Hydration and mobility of ions in solution

Impey, Roger; Madden, P. A.; McDonald, Ian R.

doi:10.1021/j150643a008

Cited by 954 publications

(960 citation statements)

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“…Recent MD simulations suggest that ions may either bind specifically and locally to oppositely charged protein surface residues (67,68) or accumulate at nonpolar surface patches (66) as a function of type (i.e., anions/cations) and size, an observation supported by SANS experiments with varying salt concentrations and type (5,33). Moreover, both MD simulations and neutron liquid diffraction show that different ions in solution affect the local structure of water molecules (e.g., coordination numbers and orientations) specifically (69,70) so that the overall effect near protein surfaces is most probably a combination of variable local charge concentrations and, concomitantly, density variations of the water molecules with respect to the bulk solvent as a function of ion type and size (71,72). The combined SAXS/SANS data presented here quantify, in a model-free way, the local variations in electronic and neutron SLDs as a function of the character and number of amino acid residues on a protein surface.…”

Section: Protein Hs Density and Ionic Composition Depend On The Surfamentioning

confidence: 95%

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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Section: Protein Hs Density and Ionic Composition Depend On The Surfamentioning

confidence: 95%

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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“…The parameter t * is usually taken to be 2 ps -a typical lifetime of a hydrogen bond in liquid water at ambient conditions, 88 which also reflects the rate of exchange of water molecules in the first hydration shell of metal ions. 48 For a metal ion to form a CIP with the carboxylic group, at least one water molecule must leave the first hydration shell to allow its place can be taken by one of the carboxyl oxygens. Therefore, we adopt the same value of t * = 2 ps in our calculations.…”

Section: Metal -Carboxylate Structure and Dynamics From Free MD Simulmentioning

confidence: 99%

“…[43][44][45] Carboxylic groups are the most important interaction sites for metal binding to these molecules, as they are for many other organic and bioorganic molecules. Experimental and theoretical studies of the hydration of metal ions [48][49][50][51][52][53] and carboxylic functional groups [54][55][56][57] show that carboxylic groups are sites of strong association of divalent ions with NOM 24,[58][59][60] and that increasing the cation charge density increases the tendency to form a contact ion pair. 44,47 Here we present a computational molecular dynamics (MD) study of the interaction of Na + , Ca 2+ , and Mg 2+ with the carboxylic groups of a TNB NOM fragment and with acetate anion that provides an improved quantitative understanding of the structure and energetics of these interactions.…”

Section: Introductionmentioning

confidence: 99%

Metal Cation Complexation with Natural Organic Matter in Aqueous Solutions: Molecular Dynamics Simulations and Potentials of Mean Force

Iskrenova-Tchoukova¹,

Kalinichev²,

2010

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Natural organic matter (NOM, or humic substance) has a known tendency to form colloidal aggregates in aqueous environments, with the composition and concentration of cationic species in solution, pH, temperature, and the composition of the NOM itself playing important roles. Strong interaction of carboxylic groups of NOM with dissolved metal cations is thought to be the leading chemical interaction in NOM supramolecular aggregation.Computational molecular dynamics (MD) study of the interactions of Na + , Mg 2+ , and Ca 2+ with the carboxylic groups of a model NOM fragment and acetate anions in aqueous solutions provides new quantitative insight into the structure, energetics, and dynamics of the interactions of carboxylic groups with metal cations, their association and the effects of cations on the colloidal aggregation of NOM molecules. Potentials of mean force and the equilibrium constants describing overall ion association and the distribution of metal cations between contact ion pairs and solvent separated ions pairs were computed from free MD simulations and restrained umbrella sampling calculations. The results provide insight into the local structural environments of metal-carboxylate association and the dynamics of exchange among these sites. All three cations prefer contact ion pair to solvent separated ion pair coordination, and Na + and Ca 2+ show a strong preference for bidentate contact ion pair formation. The average residence time of a Ca 2+ ion in a contact ion pair with the carboxylic groups is of the order of 0.5 ns, whereas the corresponding residence time of a Na + ion is only between 0.02 and 0.05 ns. The average residence times of a Ca 2+ ion in a bidentate coordinated contact ion pair vs. a monodentate coordinated contact ion pair are about 0.5 ns and about 0.08 ns, respectively. On the 10-ns time scale of our simulations, aggregation of the NOM molecules occurs in the presence of Ca 2+ but not Na + or Mg 2+ . These results agree with previous experimental observations and are explained 3 by both Ca 2+ ion-bridging between NOM molecules and decreased repulsion between the NOM molecules due to the reduced net charge of the NOM-metal complexes. Simulations on a larger scale are needed to further explore the relative importance of the different aggregation mechanisms and the stability of NOM aggregates.4

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“…Computer simulations and neutron scattering results concerning the Cl~ coordination favour a linear configuration, whereas recent NMR data propose a symmetric arrangement [19][20][21][22]. Besides the proton ( !…”

Section: Undercooled Aqueous Kf Solutionsmentioning

confidence: 99%

“…They have been assumed to follow a VTF equation also. The distance of closest approach have been taken from radial distribution functions calculated with molecular dynamics techniques [21,22]. As an illustration Fig.…”

Section: Undercooled Aqueous Kf Solutionsmentioning

confidence: 99%