| 1. |
- Antonijevic, Sasa, et al.
(författare)
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Study of water dynamics and distances in paramagnetic solids by variable-temperature two-dimensional H-2 NMR spectroscopy
- 2007
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 126:1
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Tidskriftsartikel (refereegranskat)abstract
- A recently proposed two-dimensional H-2 NMR experiment is used to measure the H-2 (spin I=1) quadrupolar and paramagnetic shift anisotropy interactions in powdered CuCl2 center dot 2D(2)O as a function of temperature. The principal components of the quadrupolar and paramagnetic shift anisotropy tensors and the Euler angles describing the orientations of the tensors in the molecular frame are determined at each temperature. For this purpose an analytical approach is introduced to extract desired parameters from motionally averaged two-dimensional line shapes where the averaging is introduced by rapid 180 degrees flips around C-2 axes of D2O molecules. This approach can be readily applied to study various materials containing water of crystallization. It is also clearly shown that the rapid continuous rotation of D2O molecules around their C-2 axes is not taking place in the studied solid in the range of temperatures between 209 and 344 K. Once the paramagnetic shift anisotropy of a deuterium atom is measured accurately it is used to estimate the distance between deuterium and the nearest copper atom bearing an unpaired electron. Excellent agreement is found between structural parameters obtained in this study and those provided by neutron and x-ray diffraction, showing that the paramagnetic shift anisotropy is a sensitive probe of distances in paramagnetic solids. (c) 2007 American Institute of Physics.
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| 2. |
- Persson Sunde, Erik, et al.
(författare)
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Cell water dynamics on multiple time scales
- 2008
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Ingår i: Proceedings of the National Academy of Sciences. - : Proceedings of the National Academy of Sciences. - 1091-6490 .- 0027-8424. ; 105:17, s. 6266-6271
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Tidskriftsartikel (refereegranskat)abstract
- 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 2H 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 model-independent 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 ≈85% of cell water in Escherichia coli and in the extreme halophile Haloarcula marismortui has bulk-like dynamics. The remaining ≈15% 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 (≈0.1%) 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.
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| 3. |
- Persson Sunde, Erik, et al.
(författare)
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Mechanism of (1)H-(14)N cross-relaxation in immobilized proteins.
- 2010
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Ingår i: Journal of Magnetic Resonance. - : Elsevier BV. - 1096-0856 .- 1090-7807. ; 203:2, s. 257-273
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Tidskriftsartikel (refereegranskat)abstract
- A resonant enhancement of the water-(1)H relaxation rate at three distinct frequencies in the range 0.5-3MHz has been observed in a variety of aqueous biological systems. These so-called quadrupole (Q) peaks have been linked to a dipolar flip-flop polarization transfer from (1)H nuclei to rapidly relaxing amide (14)N nuclei in rotationally immobilized proteins. While the Q-peak frequencies conform to the known amide (14)N quadrupole coupling parameters, a molecular model that accounts for the intensity and shape of the Q peaks has not been available. Here, we present such a model and test it against an extensive set of Q-peak data from two fully hydrated crosslinked proteins under conditions of variable temperature, pH and H/D isotope composition. We propose that polarization transfer from bulk water to amide (14)N occurs in three steps: from bulk water to a so-called intermediary proton via material diffusion/exchange, from intermediary to amide proton by cross-relaxation driven by exchange-mediated orientational randomization of their mutual dipole coupling, and from amide proton to (14)N by resonant dipolar relaxation 'of the second kind', driven by (14)N spin fluctuations, which, in turn, are induced by restricted rigid-body motions of the protein. An essentially equivalent description of the last step can be formulated in terms of coherent (1)H-->(14)N polarization transfer followed by fast (14)N relaxation. Using independent structural and kinetic information, we show that the Q peaks from these two proteins involve approximately 7 intermediary protons in internal water molecules and side-chain hydroxyl groups with residence times of order 10(-5)s. The model not only accounts quantitatively for the extensive data set, but also explains why Q peaks are hardly observed from gelatin gels.
