proposed that the exceptional activity of these AFPs depends on their ability to prevent ice growth at the basal Plane. To test the hypothesis that the hyperactivity of sbwAFP results from direct affinity to the basal Plane, we fluorescently tagged sbwAFP and visualized it on the surface of ice crystals using fluorescence microscopy. SbwAFP accumulated at the six Prism Plane corners and the two basal Planes of hexagonal ice crystals. In contrast, fluorescently tagged fish type III AFP did not adhere to the basal Planes of a single-crystal ice hemisphere. When ice crystals were grown in the presence of a mixture of type III AFP and sbwAFP, a hybrid crystal shape was produced with sbwAFP bound to the basal Planes of truncated bipyramidal crystals. These observations are consistent with the blockage of c-axial growth of ice as a result of direct interaction of sbwAFP with the basal Planes.
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structural basis for the binding of a globular antifreeze protein to ice
Nature, 1996Co-Authors: Zongchao Jia, Carl I Deluca, Heman Chao, Peter L DaviesAbstract:Antifreeze proteins (AFPs) have the unique ability to adsorb to ice and inhibit its growth. Many organisms ranging from fish to bacteria use AFPs to retard freezing or lessen the damage incurred upon freezing and thawing. The ice-binding mechanism of the long linear alpha-helical type I AFPs has been attributed to their regularly spaced polar residues matching the ice lattice along a pyramidal Plane. In contrast, it is not known how globular antifreeze proteins such as type III AFP that lack repeating ice-binding residues bind to ice. Here we report the 1.25 A crystal structure of recombinant type III AFP (QAE isoform) from eel pout (Macrozoarces americanus), which reveals a remarkably flat amphipathic ice-binding site where five hydrogen-bonding atoms match two ranks of oxygens on the [1010] ice Prism Plane in the direction, giving high ice-binding affinity and specificity. This binding site, substantiated by the structures and properties of several ice-binding site mutants, suggests that the AFP occupies a niche in the ice surface in which it covers the basal Plane while binding to the Prism face.
Sakae Tsuda - One of the best experts on this subject based on the ideXlab platform.
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Calcium-Binding Generates the Semi-Clathrate Waters on a Type II Antifreeze Protein to Adsorb onto an Ice Crystal Surface
MDPI AG, 2019Co-Authors: Tatsuya Arai, Hidemasa Kondo, Yoshiyuki Nishimiya, Yasushi Ohyama, Sakae TsudaAbstract: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
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polypentagonal ice like water networks emerge solely in an activity improved variant of ice binding protein
Proceedings of the National Academy of Sciences of the United States of America, 2018Co-Authors: Sheikh Mahatabuddin, Hidemasa Kondo, Daichi Fukami, Tatsuya Arai, Yoshiyuki Nishimiya, Rumi Shimizu, Chie Shibazaki, Motoyasu Adachi, Sakae TsudaAbstract:Polypentagonal water networks were recently observed in a protein capable of binding to ice crystals, or ice-binding protein (IBP). To examine such water networks and clarify their role in ice-binding, we determined X-ray crystal structures of a 65-residue defective isoform of a Zoarcidae-derived IBP (wild type, WT) and its five single mutants (A20L, A20G, A20T, A20V, and A20I). Polypentagonal water networks composed of ∼50 semiclathrate waters were observed solely on the strongest A20I mutant, which appeared to include a tetrahedral water cluster exhibiting a perfect position match to the ( 10 1 ¯ 0 ) first Prism Plane of a single ice crystal. Inclusion of another symmetrical water cluster in the polypentagonal network showed a perfect complementarity to the waters constructing the ( 20 2 ¯ 1 ) pyramidal ice Plane. The order of ice-binding strength was A20L
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nmr analysis of type iii antifreeze protein intramolecular dimer structural basis for enhanced activity
Journal of Biological Chemistry, 2001Co-Authors: Kazunori Miura, Hidemasa Kondo, Ai Miura, Satoru Ohgiya, Tamotsu Hoshino, Nobuaki Nemoto, Tetsuya Suetake, Leo Spyracopoulos, Sakae TsudaAbstract:Abstract The structure of a new antifreeze protein (AFP) variant, RD3, from antarctic eel pout (Rhigophila dearborni) with enhanced activity has been determined for the first time by nuclear magnetic resonance spectroscopy. RD3 comprises a unique translational topology of two homologous type III AFP globular domains, each containing one flat, ice binding Plane. The ice binding Plane of the N domain is located ∼3.5 A “behind” that of the C domain. The two ice binding Planes are located laterally with an angle of 32 ± 12° between the Planes. These results suggest that the C domain Plane of RD3 binds first to the ice {1010} Prism Plane in the 〈0001〉 direction, which induces successive ice binding of the N domain in the 〈0101〉 direction. This manner of ice binding caused by the unique structural topology of RD3 is thought to be crucial for the significant enhancement of antifreeze activity, especially at low AFP concentrations.
