Water scaffolding in collagen: Implications on protein dynamics as revealed by solid-state NMR.

Solid-state NMR studies of collagen samples of various origin confirm that the amplitude of collagen backbone and sidechain motions increases significantly on increasing the water content. This conclusion is supported by the changes observed in three different NMR observables: (i) the linewidth dependence on the (1) H decoupling frequency; (ii) (13) C CSA changes for the peptide carbonyl groups, and (iii) dephasing rates of (1) H-(13) C dipolar couplings. In particular, a nearly three-fold increase in motional amplitudes of the backbone librations about C-C(α) or N-C(α) bonds was found on increasing the added water content up to 47 wt%D2 O. Based on the frequencies of NMR observables involved, the timescale of the protein motions dependent on the added water content is estimated to be of the order of microseconds. This estimate agrees with that from wideline T2 (1) H NMR measurements. Also, our wideline (1) H NMR measurements revealed that the timescale of the microsecond motions in proteins reduces significantly on increasing the added water content, i.e., an approximately 15-fold increase in protein motional frequencies is observed on increasing the added water content to 45 wt%D2 O. The observed changes in collagen dynamics is attributed to the increase in water translational diffusion on increasing the amount of added water, which leads to more frequent "bound water"/"free water" exchange on the protein surface, accompanied by the breakage and formation of new hydrogen bonds with polar functionalities of protein

Geophysical and geochemical survey of a large marine pockmark on the Malin Shelf, Ireland

Author Posting. © American Geophysical Union, 2012. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geochemistry Geophysics Geosystems 13 (2012): Q01011, doi:10.1029/2011GC003787.Marine pockmarks are a specific type of seabed geological setting resembling craters or pits and are considered seabed surface expressions of fluid flow in the subsurface. A large composite pockmark on the Malin Shelf, off the northern coast of Ireland was surveyed and ground truthed to assess its activity and investigate fluid related processes in the subsurface. Geophysical (including acoustic and electromagnetic) data confirmed the subsurface presence of signatures typical of fluids within the sediment. Shallow seismic profiling revealed a large shallow gas pocket and typical gas related indicators such as acoustic blanking and enhanced reflectors present underneath and around the large pockmark. Sulphate profiles indicate that gas from the shallow reservoir has been migrating upwards, at least recently. However, there are no chimney structures observed in the sub-bottom data and the migration pathways are not apparent. Electromagnetic data show slightly elevated electrical conductivity on the edges of the pockmarks and a drop below regional levels within the confines of the pockmark, suggesting changes in physical properties of the sediment. Nuclear Magnetic Resonance (NMR) experiments were employed to characterize the organic component of sediments from selected depths. Very strong microbial signatures were evident in all NMR spectra but microbes outside the pockmark appear to be much more active than inside. These observations coincide with spikes in conductivity and the lateral gas bearing body suggesting that there is an increase in microbial activity and biomass when gas is present.We wish to thank the Geological Survey of Ireland, the INtegrated Mapping FOr the Sustainable Development of Ireland’s MArine Resource (INFOMAR) program, the Irish Environmental Protection Agency, Science Foundation of Ireland, QUESTOR (Queens University Belfast) and the Irish Council for Science, engineering and technology for funding this research. AJS thanks NSERC, (Strategic and Discovery Programs), the Canada Foundation for Innovation (CFI), and the Ministry of Research and Innovation (MRI) for providing Canadian funding. The survey data utilized in the research has been co‐funded by the Geological Survey of Ireland and the Offshore Irish Petroleum Infrastructure Programme (PIP; Ref. No: IS05/16 Malin Basin EM).2012-07-1

Molecular dynamics in collagen and model peptides

About a quarter of the total mass of proteins in vertebrates is collagen, so, improved knowledge of this protein is desirable and it should provide a new insight into biological interactions in human bodies. Two of the three main residues constituting collagen are proline and its derivative, hydroxyproline, which are responsible for some of the properties of collagen. Using solid-state NMR we studied the influence of water and temperature on motional changes in collagen. The results showed that increasing water content leads to significant increase of frequencies of protein motions with correlation times of the order of μs. It was found that pyrrolidine rings of L-prolines are not static in the solid state and cyclic carbon atoms librate about their mean position. Similarly, proline and hydroxyproline cyclic carbons in collagen were found to show librational dynamics. Detailed solution NMR analysis of proline peptides have been carried out. Using a two-site equilibrium model, geometries and populations of both conformers of prolines were established using the analysis of 3 J-couplings. The results of these studies were used for the verification of the performance of MD and QM calculations in the solution state. The effect of solvent on the pyrrolidine ring conformation and cis/trans rotamerisation along the amide bond preceding Pro was investigated by temperature dependent NMR followed by detailed transition state (TS) searches using QM methods. The coalescence temperature measurements were undertaken in order to determine the free energy of activation for the cis/trans-rotamerisation, which showed significant solvent dependence. The QM calculations revealed the energetic characteristics of the TS, which were in satisfactory agreement with NMR, as well as the corresponding TS geometries. For our pilot studies of a combined NMR/MD/QM approach for structure and dynamics elucidations in the solution state we chose two open chain tetrapeptides. We used an NMR/MD analysis in order to identify the most plausible structures. These conformations were used for further geometry optimisations using QM methods. In summary, a multidisciplinary approach has been developed, where experimental (NMR) and computational techniques (MD and QM) have been applied in a complementary manner in order to achieve a better understanding of proline containing peptides and collagen

