Influence of the Compatible Solute Ectoine on the Local Water Structure: Implications for the Binding of the Protein G5P to DNA

Abstract

Microorganisms accumulate molar concentrations of compatible solutes like ectoine to prevent proteins from denaturation. Direct structural or spectroscopic information on the mechanism and about the hydration shell around ectoine are scarce. We combined surface plasmon resonance (SPR), confocal Raman spectroscopy, molecular dynamics simulations, and density functional theory (DFT) calculations to study the local hydration shell around ectoine and its influence on the binding of a gene-5-protein (G5P) to a single-stranded DNA (dT25). Due to the very high hygroscopicity of ectoine, it was possible to analyze the highly stable hydration shell by confocal Raman spectroscopy. Corresponding molecular dynamics simulation results revealed a significant change of the water dielectric constant in the presence of a high molar ectoine concentration as compared to pure water. The SPR data showed that the amount of protein bound to DNA decreases in the presence of ectoine, and hence, the protein-DNA dissociation constant increases in a concentration-dependent manner. Concomitantly, the Raman spectra in terms of the amide I region revealed large changes in the protein secondary structure. Our results indicate that ectoine strongly affects the molecular recognition between the protein and the oligonucleotide, which has important consequences for osmotic regulation mechanisms.

DNA protection by ectoine from ionizing radiation: molecular mechanisms

“…36 Ectoine is known to be expelled from the first hydration shell of charged surfaces and biomolecules. 6,7,11 However, its presence in solution will inevitably decrease the amount of water around DNA in the biologically relevant target volume of 10-15 nm diameter. 20,37 Therefore, ectoine may act as a protective agent by passively displacing water from the surroundings of the DNA.…”

“…3) in the solid 4 state and in water, 5 exerts a kosmotropic effect on the local water structure [5][6][7][8] as well as an influence on protein functions. 7,[9][10][11] Moreover, various studies [12][13][14] investigated the effects of ectoine on biological damage caused by ultraviolet radiation (UV) of various wavelengths. The study by Bünger et al 13 found that UV-A (340-400 nm) irradiated human keratinocytes show a decrease in mitochondrial DNA mutations for cells pretreated with ectoine.…”

Stabilizing effect of TMAO on globular PNIPAM states: preferential attraction induces preferential hydration

“…33 Although being attractive due to its simplicity, recent articles demonstrated the limitations of this concept in terms of concentration dependent binding effects for denaturants 15,31,34 or well-known protein protectants that indeed induce denaturation. 35,36 Henceforth, the chemical properties of solutes and osmolytes have to be studied in more detail for a deeper understanding of the resulting accumulation behavior. [37][38][39][40] The properties of osmolytes and their influence on PNIPAM were already discussed in a series of publications.…”

Ectoine: a compatible solute in radio‐halophilicStenotrophomonassp.WMA‐LM19 strain to prevent ultraviolet‐induced protein damage

“…Halomonas elongata , an ectoine‐producing strain, has widely been studied, and recycled to develop the fermentation technology at large scale (Hahn et al . ). Optimal production of ectoines was conditioned by the interplay of carbon and nitrogen metabolism.…”