Analysis of Water and Hydrogen Bond Dynamics at the Surface of an Antifreeze Protein

Xu, Yao; Gnanasekaran, Ramachandran; Leitner, David M.

doi:10.1155/2012/125071

Cited by 33 publications

(32 citation statements)

References 54 publications

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“…We note that we found a similar trend for another AFP from spruce budworm Choristoneura fumiferana, which also contains a threonine-rich ice-binding plane. In that case, four point mutations, which are found experimentally to dramatically lower antifreeze activity, lead to a similar trend in the hydrogen bond dynamics as we observe here for DAFP-1 (i.e., the hydrogen bond dynamics around all planes are similar for the mutants, whereas they are significantly slower around the icebinding plane for the WT, thereby giving rise to a heterogeneous distribution of the hydration dynamics) (38). Site-specific mutation has a clear nonlocal effect on the entire ice-binding plane.…”

Section: Resultssupporting

confidence: 80%

Long-range protein–water dynamics in hyperactive insect antifreeze proteins

Meister

Ebbinghaus

et al. 2012

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

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234

221

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Antifreeze proteins (AFPs) are specific proteins that are able to lower the freezing point of aqueous solutions relative to the melting point. Hyperactive AFPs, identified in insects, have an especially high ability to depress the freezing point by far exceeding the abilities of other AFPs. In previous studies, we postulated that the activity of AFPs can be attributed to two distinct molecular mechanisms: (i) short-range direct interaction of the protein surface with the growing ice face and (ii) long-range interaction by protein-induced water dynamics extending up to 20 Å from the protein surface. In the present paper, we combine terahertz spectroscopy and molecular simulations to prove that long-range protein-water interactions make essential contributions to the high antifreeze activity of insect AFPs from the beetle Dendroides canadensis. We also support our hypothesis by studying the effect of the addition of the osmolyte sodium citrate.hydration dynamics | THz spetroscopy A ntifreeze proteins (AFPs) and antifreeze glycoproteins (AFGPs) are classes of proteins that suppress ice growth in organisms and thereby enable their survival in subfreezing habitats (1). Despite their similar function, many distinct structures have been identified so far. AFPs have been identified in several organisms, including polar fish (2), insects (3), bacteria (4), and plants (5). Their common characteristic is the depression of the freezing temperatures of ice growth of a solution without depressing the melting point equilibrium of protein solutions. This nonequilibrium phenomenon leads to a difference between the freezing and melting temperature, which is referred to as thermal hysteresis (TH). TH is used as a characteristic measure for antifreeze activity of an AFP (6). AFGPs and AFPs, as extracted from the blood of polar fish, usually exhibit up to 2°of TH activity and are termed moderately active AFPs, whereas insect AFPs can exhibit over 5°of TH and therefore, are referred to as hyperactive AFPs. The work by Raymond and DeVries (7,8) proposed a mechanism in which freezing point depression is achieved by an adsorption-inhibition mechanism, in which the proteins recognize and bind "quasiirreversibly" to an ice surface, thereby preventing growth of ice crystals. The adsorption of the protein is thought to prevent macroscopic ice growth in the hysteresis gap, but microscopic growth occurs at the interface in the form of highly curved fronts between adsorbed antifreeze molecules. This effect will cause a decrease of the local freezing temperature because of the Kelvin effect, while leaving the melting temperature relatively unaffected (7). As recently pointed out in the work by Sharp (9), antifreeze activity involves one of the most difficult recognition problems in biology, the distinction between water as liquid and ice. The initially proposed mechanism builds on a local mechanism. In particular, threonine (Thr) residues were proposed to play a decisive role: their hydroxyl groups were thought to be responsible for the high af...

