scholarly journals Enzyme catalysis captured using multiple structures from one crystal at varying temperatures

IUCrJ ◽  
2018 ◽  
Vol 5 (3) ◽  
pp. 283-292 ◽  
Author(s):  
Sam Horrell ◽  
Demet Kekilli ◽  
Kakali Sen ◽  
Robin L. Owen ◽  
Florian S. N. Dworkowski ◽  
...  
Keyword(s):  
High Resolution ◽  
Enzyme Catalysis ◽  
Density Functional ◽  
Room Temperature ◽  
Structural Information ◽  
Density Functional Theory Calculations ◽  
State Density ◽  
X Rays ◽  
Copper Site ◽  
Multiple Structures

High-resolution crystal structures of enzymes in relevant redox states have transformed our understanding of enzyme catalysis. Recent developments have demonstrated that X-rays can be used, via the generation of solvated electrons, to drive reactions in crystals at cryogenic temperatures (100 K) to generate `structural movies' of enzyme reactions. However, a serious limitation at these temperatures is that protein conformational motion can be significantly supressed. Here, the recently developed MSOX (multiple serial structures from one crystal) approach has been applied to nitrite-bound copper nitrite reductase at room temperature and at 190 K, close to the glass transition. During both series of multiple structures, nitrite was initially observed in a `top-hat' geometry, which was rapidly transformed to a `side-on' configuration before conversion to side-on NO, followed by dissociation of NO and substitution by water to reform the resting state. Density functional theory calculations indicate that the top-hat orientation corresponds to the oxidized type 2 copper site, while the side-on orientation is consistent with the reduced state. It is demonstrated that substrate-to-product conversion within the crystal occurs at a lower radiation dose at 190 K, allowing more of the enzyme catalytic cycle to be captured at high resolution than in the previous 100 K experiment. At room temperature the reaction was very rapid, but it remained possible to generate and characterize several structural states. These experiments open up the possibility of obtaining MSOX structural movies at multiple temperatures (MSOX-VT), providing an unparallelled level of structural information during catalysis for redox enzymes.

High-Resolution Scanning Electron Microscopy of Biological Specimens

1988 ◽  
Vol 46 ◽  
pp. 186-187
Author(s):  
M. Müller ◽  
R. Hermann
Keyword(s):  
High Resolution ◽  
Freeze Drying ◽  
Room Temperature ◽  
Structural Information ◽  
Freeze Substitution ◽  
Critical Point Drying ◽  
Sem Study ◽  
Major Factors ◽  
Structural Preservation ◽  
Preparation Techniques

Three major factors must be concomitantly assessed in order to extract relevant structural information from the surface of biological material at high resolution (2-3nm).Procedures based on chemical fixation and dehydration in graded solvent series seem inappropriate when aiming for TEM-like resolution. Cells inevitably shrink up to 30-70% of their initial volume during gehydration; important surface components e.g. glycoproteins may be lost. These problems may be circumvented by preparation techniques based on cryofixation. Freezedrying and freeze-substitution followed by critical point drying yields improved structural preservation in TEM. An appropriate preservation of dimensional integrity may be achieved by freeze-drying at - 85° C. The sample shrinks and may partially collapse as it is warmed to room temperature for subsequent SEM study. Observations at low temperatures are therefore a necessary prerequisite for high fidelity SEM. Compromises however have been unavoidable up until now. Aldehyde prefixation is frequently needed prior to freeze drying, rendering the sample resistant to treatment with distilled water.

scholarly journals Measurement of synchrotron-radiation-excited Kossel patterns

2016 ◽  
Vol 23 (1) ◽  
pp. 214-218 ◽  
Author(s):  
G. Bortel ◽  
G. Faigel ◽  
M. Tegze ◽  
A. Chumakov
Keyword(s):  
High Resolution ◽  
Dynamic Range ◽  
Structural Information ◽  
Photon Counting ◽  
Spot Size ◽  
Low Noise ◽  
X Rays ◽  
Technical Problems ◽  
Pixel Detectors ◽  
Exciting Beam

Kossel line patterns contain information on the crystalline structure, such as the magnitude and the phase of Bragg reflections. For technical reasons, most of these patterns are obtained using electron beam excitation, which leads to surface sensitivity that limits the spatial extent of the structural information. To obtain the atomic structure in bulk volumes, X-rays should be used as the excitation radiation. However, there are technical problems, such as the need for high resolution, low noise, large dynamic range, photon counting, two-dimensional pixel detectors and the small spot size of the exciting beam, which have prevented the widespread use of Kossel pattern analysis. Here, an experimental setup is described, which can be used for the measurement of Kossel patterns in a reasonable time and with high resolution to recover structural information.

scholarly journals Investigation of the cis–trans structures and isomerization of oligoprolines by using Raman spectroscopy and density functional theory calculations: solute–solvent interactions and effects of terminal positively charged amino acid residues

RSC Advances ◽  
2020 ◽  
Vol 10 (57) ◽  
pp. 34493-34500
Author(s):  
Mei-Chun Huang ◽  
Wei-Hao Chen ◽  
Chen-Wei Huang ◽  
Kuei-Yen Huang ◽  
Jia-Cherng Horng ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Raman Spectroscopy ◽  
Density Functional ◽  
Theoretical Calculations ◽  
Density Functional Theory Calculations ◽  
State Density ◽  
Amino Acid Residues ◽  
Functional Theory ◽  
Solvent Interactions ◽  
Positively Charged

