Explicit models of motions to analyze NMR relaxation data in proteins

Nuclear Magnetic Resonance (NMR) is a tool of choice to characterize molecular motions. In biological macromolecules, pico- to nano-second motions, in particular, can be probed by nuclear spin relaxation rates which depend on the time fluctuations of the orientations of spin interaction frames. For the past 40 years, relaxation rates have been successfully analyzed using the Model Free (MF) approach which makes no assumption on the nature of motions and reports on the effective amplitude and time-scale of the motions. However, obtaining a mechanistic picture of motions from this type of analysis is difficult at best, unless complemented with molecular dynamics (MD) simulations. In spite of their limited accuracy, such simulations can be used to obtain the information necessary to build explicit models of motions designed to analyze NMR relaxation data. Here, we present how to build such models, suited in particular to describe motions of methyl-bearing protein side-chains and compare them with the MF approach. We show on synthetic data that explicit models of motions are more robust in the presence of rotamer jumps which dominate the relaxation in methyl groups of protein side-chains. We expect this work to motivate the use of explicit models of motion to analyze MD and NMR data

Simple method for the generation of multiple homogeneous field volumes inside the bore of superconducting magnets

International audienceStandard Magnetic Resonance magnets produce a single homogeneous field volume, where the analysis is performed. Nonetheless, several modern applications could benefit from the generation of multiple homogeneous field volumes along the axis and inside the bore of the magnet. In this communication, we propose a straightforward method using a combination of ring structures of permanent magnets in order to cancel the gradient of the stray field in a series of distinct volumes. These concepts were demonstrated numerically on an experimentally measured magnetic field profile. We discuss advantages and limitations of our method and present the key steps required for an experimental validation

Investigation of smectite hydration properties by modeling experimental X-ray diffraction patterns. Part I. Montmorillonite hydration properties.

Hydration of the <1 μm size fraction of SWy-1 source clay (low-charge montmorillonite) was studied by modeling of X-ray diffraction (XRD) patterns recorded under controlled relative humidity (RH) conditions on Li-, Na-, K-, Mg-, Ca-, and Sr saturated specimens. The quantitative description of smectite hydration, based on the relative proportions of different layer types derived from the fitting of experimental XRD patterns, was consistent with previous reports of smectite hydration. However, the coexistence of smectite layer types exhibiting contrasting hydration states was systematically observed, and heterogeneity rather than homogeneity seems to be the rule for smectite hydration. This heterogeneity can be characterized qualitatively using the standard deviation of the departure from rationality of the 00l reflection series (ξ), which is systematically larger than 0.4 A when the prevailing layer type accounts for ~70% or less of the total layers (~25 of XRD patterns examined). In addition, hydration heterogeneities are not randomly distributed within smectite crystallites, and models describing these complex structures involve two distinct contributions, each containing different layer types that are randomly interstratifed. As a result, the different layer types are partially segregated in the sample. However, these two contributions do not imply the actual presence of two populations of particles in the sample. XRD profile modeling has allowed also the refinement of structural parameters, such as the location of interlayer species and the layer thickness corresponding to the different layer types, for all interlayer cations and RH values. From the observed dependence of the latter parameter on the cation ionic potential ( r/v , v = cation valency and r = ionic radius) and on RH, the following equations were derived: 36 37 Layer thickness (1W) = 12.556 + 0.3525 × ( r/v - 0.241) × (v × RH - 0.979) Layer thickness (2W) = 15.592 + 0.6472 × ( 38 r/v - 0.839) × (v × RH - 1.412) which allow the quantification of the increase of layer thickness with increasing RH for both 1W (one-water) and 2W (two-water) layers. In addition for 2W layers interlayer H2O molecules are probably distributed as a unique plane on each side of the central interlayer cation. This plane of H2O molecules is located at ~1.20 A from the central interlayer cation along the c* axis

Experimental evidence for calcium-chloride ion pairs in the interlayer of montmorillonite. A XRD profile modeling approach.

