scholarly journals How Do Size and Aggregation of Ice-binding Proteins Control their Ice Nucleation Efficiency

2018 ◽  
Author(s):  
Yuqing Qiu ◽  
Arpa Hudait ◽  
Valeria Molinero
Keyword(s):  
Amino Acid ◽  
Cell Membrane ◽  
Binding Site ◽  
Homogeneous Nucleation ◽  
Binding Proteins ◽  
Nucleation And Growth ◽  
Ice Nucleation ◽  
Nucleation Theory ◽  
Cold Temperatures ◽  
Ice Binding

Organisms that thrive at cold temperatures have evolved ice-binding proteins to manage the nucleation and growth of ice. Bacterial ice-nucleating proteins (INP) and insect hyperactive antifreeze proteins (AFP) bind ice through the same amino acid motifs, despite their opposite functions. AFPs are generally small, while INPs are long and aggregate in the cell membrane. It is not yet understood to which extent the size and aggregation determine the temperature Thet at which proteins nucleate ice. Here we address this question using molecular simulations and nucleation theory. The simulations indicate that the 2.5 nm long Tm AFP nucleates ice at 2±1 ° C above the homogeneous nucleation temperature. Addition of ice-binding loops to Tm AFP increases Thet until the length of the binding-site becomes ~4 times its width, beyond which Thet plateaus. We calculate that the INP of Ps. syringae, Ps INP, reaches its maximum Thet = -26 ° C when its binding site has 16 ice-binding loops, in excellent agreement with Thet = -25 ±1 ° C measured for an engineered 16-loop fragment of Ps INP. To further increase Thet , the proteins must aggregate. We predict Thet per number of Ps INP in the aggregate, and conclude that assemblies with 34 INP already reach Thet = -2 ° C characteristic of this bacterium. Interestingly, we find that Thet of aggregates is a non-monotonic and strongly varying function of the distance between proteins. We conclude that to achieve maximum freezing efficiency, bacteria must exert exquisite, sub-angstrom control of the distance between INP in their membrane.

scholarly journals How Do Size and Aggregation of Ice-binding Proteins Control their Ice Nucleation Efficiency

2019 ◽  
Author(s):  
Yuqing Qiu ◽  
Arpa Hudait ◽  
Valeria Molinero
Keyword(s):  
Binding Proteins ◽  
Molecular Simulations ◽  
Finite Size ◽  
Ice Nucleation ◽  
Nucleation Theory ◽  
Classical Nucleation Theory ◽  
Cold Temperatures ◽  
Ice Binding ◽  
Quantitative Understanding ◽  
Accurate Procedure

<p>Organisms that thrive at cold temperatures produce ice-binding proteins to manage the nucleation and growth of ice. Bacterial ice-nucleating proteins (INP) are typically large and form aggregates in the cell membrane, while insect hyperactive antifreeze proteins (AFP) are soluble and generally small. Experiments indicate that larger ice-binding proteins and their aggregates nucleate ice at warmer temperatures. Nevertheless, a quantitative understanding of how do size and aggregation of ice-binding proteins determine the temperature Thet at which proteins nucleate ice is still lacking. Here we address this question using molecular simulations and nucleation theory. The simulations indicate that the 2.5 nm long antifreeze protein TmAFP nucleates ice at 2±1 °C above the homogeneous nucleation temperature, in good agreement with recent experiments. We predict that the addition of ice-binding loops to TmAFP increases Thet until the length of the binding-site becomes ~4 times its width, beyond which Thet plateaus. We implement an accurate procedure to determine Thet of surfaces of finite size using classical nucleation theory and, after validating the theory against Thet of the proteins in molecular simulations, we use it to predict Thet of the INP of Ps. syringae as a function of the length and number of proteins in the aggregates. We conclude that assemblies with at most 34 INP already reach the Thet = -2 °C characteristic of this bacterium. Interestingly, we find that Thet is a strongly varying non-monotonic function of the distance between proteins in the aggregates. This indicates that to achieve maximum freezing efficiency, bacteria must exert exquisite, sub-angstrom control of the distance between INP in their membrane</p>

How Do Size and Aggregation of Ice-binding Proteins Control their Ice Nucleation Efficiency

2019 ◽  
Author(s):  
Yuqing Qiu ◽  
Arpa Hudait ◽  
Valeria Molinero
Keyword(s):  
Binding Proteins ◽  
Molecular Simulations ◽  
Finite Size ◽  
Ice Nucleation ◽  
Nucleation Theory ◽  
Classical Nucleation Theory ◽  
Cold Temperatures ◽  
Ice Binding ◽  
Quantitative Understanding ◽  
Accurate Procedure

