Water structure and interactions with protein surfaces

Raschke, Tanya M.

doi:10.1016/j.sbi.2006.03.002

Cited by 239 publications

(152 citation statements)

References 63 publications

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“…To do this, we note that studies of a wide range of aqueous model systems, from small solutes to proteins and membranes, show that the dynamic perturbation is essentially confined to water molecules in direct contact with the solute's surface (1,2,4,23,24). In other words, water outside the (first) hydration layer is practically indistinguishable from bulk water.…”

Section: Resultsmentioning

confidence: 99%

“…biomolecular hydration ͉ buried water molecules ͉ Escherichia coli ͉ Haloarcula marismortui ͉ in vivo NMR W ater, the ubiquitous biosolvent, mediates or modulates the intermolecular forces that govern the self-assembly of biological cells, it controls the rates of substrate diffusion and conformational transitions, and it participates in molecular recognition and enzyme catalysis (1)(2)(3)(4). It is therefore imperative to characterize and understand any differences between cell water and bulk water.…”

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confidence: 99%

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Cell water dynamics on multiple time scales

Persson

Halle

2008

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

189

165

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Water-biomolecule interactions have been extensively studied in dilute solutions, crystals, and rehydrated powders, but none of these model systems may capture the behavior of water in the highly organized intracellular milieu. Because of the experimental difficulty of selectively probing the structure and dynamics of water in intact cells, radically different views about the properties of cell water have proliferated. To resolve this long-standing controversy, we have measured the 2 H spin relaxation rate in living bacteria cultured in D2O. The relaxation data, acquired in a wide magnetic field range (0.2 mT-12 T) and analyzed in a modelindependent way, reveal water dynamics on a wide range of time scales. Contradicting the view that a substantial fraction of cell water is strongly perturbed, we find that Ϸ85% of cell water in Escherichia coli and in the extreme halophile Haloarcula marismortui has bulk-like dynamics. The remaining Ϸ15% of cell water interacts directly with biomolecular surfaces and is motionally retarded by a factor 15 ؎ 3 on average, corresponding to a rotational correlation time of 27 ps. This dynamic perturbation is three times larger than for small monomeric proteins in solution, a difference we attribute to secluded surface hydration sites in supramolecular assemblies. The relaxation data also show that a small fraction (Ϸ0.1%) of cell water exchanges from buried hydration sites on the microsecond time scale, consistent with the current understanding of protein hydration in solutions and crystals. biomolecular hydration ͉ buried water molecules ͉ Escherichia coli ͉ Haloarcula marismortui ͉ in vivo NMR W ater, the ubiquitous biosolvent, mediates or modulates the intermolecular forces that govern the self-assembly of biological cells, it controls the rates of substrate diffusion and conformational transitions, and it participates in molecular recognition and enzyme catalysis (1-4). It is therefore imperative to characterize and understand any differences between cell water and bulk water. Biopolymers and other solutes make up one-third of the mass of a typical cell, so this difference could be substantial. The few experimental techniques that can monitor the molecular properties of water in vivo have suffered from interpretational ambiguities, allowing widely discordant views about cell water structure and dynamics to coexist for a long time (5-7). NMR spectroscopy can provide information about cell water via the spin relaxation times of the dominant water-1 H signal (8, 9). In fact, tissue-specific variations in water relaxation times provided the impetus for developing magnetic resonance imaging (10). Unfortunately, the interpretation of water-1 H relaxation data from biological samples is confounded by crossrelaxation, intermolecular paramagnetic couplings, and protonexchange modulation of the nuclear shielding (11,12). Here, we circumvent these complications by measuring the relaxation rate of the longitudinal water-2 H magnetization from cells cultured in D 2 O. We have chosen to study...

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Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

Cell water dynamics on multiple time scales

Persson

Halle

2008

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

189

165

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“…Hydration water is an integral part of biomacromolecules and plays a crucial role in their activity and stability, as well as in intermolecular interactions (1)(2)(3). Despite its importance, gaining insight into the molecular mechanisms and structures of hydration water has been challenging and has led to conflicting descriptions, mainly due to its dynamic nature, which can be affected by various factors in the surrounding environment, including physicochemical properties of the solute molecules, as well as solvent composition, in particular, the presence of ions (4)(5)(6).…”

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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“…Charged groups on the surfaces of proteins and low-molecular-mass compounds interact with water molecules through electrostatic interactions (Fennema, 1996;Raschke, 2006). The unit compressibility contribution of a charged protein surface, cha γ , being equal to (-15 ± 10) ×10 -6 cm 3 mol -1 bar -1 Å -2 , is similar to that for glycine (-20 ×10 -6 cm 3 mol -1 bar -1 Å -2 ) suggesting that proteins and low molecular mass compounds have similar hydration shells of charged groups as each other, where water molecules are strongly oriented in the electrostatic field of the charged groups (Kharakoz, 1991, Chalikian et al, 1993.…”

Section: Interpretation Of Compressibilitymentioning

confidence: 99%

“…It has been pointed out that polar groups (with an absolute partial charge |q i |>0.3e excluding charged groups) interact with water molecules directly through hydrogen bonds, whereas non-polar groups enhance hydrogen bonds among water molecules themselves, favouring the formation of clathrates around the non-polar groups by water molecules (Fennema, 1996;Raschke, 2006). found that the unit compressibility contribution of polar protein surfaces, pol γ , is almost three times more negative than that for an amino acid obtained by Kharakoz (1991).…”

Section: Interpretation Of Compressibilitymentioning

confidence: 99%