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Section: Resultssupporting

confidence: 80%

Long-range protein–water dynamics in hyperactive insect antifreeze proteins

Meister

Ebbinghaus

et al. 2012

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

Self Cite

234

221

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“…Interestingly, the enhancement of water -water H-bond lifetime upon gradual addition of TMU in aqueous solution resembles the slowing down of water confined in carbon nanotube [105] and water at the surface of an antifreeze protein. [106] Therefore, it may be stated that the presence of TMU slows down the H-bond dynamics in some ways similar to those operative inside the confinement and at the micelle and protein surfaces. One of the frames from the simulation trajectory at X TMU ¼ 0.2 is shown in Figure 9 which depicts the alignment of water and TMU molecules in the binary mixture.…”

Section: Molecular Simulation 477mentioning

confidence: 99%

Hydrogen-bond dynamics of water in presence of an amphiphile, tetramethylurea: signature of confinement-induced effects

Indra

Biswas

2014

Molecular Simulation

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Various experimental and simulation studies have suggested that the presence of amphiphilic molecules in aqueous solutions substantially perturbs the tetrahedral hydrogen-bond (H-bond) network of neat liquid water. Such structural perturbation is expected to impact H-bond lifetime of liquid water. Tetramethylurea (TMU) is an example of an amphiphile because it possesses both hydrophobic and hydrophilic moieties. Molecular dynamics simulations of (water þ TMU) binary mixtures at various compositions have been performed in order to investigate the microscopic mechanism through which the amphiphiles influence the H-bond dynamics of liquid water at room temperature. Present simulations indicate lengthening of both water -water H-bond lifetime and H-bond structural relaxation time upon addition of TMU in aqueous solution. At the highest TMU mole fraction studied, H-bond lifetime and structural relaxation time are, respectively, , 4 and , 8 times longer than those in neat water. This is comparable with the slowing down of H-bond dynamics for water molecules confined in cyclodextrin cavities. Simulated relaxation profiles are multi-exponential in character at all mixture compositions, and simulated radial distribution functions suggest enhanced water -water and water -TMU interactions upon addition of TMU. No evidence for complete encapsulation of TMU by water H-bond network has been found.

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“…In MD simulation, usually the geometric or the energetic criteria are used to define an HB. Classical atomistic MD simulations have revealed that the relaxation of water−water HB is much faster than that of the protein−water HB . A correlation is established between protein water HB dynamics with the biological activity.…”

Section: Introductionmentioning

confidence: 99%

“…Classical atomistic MD simulations have revealed that the relaxation of waterÀ water HB is much faster than that of the proteinÀ water HB. [36,37] A correlation is established between protein water HB dynamics with the biological activity. Thus, important insight can be drawn from studies of solvation dynamics which can shed light on the role of different factors influencing the water dynamics to modulate the behavior of the protein.…”

Section: Introductionmentioning

confidence: 99%

Choline Chloride as a Nano‐Crowder Protects HP‐36 from Urea‐Induced Denaturation: Insights from Solvent Dynamics and Protein‐Solvent Interactions

et al. 2020

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Urea at sufficiently high concentration unfolds the secondary structure of proteins leading to denaturation. In contrast, choline chloride (ChCl) and urea, in 1 : 2 molar ratio, form a deep eutectic mixture, a liquid at room temperature, protecting proteins from denaturation. In order to get a microscopic picture of this phenomenon, we perform extensive all‐atom molecular dynamics simulations on a model protein, HP‐36. Based on our calculation of Kirkwood‐Buff integrals, we analyze the relative accumulation of urea and ChCl around the protein. Additional insights are drawn from the translational and rotational dynamics of solvent molecules and hydrogen bond auto‐correlation functions. In the presence of urea, water shows slow subdiffusive dynamics around the protein owing to a strong interaction of water with the backbone atoms. Urea also shows subdiffusive motion. The addition of ChCl further slows down the dynamics of urea, restricting its accumulation around the protein backbone. Adding to this, choline cations in the first solvation shell of the protein show the strongest subdiffusive behavior. In other words, ChCl acts as a nano‐crowder by excluding urea from the protein backbone and thereby slowing down the dynamics of water around the protein. This prevents the protein from denaturation and makes it structurally rigid, which is supported by the smaller radius of gyration and root mean square deviation values of HP‐36.

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Analysis of Water and Hydrogen Bond Dynamics at the Surface of an Antifreeze Protein

Cited by 33 publications

References 54 publications

Long-range protein–water dynamics in hyperactive insect antifreeze proteins

Long-range protein–water dynamics in hyperactive insect antifreeze proteins

Hydrogen-bond dynamics of water in presence of an amphiphile, tetramethylurea: signature of confinement-induced effects

Choline Chloride as a Nano‐Crowder Protects HP‐36 from Urea‐Induced Denaturation: Insights from Solvent Dynamics and Protein‐Solvent Interactions

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