Montmorillonite was equilibrated with high normality Cl - solutions to assess the possible presence of MeCl + ion pairs in smectite interlayers which is suggested by chemical modeling of cation exchange experimental studies. Structural modifications induced by the presence of such ion pairs, and more especially those related to smectite hydration properties, were characterized from the modeling of experimental X-ray diffraction (XRD) profiles. As compared to those obtained from samples prepared at low ionic strength, XRD patterns from samples equilibrated in high ionic strength CaCl2 solutions exhibited a small positional shift of 0

New insights on the distribution of interlayer water in bi-hydrated smectite from X-ray diffraction profile modeling 00l reflections

International audienceThe interlayer configuration proposed by Moore and Reynolds and commonly used to reproduce the 00l reflections of bi-hydrated smectite is shown to be inconsistent with experimental X-ray diffraction data. 1 The alternative configuration of interlayer species with cations located in the mid-plane of the interlayer and one sheet of H2O molecules on each side of this plane is also shown to imperfectly describe the actual structure of bi-hydrated smectites. Specifically, the thermal fluctuation of atomic positions (Debye-Waller factor) used to describe the positional disorder of interlayer H2O molecules has to be increased to unrealistic values to satisfactorily reproduce experimental X-ray diffraction data when using this model. A new configuration is thus proposed for the interlayer structure of bi-hydrated smectite. Cations are located in the mid-plane of the interlayer whereas H2O molecules are scattered about two main positions according to Gaussian-shaped distributions. This configuration allows reproducing all 00l reflections with a high precision, with only one new variable parameter (width of the Gaussian function). The proposed configuration is consistent with those derived from Monte-Carlo calculations and allows matching more closely the amount of interlayer water that can be determined independently from water vapor adsorption/desorption isotherm experiments. In addition, the proposed configuration of interlayer species appears valid for both dioctahedral and trioctahedral smectites exhibiting octahedral and tetrahedral substitutions, respectively, thus not allowing to differentiate these expandable 2:1 phyllosilicates from their respective interlayer configuration

Hydration Properties and Interlayer Organization of Water and Ions in Synthetic Na-Smectite with Tetrahedral Layer Charge. Part 1. Results from X-ray Diffraction Profile Modeling

International audienceThe dehydration of two Na-saturated synthetic saponites with contrasting layer charge was studied by modeling the X-ray diffraction (XRD) patterns recorded along a water vapor desorption isotherm. The interlayer configurations used to reproduce the XRD data over a large angular range include Na+ cations located in the interlayer midplane and H2O molecules normally distributed about one or two main positions for mono- and bihydrated layers, respectively. Although strongly reduced in comparison to natural smectites, hydration heterogeneity was systematically observed for these synthetic saponites, especially along the transition between two hydration states. Using improved models for the description of the interlayer organization, the influence of layer charge on the structure of interlayer water can be precisely assessed. In addition, the comparison with water contents obtained from water vapor gravimetry experiments allows discriminating the relative contributions of H2O molecules from 1W and 2W interlayers (crystalline water) and from the pore space network

Investigation of dioctahedral smectite hydration properties by modeling of X-ray diffraction profiles: Influence of layer charge and charge location

International audienceHydration of the <1 μm size fraction of a high-charge montmorillonite (Clay Minerals Society Source Clay SAz-1), and of low- and high-charge beidellites (Source Clays SbId-1 and SbCa-1, respectively) was studied by modeling of X-ray diffraction patterns recorded under controlled relative humidity (RH) for Sr- and/or Ca-saturated specimens. The influence of layer charge and charge location on smectite hydration was studied. Distribution of layers with different hydration states (dehydrated – 0W, monohydrated – 1W, bi-hydrated – 2W, or tri-hydrated – 3W) within smectite crystals often leads to two distinct contributions to the X-ray diffraction pattern, each contribution having different layer types randomly interstratified. Structure models are more heterogeneous for beidellite than for montmorillonite. For beidellite, two distinct populations of particles with different coherent scattering domain sizes account for the heterogeneity. Increased hydration heterogeneity in beidellite originates also from the presence of 0W (non-expandable) and of 1W layers under high relative humidity (RH) conditions. Similarly, after ethylene-glycol (EG) solvation, some beidellite layers incorporate only one plane of EG molecules whereas homogeneous swelling was observed for montmorillonite with the systematic presence of two planes of EG molecules. For montmorillonite and beidellite, the increase of layer charge shifts the 2W-to-1W and the 1W-to-0W transitions towards lower RH values. For all samples, layer thickness of 0W, 1W, and 2W layer types was similar to that determined for low-charge SWy-1 montmorillonite (Source Clay SWy-1), and no change of layer thickness was observed as a function of the amount or of the location of layer charge. Layer thickness however increased with increasing RH conditions