Ido Braslavsky - One of the best experts on this subject based on the ideXlab platform.
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experimental correlation between thermal hysteresis activity and the distance between antifreeze proteins on an ice surface
RSC Advances, 2015Co-Authors: Ran Drori, Peter L Davies, Ido BraslavskyAbstract:Antifreeze proteins (AFPs) aid the survival of cold-adapted organisms by inhibiting the growth of ice crystals in the organism. The binding of AFPs to ice separates the melting point from the freezing point of the ice crystal (thermal hysteresis, TH). Although AFPs were discovered more than 40 years ago, the mechanism by which they inhibit ice growth remains unclear. The distance between surface-bound AFPs is thought to correlate directly with the TH activity; however, this correlation has never been experimentally established. A novel microfluidics system was used here to obtain ice crystals covered with GFP-tagged AFPs in an AFP-free solution. This method permits calculation of the surface density of bound AFPs. Fluorescence intensity analysis revealed that the distance between ∼3 nm-long AFPs on the ice surface was 7–35 nm, depending on the AFP solution concentration and time of its exposure to ice. A direct correlation between these distances and the measured TH activity was found for a representative insect AFP, but not for a typical fish AFP. Insect AFPs accumulate over multiple ice crystal Planes, especially the basal Plane. Fish AFPs, which cannot bind to the basal Plane, change the shape of the crystal to minimize the basal Plane area. Thus, we postulate that the surface density of fish AFPs on the Prism Plane is not directly indicative of the TH activity, which ends when ice grows out of the basal Plane and is a function of the basal Plane area. These results significantly contribute to our understanding of the AFP mechanism and will be helpful in applying these proteins in different fields.
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compound ice binding site of an antifreeze protein revealed by mutagenesis and fluorescent tagging
Biochemistry, 2010Co-Authors: Christopher P Garnham, Ido Braslavsky, Adam J Middleton, Aditya Natarajan, Mike J Kuiper, Peter L DaviesAbstract:By binding to the surface of ice crystals, type III antifreeze protein (AFP) can depress the freezing point of fish blood to below that of freezing seawater. This 7-kDa globular protein is encoded by a multigene family that produces two major isoforms, SP and QAE, which are 55% identical. Disruptive mutations on the ice-binding site of type III AFP lower antifreeze activity but can also change ice crystal morphology. By attaching green fluorescent protein to different mutants and isoforms and by examining the binding of these fusion proteins to single-crystal ice hemispheres, we show that type III AFP has a compound ice-binding site. There are two adjacent, flat, ice-binding surfaces at 150° to each other. One binds the primary Prism Plane of ice; the other, a pyramidal Plane. Steric mutations on the latter surface cause elongation of the ice crystal as primary Prism Plane binding becomes dominant. SP isoforms naturally have a greatly reduced ability to bind the Prism Planes of ice. Mutations that make th...
