Unveiling the pathway to Z-DNA in the protein-induced B–Z transition

Left-handed Z-DNA is an extraordinary conformation of DNA, which can form by special sequences under specific biological, chemical or physical conditions. Human ADAR1, prototypic Z-DNA binding protein (ZBP), binds to Z-DNA with high affinity. Utilizing single-molecule FRET assays for Z-DNA forming sequences embedded in a long inactive DNA, we measure thermodynamic populations of ADAR1-bound DNA conformations in both GC and TG repeat sequences. Based on a statistical physics model, we determined quantitatively the affinities of ADAR1 to both Z-form and B-form of these sequences. We also reported what pathways it takes to induce the B–Z transition in those sequences. Due to the high junction energy, an intermediate B* state has to accumulate prior to the B–Z transition. Our study showing the stable B* state supports the active picture for the protein-induced B–Z transition that occurs under a physiological setting. (c)The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research

Two-Dimensional Infrared Spectroscopy and Molecular Dynamics Simulation Studies of Nonaqueous Lithium Ion Battery Electrolytes

Lithium ion battery (LIB) technology is undoubtedly indispensable to modern life. However, despite enormous and extended effort to improve LIB performance, our understanding of the underlying principles and mechanisms of lithium ion transport in nonaqueous LIB electrolytes remained limited until recently. There is a particular lack of knowledge of the microscopic solvation structures and fluctuation dynamics around charge carriers in real electrolytes. Typical electrolytes found in commercially available LIBs consist of lithium salts and mixed carbonate solvents, with the latter playing an essential role in promoting lithium ion transport and forming an electrically stable solid electrolyte interphase. Although a number of linear spectroscopic studies of LIB electrolytes aiming at understanding the complex nature of lithium ion solvation processes have been reported, the notion that each lithium ion is strongly solvated by carbonate molecules to form a long-lasting solvation sheath structure has remained the subject of intense debate. Here, we present the results of FTIR, fs IR pump-probe, two-dimensional IR spectroscopy, and molecular dynamics simulations reported by us and others and discuss the possible interplay of picosecond solvation dynamics and macroscopic ion transport processes within the framework of the fluctuation-dissipation relationship. Further, by measuring the time-dependent fluctuations and spectral diffusions of carbonate carbonyl stretch modes that act as excellent infrared probes for the local electrostatic environment, we show that lithium cations are not only solvated by carbonate molecules but also interact with counteranions at equilibrium depending on solvent composition. Molecular dynamics simulations support the notion that rapid chemical exchanges between carbonate solvent molecules in the first and outer solvation shells are critical for describing mobile lithium ion transport phenomena. We thus anticipate that time-resolved coherent multidimensional vibrational spectroscopy is capable of providing decisive evidence on the ultrafast solvent dynamics of various electrolytes, which is potentially helpful for designing improved and more efficient LIB electrolytes in the future. © 2019 American Chemical Societ

Vibrational Lifetime of the SCN Protein Label in H2O and D2O Reports Site-Specific Solvation and Structure Changes during PYP's Photocycle

© 2019 American Chemical Society.The application of vibrational labels such as thiocyanate »(-S-CN) for studying protein structure and dynamics is thriving. Absorption spectroscopy is usually employed to obtain wavenumber and line shape of the label. An observable of great significance might be the vibrational lifetime, which can be obtained by pump probe or 2D-IR spectroscopy. Due to the insulating effect of the heavy sulfur atom in the case of the SCN label, the lifetime of the CN oscillator is expected to be particularly sensitive to its surrounding as it is not dominated by through-bond relaxation. We therefore investigate the vibrational lifetime of the SCN label at various positions in the blue light sensor protein Photoactive Yellow Protein (PYP) in the ground state and signaling state of the photoreceptor. We find that the vibrational lifetime of the CN stretching mode is strongly affected both by its protein environment and by the degree of exposure to the solvent. Even for label positions where the line shape and wavenumber observed by FTIR are barely changing upon activation of the photoreceptor, we find that the lifetime can change considerably. To obtain an unambiguous measure for the solvent exposure of the labeled site, we show that it is imperative to compare the lifetimes in H2O and D2O. Importantly, the lifetimes shorten in H2O as compared to D2O for water exposed labels, while they stay largely the same for buried labels. We quantify this effect by defining a solvent exclusion coefficient (SEC). The response of the label's vibrational lifetime to its solvent exposure renders it a suitable universal probe for protein investigations. This applies even to systems that are otherwise hard to address, such as transient or short-lived states, which could be created during a protein's working cycle (as here in PYP) or during protein folding. It is also applicable to flexible systems (intrinsically disordered proteins), protein-protein and protein-membrane interaction

Selective suppression of CARS signal with two competing stimulated Raman scattering processes

Coherent anti-Stokes Raman scattering (CARS) spectroscopy and microscopy have been used in studying the structure and dynamics of a wide range of chemical and biological systems. However, the spatial resolution of CARS microscopy is still limited by the diffraction barrier, and hence a suitable scheme to selectively switch off the CARS imaging signal is essential for super-resolution CARS microscopy. Here, we present theoretical descriptions about three different ways to selectively suppress the pump-Stokes-pump two-beam CARS signal by employing three-beam double stimulated Raman scattering (SRS) schemes. Using a semiclassical theory for the interaction of radiation with the Raman-active molecule, we obtain coupled differential equations for the intensities of the pump, Stokes, depletion, and the generated CARS signal fields. We find approximate solutions of these coupled differential equations. They are then used to show that the pump-Stokes-pump CARS signal can be selectively suppressed by increasing the added depletion beam intensity, when the three injected beam frequencies are tuned in such a way that they can induce two SRS processes simultaneously. To show that these switching-off methods can be used to develop super-resolution CARS imaging techniques, we numerically calculate the full-width-at-half-maximum of the CARS imaging point spread function assuming that the spatial profiles of the pump and Stokes beams are Gaussian functions and that the spatial profile of the depletion beam is doughnut-shaped. We anticipate that the proposed selective CARS suppression schemes will be of use in developing super-resolution, label-free CARS microscopy. ? 2018 Author(s