Molecular dynamics simulations of microstructure and mixing dynamics of cryoprotective solvents in water and in the presence of a lipid membrane

Kyrychenko, Alexander; Dyubko, T. S.

doi:10.1016/j.bpc.2008.04.004

Cited by 31 publications

(27 citation statements)

References 64 publications

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“…The two conformations are likely similar to those seen in the crystalline state for POPC and DMPC based on the similar chemical shifts (Bruzik and Harwood, 1997; Nomura et al, 2011). The interfacial location of cryoprotectants is consistent with X-ray diffraction data (Yu and Quinn, 2000) and molecular dynamics simulations of DMSO-bound membranes (Kyrychenko and Dyubko, 2008). At this interfacial location, the polar groups of cryoprotectants can form hydrogen bonds with the lipid headgroup and backbone, thus locking lipids into a small number of conformations.…”

Section: Discussionsupporting

confidence: 74%

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Cryoprotection of lipid membranes for high-resolution solid-state NMR studies of membrane peptides and proteins at low temperature

Lee

Hong

2014

J Biomol NMR

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Solid-state NMR spectra of membrane proteins often show significant line broadening at cryogenic temperatures. Here we investigate the effects of several cryoprotectants to preserve the spectral resolution of lipid membranes and membrane peptides at temperatures down to ~200 K. Trehalose, glycerol, dimethylsulfoxide (DMSO), dimethylformamide (DMF), and polyethylene glycol (PEG), were chosen. These compounds are commonly used in protein crystallography and cryobiology. 13C and 1H MAS spectra of several types of lipid membranes show that DMSO provides the best resolution enhancement over unprotected membranes and also best retards ice formation at low temperature. DMF and PEG-400 show slightly weaker cryoprotection, while glycerol and trehalose neither prevent membrane line broadening nor prevent ice formation under the conditions of our study. Neutral saturated-chain phospholipids are the most amenable to cryoprotection, whereas negatively charged and unsaturated lipids attenuate cryoprotection. 13C-1H dipolar couplings and 31P chemical shift anisotropies indicate that high spectral resolution at low temperature is correlated with stronger immobilization of the lipids at high temperature, indicating that line narrowing results from reduction of the conformational space sampled by the lipid molecules at high temperature. DMSO selectively narrowed the linewidths of the most disordered residues in the influenza M2 transmembrane peptide, while residues that exhibit narrow linewidths in the unprotected membrane are less impacted. A relatively rigid β-hairpin antimicrobial peptide, PG-1, showed a linewidth increase of ~0.5 ppm over a ~70 K temperature drop both with and without cryoprotection. Finally, a short-chain saturated lipid, DLPE, exhibits excellent linewidths, suggesting that it may be a good medium for membrane protein structure determination. The three best cryoprotectants found in this work – DMSO, PEG, and DMF - should be useful for low-temperature membrane-protein structural studies by SSNMR without compromising spectral resolution.

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Section: Discussionsupporting

confidence: 74%

“…This is consistent with the trend of freezing-point depression by these compounds. Molecular dynamics simulations indicate that cryoprotectants with similarly high water miscibility can have different molecular interactions with water: DMSO equilibrates with water much faster than glycerol and ethylene glycol (Kyrychenko and Dyubko, 2008). …”

Section: Discussionmentioning

confidence: 99%

Cryoprotection of lipid membranes for high-resolution solid-state NMR studies of membrane peptides and proteins at low temperature

Lee

Hong

2014

J Biomol NMR

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“…Alcohol molecules were uniformly distributed in the water boxes in order to reduce the mixing time of the alcohol clusters. 18 After completing the system construction, a short time of 2 ps was conducted to minimize the energy of the binary mixture and then a run for 4.0 ns was carried out to fully equilibrate the system.…”

Section: Model and Methodologymentioning

confidence: 99%

Molecular Dynamics Investigation of the Effects of Concentration on Hydrogen Bonding in Aqueous Solutions of Methanol, Ethylene Glycol and Glycerol

Zhang¹,

Li²,

Chen³

et al. 2013

Bulletin of the Korean Chemical Society

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Hydrogen bonding interaction between alcohols and water molecules is an important characteristic in the aqueous solutions of alcohols. In this paper, a series of molecular dynamics simulations have been performed to investigate the aqueous solutions of low molecular weight alcohols (methanol, ethylene glycol and glycerol) at the concentrations covering a broad range from 1 to 90 mol %. The work focuses on studying the effect of the alcohols molecules on the hydrogen bonding of water molecules in binary mixtures. By analyzing the hydrogen bonding ability of the hydroxyl (-OH) groups for the three alcohols, it is found that the hydroxyl group of methanol prefers to form more hydrogen bonds than that of ethylene glycol and glycerol due to the intra-and intermolecular effects. It is also shown that concentration has significant effect on the ability of alcohol molecule to hydrogen bond water molecules. Understanding the hydrogen bonding characteristics of the aqueous solutions is helpful to reveal the cryoprotective mechanisms of methanol, ethylene glycol and glycerol in aqueous solutions.

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“…The potency of CPAs mainly depends upon their probable 47 parameters like the number and spatial arrangement of \OH groups, 48 molecular weight, rate and ability of penetration across the cell mem- 49 brane, most populated, and predominant and stable conformations in 50 aqueous environment [15]. These potential parameters play an impor- 51 tant role in employing the CPAs at freezing temperature in long-term 52 storage of biomaterials and stabilization of biological macromolecules.…”

mentioning

confidence: 99%

“…■ DEG-water hydrogen bonding interaction study is a prototype 467 model to investigate the hydrophilic interaction of diethylene glycol 468 molecules particularly in dominant conformations (g − g + t-tg − t, 469 g + g + t-tg − g + , g − g + t-tg − g − and g + g + t-tg − t) across a 470 palmitoyloleoylphosphatidylcholine (POPC) lipid bilayer through 471 MD studies [51]. Calculated (g − g + t-tg − t-monomer in gas phase and g − g + t-tg − t-(water) 5 in solvation phase) and available experimental (DEG and DEG in water-1.0 m) vibrational frequencies t4:3 (in cm −1 ).…”

mentioning

confidence: 99%

Ultrasonic, DFT and FT-IR studies on hydrogen bonding interactions in aqueous solutions of diethylene glycol

Raman

Kesavan

Senthilkumar

et al. 2015

Journal of Molecular Liquids

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Molecular dynamics simulations of microstructure and mixing dynamics of cryoprotective solvents in water and in the presence of a lipid membrane

Cited by 31 publications

References 64 publications

Cryoprotection of lipid membranes for high-resolution solid-state NMR studies of membrane peptides and proteins at low temperature

Cryoprotection of lipid membranes for high-resolution solid-state NMR studies of membrane peptides and proteins at low temperature

Molecular Dynamics Investigation of the Effects of Concentration on Hydrogen Bonding in Aqueous Solutions of Methanol, Ethylene Glycol and Glycerol

Ultrasonic, DFT and FT-IR studies on hydrogen bonding interactions in aqueous solutions of diethylene glycol

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