The biological function of an insect antifreeze protein simulated by molecular dynamics

Kuiper, Michael J.; Morton, Craig J.; Abraham, Sneha Elizabeth; Gray‐Weale, Angus

doi:10.7554/elife.05142

Cited by 90 publications

(127 citation statements)

References 57 publications

(70 reference statements)

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“…This theory has recently been supported via molecular simulation work by Naullage et al (9), who accurately calculated ∆T from θ and d for a model system. Additionally, Kuiper et al (10) confirmed that the binding of an AFP to the ice front is nearly irreversible in microsecond-long simulations, agreeing with earlier experimental evidence (11). However, how does the AFP first recognize and bind to a small quantity of solid water in a vast reservoir of liquid water?…”

Section: ∆T = αPsupporting

confidence: 58%

Combined molecular dynamics and neural network method for predicting protein antifreeze activity

Kozuch

Stillinger

Debenedetti

2018

Proc. Natl. Acad. Sci. U.S.A.

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Antifreeze proteins (AFPs) are a diverse class of proteins that depress the kinetically observable freezing point of water. AFPs have been of scientific interest for decades, but the lack of an accurate model for predicting AFP activity has hindered the logical design of novel antifreeze systems. To address this, we perform molecular dynamics simulation for a collection of well-studied AFPs. By analyzing both the dynamic behavior of water near the protein surface and the geometric structure of the protein, we introduce a method that automatically detects the ice binding face of AFPs. From these data, we construct a simple neural network that is capable of quantitatively predicting experimentally observed thermal hysteresis from a trio of relevant physical variables. The model’s accuracy is tested against data for 17 known AFPs and 5 non-AFP controls.

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Section: ∆T = αPsupporting

confidence: 58%

Combined molecular dynamics and neural network method for predicting protein antifreeze activity

Kozuch

Stillinger

Debenedetti

2018

Proc. Natl. Acad. Sci. U.S.A.

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“…B) Molecular dynamics results showing Spruce Budworm AFP with ordered water on AFP surface binding to the prism plane of ice. Reproduced with permission . Copyright 2015, eLife Sciences Publications.…”

Section: Facially Amphiphilic Non‐ice‐binding Materials and Compoundsmentioning

confidence: 99%

Mimicking the Ice Recrystallization Activity of Biological Antifreezes. When is a New Polymer “Active”?

Biggs

Stubbs

Graham

et al. 2019

Macromolecular Bioscience

101

173

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Antifreeze proteins and ice‐binding proteins have been discovered in a diverse range of extremophiles and have the ability to modulate the growth and formation of ice crystals. Considering the importance of cryoscience across transport, biomedicine, and climate science, there is significant interest in developing synthetic macromolecular mimics of antifreeze proteins, in particular to reproduce their property of ice recrystallization inhibition (IRI). This activity is a continuum rather than an “on/off” property and there may be multiple molecular mechanisms which give rise to differences in this observable property; the limiting concentrations for ice growth vary by more than a thousand between an antifreeze glycoprotein and poly(vinyl alcohol), for example. The aim of this article is to provide a concise comparison of a range of natural and synthetic materials that are known to have IRI, thus providing a guide to see if a new synthetic mimic is active or not, including emerging materials which are comparatively weak compared to antifreeze proteins, but may have technological importance. The link between activity and the mechanisms involving either ice binding or amphiphilicity is discussed and known materials assigned into classes based on this.

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“…Hydration shell structure in bulk water Some IBPs indirectly bind to ice through ordered "ice-like" or "clathrate-like" hydration water molecules, which are formed beside regularly spaced residues on the ice-binding site of IBP. Although the three-dimensional structure of these bound water molecules is distinct from the ice, it extensively matches the spacing of water molecules in ice lattice and forms hydrogen bonds with them [14][15][16]61 .…”

Section: Putative Ibs Inferred From Structural Analysismentioning

confidence: 99%

“…The icebinding site (IBS), often determined by point mutagenesis, is described as a broad, flat, somewhat hydrophobic surface. IBPs exhibit various ice-binding mechanisms driven by hydrogen bonding 9 , hydrophobic interaction [10][11][12][13] , and anchored clathrate motif [14][15][16] . The IBPs from the sea-ice diatom Fragilariopsis cylindrus (fcIBP), a dominant species within polar sea-ice microbial assemblages, belong to an IBP family very common among psychrophilic microorganisms 17 .…”

mentioning

confidence: 99%

Multiple binding modes of a moderate ice-binding protein from a polar microalga

Kondo

Mochizuki

Bayer‐Giraldi

2018

Phys. Chem. Chem. Phys.

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Ice-binding proteins (IBPs) produced by cold-tolerant organisms interact with ice and strongly control crystal growth. The molecular basis for the different magnitudes of activity displayed by various IBPs (moderate and hyperactive) has not yet been clarified. Previous studies questioned whether the moderate activity of some IBPs relies on their weaker binding modus to the ice surface, compared to hyperactive IBPs, rather than relying on binding only to selected faces of the ice crystal. We present the structure of one moderate IBP from the sea-ice diatom Fragilariopsis cylindrus (fcIBP) as determined by X-ray crystallography and investigate the protein's binding modes to the growing ice-water interface using molecular dynamics simulations. The structure of fcIBP is the IBP-1 fold, defined by a discontinuous β-solenoid delimitated by three faces (A, B and C-faces) and braced by an α-helix. The fcIBP structure shows capping loops on both N- and C-terminal parts of the solenoid. We show that the protein adsorbs on both the prism and the basal faces of ice crystals, confirming experimental results. The fcIBP binds irreversibly to the prism face using the loop between the B and the C-faces, involving also the B-face in water immobilization despite its irregular structure. The α-helix attaches the protein to the basal face with a partly reversible modus. Our results suggest that fcIBP has a looser attachment to ice and that this weaker binding modus is the basis to explain the moderate activity of fcIBP.

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The biological function of an insect antifreeze protein simulated by molecular dynamics

Cited by 90 publications

References 57 publications

Combined molecular dynamics and neural network method for predicting protein antifreeze activity

Combined molecular dynamics and neural network method for predicting protein antifreeze activity

Mimicking the Ice Recrystallization Activity of Biological Antifreezes. When is a New Polymer “Active”?

Multiple binding modes of a moderate ice-binding protein from a polar microalga

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