Antifreeze protein hydration waters: Unstructured unless bound to ice

Marks, Sean M.; Patel, Amish J.

doi:10.1073/pnas.1810812115

Cited by 27 publications

(15 citation statements)

References 24 publications

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“…We note that although we have primarily discussed SWIPES in the context of surface-liquid-vapor systems, it can also be extended in a straightforward manner to other interfacial systems, such as surface-liquid-liquid or surfaceliquid-solid systems. By biasing an appropriate order parameter to control the extent to which a surface is covered by one phase relative to another, the method presented here can be generalized to characterize the preference of a surface for one liquid over another, or for a crystalline solid over its coexisting liquid 32,[67][68][69] . We further note that our approach can also be used to estimate the free energetic cost for wetting surfaces with nanoscale heterogeneities, such as chemically patterned surfaces or surfaces with nanoscale texture; for such surfaces, the notion of a contact angle itself may break down, and even if it can be defined unambiguously, estimating the contact angle from droplet geometry may be non-trivial [70][71][72][73][74][75][76] .…”

Section: E Conclusion and Outlookmentioning

confidence: 99%

Characterizing surface wetting and interfacial properties using enhanced sampling (SWIPES)

et al. 2019

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We introduce an accurate and efficient method for characterizing surface wetting and interfacial properties, such as the contact angle made by a liquid droplet on a solid surface, and the vapor-liquid surface tension of a fluid. The method makes use of molecular simulations in conjunction with the indirect umbrella sampling technique to systematically wet the surface and estimate the corresponding free energy. To illustrate the method, we study the wetting of a family of Lennard-Jones surfaces by water. We estimate contact angles for surfaces with a wide range of attractions for water by using our method and also by using droplet shapes. Notably, as surface -water attractions are increased, our method is able to capture the transition from partial to complete wetting. Finally, the method is straightforward to implement and computationally efficient, providing accurate contact angle estimates in roughly 5 nanoseconds of simulation time. A. IntroductionWetting of solid surfaces by fluids is important in diverse disciplines, including but not limited to surface chemistry, materials characterization, oil and gas recovery 1-5 . In general, the wettability of a solid by a fluid is characterized by a wetting coefficient, k ≡ (γ SV − γ SL )/γ VL , where γ represents surface tension, and the subscripts correspond to the coexisting vapor (V), liquid (L) and solid (S) phases. The wetting coefficient is also related to the contact angle (θ ) that a liquid droplet (surrounded by its vapor) makes with a solid surface; according to Young's equation, cos θ = (γ SV − γ SL )/γ VL = k. Thus, the extent to which a fluid prefers to wet a solid, or the preference of the solid for the

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Section: E Conclusion and Outlookmentioning

confidence: 99%

Characterizing surface wetting and interfacial properties using enhanced sampling (SWIPES)

et al. 2019

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“…The nature of the interactions that determine the binding to the ice surface has been widely debated: a spatial match between the polar residues of the IBS and the oxygen–oxygen distance in the ice lattice has been repeatedly noted, − pointing to a critical role of hydrogen bonds in the protein–ice binding. However, IBSs also typically show a relevant hydrophobic content, suggesting that hydrophobic groups might also be involved in ice binding, − with the idea that the release of constrained waters from hydrophobic groups on the IBS might provide a thermodynamic driving force for ice binding . Another key question is how AFPs are able to recognize ice prior to binding in a vast excess of water.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2019

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Antifreeze proteins (AFPs) have the ability to inhibit ice growth by binding to ice nuclei. Their ice-binding mechanism is still unclear, yet the hydration layer is thought to play a fundamental role. Here, we use molecular dynamics simulations to characterize the hydration shell of two AFPs and two non-AFPs. The calculated shell thickness and density of the AFPs do not feature any relevant difference with respect to the non-AFPs. Moreover, the hydration shell density is always higher than the bulk density and, thus, no low-density, ice-like layer is detected at the ice-binding surface (IBS) of AFPs. Instead, we observe local water-density differences in AFPs between the IBS (lower density) and the non-IBS (higher density). The lower solvent density at the ice-binding site can pave the way to the protein binding to ice nuclei, while the higher solvent density at the non-ice-binding surfaces might provide protection against ice growth.

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“…Smaller protein molecules, such as lysozyme, were found to partition even further from the ice interface, in line with our simulations. We note that a different behavior from the one observed here can be found for a specialized class of proteins, antifreeze proteins (AFPs), that can directly bind to ice nuclei and prevent them from growing. − …”

Section: Resultsmentioning

confidence: 99%

Heightened Cold-Denaturation of Proteins at the Ice–Water Interface

et al. 2020

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The process of freezing proteins is widely used in applications ranging from processing and storage of biopharmaceuticals to cryo-EM analysis of protein complexes. The formation of an ice−water interface is a critical destabilization factor for the protein, which can be offset by the use of cryo-protectants. Using molecular dynamics simulation, we demonstrate that the presence of the ice−water interface leads to a lowering of the free-energy barrier for unfolding, resulting in rapid unfolding of the protein. The unfolding process does not require direct adsorption of the protein to the surface, but is rather mediated by nearby liquid molecules that show an increased tendency for hydrating nonpolar groups. The observed enhancement in the cold denaturation process upon ice formation can be mitigated by addition of glucose, which acts as a cryoprotectant through preferential exclusion from side chains of the protein.

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Antifreeze protein hydration waters: Unstructured unless bound to ice

Cited by 27 publications

References 24 publications

Characterizing surface wetting and interfacial properties using enhanced sampling (SWIPES)

Characterizing surface wetting and interfacial properties using enhanced sampling (SWIPES)

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

Heightened Cold-Denaturation of Proteins at the Ice–Water Interface

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