Is dynamic heterogeneity of water in presence of a protein denaturing agent different from that in presence of a protein stabilizer? A molecular dynamics simulation study

Indra, Sandipa; Biswas, Ranjit

doi:10.1007/s12039-016-1194-x

Cited by 16 publications

(20 citation statements)

References 69 publications

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“…The sluggish translational, rotational and hydrogen bond dynamics for the three components in PWUC system confirm the correlated slowdown of all the three components around the protein, which can also be attributed to the spatial arrangement of the bulky molecules of denaturant and the protecting osmolyte. This kind of slower motion of water and other co‐solvents around a protein is also reported earlier for different denaturants or protecting osmolytes . This type of dynamics modulates the rigidity of the surrounding environment and turns it into a slowly moving solvent shell around the protein which imposed a restriction in conformational flexibility of protein in the ternary mixture and even in PWC system reflected in the RMSD‐vs‐R g plot (Figure ).…”

Section: Discussionsupporting

confidence: 76%

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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Section: Discussionsupporting

confidence: 76%

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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“…[58][59][60][61][62][63] Molecular dynamics simulations have shown that water-TMAO interaction is stronger than that of watertetramethylurea. 64 This is in line with an earlier study by Paul et al 65 Despite having a similar structural framework, tert-butyl alcohol and TMAO show a drastic difference in their behaviors on the water structure. 26 The presence of multiple potential hydrogen bonding sites is responsible for the interference of urea into the tetrahedral structure of water.…”

Section: Introductionsupporting

confidence: 88%

Microscopic structural features of water in aqueous–reline mixtures of varying compositions

Sarkar

Maity

Chakrabarti

2021

Phys. Chem. Chem. Phys.

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“…τ In our case, the simulated value of the ratio of translational and rotational diffusion constant (D T /D R ) is not equal to the value obtained from the hydrodynamic prediction. A recent simulation study 38 has also shown the similar kind of break-down of this expected constancy even for ambient aqueous solutions.…”

Section: Coupling Between Translational and Rotational Diffusionsupporting

confidence: 56%

Dynamics of a binary mixture of non-spherical molecules: Test of hydrodynamic predictions

Sarkar

Samanta

Bagchi

2018

The Journal of Chemical Physics

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We consider a new class of model systems to study systematically the role of molecular shape in the transport properties of dense liquids. Our model is a liquid binary mixture where both the molecules are non-spherical and characterized by a collection of parameters. Although in the real world most of the molecules are non-spherical, only a limited number of theoretical studies exist on the effects of molecular shapes and hardly any have addressed the validity of the hydrodynamic predictions of rotational and translational diffusion of these shapes in liquids. In this work, we study a model liquid consisting of a mixture of prolate and oblate (80:20 mixture) ellipsoidals with interactions governed by a modified Gay-Berne potential for a particular aspect ratio (ratio of the length and diameter of the ellipsoids), at various temperature and pressure conditions.We report calculations of transport properties of this binary mixture by varying temperature over a wide range, at a fixed pressure. We find that for the pressure-density conditions studied, there is no signature of any phase separation, except transitions to the crystalline phase at low temperatures and relatively low pressure (the reason we largely confined our studies to high pressure). We find that for our model binary mixture, both the stick and slip hydrodynamic predictions break down in a major fashion, for both prolates and oblates and particularly so for rotation. Moreover, prolates and oblates themselves display different dynamical features in the mean square displacement and in orientational time correlation functions.

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Is dynamic heterogeneity of water in presence of a protein denaturing agent different from that in presence of a protein stabilizer? A molecular dynamics simulation study

Cited by 16 publications

References 69 publications

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

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

Microscopic structural features of water in aqueous–reline mixtures of varying compositions

Dynamics of a binary mixture of non-spherical molecules: Test of hydrodynamic predictions

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