Translational diffusion of hydration water correlates with functional motions in folded and intrinsically disordered proteins

Schirò, Giorgio; Fichou, Yann; Gallat, Francois Xavier; Wood, Kathleen; Gabel, Frank; Moulin, Martine; Härtlein, Michael; Heyden, Matthias; Colletier, J.P.; Orecchini, A.; Paciaroni, Alessandro; Wuttke, Joachim; Tobias, Douglas J.; Weik, Martin H.

doi:10.1038/ncomms7490

Cited by 221 publications

(250 citation statements)

References 66 publications

(93 reference statements)

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“…There is good evidence that the large-amplitude motions of proteins are mediated by the translational diffusion of water. 116 However, the details are far from clear. Overall, the field does not yet seem to have determined whether dynamic water is important to the thermodynamics or kinetics of protein folding, ligand binding, or enzyme catalysis.…”

Section: Recognition Mimicry and Interactions With Biomoleculesmentioning

confidence: 99%

Collaborative routes to clarifying the murky waters of aqueous supramolecular chemistry

et al. 2017

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Collaborative routes to clarifying the murky waters of aqueous supramolecular chemistry. AbstractOn planet Earth, water is everywhere: the majority of the surface is covered with it; it is a key component of all life; its vapor and droplets fill the lower atmosphere; even rocks contain it and undergo geomorphological changes because of it. A community of physical scientists largely drives studies of the chemistry of water and aqueous solutions, with expertise in biochemistry, spectroscopy, and computer modeling. More recently however, supramolecular chemistry -with its expertise in macrocyclic synthesis and measuring supramolecular interactions -have renewed their interest in water-mediated non-covalent interactions. These two groups offer complementary expertise that, if harnessed, offers to accelerate our understanding of aqueous supramolecular chemistry and water writ large. This review summarizes the state-of-the-art of the two fields, and highlights where there is latent chemical space for collaborative exploration by the two groups. 4Water is ubiquitous and essential to life on planet Earth. A full understanding of aqueous solutions is therefore of significance to a wide range of fields within the atmospheric, environmental, biological and geological sciences. Within the chemical sciences, a deeper appreciation of how non-covalent interactions and chemical transformations are influenced by water would benefit a variety of fields. However, as we highlight here, there are many open questions regarding the chemical and physical properties of aqueous solutions.The aqueous realm is frequently bifurcated into the Hofmeister and hydrophobic effects, phenomena that respectively deal with the properties of solutions of salts and relatively nonpolar molecules. However, it is becoming increasingly evident that these areas do in fact frequently overlap; two prime examples being the accumulation of large polarizable anions at the air-water interface, 1-5 and the favorable interactions of polarizable anions with non-polar surfaces. [6][7][8][9][10][11][12][13][14][15] Thus the hydrophobic and Hofmeister effects are but part of a greater continuum of aqueous supramolecular chemistry, with many important and outstanding questions regarding the influence of the different kinds of non-covalent interactions involved.Studies of water and aqueous solutions have mostly been driven by the physical sciences community, a broad range of scientists whose expertise in spectroscopy, computer modeling, and biochemistry (to name just three areas) has generally not involved macrocycles or host molecules in general. However, for some time now, supramolecular chemists -with their expertise in macrocyclic synthesis and measuring weak non-covalent interactions -have been travelling a parallel course of exploration. This Review, inspired by discussions between sixteen members of each community at a recent workshop, 16 is an attempt to summarize what we know about aqueous solutions, what we do not know about them, and where the two communit...

