TY  - JOUR
A1  - Oprzeska-Zingrebe, Ewa Anna
A1  - Meyer, Susann
A1  - Roloff, Alexander
A1  - Kunte, Hans-Jörg
A1  - Smiatek, Jens
T1  - Influence of compatible solute ectoine on distinct DNA structures
BT  - thermodynamic insights into molecular binding mechanisms and destabilization effects
JF  - Physical chemistry, chemical physics : a journal of European Chemical Societies
N2  - In nature, the cellular environment of DNA includes not only water and ions, but also other components and co-solutes, which can exert both stabilizing and destabilizing effects on particular oligonucleotide conformations. Among them, ectoine, known as an important osmoprotectant organic co-solute in a broad range of pharmaceutical products, turns out to be of particular relevance. In this article, we study the influence of ectoine on a short single-stranded DNA fragment and on double-stranded helical B-DNA in aqueous solution by means of atomistic molecular dynamics (MD) simulations in combination with molecular theories of solution. Our results demonstrate a conformation-dependent binding behavior of ectoine, which favors the unfolded state of DNA by a combination of electrostatic and dispersion interactions. In conjunction with the Kirkwood-Buff theory, we introduce a simple framework to compute the influence of ectoine on the DNA melting temperature. Our findings reveal a significant linear decrease of the melting temperature with increasing ectoine concentration, which is found to be in qualitative agreement with results from denaturation experiments. The outcomes of our computer simulations provide a detailed mechanistic rationale for the surprising destabilizing influence of ectoine on distinct DNA structures.
Y1  - 2018
U6  - https://doi.org/10.1039/c8cp03543a
SN  - 1463-9076
SN  - 1463-9084
VL  - 20
IS  - 40
SP  - 25861
EP  - 25874
PB  - Royal Society of Chemistry
CY  - Cambridge
ER  - 
TY  - JOUR
A1  - Hahn, Marc Benjamin
A1  - Solomun, Tihomir
A1  - Wellhausen, Robert
A1  - Hermann, Sabrina
A1  - Seitz, Harald
A1  - Meyer, Susann
A1  - Kunte, Hans-Jörg
A1  - Zeman, Johannes
A1  - Uhlig, Frank
A1  - Smiatek, Jens
A1  - Sturm, Heinz
T1  - Influence of the Compatible Solute Ectoine on the Local Water Structure: Implications for the Binding of the Protein G5P to DNA
JF  - The journal of physical chemistry : B, Condensed matter, materials, surfaces, interfaces & biophysical chemistry
N2  - 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-S-protein (G5P) to a single-stranded DNA (dT(25)). 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 oligonudeotide, which has important consequences for osmotic regulation mechanisms.
Y1  - 2015
U6  - https://doi.org/10.1021/acs.jpcb.5b09506
SN  - 1520-6106
VL  - 119
IS  - 49
SP  - 15212
EP  - 15220
PB  - American Chemical Society
CY  - Washington
ER  - 
TY  - JOUR
A1  - Niskanen, Johannes
A1  - Sahle, Christoph J.
A1  - Gilmore, Keith
A1  - Uhlig, Frank
A1  - Smiatek, Jens
A1  - Föhlisch, Alexander
T1  - Disentangling structural information from core-level excitation spectra
JF  - Physical review : E, Statistical, nonlinear and soft matter physics
N2  - Core-level spectra of liquids can be difficult to interpret due to the presence of a range of local environments. We present computational methods for investigating core-level spectra based on the idea that both local structural parameters and the x-ray spectra behave as functions of the local atomic configuration around the absorbing site. We identify correlations between structural parameters and spectral intensities in defined regions of interest, using the oxygen K-edge excitation spectrum of liquid water as a test case. Our results show that this kind of analysis can find the main structure-spectral relationships of ice, liquid water, and supercritical water.
Y1  - 2017
U6  - https://doi.org/10.1103/PhysRevE.96.013319
SN  - 2470-0045
SN  - 2470-0053
VL  - 96
PB  - American Physical Society
CY  - College Park
ER  -