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| 4. |
- Persson Sunde, Erik, et al.
(författare)
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Nanosecond to Microsecond Protein Dynamics Probed by Magnetic Relaxation Dispersion of Buried Water Molecules
- 2008
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 1520-5126 .- 0002-7863. ; 130:5, s. 1774-1787
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Tidskriftsartikel (refereegranskat)abstract
- Large-scale protein conformational motions on nanosecond – microsecond time scales are important for many biological processes, but remain largely unexplored because of methodological limitations. NMR relaxation methods can access these time scales if protein tumbling is prevented, but the isotropy required for high-resolution solution NMR is then lost. However, if the immobilized protein molecules are randomly oriented, the water 2H and 17O spins relax as in a solution of freely tumbling protein molecules, with the crucial difference that they now sample motions on all time scales up to ~100 μs. In particular, the exchange rates of internal water molecules can be determined directly from the 2H or 17O magnetic relaxation dispersion (MRD) profile. This possibility opens up a new window for characterizing the motions of individual internal water molecules as well as the large-scale protein conformational fluctuations that govern the exchange rates of structural water molecules. We introduce and validate this new NMR method by presenting and analyzing an extensive set of 2H and 17O MRD data from cross-linked gels of two model proteins: bovine pancreatic trypsin inhibitor and ubiquitin. We determine residence times and order parameters of four internal water molecules in these proteins and show that they are quantitatively consistent with the information available from crystallography and solution MRD. We also show how slow motions of side-chains bearing labile hydrogens can be monitored by the same approach. Proteins of any size can be studied at physiological hydration levels with this method.
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| 5. |
- Persson Sunde, Erik, et al.
(författare)
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Slow Internal Protein Dynamics from Water 1H Magnetic Relaxation Dispersion
- 2009
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 1520-5126 .- 0002-7863. ; 131:51, s. 18214-18214
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Tidskriftsartikel (refereegranskat)abstract
- To probe internal motions in proteins on the 10−8−10−5 s time scale by NMR relaxation, it is necessary to eliminate protein tumbling. Here, we examine to what extent magnetic relaxation dispersion (MRD) experiments on the water 1H resonance report on protein motions in this time window. We also perform a critical test of two physically distinct mechanisms that have been proposed to explain and interpret 1H MRD profiles from immobilized proteins: the exchange-mediated orientational randomization (EMOR) mechanism and the two-phase spin-fracton (2PSF) mechanism. For these purposes, we report the 1H MRD profiles from protonated and partially deuterated ubiquitin, cross-linked by glutaraldehyde. The EMOR approach, with the crystal structure of ubiquitin as input, accounts quantitatively for the MRD data and shows that hydroxyl-bearing side chains undergo large-amplitude motions on the microsecond time scale. In contrast, the 2PSF model, which attributes 1H relaxation to small-amplitude backbone vibrations that propagate in a low-dimensional fractal space, fails qualitatively in describing the effect of H→D substitution. These findings appear to resolve the long-standing controversy over the molecular basis of water-1H relaxation in systems containing rotationally immobilized macromolecules, including biological tissue.
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| 6. |
- Persson Sunde, Erik, et al.
(författare)
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The physical state of water in bacterial spores.
