scholarly journals Thermal contraction of aqueous glycerol and ethylene glycol solutions for optimized protein-crystal cryoprotection

2016 ◽  
Vol 72 (6) ◽  
pp. 742-752 ◽  
Author(s):  
Chen Shen ◽  
Ethan F. Julius ◽  
Timothy J. Tyree ◽  
David W. Moreau ◽  
Hakan Atakisi ◽  
...  

The thermal contraction of aqueous cryoprotectant solutions on cooling to cryogenic temperatures is of practical importance in protein cryocrystallography and in biological cryopreservation. In the former case, differential contraction on cooling of protein molecules and their lattice relative to that of the internal and surrounding solvent may lead to crystal damage and the degradation of crystal diffraction properties. Here, the amorphous phase densities of aqueous solutions of glycerol and ethylene glycol atT= 77 K have been determined. Densities with accuracies of <0.5% to concentrations as low as 30%(w/v) were determined by rapidly cooling drops with volumes as small as 70 pl, assessing their optical clarity and measuring their buoyancy in liquid nitrogen–argon solutions. The use of these densities in contraction matching of internal solvent to the available solvent spaces is complicated by several factors, most notably the exclusion of cryoprotectants from protein hydration shells and the expected deviation of the contraction behavior of hydration water from bulk water. The present methods and results will assist in developing rational approaches to cryoprotection and an understanding of solvent behavior in protein crystals.

2012 ◽  
Vol 24 (6) ◽  
pp. 064103 ◽  
Author(s):  
Francesco Mallamace ◽  
Carmelo Corsaro ◽  
Piero Baglioni ◽  
Emiliano Fratini ◽  
Sow-Hsin Chen

1979 ◽  
Vol 34 (12) ◽  
pp. 1424-1435 ◽  
Author(s):  
P. Bopp ◽  
W. Dietz ◽  
K. Heinzinger

Abstract The central force model for water has been employed in a molecular dynamics simulation of a 2.2 molal NaCl solution. The structural properties of the solution obtained are compared with results of previous simulations where the ST2 model of water was used. Preliminary results on the influence of the ions on the water molecule geometry in the hydration shells are reported. The spectral densities calculated from the hydrogen velocity autocorrelation functions by Fourier transformation indicate differences in the librational and vibrational frequencies between bulk water and hydration water of Na+ and Cl-.


2021 ◽  
Vol 9 ◽  
Author(s):  
Hiroshi Nakagawa ◽  
Taro Tamada

Protein hydration is crucial for the stability and molecular recognition of a protein. Water molecules form a hydration water network on a protein surface via hydrogen bonds. This study examined the hydration structure and hydrogen bonding state of a protein, staphylococcal nuclease, at various hydration levels in its crystalline state by all-atom molecular dynamics (MD) simulation. Hydrophilic residues were more hydrated than hydrophobic residues. As the water content increases, both types of residues were uniformly more hydrated. The number of hydrogen bonds per single water asymptotically approaches 4, the same as bulk water. The distances and angles of hydrogen bonds in hydration water in the protein crystal were almost the same as those in the tetrahedral structure of bulk water regardless of the hydration level. The hydrogen bond structure of hydration water observed by MD simulations of the protein crystalline state was compared to the Hydrogen and Hydration Database for Biomolecule from experimental protein crystals.


2010 ◽  
Vol 43 (2) ◽  
pp. 341-346 ◽  
Author(s):  
Yu Kitago ◽  
Nobuhisa Watanabe ◽  
Isao Tanaka

Use of longer-wavelength X-rays has advantages for the detection of small anomalous signals from light atoms, such as sulfur, in protein molecules. However, the accuracy of the measured diffraction data decreases at longer wavelengths because of the greater X-ray absorption. The capillary-top mounting method (formerly the loopless mounting method) makes it possible to eliminate frozen solution around the protein crystal and reduces systematic errors in the evaluation of small anomalous differences. However, use of this method requires custom-made tools and a large amount of skill. Here, the development of a device that can freeze the protein crystal semi-automatically using the capillary-top mounting method is described. This device can pick up the protein crystal from the crystallization drop using a micro-manipulator, and further procedures, such as withdrawal of the solution around the crystal by suction and subsequent flash freezing of the protein crystal, are carried out automatically. This device makes it easy for structural biologists to use the capillary-top mounting method for sulfur single-wavelength anomalous diffraction phasing using longer-wavelength X-rays.


2014 ◽  
Vol 90 (4) ◽  
Author(s):  
Zhe Wang ◽  
Emiliano Fratini ◽  
Mingda Li ◽  
Peisi Le ◽  
Eugene Mamontov ◽  
...  

1969 ◽  
Vol 24 (10) ◽  
pp. 1502-1511
Author(s):  
Karl Heinzinger

Abstract There are two kinds of water in CuSO4·5H2O differing by their binding in the crystal. The oxygen of four water molecules is bonded to the copper ion, that of the fifth molecule is hydrogen bonded. It is shown that the D/H ratios of these two kinds of water differ by 5.7%, the light isotope being enriched in the water molecules coordinated with the copper ion. The results show that there is no exchange of the hydrogen isotopes during the time needed for dehydration at room temperature which takes several days. The assumption has been confirmed that the water coordinated with the copper ion leaves the crystal first on dehydration at temperatures below 50 °C. Additional measurements of the separation factor for the hydrogen isotopes between water vapor and copper sulfate solutions allow conclusions on the fractionation of the hydrogen isotopes between bulk water and hydration water in aqueous solutions.


1973 ◽  
Vol 28 (2) ◽  
pp. 137-141 ◽  
Author(s):  
D. Götz ◽  
K. Heinzinger

The fractionation of the oxygen isotopes in solutions of LiCl, NaCl. KCl, KBr, KJ and CsCl with H2O and D2O as solvent has been measured at 25 °C by means of the CO2-equilibration technique. As opposed to earlier measurements a slight anion dependence for the potassium halides has been found in H2O. This anion effect is much more pronounced in D2O. It even leads to a change in the directions of the 180 enrichment between cationic hydration water and bulk water for KCl and KBr. The absolute values of the fractionation factors for LiCl and CsCl, which differ in sign in H2O in agreement with positive and negative cationic hydration, respectively, as known from other kinds of measurements, is increased for LiCl and decreased for CsCl in D2O. There is no fractionation of the oxygen isotopes between hydration water and bulk water in both solvents for NaCl.The solvent isotope effect is explained by the stronger anion influence on the structure of the bulk water in D2O as compared with H2O. This stronger influence is expected because of the higher structural order in D2O than in H2O at the same temperature.


ChemPhysChem ◽  
2006 ◽  
Vol 7 (10) ◽  
pp. 2126-2133 ◽  
Author(s):  
Irena Danielewicz-Ferchmin ◽  
Ewa M. Banachowicz ◽  
A. Ryszard Ferchmin

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