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DDC: 540 × Subject: Molecular Dynamics Simulation ×

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Now showing 1 - 3 of 3
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    Water Dynamics in the Hydration Shells of Biomolecules
    (Washington, DC : ACS Publ., 2017) Laage, Damien; Elsaesser, Thomas; Hynes, James T.
    The structure and function of biomolecules are strongly influenced by their hydration shells. Structural fluctuations and molecular excitations of hydrating water molecules cover a broad range in space and time, from individual water molecules to larger pools and from femtosecond to microsecond time scales. Recent progress in theory and molecular dynamics simulations as well as in ultrafast vibrational spectroscopy has led to new and detailed insight into fluctuations of water structure, elementary water motions, electric fields at hydrated biointerfaces, and processes of vibrational relaxation and energy dissipation. Here, we review recent advances in both theory and experiment, focusing on hydrated DNA, proteins, and phospholipids, and compare dynamics in the hydration shells to bulk water.
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    Excited-state relaxation of hydrated thymine and thymidine measured by liquid-jet photoelectron spectroscopy: experiment and simulation
    (Washington, DC : ACS Publications, 2015) Buchner, Franziska; Nakayama, Akira; Yamazaki, Shohei; Ritze, Hans-Hermann; Lübcke, Andrea
    Time-resolved photoelectron spectroscopy is performed on thymine and thymidine in aqueous solution to study the excited-state relaxation dynamics of these molecules. We find two contributions with sub-ps lifetimes in line with recent excited-state QM/MM molecular dynamics simulations (J. Chem. Phys.2013, 139, 214304). The temporal evolution of ionization energies for the excited ππ* state along the QM/MM molecular dynamics trajectories were calculated and are compatible with experimental results, where the two contributions correspond to the relaxation paths in the ππ* state involving different conical intersections with the ground state. Theoretical calculations also show that ionization from the nπ* state is possible at the given photon energies, but we have not found any experimental indication for signal from the nπ* state. In contrast to currently accepted relaxation mechanisms, we suggest that the nπ* state is not involved in the relaxation process of thymine in aqueous solution.
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    The influence of the Δk280 mutation and N- or C-terminal extensions on the structure, dynamics, and fibril morphology of the tau R2 repeat
    (London [u.a.] : Royal Society of Chemistry, 2014) Raz, Y.; Adler, J.; Vogel, A.; Scheidt, H.A.; Häupl, T.; Abel, B.; Huster, D.; Miller, Y.
    Tau is a microtubule-associated protein and is involved in microtubule assembly and stabilization. It consists of four repeats that bind to the microtubule. The ΔK280 deletion mutation in the tau R2 repeat region is directly associated with the development of the frontotemporal dementia parkinsonism linked to chromosome 17 (FTDP-17). This deletion mutation is known to accelerate tau R2 repeat aggregation. However, the secondary and the tertiary structures of the self-assembled ΔK280 tau R2 repeat mutant aggregates are still controversial. Moreover, it is unclear whether extensions by one residue in the N- or the C-terminus of this mutant can influence the secondary or the tertiary structure. Herein, we combine solid-state NMR, atomic force microscopy, electron microscopy and all-atom explicit molecular dynamics simulations to investigate the effects of the deletion mutation and the N- and the C-terminal extension of this mutant on the structure. Our main findings show that the deletion mutation induces the formation of small aggregates, such as oligomers, and reduces the formation of fibrils. However, the extensions in the N- or the C-terminus revealed more fibril formation than small aggregates. Further, in the deletion mutation only one structure is preferred, while the N- and the C-terminal extensions strongly lead to polymorphic states. Finally, our broad and combined experimental and computational techniques provide direct structural information regarding ΔK280 tau R2 repeat mutant aggregates and their extensions in the N- and C-terminii by one residue.