- 2009
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Ingår i: Proceedings of the National Academy of Sciences. - : Proceedings of the National Academy of Sciences. - 1091-6490 .- 0027-8424. ; 106:46, s. 19334-19339
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Tidskriftsartikel (refereegranskat)abstract
- The bacterial spore, the hardiest known life form, can survive in a metabolically dormant state for many years and can withstand high temperatures, radiation, and toxic chemicals. The molecular basis of spore dormancy and resistance is not understood, but the physical state of water in the different spore compartments is thought to play a key role. To characterize this water in situ, we recorded the water 2H and 17O spin relaxation rates in D2O-exchanged Bacillus subtilis spores over a wide frequency range. The data indicate high water mobility throughout the spore, comparable with binary protein–water systems at similar hydration levels. Even in the dense core, the average water rotational correlation time is only 50 ps. Spore dormancy therefore cannot be explained by glass-like quenching of molecular diffusion but may be linked to dehydration-induced conformational changes in key enzymes. The data demonstrate that most spore proteins are rotationally immobilized, which may contribute to heat resistance by preventing heat-denatured proteins from aggregating irreversibly. We also find that the water permeability of the inner membrane is at least 2 orders of magnitude lower than for model membranes, consistent with the reported high degree of lipid immobilization in this membrane and with its proposed role in spore resistance to chemicals that damage DNA. The quantitative results reported here on water mobility and transport provide important clues about the mechanism of spore dormancy and resistance, with relevance to food preservation, disease prevention, and astrobiology.
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| 7. |
- Persson Sunde, Erik
(författare)
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Water and Protein Dynamics in Biological Systems Studied by Magnetic Relaxation Dispersion
- 2009
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The results presented in this thesis demonstrate that the magnetic relaxation dispersion (MRD) technique can provide information of relevance to protein biophysics, magnetic resonance imaging and cell biology. By immobilizing proteins with covalent cross-links, intermittent protein dynamics on the previously inaccessible ns-µs time scale could be probed with MRD via the exchange of water molecules between internal cavities and the surrounding bulk solvent phase. Persistent side-chain dynamics on the same time scale could also be probed via labile hydrogens that exchange with bulk water. A critical test of two physically distinct mechanisms that are used to interpret 1H MRD profiles from immobilized proteins was performed. A quantitative analysis of the 1H profiles from protonated and partially deuterated ubiquitin resolved the long-standing controversy over the molecular basis of water-1H relaxation in systems containing immobilized macromolecules, including biological tissue. The molecular mechanisms behind the 1H-14N magnetization transfer, the so called quadrupolar peaks, observed in immobilized systems was also investigated. The state of water in living cells is of fundamental biological importance, but previous attempts to characterize cell water have been inconclusive. MRD experiments on deuterated cell water are reported that, for the first time, quantify the slowing down of all intracellular water and rule out the idea of a highly perturbed cytoplasm. Water 2H and 17O MRD was also used to address a related problem of both fundamental and practical importance: the molecular mechanism behind the exceptional heat resistance and dormancy of bacterial spores. The dehydrated core region is thought to play a key role but little is known about the physical state of water in the different spore compartments or about the rate of water transport among them. These questions could be answered by monitoring the water dynamics in the different compartments of B. subtilis spores.
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| 8. |
- Qvist, Johan, et al.
(författare)
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Rotational dynamics in supercooled water from nuclear spin relaxation and molecular simulations.
- 2012
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 136:20
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Tidskriftsartikel (refereegranskat)abstract
- Structural dynamics in liquid water slow down dramatically in the supercooled regime. To shed further light on the origin of this super-Arrhenius temperature dependence, we report high-precision (17)O and (2)H NMR relaxation data for H(2)O and D(2)O, respectively, down to 37 K below the equilibrium freezing point. With the aid of molecular dynamics (MD) simulations, we provide a detailed analysis of the rotational motions probed by the NMR experiments. The NMR-derived rotational correlation time τ(R) is the integral of a time correlation function (TCF) that, after a subpicosecond librational decay, can be described as a sum of two exponentials. Using a coarse-graining algorithm to map the MD trajectory on a continuous-time random walk (CTRW) in angular space, we show that the slowest TCF component can be attributed to large-angle molecular jumps. The mean jump angle is ∼48° at all temperatures and the waiting time distribution is non-exponential, implying dynamical heterogeneity. We have previously used an analogous CTRW model to analyze quasielastic neutron scattering data from supercooled water. Although the translational and rotational waiting times are of similar magnitude, most translational jumps are not synchronized with a rotational jump of the same molecule. The rotational waiting time has a stronger temperature dependence than the translation one, consistent with the strong increase of the experimentally derived product τ(R) D(T) at low temperatures. The present CTRW jump model is related to, but differs in essential ways from the extended jump model proposed by Laage and co-workers. Our analysis traces the super-Arrhenius temperature dependence of τ(R) to the rotational waiting time. We present arguments against interpreting this temperature dependence in terms of mode-coupling theory or in terms of mixture models of water structure.
