Gas-sensitive biological crystals processed in pressurized oxygen and krypton atmospheres: deciphering gas channels in proteins using a novel `soak-and-freeze' methodology

2016 ◽  
Vol 49 (5) ◽  
pp. 1478-1487 ◽  
Author(s):  
Bénédicte Lafumat ◽  
Christoph Mueller-Dieckmann ◽  
Gordon Leonard ◽  
Nathalie Colloc'h ◽  
Thierry Prangé ◽  
...  
Keyword(s):  
High Pressure ◽  
Molecular Oxygen ◽  
Gas Pressure ◽  
Biological Molecules ◽  
Urate Oxidase ◽  
Biological Processes ◽  
X Ray ◽  
Pressure Cell ◽  
Sufficient Detail ◽  
Wide Range

Molecular oxygen (O2) is a key player in many fundamental biological processes. However, the combination of the labile nature and poor affinity of O2 often makes this substrate difficult to introduce into crystals at sufficient concentrations to enable protein/O2 interactions to be deciphered in sufficient detail. To overcome this problem, a gas pressure cell has been developed specifically for the `soak-and-freeze' preparation of crystals of O2-dependent biological molecules. The `soak-and-freeze' method uses high pressure to introduce oxygen molecules or krypton atoms (O2 mimics) into crystals which, still under high pressure, are then cryocooled for X-ray data collection. Here, a proof of principle of the gas pressure cell and the methodology developed is demonstrated with crystals of enzymes (lysozyme, thermolysin and urate oxidase) that are known to absorb and bind molecular oxygen and/or krypton. The successful results of these experiments lead to the suggestion that the soak-and-freeze method could be extended to studies involving a wide range of gases of biological, medical and/or environmental interest, including carbon monoxide, ethylene, methane and many others.

The subatomic resolution study of laccase inhibition by chloride and fluoride anions using single-crystal serial crystallography: insights into the enzymatic reaction mechanism

2019 ◽  
Vol 75 (9) ◽  
pp. 804-816 ◽  
Author(s):  
Konstantin M. Polyakov ◽  
Sergei Gavryushov ◽  
Tatiana V. Fedorova ◽  
Olga A. Glazunova ◽  
Alexander N. Popov
Keyword(s):  
Molecular Oxygen ◽  
Enzymatic Reaction ◽  
Copper Ion ◽  
Data Sets ◽  
X Ray Diffraction ◽  
Fluoride Ions ◽  
X Ray ◽  
Mechanism Of Inhibition ◽  
Wide Range ◽  
Oxygen Ligand

Laccases are enzymes that catalyze the oxidation of a wide range of organic and inorganic substrates accompanied by the reduction of molecular oxygen to water. Here, a subatomic resolution X-ray crystallographic study of the mechanism of inhibition of the laccase from the basidiomycete fungus Steccherinum murashkinskyi by chloride and fluoride ions is presented. Three series of X-ray diffraction data sets were collected with increasing doses of absorbed X-ray radiation from a native S. murashkinskyi laccase crystal and from crystals of complexes of the laccase with chloride and fluoride ions. The data for the native laccase crystal confirmed the previously deduced enzymatic mechanism of molecular oxygen reduction. The structures of the complexes allowed the localization of chloride and fluoride ions in the channel near the T2 copper ion. These ions replace the oxygen ligand of the T2 copper ion in this channel and can play the role of this ligand in the enzymatic reaction. As follows from analysis of the structures from the increasing dose series, the inhibition of laccases by chloride and fluoride anions can be explained by the fact that the binding of these negatively charged ions at the position of the oxygen ligand of the T2 copper ion impedes the reduction of the T2 copper ion.

scholarly journals High pressure studies of L-Serine-L-Ascorbic acid co-crystal

2014 ◽  
Vol 70 (a1) ◽  
pp. C988-C988
Author(s):  
Sergey Arkhipov ◽  
Boris Zakharov ◽  
Elena Boldyreva
Keyword(s):  
High Pressure ◽  
Ascorbic Acid ◽  
Hydrogen Bonds ◽  
Single Crystal ◽  
Crystal Engineering ◽  
Mixed Crystals ◽  
Study Phase ◽  
X Ray Diffraction ◽  
X Ray ◽  
Wide Range

"Experiments for studying crystalline materials under extreme conditions are a powerful tool for investigating ""structure-property"" relationships. They also give information on the behavior of hydrogen bonds and are important both for materials science and crystal engineering. In addition, many processes in the living organisms are also related to mechanical stress. One of the most interesting tasks is to identify factors which influence the stability of a structure, or a part of the structure, at high pressure. Experiments on the systematic study of compounds in a wide range of pressures allow us to accumulate data that can be used to solve this problem. For a more complete picture, the mixed crystals of the selected compound are studied. Investigation of mixed crystals and cocrystals of interest can be compared with the crystals of individual compounds. We have chosen the structure of L-serine - L-ascorbic acid to be compared with those of L-serine and L-ascorbic acids for such a study. Phase transitions were previously reported to be induced by increasing pressure in both L-serine [1] and L-ascorbic acid [2]; moreover, the structure of L-serine was followed at multiple pressures by single-crystal and powder X-ray diffraction[3]. L-serine – L-ascorbic acid co-crystal was studied in the pressure range 0-5.4 GPa (at multiple points at every 0.5-0.7 GPa) by single-crystal X-ray diffraction and Raman spectroscopy. A phase transition has been detected and some rearrangement in the network of hydrogen bonds was observed. The high pressure data were compared with those for the individual structures of the L-serine and L-ascorbic acid. This work was supported by RFBR (grants 12–03-31541, 14-03-31866, 13-03-92704, 14-03-00902 ), Ministry of Science and Education of Russia and Russian Academy of Sciences."

