scholarly journals Xtrapol8: automatic elucidation of low-occupancy intermediate-states in crystallographic studies

2022 ◽  
Author(s):  
Elke De Zitter ◽  
Nicolas Coquelle ◽  
Thomas R.M. Barends ◽  
Jacques-Philippe Colletier
Keyword(s):  
Bayesian Statistics ◽  
Structure Determination ◽  
Intermediate State ◽  
Time Resolved ◽  
Structure Factors ◽  
Intermediate States ◽  
Conventional Methods ◽  
Unstable States

Unstable states studied in kinetic, time-resolved and ligand-based crystallography are often characterized by a low occupancy, hindering structure determination by conventional methods. To automatically extract such structures, we developed Xtrapol8, a program which (i) applies various flavors of Bayesian-statistics weighting to generate the most informative Fourier difference maps; (ii) determines the occupancy of the intermediate state; (iii) calculates various types of extrapolated structure factors, and (iv) refines the corresponding structures.

Structure determination of modulated structures by powder X-ray diffraction and electron diffraction

2016 ◽  
Vol 3 (11) ◽  
pp. 1351-1362 ◽  
Author(s):  
Zhengyang Zhou ◽  
Lukáš Palatinus ◽  
Junliang Sun
Keyword(s):  
Electron Diffraction ◽  
Structure Determination ◽  
X Ray Diffraction ◽  
X Ray ◽  
Modulated Structures ◽  
Conventional Methods

The combination of PXRD and ED is applied to determine modulated structures which resist solution by more conventional methods.

scholarly journals Enzymatic evolution driven by entropy production

2018 ◽  
Author(s):  
A. Arango-Restrepo ◽  
J.M. Rubi ◽  
D. Barragán
Keyword(s):  
Enzyme Kinetics ◽  
Entropy Production ◽  
Intermediate State ◽  
State Energy ◽  
Structural Evolution ◽  
Thermodynamic Efficiency ◽  
Total Entropy ◽  
Enzymatic Process ◽  
Intermediate States ◽  
Evolution Proceeds

AbstractWe show that the structural evolution of enzymes is largely influenced by the entropy produced in the enzymatic process. We have computed this quantity for the case in which the process has unstable and metastable intermediate states. By assuming that the kinetics takes place along a potential barrier, we have found that the behavior of the total entropy produced is a non-monotonic function of the intermediate state energy. By diminishing the number of metastable intermediate states, the total entropy produced decreases and consequently the enzyme kinetics and the thermodynamic efficiency are enhanced. Minimizing locally the total entropy produced for an enzymatic process with metastable intermediate states, the kinetics and the thermodynamic efficiency are raised. In contrast, in the absence of metastable intermediate states, a maximum of the entropy produced results in an improvement of the kinetic performance although the thermodynamic efficiency diminishes. Our results show that the enzymatic evolution proceeds not only to enhance the kinetics but also to optimize the total entropy produced.

Apparatus for the measurement of the electronic excited-state structure of single crystals using X-ray diffraction

1994 ◽  
Vol 27 (5) ◽  
pp. 727-732 ◽  
Author(s):  
M. A. White ◽  
M. R. Pressprich ◽  
P. Coppens ◽  
D. D. Coppens
Keyword(s):  
Excited States ◽  
Modulation Method ◽  
State Structure ◽  
X Ray Diffraction ◽  
Time Resolved ◽  
X Ray ◽  
Electronic Excited States ◽  
Structure Factors ◽  
Counting Statistics ◽  
Mechanical Chopper

Instrumentation for measuring the X-ray diffraction pattern of optically excited crystals is described. The experiment uses a high-power (~1 W) laser and a single-crystal diffractometer equipped with a helium cryostat (T < 70 K). The laser beam is modulated by a mechanical chopper and the diffraction signal gated in synchronization with the chopper phase. The modulation method is capable of observing small changes (down to about 0.01%) in the structure factors upon excitation of a fraction of the molecules in the crystal, given adequate counting statistics. The technique can be used for relatively long lived electronic excited states (τ ≃ 0.1–10 ms). The optical system is also suitable for time-resolved measurements using the time structure of synchrotron radiation.

scholarly journals The Extended PLATON/SQUEEZE Tool in the Context of Twinning and SHELXL2014

2014 ◽  
Vol 70 (a1) ◽  
pp. C1436-C1436 ◽  
Author(s):  
Anthony Spek
Keyword(s):  
Structure Determination ◽  
Fourier Transformation ◽  
Ad Hoc ◽  
Solvent Mixtures ◽  
Density Peaks ◽  
Difference Density ◽  
Valence States ◽  
Structure Factors ◽  
Density Map ◽  
Solvent Molecules

