Temperature dependence of protein-hydration hydrodynamics by molecular dynamics simulations

Lau, Edmond Y.; Krishnan, Viswanathan V

doi:10.1016/j.bpc.2007.07.004

Cited by 4 publications

(4 citation statements)

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“…The relative small effect on the average diffusion constant, as well as average relaxation times, for the hydration water of proteins as compared to bulk water is well established by experimental studies using different techniques, such as neutron scattering, 9,39,40 various NMR techniques, 41,42 and by MD simulations. [43][44][45] A similar slowing down of the dynamics is, furthermore, not only typical for protein hydration water but also for hydration water in other biological systems, such as lipid membranes 46 and carbohydrates, 47 but in sharp contrast to water confined in many hydrophilic model systems and geological systems, such as a molecular sieve of pore size 10 Å ͑Ref. 48͒ and a fully hydrated clay, 49 where the diffusion constant is reduced by as much as a factor 30 or more at room temperature.…”

Section: Discussionmentioning

confidence: 99%

Dynamics of a protein and its surrounding environment: A quasielastic neutron scattering study of myoglobin in water and glycerol mixtures

Jansson

Kargl

Fernandez-Alonso

et al. 2009

The Journal of Chemical Physics

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In this quasielastic neutron scattering (QENS) study we have investigated the relation between protein and solvent dynamics. Myoglobin in different water:glycerol mixtures has been studied in the temperature range of 260-320 K. In order to distinguish between solvent and protein dynamics we have measured protonated as well as partly deuterated samples. As commonly observed for bulk as well as for confined water, the dynamics of the surrounding solvent is well described by a jump diffusion model. The intermediate scattering function I(Q,t) from the protein (partly deuterated samples) was analyzed by fitting a single Kohlrausch-Williams-Watts (KWW) stretched exponential function to the data. However, due to the limited experimental time window, two different curve fitting approaches were used. The first one was performed with the assumption that I(Q,t) decays to zero at long times, i.e., it was assumed that all protein relaxations that are observed on the experimental time scale, as well as would be observed on longer time scales, can be described by a single KWW function. In the second approach we instead assumed that both the protein relaxation time tau(p) and the stretching parameter beta(KWW) were Q-independent, i.e., we assumed that the protein dynamics is dominated by more local motions. Advantages and disadvantages of both approaches are discussed. The first approach appears to work best at higher Q-values, indicating a power law relation of the Q-dependent protein dynamics for all samples and temperatures, whereas the second approach seems to work at lower Q-values, where the expected confined diffusion of hydrogen atoms in the protein gives the assumed Q-independent relaxation time. Independent of the chosen approach we find a significant correlation between the average relaxation time of the protein and the diffusion constant (or in this case the related relaxation time) of the solvent. However, the correlation is not perfect since the average relaxation time of the protein is more strongly dependent on the total amount of solvent than the diffusion constant of the solvent itself. Thus, the average relaxation time of the protein decreases not only with increasing solvent mobility, but also with increasing solvent content.

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Section: Discussionmentioning

confidence: 99%

Dynamics of a protein and its surrounding environment: A quasielastic neutron scattering study of myoglobin in water and glycerol mixtures

Jansson

Kargl

Fernandez-Alonso

et al. 2009

The Journal of Chemical Physics

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“…In addition, we analysed the effect of water on the dielectric properties of materials studied. The interaction of waterunmodified collagen in the solid state has been extensively studied by many authors [18,[32][33][34][35][36][37][38][39][40]. The data obtained concerned the classification of water associated with collagen into…”

Section: Introductionmentioning

confidence: 99%

The effect of different methods of cross-linking of collagen on its dielectric properties

Marzec¹,

Pietrucha²

2008

Biophysical Chemistry

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This paper reports on the effect of different methods of collagen cross-linking on its dielectric properties. In order to obtain collagen-hyaluronic acid (HA) scaffolds, collagen was first dehydrated by a combination of thermal and vacuum drying (DHT) and then treated with the chemical reagent carbodiimide (EDC/NHS) for final cross-linking. The measurements of the relative permittivity epsilon' and the dielectric loss epsilon'' for all materials were carried over the frequency range of 10 Hz-100 kHz and at temperatures from 22 to 260 degrees C. The results for these samples reveal distinct relaxation processes at low temperatures, below 140 degrees C and at higher temperatures as broad peak around 230 degrees C. The first and second relaxation are associated with changes in the secondary structure of collagen accompanied by the release of water and with the denaturation of dry collagen, respectively. The influence of cross-linking on the permittivity of collagen is significant over the entire temperature range.

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“…The interaction between water and proteins [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16][17][18] has been attracting considerable attention in the fields of food, pharmaceutical, and biomedical sciences. The idea of bound water is essential for understanding the interaction between water and proteins.…”

Section: Introductionmentioning

confidence: 99%

“…Many experimental works on characterizing the bound water, such as those involving nuclear magnetic resonance (NMR), [3][4][5][6][7]19,20) differential scanning calorimetry (DSC), 8,9,[20][21][22][23][24][25][26][27] dielectric measurements, [10][11][12][13][14][15]28,29) and infrared (IR) and Raman spectroscopies, have been performed. 9,26,[29][30][31] These experimental studies, together with molecular dynamic (MD) simulations [15][16][17][18] for water-containing hydrophilic molecules, have revealed the following three types of water that surrounds protein molecules: strongly bound, weakly bound, and free waters. Among those types of water, the weakly bound water has attracted considerable attention, because it is known that the properties of materials that contain water strongly depend on this type of water.…”

Section: Introductionmentioning

confidence: 99%

Bound states of water in gelatin discriminated by near-infrared spectroscopy

Otsuka

Shirakashi

Hirakawa

2017

Jpn. J. Appl. Phys.

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By near-infrared spectroscopy, we classified water molecules in hydrated gelatin membranes in a drying process. Absorbance spectra in the frequency range of 4500–5500 cm−1 were resolved into three peaks, S0, S1, and S2, that correspond to water molecules with different hydrogen bond states. From the areas of the absorbance peaks as a function of the water content of gelatin, together with the information on the freezing properties of water measured by differential scanning calorimetry, we found that, when the water content is less than 20%, free water disappears and only weakly and strongly bound waters remain. We also found that the weakly bound water consists of S0, S1, and S2 water molecules with a simple composition of . Using this information, most of the freezable water was determined to be free water. Our classification provides a simple method of estimating the retention and freezing properties of processed foods or drugs by infrared spectroscopy.

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Temperature dependence of protein-hydration hydrodynamics by molecular dynamics simulations

Cited by 4 publications

References 73 publications

Dynamics of a protein and its surrounding environment: A quasielastic neutron scattering study of myoglobin in water and glycerol mixtures

Dynamics of a protein and its surrounding environment: A quasielastic neutron scattering study of myoglobin in water and glycerol mixtures

The effect of different methods of cross-linking of collagen on its dielectric properties

Bound states of water in gelatin discriminated by near-infrared spectroscopy

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