<p>Organisms that thrive at cold temperatures produce ice-binding proteins to manage the nucleation and growth of ice. Bacterial ice-nucleating proteins (INP) are typically large and form aggregates in the cell membrane, while insect hyperactive antifreeze proteins (AFP) are soluble and generally small. Experiments indicate that larger ice-binding proteins and their aggregates nucleate ice at warmer temperatures. Nevertheless, a quantitative understanding of how do size and aggregation of ice-binding proteins determine the temperature Thet at which proteins nucleate ice is still lacking. Here we address this question using molecular simulations and nucleation theory. The simulations indicate that the 2.5 nm long antifreeze protein TmAFP nucleates ice at 2±1 °C above the homogeneous nucleation temperature, in good agreement with recent experiments. We predict that the addition of ice-binding loops to TmAFP increases Thet until the length of the binding-site becomes ~4 times its width, beyond which Thet plateaus. We implement an accurate procedure to determine Thet of surfaces of finite size using classical nucleation theory and, after validating the theory against Thet of the proteins in molecular simulations, we use it to predict Thet of the INP of Ps. syringae as a function of the length and number of proteins in the aggregates. We conclude that assemblies with at most 34 INP already reach the Thet = -2 °C characteristic of this bacterium. Interestingly, we find that Thet is a strongly varying non-monotonic function of the distance between proteins in the aggregates. This indicates that to achieve maximum freezing efficiency, bacteria must exert exquisite, sub-angstrom control of the distance between INP in their membrane</p>

scholarly journals Ice Nucleation Properties of Ice-binding Proteins from Snow Fleas

Biomolecules ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 532 ◽  
Author(s):  
Akalabya Bissoyi ◽  
Naama Reicher ◽  
Michael Chasnitsky ◽  
Sivan Arad ◽  
Thomas Koop ◽  
...  
Keyword(s):  
Binding Proteins ◽  
Thermal Hysteresis ◽  
Ice Nucleation ◽  
Ice Crystals ◽  
Nucleation Theory ◽  
Classical Nucleation Theory ◽  
Ice Binding ◽  
Nucleation Activity ◽  
Ice Shell ◽  
Ice Nucleation Activity

Ice-binding proteins (IBPs) are found in many organisms, such as fish and hexapods, plants, and bacteria that need to cope with low temperatures. Ice nucleation and thermal hysteresis are two attributes of IBPs. While ice nucleation is promoted by large proteins, known as ice nucleating proteins, the smaller IBPs, referred to as antifreeze proteins (AFPs), inhibit the growth of ice crystals by up to several degrees below the melting point, resulting in a thermal hysteresis (TH) gap between melting and ice growth. Recently, we showed that the nucleation capacity of two types of IBPs corresponds to their size, in agreement with classical nucleation theory. Here, we expand this finding to additional IBPs that we isolated from snow fleas (the arthropod Collembola), collected in northern Israel. Chemical analyses using circular dichroism and Fourier-transform infrared spectroscopy data suggest that these IBPs have a similar structure to a previously reported snow flea antifreeze protein. Further experiments reveal that the ice-shell purified proteins have hyperactive antifreeze properties, as determined by nanoliter osmometry, and also exhibit low ice-nucleation activity in accordance with their size.

scholarly journals Ankyrin-binding proteins related to nervous system cell adhesion molecules: candidates to provide transmembrane and intercellular connections in adult brain.

1993 ◽  
Vol 121 (1) ◽  
pp. 121-133 ◽  
Author(s):  
J Q Davis ◽  
T McLaughlin ◽  
V Bennett
Keyword(s):  
Nervous System ◽  
Cell Adhesion ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Binding Site ◽  
Adhesion Molecules ◽  
Cell Adhesion Molecules ◽  
Binding Proteins ◽  
Cytoplasmic Domain ◽  
System Cell

A major class of ankyrin-binding glycoproteins have been identified in adult rat brain of 186, 155, and 140 kD that are alternatively spliced products of the same pre-mRNA. Characterization of cDNAs demonstrated that ankyrin-binding glycoproteins (ABGPs) share 72% amino acid sequence identity with chicken neurofascin, a membrane-spanning neural cell adhesion molecule in the Ig super-family expressed in embryonic brain. ABGP polypeptides have the following features consistent with a role as ankyrin-binding proteins in vitro and in vivo: (a) ABGPs and ankyrin associate as pure proteins in a 1:1 molar stoichiometry; (b) the ankyrin-binding site is located in the COOH-terminal 21 kD of ABGP186 which contains the predicted cytoplasmic domain; (c) ABGP186 is expressed at approximately the same levels as ankyrin (15 pmoles/milligram of membrane protein); and (d) ABGP polypeptides are co-expressed with the adult form of ankyrinB late in postnatal development and are colocalized with ankyrinB by immunofluorescence. Similarity in amino acid sequence and conservation of sites of alternative splicing indicate that genes encoding ABGPs and neurofascin share a common ancestor. However, the major differences in developmental expression reported for neurofascin in embryos versus the late postnatal expression of ABGPs suggest that ABGPs and neurofascin represent products of gene duplication events that have subsequently evolved in parallel with distinct roles. The predicted cytoplasmic domains of rat ABGPs and chicken neurofascin are nearly identical to each other and closely related to a group of nervous system cell adhesion molecules with variable extracellular domains, which includes L1, Nr-CAM, and Ng-CAM of vertebrates, and neuroglian of Drosophila. The ankyrin-binding site of rat ABGPs is localized to the C-terminal 200 residues which encompass the cytoplasmic domain, suggesting the hypothesis that ability to associate with ankyrin may be a shared feature of neurofascin and related nervous system cell adhesion molecules.