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| 9. |
- Qvist, Johan, et al.
(författare)
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Time scales of water dynamics at biological interfaces: peptides, proteins and cells
- 2009
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Ingår i: Faraday Discussions. - : Royal Society of Chemistry (RSC). - 1364-5498. ; 141:1, s. 131-144
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Tidskriftsartikel (refereegranskat)abstract
- Water 2H and 17O spin relaxation is used to study water dynamics in the hydration layers of two small peptides, two globular proteins and in living cells of two microorganisms. The dynamical heterogeneity of hydration water is characterized by performing relaxation measurements over a wide temperature range, extending deeply into the supercooled regime, or by covering a wide frequency range. Protein hydration layers can be described by a power-law distribution of rotational correlation times with an exponent close to 2. This distribution comprises a small fraction of protein-specific hydration sites, where water rotation is strongly retarded, and a dominant fraction of generic hydration sites, where water rotation is as fast as in the hydration shells of small peptides. The generic dynamic perturbation factor is less than 2 at room temperature and exhibits a maximum near 260 K. The dynamic perturbation is induced by H-bond constraints that interfere with the cooperative mechanism that facilitates rotation in bulk water. Because these constraints are temperature-independent, hydration water does not follow the super-Arrhenius temperature dependence of bulk water. Water in living cells behaves as expected from studies of simpler model systems, the only difference being a larger fraction of secluded (strongly perturbed) hydration sites associated with the supramolecular organization in the cell. Intracellular water that is not in direct contact with biopolymers has essentially the same dynamics as bulk water. There is no significant difference in cell water dynamics between mesophilic and halophilic organisms, despite the high K+ and Na+ concentrations in the latter.
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| 10. |
- Vaca Chavez, Fabian, et al.
(författare)
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Internal water molecules and magnetic relaxation in agarose gels
- 2006
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 1520-5126 .- 0002-7863. ; 128:14, s. 4902-4910
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Tidskriftsartikel (refereegranskat)abstract
- Agarose gels have long been known to produce exceptionally large enhancements of the water H-1 and H-2 magnetic relaxation rates. The molecular basis for this effect has not been clearly established, despite its potential importance for a wide range of applications of agarose gels, including their use as biological tissue models in magnetic resonance imaging. To resolve this issue, we have measured the 2 H magnetic relaxation dispersion profile from agarose gels over more than 4 frequency decades. We find a very large dispersion, which, at neutral pH, is produced entirely by internal water molecules, exchanging with bulk water on the time scale 10(-8)-10(-6) s. The most long-lived of these dominate the dispersion and give rise to a temperature maximum in the low-frequency relaxation rate. At acidic pH, there is also a low-frequency contribution from hydroxyl deuterons exchanging on a time scale of 10(-4)S. Our analysis of the dispersion profiles is based on a nonperturbative relaxation theory that remains valid outside the conventional motional- narrowing regime. The results of this analysis suggest that the internal water molecules responsible for the dispersion are located in the central cavity of the agarose double helix, as previously proposed on the basis of fiber diffraction data. The magnetic relaxation mechanism invoked here, where spin relaxation is induced directly by molecular exchange, also provides a molecular basis for understanding the water H-1 relaxation behavior that governs the intrinsic magnetic resonance image contrast in biological tissue.
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