Espiritualidade e comportamentos de cidadania organizacional : expressões de cidadania nas organizações : um estudo de caso

Dissertação de Mestrado em Relações Internacionais apresentada à Universidade AbertaA questão que deu origem à dissertação visava descortinar a influência da dimensão espiritual nos comportamentos do indivíduo, mormente nas organizações. Dada a condição da autora trabalhar na organização, objeto do estudo de caso, foi necessário criar um dispositivo que a ajudasse a distanciar-se, de modo a poder analisá-la com maior objetividade. Nesse contexto, foi construído um modelo de análise ancorado no quadro teórico de referência, a partir do qual se concebeu o questionário para a recolha de dados. Este integrou um conjunto de 31 afirmações, cada uma das quais apelando ao preenchimento de duas escalas de Lickert (sobre a situação percecionada e a situação desejada), bem como algumas variáveis caracterizadoras dos inquiridos (o sexo, a idade, a categoria profissional, as habilitações literárias e a dimensão espiritual no seu comportamento organizacional). O questionário foi aplicado a uma amostra de 158 colaboradores da Universidade Aberta, entre pessoal docente e não docente, com o intuito de analisar as perceções dos inquiridos. O questionário foi elaborado na ferramenta Limesurvey e para o tratamento dos dados utilizamos o EXCEL. Apresentámos os resultados de forma descritiva utilizando para o efeito as frequências absolutas e relativas e a média. Fizemos contagens simples para apurar as respostas procurando encontrar a relação entre as diversas variáveis em estudo. Por fim e após a análise dos dados chegámos a algumas conclusões que são respostas às questões de investigação, nomeadamente: que os comportamentos de cidadania organizacional sofrem a influência da dimensão espiritual, que esta dimensão é reflexo da educação/socialização e que o modelo de análise deste trabalho revela a interdependência entre a dimensão espiritual e os comportamentos de cidadania. Sugerimos que a Liderança, enquanto variável, seja estudada numa perspectiva espiritual em pesquisas futuras, pela importância que adquire nas organizações e no condicionamento dos comportamentos de cidadania organizacional

The spalling decay of building bioclastic limestones of Provence (South East of France): From clay minerals swelling to hydric dilation

International audienceMedieval historical monuments of the Provence region (South East of France) were erected with bioclastic limestones and display different sensitivities to spalling decay. The present study aims at understanding the physical processes at play as well as the internal properties governing its intensity. Limestones of contrasting sensitivity to spalling were compared to a reference type, unaffected by this decay, by means of petrography, petrophysic, mineralogy, and hydromechanics. The obtained results highlighted that the various sensitivities can be explained by the deformation recorded during water content variation (hydric dilation). A clay fraction was systematically detected within the mineralogical composition except for the reference material, and some swelling layers were identified in ontmorillonite/glauconite mixed layer minerals. A specific quantification procedure based on the combination of transmission electron microscopy coupled to an energy-dispersive X-ray spectrometer (TEM–EDX) and profile modeling of X-ray diffraction patterns was applied. A strong relationship between swelling layer content and hydric dilation of limestones was evidenced and corroborated the spalling sensitivity. Further interpretation of results showed that swelling layers localization within the texture significantly influence hydric dilation kinetics. Eventually, a mechanical softening was measured after water saturation. This behavior seems unrelated to the clay mineral content and its relative influence on spalling should be examined

Understanding the Methyl-TROSY effect over a wide range of magnetic fields

The use of relaxation interference in the methyl Transverse Relaxation-Optimized SpectroscopY (TROSY) experiment has opened new avenues for the study of large proteins and protein assemblies in nuclear magnetic resonance. So far, the theoretical description of the methyl-TROSY experiment has been limited to the slow-tumbling approximation, which is correct for large proteins on high field spectrometers. In a recent paper, favorable relaxation interference was observed in the methyl groups of a small protein at a magnetic field as low as 0.33 T, well outside the slow-tumbling regime. Here, we present a model to describe relaxation interference in methyl groups over a broad range of magnetic fields, not limited to the slow-tumbling regime. We predict that the type of multiple-quantum transitions that show favorable relaxation properties change with the magnetic field. Under the condition of fast methyl-group rotation, methyl-TROSY experiments can be recorded over the entire range of magnetic fields from a fraction of 1 T up to 100 T