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Section: Recognition Mimicry and Interactions With Biomoleculesmentioning

confidence: 99%

Collaborative routes to clarifying the murky waters of aqueous supramolecular chemistry

et al. 2017

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“…High-resolution structural studies by x-ray crystallography or NMR, molecular dynamics (MD) simulations, solution scattering, and other biophysical studies have provided information on water-macromolecule interactions in specific systems (7)(8)(9)(10). NMR and neutron spectroscopy have revealed altered mobility of water molecules on protein surfaces with respect to the bulk (11)(12)(13)(14)(15), and time-resolved vibrational spectroscopy has revealed distinctive dynamics of solvation near the active sites of enzymes during catalysis with respect to bulk solvent (16). Increased water density in the first hydration shell (HS), as well as surface-specific differences in the organization of the hydration water, have been reported by MD simulations (17)(18)(19)(20) and have been described thermodynamically in terms of electrorestriction (21).…”

Section: Introductionmentioning

confidence: 99%

SAXS/SANS on Supercharged Proteins Reveals Residue-Specific Modifications of the Hydration Shell

Kim

Martel

Girard

et al. 2016

Biophysical Journal

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Water molecules in the immediate vicinity of biomacromolecules, including proteins, constitute a hydration layer characterized by physicochemical properties different from those of bulk water and play a vital role in the activity and stability of these structures, as well as in intermolecular interactions. Previous studies using solution scattering, crystallography, and molecular dynamics simulations have provided valuable information about the properties of these hydration shells, including modifications in density and ionic concentration. Small-angle scattering of x-rays (SAXS) and neutrons (SANS) are particularly useful and complementary techniques to study biomacromolecular hydration shells due to their sensitivity to electronic and nuclear scattering-length density fluctuations, respectively. Although several sophisticated SAXS/SANS programs have been developed recently, the impact of physicochemical surface properties on the hydration layer remains controversial, and systematic experimental data from individual biomacromolecular systems are scarce. Here, we address the impact of physicochemical surface properties on the hydration shell by a systematic SAXS/SANS study using three mutants of a single protein, green fluorescent protein (GFP), with highly variable net charge (þ36, À6, and À29). The combined analysis of our data shows that the hydration shell is locally denser in the vicinity of acidic surface residues, whereas basic and hydrophilic/hydrophobic residues only mildly modify its density. Moreover, the data demonstrate that the density modifications result from the combined effect of residue-specific recruitment of ions from the bulk in combination with water structural rearrangements in their vicinity. Finally, we find that the specific surface-charge distributions of the different GFP mutants modulate the conformational space of flexible parts of the protein.

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“…This latter temperature depends on a number of factors, including the resolution of the spectrometer, i.e., effectively the time period over which the atomic displacements are recorded [14,15]. This phenomenology has attracted significant attention since enhanced flexibility and, therefore, the ability to perform biological function can develop at T > T d [16].…”

Section: Introductionmentioning

confidence: 99%

Dynamical and orientational structural crossovers in low-temperature glycerol

2016

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Mean square displacements of hydrogen atoms in glass-forming materials and proteins, as reported by incoherent elastic neutron scattering, show kinks in their temperature dependence. This crossover, known as the dynamical transition, connects two approximately linear regimes. It is often assigned to the dynamical freezing of subsets of molecular modes at the point of equality between their corresponding relaxation times and the instrumental observation window. The origin of the dynamical transition in glass-forming glycerol is studied here by extensive molecular dynamics simulations. We find the dynamical transition to occur for both the center of mass translations and the molecular rotations at the same temperature, insensitive to changes of the observation window. Both the translational and rotational dynamics of glycerol show a dynamic crossover from the structural to a secondary relaxation at the temperature of the dynamical transition. A significant and discontinuous increase in the orientational Kirkwood factor and in the dielectric constant is observed in the same range of temperatures. We, however, do not find any indications of a true thermodynamic transition to an ordered low-temperature phase. We therefore suggest that all observed crossovers are dynamic in character. The increase in the dielectric constant is related to the dynamic freezing of dipolar domains on the time-scale of simulations.

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Translational diffusion of hydration water correlates with functional motions in folded and intrinsically disordered proteins

Cited by 221 publications

References 66 publications

Collaborative routes to clarifying the murky waters of aqueous supramolecular chemistry

Collaborative routes to clarifying the murky waters of aqueous supramolecular chemistry

SAXS/SANS on Supercharged Proteins Reveals Residue-Specific Modifications of the Hydration Shell

Dynamical and orientational structural crossovers in low-temperature glycerol

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