Search results for "molecular-dynamics"
showing 10 items of 33 documents
Negatively Charged Gangliosides Promote Membrane Association of Amphipathic Neurotransmitters
2018
Lipophilic neurotransmitters (NTs) such as dopamine are chemical messengers enabling neurotransmission by adhering onto the extracellular surface of the post-synaptic membrane in a synapse, followed by binding to their receptors. Previous studies have shown that the strength of the NT-membrane association is dependent on the lipid composition of the membrane. Negatively charged lipids such as phosphatidylserine, phosphatidylglycerol, and phosphatidic acid have been indicated to promote NT-membrane binding, however these anionic lipids reside almost exclusively in the intracellular leaflet of the post-synaptic membrane instead of the extracellular leaflet facing the synaptic cleft. Meanwhile…
Post-tilleyite, a dense calcium silicate-carbonate phase
2019
Scientific reports 9(1), 7898 (2019). doi:10.1038/s41598-019-44326-9
Characterization of the interaction of the antifungal and cytotoxic cyclic glycolipopeptide hassallidin with sterol-containing lipid membranes.
2019
Hassallidins are cyclic glycolipopeptides produced by cyanobacteria and other prokaryotes. The hassallidin structure consists of a peptide ring of eight amino acids where a fatty acid chain, additional amino acids, and sugar moieties are attached. Hassallidins show antifungal activity against several opportunistic human pathogenic fungi, but does not harbor antibacterial effects. However, they have not been studied on mammalian cells, and the mechanism of action is unknown. We purified hassallidin D from cultured cyanobacterium Anabaena sp. UHCC 0258 and characterized its effect on mammalian and fungal cells. Ultrastructural analysis showed that hassallidin D disrupts cell membranes, causin…
Chemical Identification at the Solid–Liquid Interface
2017
Solid-liquid interfaces are decisive for a wide range of natural and technological processes, including fields as diverse as geochemistry and environmental science as well as catalysis and corrosion protection. Dynamic atomic force microscopy nowadays provides unparalleled structural insights into solid-liquid interfaces, including the solvation structure above the surface. In contrast, chemical identification of individual interfacial atoms still remains a considerable challenge. So far, an identification of chemically alike atoms in a surface alloy has only been demonstrated under well-controlled ultrahigh vacuum conditions. In liquids, the recent advent of three-dimensional force mapping…
Tracking Ca2+ ATPase intermediates in real time by x-ray solution scattering
2020
Sarco/endoplasmic reticulum Ca2+ ATPase (SERCA) transporters regulate calcium signaling by active calcium ion reuptake to internal stores. Structural transitions associated with transport have been characterized by x-ray crystallography, but critical intermediates involved in the accessibility switch across the membrane are missing. We combined time-resolved x-ray solution scattering (TR-XSS) experiments and molecular dynamics (MD) simulations for real-time tracking of concerted SERCA reaction cycle dynamics in the native membrane. The equilibrium [Ca2] E1 state before laser activation differed in the domain arrangement compared with crystal structures, and following laser-induced release o…
Assessment of the Potential Energy Hypersurfaces in Thymine within Multiconfigurational Theory: CASSCF vs. CASPT2
2016
The present study provides new insights into the topography of the potential energy hypersurfaces (PEHs) of the thymine nucleobase in order to rationalize its main ultrafast photochemical decay paths by employing two methodologies based on the complete active space self-consistent field (CASSCF) and the complete active space second-order perturbation theory (CASPT2) methods: (i) CASSCF optimized structures and energies corrected with the CASPT2 method at the CASSCF geometries and (ii) CASPT2 optimized geometries and energies. A direct comparison between these strategies is drawn, yielding qualitatively similar results within a static framework. A number of analyses are performed to assess t…
Structural, vibrational and electrical study of compressed BiTeBr
2016
Compresed BiTeBr has been studied from a joint experimental and theoretical perspective. Room-temperature x-ray diffraction, Raman scattering, and transport measurements at high pressures have been performed in this layered semiconductor and interpreted with the help of ab initio calculations. A reversible first-order phase transition has been observed above 6–7 GPa, but changes in structural, vibrational, and electrical properties have also been noted near 2 GPa. Structural and vibrational changes are likely due to the hardening of interlayer forces rather than to a second-order isostructural phase transition while electrical changes are mainly attributed to changes in the electron mobilit…
Journeys from quantum optics to quantum technology
2017
Sir Peter Knight is a pioneer in quantum optics which has now grown to an important branch of modern physics to study the foundations and applications of quantum physics. He is leading an effort to develop new technologies from quantum mechanics. In this collection of essays, we recall the time we were working with him as a postdoc or a PhD student and look at how the time with him has influenced our research.
High-pressure structural and elastic properties of Tl2O3
2014
The structural properties of Thallium (III) oxide (Tl2O3) have been studied both experimentally and theoretically under compression at room temperature. X-ray powder diffraction measurements up to 37.7 GPa have been complemented with ab initio total-energy calculations. The equation of state of Tl2O3 has been determined and compared to related compounds. It has been found experimentally that Tl2O3 remains in its initial cubic bixbyite-type structure up to 22.0 GPa. At this pressure, the onset of amorphization is observed, being the sample fully amorphous at 25.2 GPa. The sample retains the amorphous state after pressure release. To understand the pressure-induced amorphization process, we h…
Membrane Structure of Aquaporin Observed with Combined Experimental and Theoretical Sum Frequency Generation Spectroscopy
2021
High-resolution structural information on membrane proteins is essential for understanding cell biology and for the structure-based design of new medical drugs and drug delivery strategies. X-ray diffraction (XRD) can provide angstrom-level information about the structure of membrane proteins, yet for XRD experiments, proteins are removed from their native membrane environment, chemically stabilized, and crystallized, all of which can compromise the conformation. Here, we describe how a combination of surface-sensitive vibrational spectroscopy and molecular dynamics simulations can account for the native membrane environment. We observe the structure of a glycerol facilitator channel (GlpF)…