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Direct Visualization of Spruce Budworm Antifreeze Protein Interacting with Ice Crystals: Basal Plane Affinity Confers Hyperactivity
Biophysical journal, 2008Co-Authors: Natalya Pertaya, Peter L Davies, Christopher B. Marshall, Yeliz Celik, Ido BraslavskyAbstract:Antifreeze proteins (AFPs) protect certain organisms from freezing by adhering to ice crystals, thereby preventing their growth. All AFPs depress the nonequilibrium freezing temperature below the melting point; however AFPs from overwintering insects, such as the spruce budworm (sbw) are 10–100 times more effective than most fish AFPs. It has been proposed that the exceptional activity of these AFPs depends on their ability to prevent ice growth at the basal Plane. To test the hypothesis that the hyperactivity of sbwAFP results from direct affinity to the basal Plane, we fluorescently tagged sbwAFP and visualized it on the surface of ice crystals using fluorescence microscopy. SbwAFP accumulated at the six Prism Plane corners and the two basal Planes of hexagonal ice crystals. In contrast, fluorescently tagged fish type III AFP did not adhere to the basal Planes of a single-crystal ice hemisphere. When ice crystals were grown in the presence of a mixture of type III AFP and sbwAFP, a hybrid crystal shape was produced with sbwAFP bound to the basal Planes of truncated bipyramidal crystals. These observations are consistent with the blockage of c-axial growth of ice as a result of direct interaction of sbwAFP with the basal Planes.
Hidemasa Kondo - One of the best experts on this subject based on the ideXlab platform.
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Calcium-Binding Generates the Semi-Clathrate Waters on a Type II Antifreeze Protein to Adsorb onto an Ice Crystal Surface
MDPI AG, 2019Co-Authors: Tatsuya Arai, Hidemasa Kondo, Yoshiyuki Nishimiya, Yasushi Ohyama, Sakae TsudaAbstract: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
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polypentagonal ice like water networks emerge solely in an activity improved variant of ice binding protein
Proceedings of the National Academy of Sciences of the United States of America, 2018Co-Authors: Sheikh Mahatabuddin, Hidemasa Kondo, Daichi Fukami, Tatsuya Arai, Yoshiyuki Nishimiya, Rumi Shimizu, Chie Shibazaki, Motoyasu Adachi, Sakae TsudaAbstract:Polypentagonal water networks were recently observed in a protein capable of binding to ice crystals, or ice-binding protein (IBP). To examine such water networks and clarify their role in ice-binding, we determined X-ray crystal structures of a 65-residue defective isoform of a Zoarcidae-derived IBP (wild type, WT) and its five single mutants (A20L, A20G, A20T, A20V, and A20I). Polypentagonal water networks composed of ∼50 semiclathrate waters were observed solely on the strongest A20I mutant, which appeared to include a tetrahedral water cluster exhibiting a perfect position match to the ( 10 1 ¯ 0 ) first Prism Plane of a single ice crystal. Inclusion of another symmetrical water cluster in the polypentagonal network showed a perfect complementarity to the waters constructing the ( 20 2 ¯ 1 ) pyramidal ice Plane. The order of ice-binding strength was A20L
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nmr analysis of type iii antifreeze protein intramolecular dimer structural basis for enhanced activity
Journal of Biological Chemistry, 2001Co-Authors: Kazunori Miura, Hidemasa Kondo, Ai Miura, Satoru Ohgiya, Tamotsu Hoshino, Nobuaki Nemoto, Tetsuya Suetake, Leo Spyracopoulos, Sakae TsudaAbstract:Abstract The structure of a new antifreeze protein (AFP) variant, RD3, from antarctic eel pout (Rhigophila dearborni) with enhanced activity has been determined for the first time by nuclear magnetic resonance spectroscopy. RD3 comprises a unique translational topology of two homologous type III AFP globular domains, each containing one flat, ice binding Plane. The ice binding Plane of the N domain is located ∼3.5 A “behind” that of the C domain. The two ice binding Planes are located laterally with an angle of 32 ± 12° between the Planes. These results suggest that the C domain Plane of RD3 binds first to the ice {1010} Prism Plane in the 〈0001〉 direction, which induces successive ice binding of the N domain in the 〈0101〉 direction. This manner of ice binding caused by the unique structural topology of RD3 is thought to be crucial for the significant enhancement of antifreeze activity, especially at low AFP concentrations.