scholarly journals A high pressure cell for small angle X-ray scattering

1993 ◽  
Vol 03 (C8) ◽  
pp. C8-487-C8-490 ◽  
Author(s):  
M. LORENZEN ◽  
C. RIEKEL ◽  
A. EICHLER ◽  
D. HÄUSSERMANN
Keyword(s):  
High Pressure ◽  
Small Angle ◽  
High Pressure Cell ◽  
X Ray ◽  
Pressure Cell ◽  
X Ray Scattering ◽  
Ray Scattering

Chemical and Biological Evaluation of Thiosemicarbazone-Bearing Heterocyclic Metal Complexes

2020 ◽  
Vol 20 ◽  
Author(s):  
Ana I. Matesanz ◽  
Jorge M. Herrero ◽  
Adoración G. Quiroga
Keyword(s):  
Biological Properties ◽  
Biological Evaluation ◽  
Biological Molecules ◽  
Biological Processes ◽  
Binding Modes ◽  
Future Studies ◽  
Vitamine B12 ◽  
Electronic Delocalization ◽  
Wide Range ◽  
Electronic And Structural Properties

: Thiosemicarbazones (TSCNs) constitute a broad family of compounds (R1R2C=N-NH-C(S)-NR3R4) particularly attractive because many of them display some biological activity against a wide range of microorganisms and cancer cells. Their activity can be related with their electronic and structural properties, which offer a rich set of donor atoms for metal coordination and a high electronic delocalization providing different binding modes for biomolecules. Heterocycles such as pyrrole, imidazole and triazole are present in biological molecules such as Vitamine B12 and amino acids and could potentially target multiple biological processes. Considering this, we have explored the chemistry and biological properties of thiosemicarbazones series and their complexes bearing heterocycles such as pyrrole, imidazole, thiazole and triazole. We focus at the chemistry and cytotoxicity of those derivatives to find out the structure activity relationships, and particularly we analyzed those examples with the TSCN units in which the mechanism of action information has been profoundly studied and pathways determined, to promote future studies for heterocycle derivatives.

Innovative High Gas Pressure Microscopy Chamber Designed for Biological Cell Observation

2016 ◽  
Vol 22 (1) ◽  
pp. 63-70 ◽  
Author(s):  
Mélanie Ragon ◽  
Hue Nguyen Thi Minh ◽  
Stéphane Guyot ◽  
Pauline Loison ◽  
Gaëtan Burgaud ◽  
...  
Keyword(s):  
High Pressure ◽  
Real Time ◽  
Gas Pressure ◽  
Biological Cell ◽  
Liquid Pressure ◽  
Observation Window ◽  
Yeast Strains ◽  
Observation Area ◽  
Wide Range ◽  
Real Time Visualization

AbstractAn original high-pressure microscopy chamber has been designed for real-time visualization of biological cell growth during high isostatic (gas or liquid) pressure treatments up to 200 MPa. This new system is highly flexible allowing cell visualization under a wide range of pressure levels as the thickness and the material of the observation window can be easily adapted. Moreover, the design of the observation area allows different microscope objectives to be used as close as possible to the observation window. This chamber can also be temperature controlled. In this study, the resistance and optical properties of this new high-pressure chamber have been tested and characterized. The use of this new chamber was illustrated by a real-time study of the growth of two different yeast strains – Saccharomyces cerevisiae and Candida viswanathii – under high isostatic gas pressure (30 or 20 MPa, respectively). Using image analysis software, we determined the evolution of the area of colonies as a function of time, and thus calculated colony expansion rates.

A 109Pa high-pressure cell for X-ray and optical measurements. Erratum

1993 ◽  
Vol 26 (4) ◽  
pp. 619-619
Author(s):  
M. Leszczynski ◽  
S. Podlasin ◽  
T. Suski
Keyword(s):  
High Pressure ◽  
Optical Measurements ◽  
High Pressure Cell ◽  
X Ray ◽  
Pressure Cell

Energy Dispersive Diffraction in a Diamond Anvil High Pressure Cell Using Synchrotron and Conventional X-Radiation

1983 ◽  
Vol 27 ◽  
pp. 331-337
Author(s):  
David R. Black ◽  
Carmen S. Menoni ◽  
Ian L. Spain
Keyword(s):  
High Pressure ◽  
Energy Dispersive ◽  
X Rays ◽  
High Pressure Cell ◽  
X Ray ◽  
Detection Techniques ◽  
Wide Range ◽  
Diamond Anvil ◽  
Experimental Geometry ◽  
Energy Dispersive Diffraction

A wide range of structural studies have been carried out in high pressure diamond anvil cells using x-rays. The most common experimental geometry is shown in Fig. 1a. The incident x-ray beam passes axially through the first diamond and enters the sample, typically 100-300 μm in diameter and 20-100 μm thick; the diffracted x-rays exit via the second diamond. Energy-dispersive detection techniques (EDXRD) have been used. However the intensity of diffracted radiation from the sample is weak, so that typical exposure times with a conventional, fixed anode, x-ray source are typically one to several days.Accordingly, higher intensity radiation from synchrotron sources has been used for these experiments.

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