Drying kinetics of deformable and cracking nano-porous gels

The desiccation of porous materials encompasses a wide range of technological and industrial processes and is acutely sensitive to the hierarchical structure of the porous materials resulting in complex dynamics which are challenging to unravel. Macroscopic observations of the surface and geometry of model colloidal gels during desiccation under controlled air flow highlight the role of crack formation in drying. The density of cracks and their rate of appearance depend on the initial solid fraction of the gels and their adherence to the substrate. While under certain conditions cracking leads to an increase of the drying rate, in other cases cracking allows for its conservation over an extended period of the drying process. Nevertheless, as long as the sample is saturated with water, each piece within the sample shrinks isotropically as if it were an independent drying system. By simulating the airflow around the sample and inside the crack cavities, we show the existence of a perturbation in the air velocity in the vicinity of the crack cavity whose scale depends on the aspect ratio (depth/width) of the latter. On this basis, we propose a simple model which predicts the observed drying rate variations encountered while the sample cracks; and further enables to simulate the desiccation for a designated crack density

Unraveling the long-term stabilization mechanisms of organic materials in soils by physical fractionation and NMR spectroscopy

The fundamental mechanisms whereby organic inputs stabilize in soil are poorly resolved, which limits our current capacity to predict the dynamics of soil organic matter (OM) turnover and its influence on soil quality and functioning. Here we fractionated soil OM from long-term experimental field plots either unamended or amended with two organic materials of different quality (i.e., solid cattle manure and crop residues) for 44 years into five measurable and meaningful pools directly related to conceptual preservation mechanisms: dissolved OM, mineral-free particulate OM located outside aggregates (unprotected from decomposition), OM occluded within both macroaggregates and microaggregates (weakly and strongly protected by physical mechanisms, respectively), and OM intimately associated with soil mineral particles (protected by chemical mechanisms). Compared to the unamended soil, the application of cattle manure and crop residues increased total organic C content by 35 and 10%, respectively. Most of these increases (up to 60 and 72% for cattle manure and crop residues, respectively) were explained by the mineral-associated OM pool, followed by the intra-microaggreggate OM fraction. In general, the distribution and dynamics of N content paralleled those of C content. As determined by a range of modern nuclear magnetic resonances (NMR) techniques, including 13C cross polarization magic angle spinning (MAS), 1H high resolution (HR)-MAS, and 1H-13C heteronuclear single quantum coherence HR-MAS NMR, the mineral-associated OM fraction was found to be predominately of microbial origin, unlike free and intra-aggregate OM pools, which were dominated by plant structures at different stages of decomposition. As a whole, our results indicate that the main mechanism by which organic inputs are stabilized and OM accrues in soils is not the physical and chemical protection of undecayed or partially degraded organic structures, but the adsorption on mineral surfaces of microbial biomass and microbial by-products resulting from microbial growth, transformation, and degradation processes. It is possible that organic amendments increase more than previously thought the microbial populations of the soil, which live, thrive, and die in close association with the mineral surfaces. This mechanism appears to be enhanced with the addition of stable organic materials

Drying kinetics of deformable and cracking nano-porous gels

The desiccation of porous materials encompasses a wide range of technological and industrial processes and is acutely sensitive to the hierarchical structure of the porous materials resulting in complex dynamics which are challenging to unravel. Macroscopic observations of the surface and geometry of model colloidal gels during desiccation under controlled air flow highlight the role of crack formation in drying. The density of cracks and their rate of appearance depend on the initial solid fraction of the gels and their adherence to the substrate. While under certain conditions cracking leads to an increase of the drying rate, in other cases cracking allows for its conservation over an extended period of the drying process. Nevertheless, as long as the sample is saturated with water, each piece within the sample shrinks isotropically as if it were an independent drying system. By simulating the airflow around the sample and inside the crack cavities, we show the existence of a perturbation in the air velocity in the vicinity of the crack cavity whose scale depends on the aspect ratio (depth/width) of the latter. On this basis, we propose a simple model which predicts the observed drying rate variations encountered while the sample cracks; and further enables to simulate the desiccation for a designated crack density