Atomic Resolution Insight into Sac7d Protein Binding to DNA and Associated Global Changes by Molecular Dynamics Simulations

Sac7d is a small, thermostable protein that induces large helical deformations in DNA upon association. Starting from multiple initial placements of the unbound Sac7d structure relative to a B‐DNA oligonucleotide, molecular dynamics (MD) simulations were employed to directly follow several successful binding events at atomic resolution that resulted in structures in close agreement with the native complex geometry. The final native complex formed rapidly within tenths of nanoseconds and included simultaneous large‐scale kinking, groove opening, twisting, and intercalation in the target DNA. The simulations indicate that the complex formation process involves initial non‐native contacts that helped in reaching the final bound state, with residues intercalated at the center of the kinked DNA. It was also possible to identify several long‐lived trapped intermediate states of the binding process and to follow sliding processes of Sac7d along the DNA minor groove.     

On the limit Sobolev regularity for Dirichlet and Neumann problems on Lipschitz domains

We construct a bounded C¹ domain Ω in for which the regularity for the Dirichlet and Neumann problems for the Laplacian cannot be improved, that is, there exists f in such that the solution of in Ω and either on or on is contained in but not in for any . An analogous result holds for Sobolev spaces with .     

The length and depth of algebraic groups

Mathematische Zeitschrift - Let G be a connected algebraic group. An unrefinable chain of G is a chain of subgroups $$G = G_0> G_1> \cdots > G_t = 1$$ , where each $$G_i$$ is a...     

Emergent biaxiality in nematic microflows illuminated by a laser beam

Anisotropic fluids (e.g. liquid crystals) offer a remarkable promise as optofluidic materials owing to the directional, tunable, and coupled interactions between the material, flow, and the optical fields. Here we present a comprehensive in silico treatment of this anisotropic interaction by performing nonequilibrium molecular dynamics simulations. We quantify the response of a nematic liquid crystal (NLC) undergoing a Poiseuille flow in the Stokes regime, while being illuminated by a laser beam incident perpendicular to the flow direction. We adopt a minimalistic model to capture the interactions, accounting for two features: first, the laser heats up the NLC locally; and second, the laser polarises the NLC and exerts an optical torque that tends to reorient molecules of the nematic phase. Because of this reorientation the liquid crystal exhibits small regions of biaxiality, where the nematic director is one symmetry axis and the axis of rotation for the reorientation of the molecules is the other one. We find that the relative strength of the viscous and the optical torques mediates the flow-induced response of the biaxial regions, thereby tuning the emergence, shape and location of the regions of enhanced biaxiality. The mechanistic framework presented here promises experimentally tractable routes toward novel optofluidic applications based on material-flow-light interactions.     

Water Docking Bias in [4]Helicene

We report on the one‐ and two‐water clusters of [4]helicene, the smallest polycyclic aromatic hydrocarbon with a helical sense, which were captured in the gas phase using high‐resolution rotational spectroscopy. The structures of the complexes are unambiguously revealed using microwave spectra of isotopically enriched species. In the one‐water cluster, the apparent splitting pattern is consistent with a tunneling motion that encompasses an exchange of strongly and weakly bonded water hydrogens. This motion is “locked” in the two‐water cluster. The relevant intermolecular contacts, symmetry, and aromaticity effects are unveiled for the microsolvated chiral topologies. These observations entail the first glance at the structures and internal dynamics of the water binding motifs of a chiral polycyclic aromatic hydrocarbon.     

W-shaped mesogens and variations of their molecular structure

New bent-core liquid crystalline dimers with W-shaped molecular geometry have been prepared and studied. We have modified the dimer shape by variation of the connecting part between two bent-core units and changing the terminal chains (perfluoroalkyl, siloxanealkyl). Additionally, we have altered the inner bend angle value (120°, 60° and 148°) by utilization of different aromatic units. Mesomorphic properties of new dimers were established based on the texture observation in the polarizing microscope and DSC measurements. Moreover, x-ray structural analysis has been performed for selected dimers to confirm phase identification. For most of the studied dimers, nematic or columnar phases have been detected, for several compounds appearing in a nematic-columnar phase sequence on cooling from the isotropic phase. The studied dimers showed richer polymorphism than their monomeric counterparts.     

Photooptical Properties of Polymethacrylates Having Cyanoazobenzene‐Containing Side Groups with Lateral Methyl Substituents and Different Spacer Length

New photochromic polymethacrylates with different spacer length having azobenzene side groups and lateral methyl substituents were synthesized. The phase behavior of polymethacrylates and their photooptical properties were studied and compared with unsubstituted analogues. It is shown that an introduction of lateral methyl substituents results in almost complete suppression of liquid crystalline (LC) phase formation and strong decrease of photoinduced dichroism values. It is found that rates of the photoinduced E‐Z isomerization and back thermal Z‐E isomerization are almost independent on spacer lengths. Due to the presence of lateral substituents, the photoinduced azobenzene Z‐form shows remarkable long lifetime, and back thermal conversion at room temperature takes more than 10 days. Specific peculiarities of the photoorientation process in polymer films under the polarized UV and visible light action were studied and their mechanism is suggested. © 2019 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2019 , 57, 1337–1342     

Capacitive Sensor to Monitor Enzyme Activity by Following Degradation of Macromolecules in Real Time

Applied Biochemistry and Biotechnology - A capacitive sensor was developed to analyze the presence and enzymatic activity of a model protease from standard solutions by following the degradation of...     

On Electrostatics,Covalency, and Chemical Dashes: Physical Interactions versus Chemical Bonds

The increasing availability of real-space interaction energies between quantum atoms or fragments that provide a chemically intuitive decomposition of intrinsic bond energies into electrostatic and covalent terms [see, for instance, Chem. Eur. J. 2018 , 24, 9101] provides evidence for differences between the physicist's concept of interaction and the chemist's concept of a bond. Herein, it is argued that, for the former, all types of interactions are treated equally, whereas, for the latter, only the covalent short-range interactions have actually been used to build intuition about chemical graphs and chemical bonds. This has led to the bonding role of long-range Coulombic terms in molecular chemistry being overlooked. Simultaneously, blind consideration of electrostatic terms in chemical bonding parlance may lead to confusion. The relationship between these concepts is examined herein, and some notes of caution on how to merge them are proposed.