The Effect of Natural Osmolyte Mixtures on the Temperature-Pressure Stability of the Protein RNase A

2018 ◽  
Vol 232 (5-6) ◽  
pp. 615-634 ◽  
Author(s):  
Loana Arns ◽  
Vitor Schuabb ◽  
Shari Meichsner ◽  
Melanie Berghaus ◽  
Roland Winter
Keyword(s):  
Deep Sea ◽  
Rnase A ◽  
Scattering Data ◽  
Hydration Water ◽  
Angle Scattering ◽  
Hydrated Protein ◽  
Unfolded State ◽  
Pressure Stability ◽  
Temperature And Pressure ◽  
A Minor

Abstract In biological cells, osmolytes appear as complex mixtures with variable compositions, depending on the particular environmental conditions of the organism. Based on various spectroscopic, thermodynamic and small-angle scattering data, we explored the effect of two different natural osmolyte mixtures, which are found in shallow-water and deep-sea shrimps, on the temperature and pressure stability of a typical monomeric protein, RNase A. Both natural osmolyte mixtures stabilize the protein against thermal and pressure denaturation. This effect seems to be mainly caused by the major osmolyte components of the osmolyte mixtures, i.e. by glycine and trimethylamine-N-oxide (TMAO), respectively. A minor compaction of the structure, in particular in the unfolded state, seems to be largely due to TMAO. Differences in thermodynamic properties observed for glycine and TMAO, and hence also for the two osmolyte mixtures, are most likely due to different solvation properties and interactions with the protein. Different from TMAO, glycine seems to interact with the amino acid side chains and/or the backbone of the protein, thus competing with hydration water and leading to a less hydrated protein surface.

Pushing the Envelope

2018 ◽  
Author(s):  
Eaton E. Lattman ◽  
Thomas D. Grant ◽  
Edward H. Snell
Keyword(s):  
High Resolution ◽  
Electron Density ◽  
Structural Information ◽  
Hydration Shell ◽  
Three Dimensional ◽  
Scattering Data ◽  
Saxs Data ◽  
Electron Density Function ◽  
Angle Scattering ◽  
Iterative Structure

Direct electron density determination from SAXS data opens up new opportunities. The ability to model density at high resolution and the implicit direct estimation of solvent terms such as the hydration shell may enable high-resolution wide angle scattering data to be used to calculate density when combined with additional structural information. Other diffraction methods that do not measure three-dimensional intensities, such as fiber diffraction, may also be able to take advantage of iterative structure factor retrieval. While the ability to reconstruct electron density ab initio is a major breakthrough in the field of solution scattering, the potential of the technique has yet to be fully uncovered. Additional structural information from techniques such as crystallography, NMR, and electron microscopy and density modification procedures can now be integrated to perform advanced modeling of the electron density function at high resolution, pushing the boundaries of solution scattering further than ever before.

scholarly journals 2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update

2017 ◽  
Vol 73 (9) ◽  
pp. 710-728 ◽  
Author(s):  
Jill Trewhella ◽  
Anthony P. Duff ◽  
Dominique Durand ◽  
Frank Gabel ◽  
J. Mitchell Guss ◽  
...  
Keyword(s):  
Small Angle ◽  
Task Force ◽  
Data Bank ◽  
Small Angle Scattering ◽  
Scattering Data ◽  
Quality Data ◽  
Angle Scattering ◽  
Publication Guidelines ◽  
Guidelines And Recommendations

In 2012, preliminary guidelines were published addressing sample quality, data acquisition and reduction, presentation of scattering data and validation, and modelling for biomolecular small-angle scattering (SAS) experiments. Biomolecular SAS has since continued to grow and authors have increasingly adopted the preliminary guidelines. In parallel, integrative/hybrid determination of biomolecular structures is a rapidly growing field that is expanding the scope of structural biology. For SAS to contribute maximally to this field, it is essential to ensure open access to the information required for evaluation of the quality of SAS samples and data, as well as the validity of SAS-based structural models. To this end, the preliminary guidelines for data presentation in a publication are reviewed and updated, and the deposition of data and associated models in a public archive is recommended. These guidelines and recommendations have been prepared in consultation with the members of the International Union of Crystallography (IUCr) Small-Angle Scattering and Journals Commissions, the Worldwide Protein Data Bank (wwPDB) Small-Angle Scattering Validation Task Force and additional experts in the field.

scholarly journals Effects of Temperature and Pressure on Sulfate Reduction and Anaerobic Oxidation of Methane in Hydrothermal Sediments of Guaymas Basin

2004 ◽  
Vol 70 (2) ◽  
pp. 1231-1233 ◽  
Author(s):  
Jens Kallmeyer ◽  
Antje Boetius
Keyword(s):  
Sulfate Reduction ◽  
Deep Sea ◽  
Anaerobic Oxidation Of Methane ◽  
Anaerobic Oxidation ◽  
Guaymas Basin ◽  
Oxidation Of Methane ◽  
Hydrothermal Sediments ◽  
Deep Sea Sediments ◽  
Effects Of Temperature ◽  
Temperature And Pressure

ABSTRACT Rates of sulfate reduction (SR) and anaerobic oxidation of methane (AOM) in hydrothermal deep-sea sediments from Guaymas Basin were measured at temperatures of 5 to 200°C and pressures of 1 × 105, 2.2 × 107, and 4.5 × 107 Pa. A maximum SR of several micromoles per cubic centimeter per day was found at between 60 and 95°C and 2.2 × 107 and 4.5 × 107 Pa. Maximal AOM was observed at 35 to 90°C but generally accounted for less than 5% of SR.