The low-wavenumber Raman spectra in combination with theoretical calculations via solid-state density functional theory (DFT)-D3 are displayed. The vibrational structures and interaction with solvent of poly-l-proline and the oligoproline P12 series are identified.

scholarly journals High-Pressure Structural Behavior and Equation of State of Kagome Staircase Compound, Ni3V2O8

Crystals ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 910
Author(s):  
Daniel Diaz-Anichtchenko ◽  
Robin Turnbull ◽  
Enrico Bandiello ◽  
Simone Anzellini ◽  
Daniel Errandonea
Keyword(s):  
High Pressure ◽  
Equation Of State ◽  
Density Functional ◽  
Room Temperature ◽  
Ambient Pressure ◽  
Density Functional Theory Calculations ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters ◽  
A Chain

We report on high-pressure synchrotron X-ray diffraction measurements on Ni3V2O8 at room-temperature up to 23 GPa. According to this study, the ambient-pressure orthorhombic structure remains stable up to the highest pressure reached in the experiments. We have also obtained the pressure dependence of the unit-cell parameters, which reveals an anisotropic compression behavior. In addition, a room-temperature pressure–volume third-order Birch–Murnaghan equation of state has been obtained with parameters: V0 = 555.7(2) Å3, K0 = 139(3) GPa, and K0′ = 4.4(3). According to this result, Ni3V2O8 is the least compressible kagome-type vanadate. The changes of the crystal structure under compression have been related to the presence of a chain of edge-sharing NiO6 octahedral units forming kagome staircases interconnected by VO4 rigid tetrahedral units. The reported results are discussed in comparison with high-pressure X-ray diffraction results from isostructural Zn3V2O8 and density-functional theory calculations on several isostructural vanadates.

Synthesis, Structure, and Visible Phosphorescence Emission of Novel CuI Coordination Polymers Based on 4,4′-Bis(3-pyridyl)-2,2′-bis(hydroxylmethyl) Biphenyl

2015 ◽  
Vol 68 (2) ◽  
pp. 307 ◽  
Author(s):  
Guo-Xia Jin ◽  
Jian-Ping Ma ◽  
Chuan-Zhi Sun ◽  
Yu-Bin Dong
Keyword(s):  
Coordination Polymers ◽  
Density Functional ◽  
Room Temperature ◽  
Emission Spectra ◽  
Density Functional Theory Calculations ◽  
X Ray Diffraction ◽  
Ligand Charge Transfer ◽  
Yellow Orange ◽  
The Difference ◽  
1D Chains

Four new CuI coordination polymers, [(CuCl)L]n (1), {[(CuCl)2L2]·(H2O)}n (2), [(CuBr)L]n (3), and {[(CuBr)2L2]·(H2O)}n (4), were obtained from a new ligand 4,4′-bis(3-pyridyl)-2,2′-bis(hydroxylmethyl) biphenyl (L) and characterized by single-crystal X-ray diffraction. In 1 and 3, the rhombic [Cu2(μ-X)2] units are connected to each other by the bidentate linkers to form an infinite 1D double chain (X = Cl, Br). Such 1D chains are arranged into a 2D sheet through inter-chain π···π interactions. In 2 and 4, there are similar 1D double chains, but different inter-chain arrangement. Such 1D chains are connected into a 2D layer and further arranged in an ABAB fashion through O–H···X hydrogen bonds. The emission spectra and lifetimes in the microsecond range were measured at room temperature and at 77 K. Complexes 1 and 3 exhibit strong orange and yellow–orange emission in the solid state at room temperature, and were assigned to X-and M-to-ligand charge transfer excited states based on density functional theory calculations. The emission property of 2 and 4 was distinctly different from that of 1 and 3, probably due to the difference in coordination environments of the CuI centres as well as the dissimilar intermolecular arrangement.

Terahertz spectroscopy and solid-state density functional theory calculations of structural isomers: Nicotinic acid, isonicotinic acid and 2-picolinic acid

2017 ◽  
Vol 31 (13) ◽  
pp. 1750149 ◽  
Author(s):  
Ling Ding ◽  
Wen-Hui Fan ◽  
Xu Chen ◽  
Ze-You Chen ◽  
Chao Song
Keyword(s):  
Density Functional Theory ◽  
Nicotinic Acid ◽  
Density Functional ◽  
Isonicotinic Acid ◽  
Picolinic Acid ◽  
Molecular Crystals ◽  
Density Functional Theory Calculations ◽  
State Density ◽  
Functional Theory ◽  
Absorption Features

We report, for the first time to our knowledge, the terahertz (THz) spectra of isonicotinic acid and 2-picolinic acid. The distinct THz spectral differences among these two isomers and nicotinic acid have also been observed, indicating that the THz vibrational modes are highly sensitive to the structural differences even in similar molecular crystals. Besides, solid-state density functional theory calculations reveal better qualitative agreement with the measured absorption features, which are related to the molecular vibrations of nicotinic acid and isonicotinic acid. As for 2-picolinic acid, the calculation based on the primitive cell reproduces the absorption features at 1.46, 1.82 and 2.46 THz originating from intermolecular vibrations. These results suggest that THz spectra can identify the complex intermolecular interactions even in similar molecular crystals, which shows potential applications in identifying isomers in food and pharmaceutical production.

Sign in / Sign up

Export Citation Format

Share Document