The completion of a single crystal structure determination is often hampered by the presence of disordered solvent molecules of crystallization. The often not interesting details of that solvent disorder and its contribution to the calculated structure factors has to be modelled in some way in order to obtain publishable results. Current refinement programs include suitable constraints and restraints for a stable refinement of a discrete disorder model. This is often the preferred procedure, in particular when charge balances and valence states are relevant. Unfortunately, a discrete disorder model is not always feasible. Examples include solvent molecules in infinite channels or structures including unknown solvents or solvent mixtures. In such cases the iterative back-Fourier transformation of the content of the disordered solvent volume in a difference density map can be attempted as the contribution to the calculated structure factors. Back-Fourier transformation of disordered solvent regions was prototyped by us nearly 25 years ago (van der Sluis & Spek, 1990) around the, at that time widely used, SHELX76 refinement program. The original reason for its development was the structure determination of a pharmaceutical that contained infinite channels filled with ridges of electron density in the difference density map rather than discrete density peaks (van der Sluis & Spek, 1990). The preliminary implementation of a successful prototype procedure (called BYPASS) was complex and found not to be easily distributable due to its dependence on many (local) ad-hoc programs. A new distributable version, compatible with the next generation refinement program SHELXL97, was implemented as the SQUEEZE tool in the program package PLATON Spek, 2009). The new SHELXL2014 refinement program allows for an even more elegant implementation of the SQUEEZE tool including the possibility to apply it also for twinned structures. Examples and restrictions will be discussed.

scholarly journals New methods in time-resolved Laue pump–probe crystallography at synchrotron sources

2015 ◽  
Vol 22 (2) ◽  
pp. 280-287 ◽  
Author(s):  
Philip Coppens ◽  
Bertrand Fournier
Keyword(s):  
Ground State ◽  
Initial Assessment ◽  
Ratio Method ◽  
Ground State Structure ◽  
Data Sets ◽  
State Structure ◽  
Time Resolved ◽  
Structure Factors ◽  
Unit Cells ◽  
Diffraction Patterns

Newly developed methods for time-resolved studies using the polychromatic and in particular the pink-Laue technique, suitable for medium and small-size unit cells typical in chemical crystallography, are reviewed. The order of the sections follows that of a typical study, starting with a description of the pink-Laue technique, followed by the strategy of data collection for analysis with the RATIO method. Novel procedures are described for spot integration, orientation matrix determination for relatively sparse diffraction patterns, scaling of multi-crystal data sets, use of Fourier maps for initial assessment and analysis of results, and least-squares refinement of photo-induced structural and thermal changes. In the calculation of Fourier maps a ground-state structure model, typically based on monochromatic results, is employed as reference, and the laser-ON structure factors for the Fourier summations are obtained by multiplying the reference ground-state structure factors by the square root of the experimental ON/OFF ratios. A schematic of the procedure followed is included in the conclusion section.

scholarly journals Biophysical properties of intermediate states of EMT outperform both epithelial and mesenchymal states

2019 ◽  
Author(s):  
Yoran Margaron ◽  
Tomoaki Nagai ◽  
Laurent Guyon ◽  
Laetitia Kurzawa ◽  
Anne-Pierre Morel ◽  
...  
Keyword(s):  
Mechanical Properties ◽  
Tumor Cell ◽  
Intermediate State ◽  
Mesenchymal Cells ◽  
Primary Breast Tumor ◽  
Tumor Cell Dissemination ◽  
Intermediate States ◽  
Defined Culture ◽  
Contractile Forces ◽  
Cell Dissemination

AbstractPotential metastatic cells can dissociate from a primary breast tumor by undergoing an epithelial-to-mesenchymal transmission (EMT). Recent work has revealed that cells in intermediate states of EMT acquire an augmented capacity for tumor-cell dissemination. These states have been characterized by molecular markers, but the structural features and the cellular mechanisms that underlie the acquisition of their invasive properties are still unknown. Using human mammary epithelial cells, we generated cells in intermediate states of EMT through the induction of a single EMT-inducing transcription factor, ZEB1, and cells in a mesenchymal state by stimulation with TGFβ. In stereotypic and spatially-defined culture conditions, the architecture, internal organization and mechanical properties of cells in the epithelial, intermediate and mesenchymal state were measured and compared. We found that the lack of intercellular cohesiveness in epithelial and mesenchymal cells can be detected early by microtubule destabilization and the repositioning of the centrosome from the cell-cell junction to the cell center. Consistent with their high migration velocities, cells in intermediate states produced low contractile forces compared with epithelial and mesenchymal cells. The high contractile forces in mesenchymal cells powered a retrograde flow pushing the nucleus away from cell adhesion to the extracellular matrix. Therefore, cells in intermediate state had structural and mechanical properties that were distinct but not necessarily intermediate between epithelial and mesenchymal cells. Based on these observations, we found that a panel of triple-negative breast cancer lines had intermediate rather than mesenchymal characteristics suggesting that the structural and mechanical properties of the intermediate state are important for understanding tumor-cell dissemination.

Origin of strong red emission in Er3+-based upconversion materials: role of intermediate states and cross relaxation

2019 ◽  
Vol 21 (43) ◽  
pp. 24026-24033 ◽  
Author(s):  
Chiho Lee ◽  
Heeyeon Park ◽  
Woong Kim ◽  
Sungnam Park
Keyword(s):  
Upconversion Luminescence ◽  
Photoluminescence Spectroscopy ◽  
Cross Relaxation ◽  
Time Resolved ◽  
Red Emission ◽  
Intermediate States ◽  
Time Resolved Photoluminescence

Comprehensive NIR-to-visible upconversion luminescence mechanism in Er3+-based materials is elucidated by wavelength-dependent, power-dependent, and time-resolved photoluminescence spectroscopy.

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