Comparison of iterative desmearing procedures for one-dimensional small-angle scattering data

2011 ◽  
Vol 44 (1) ◽  
pp. 32-42 ◽  
Author(s):  
Thomas Vad ◽  
Wiebke F. C. Sager
Keyword(s):  
Small Angle ◽  
Incident Beam ◽  
Scattering Data ◽  
Data Sets ◽  
Convergence Criteria ◽  
Small Momentum Transfer ◽  
One Dimensional ◽  
Noise Filter ◽  
Large Numbers ◽  
Angle Scattering

Two simple iterative desmearing procedures – the Lake algorithm and the Van Cittert method – have been investigated by introducing different convergence criteria using both synthetic and experimental small-angle neutron scattering data. Implementing appropriate convergence criteria resulted in stable and reliable solutions in correcting resolution errors originating from instrumental smearing,i.e.finite collimation and polychromaticity of the incident beam. Deviations at small momentum transfer for concentrated ensembles of spheres encountered in earlier studies are not observed. Amplification of statistical errors can be reduced by applying a noise filter after desmearing. In most cases investigated, the modified Lake algorithm yields better results with a significantly smaller number of iterations and is, therefore, suitable for automated desmearing of large numbers of data sets.

A Study of Beryllium-Based Materials and Comparison of Their X-Ray Homogeneities According to Small-Angle Scattering Data

2018 ◽  
Vol 63 (6) ◽  
pp. 874-882 ◽  
Author(s):  
A. A. Semenov ◽  
V. V. Volkov ◽  
A. V. Zabrodin ◽  
V. V. Gorlevskii ◽  
M. S. Sheverdyaev ◽  
...  
Keyword(s):  
Small Angle ◽  
Small Angle Scattering ◽  
Scattering Data ◽  
X Ray ◽  
Angle Scattering

scholarly journals Small-angle scattering data representation in SASCIF and integrative/hybrid methods dictionary

2017 ◽  
Vol 73 (a2) ◽  
pp. C1441-C1441
Author(s):  
Brinda Vallat ◽  
Benjamin Webb ◽  
John Westbrook ◽  
Andrej Sali ◽  
Helen Berman
Keyword(s):  
Small Angle ◽  
Hybrid Methods ◽  
Data Representation ◽  
Small Angle Scattering ◽  
Scattering Data ◽  
Angle Scattering

scholarly journals The canSAS standard for storing reduced one-dimensional small-angle scattering data in XML files

2008 ◽  
Vol 64 (a1) ◽  
pp. C554-C554
Author(s):  
P.R. Jemian ◽  
A.J. Jackson ◽  
S.M. King ◽  
K.C. Littrell ◽  
A.R.J. Nelson ◽  
...  
Keyword(s):  
Small Angle ◽  
Small Angle Scattering ◽  
Scattering Data ◽  
One Dimensional ◽  
Angle Scattering

Small-angle scattering of interacting particles. II. Generalized indirect Fourier transformation under consideration of the effective structure factor for polydisperse systems

1999 ◽  
Vol 32 (2) ◽  
pp. 197-209 ◽  
Author(s):  
B. Weyerich ◽  
J. Brunner-Popela ◽  
O. Glatter
Keyword(s):  
Form Factor ◽  
Small Angle ◽  
Structure Factor ◽  
Fourier Transformation ◽  
Hard Spheres ◽  
Small Angle Scattering ◽  
Scattering Data ◽  
Model Free ◽  
Angle Scattering ◽  
The Gift

The indirect Fourier transformation (IFT) is the method of choice for the model-free evaluation of small-angle scattering data. Unfortunately, this technique is only useful for dilute solutions because, for higher concentrations, particle interactions can no longer be neglected. Thus an advanced technique was developed as a generalized version, the so-called generalized indirect Fourier transformation (GIFT). It is based on the simultaneous determination of the form factor, representing the intraparticle contributions, and the structure factor, describing the interparticle contributions. The former can be determined absolutely free from model assumptions, whereas the latter has to be calculated according to an adequate model. In this paper, various models for the structure factor are compared,e.g.the effective structure factor for polydisperse hard spheres, the averaged structure factor, the local monodisperse approximation and the decoupling approximation. Furthermore, the structure factor for polydisperse rod-like particles is presented. As the model-free evaluation of small-angle scattering data is an essential point of the GIFT technique, the use of a structure factor without any influence of the form amplitude is advisable, at least during the first evaluation procedure. Therefore, a series of simulations are performed to check the possibility of the representation of various structure factors (such as the effective structure factor for hard spheres or the structure factor for rod-like particles) by the less exact but much simpler averaged structure factor. In all the observed cases, it was possible to recover the exact form factor with a free determined parameter set for the structure factor. The resulting parameters of the averaged structure factor have to be understood as apparent model parameters and therefore have only limited physical relevance. Thus the GIFT represents a technique for the model independent evaluation of scattering data with a minimum ofa prioriinformation.

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