scholarly journals Water structure and dynamics in the hydration layer of a type III anti-freeze protein

2018 ◽  
Vol 20 (10) ◽  
pp. 6996-7006 ◽  
Author(s):  
Z. Faidon Brotzakis ◽  
Ilja K. Voets ◽  
Huib J. Bakker ◽  
Peter G. Bolhuis
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Binding Site ◽  
Water Structure ◽  
Hydration Water ◽  
Tetrahedral Structure ◽  
Structure And Dynamics ◽  
Ice Binding ◽  
Left And Right ◽  
Middle Panel

The tetrahedral structure of hydration water (S) and its reorientation decay time (τ) correlates negatively for selected amino-acids in the vicinity of the ice binding site (left and right panels) of the antifreeze protein, but positively for the ice binding site central amino-acid (middle panel).

scholarly journals Significance of conservative asparagine residues in the thermal hysteresis activity of carrot antifreeze protein

2004 ◽  
Vol 377 (3) ◽  
pp. 589-595 ◽  
Author(s):  
Dang-Quan ZHANG ◽  
Bing LIU ◽  
Dong-Ru FENG ◽  
Yan-Ming HE ◽  
Shu-Qi WANG ◽  
...  
Keyword(s):  
Amino Acid ◽  
Binding Site ◽  
Tandem Repeat ◽  
Thermal Hysteresis ◽  
Three Dimensional ◽  
Antifreeze Protein ◽  
Three Dimensional Model ◽  
Prism Plane ◽  
Thermal Hysteresis Activity ◽  
Ice Binding

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.

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 Proteins Associated with an Antarctic Cyanobacterium, Nostoc sp. HG1

2020 ◽  
Vol 87 (2) ◽  
Author(s):  
James A. Raymond ◽  
Michael G. Janech ◽  
Marco Mangiagalli
Keyword(s):  
Amino Acid ◽  
Binding Proteins ◽  
Great Majority ◽  
Outer Cell ◽  
Polar Regions ◽  
Amino Acid Motif ◽  
Sequence Analyses ◽  
Ice Binding ◽  
Outer Cell Membrane ◽  
Genes Encoding

ABSTRACT Ice-binding proteins (IBPs) have been identified in numerous polar algae and bacteria, but so far not in any cyanobacteria, despite the abundance of cyanobacteria in polar regions. We previously reported strong IBP activity associated with an Antarctic Nostoc species. In this study, to identify the proteins responsible, as well as elucidate their origin, we sequenced the DNA of an environmental sample of this species, designated Nostoc sp. HG1, and its bacterial community and attempted to identify IBPs by looking for known IBPs in the metagenome and by looking for novel IBPs by tandem mass spectrometry (MS/MS) proteomics analyses of ice affinity-purified proteins. The metagenome contained over 116 DUF3494-type IBP genes, the most common type of IBP identified so far. One of the IBPs could be confidently assigned to Nostoc, while the others could be attributed to diverse bacteria, which, surprisingly, accounted for the great majority of the metagenome. Recombinant Nostoc IBPs (nIBPs) had strong ice-structuring activities, and their circular dichroism spectra were consistent with the secondary structure of a DUF3494-type IBP. nIBP is unusual in that it is the only IBP identified so far to have a PEP (amino acid motif) C-terminal signal, a signal that has been associated with anchoring to the outer cell membrane. These results suggest that the observed IBP activity of Nostoc sp. HG1 was due to a combination of endogenous and exogenous IBPs. Amino acid and nucleotide sequence analyses of nIBP raise the possibility that it was acquired from a planctomycete. IMPORTANCE The horizontal transfer of genes encoding ice-binding proteins (IBPs), proteins that confer freeze-thaw tolerance, has allowed many microorganisms to expand their ranges into polar regions. One group of microorganisms for which nothing is known about its IBPs is cyanobacteria. In this study, we identified a cyanobacterial IBP and showed that it was likely acquired from another bacterium, probably a planctomycete. We also showed that a consortium of IBP-producing bacteria living with the Nostoc contribute to its IBP activity.

How Size and Aggregation of Ice-Binding Proteins Control Their Ice Nucleation Efficiency

2019 ◽  
Vol 141 (18) ◽  
pp. 7439-7452 ◽  
Author(s):  
Yuqing Qiu ◽  
Arpa Hudait ◽  
Valeria Molinero
Keyword(s):  
Binding Proteins ◽  
Ice Nucleation ◽  
Ice Binding
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