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Hendrik Göddeke, M Hadi Timachi, Cedric A Hutter, Laura Galazzo, Markus A Seeger, Mikko Karttunen, Enrica Bordignon, Lars V Schäfer
ATP-binding cassette (ABC) transporters are ATP-driven molecular machines, in which ATP binding and hydrolysis in the nucleotide-binding domains (NBDs) is chemo-mechanically coupled to large-scale, alternating access conformational changes in the transmembrane domains (TMDs), ultimately leading to the translocation of substrates across biological membranes. The precise nature of the structural dynamics behind the large-scale conformational transition as well as the coupling of NBD and TMD motions is still unresolved...
March 16, 2018: Journal of the American Chemical Society
Ognjen Perišić
Physical interactions between proteins are often difficult to decipher. The aim of this paper is to present an algorithm that is designed to recognize binding patches and supporting structural scaffolds of interacting heterodimer proteins using the Gaussian Network Model (GNM). The recognition is based on the (self) adjustable identification of kinetically hot residues and their connection to possible binding scaffolds. The kinetically hot residues are residues with the lowest entropy, i.e., the highest contribution to the weighted sum of the fastest modes per chain extracted via GNM...
March 16, 2018: Pharmaceuticals
Jiaohan Guo, Kevin Black, Jiawen Hu, Mahi R Singh
We developed a theory for the fluorescence (FL) for quantum emitter and double metallic nanoshell dimer hybrids using the density matrix method. The dimer is made from two identical double metallic nanoshells, which are made of a dielectric core, a gold metallic shell and a dielectric spacer layer. The quantum emitters are deposited on the surface of the spacer layers of the dimers due to the electrostatic absorptions. We consider that dimer hybrids are surrounded by biological cells. This can be achieved by injecting them in human or animal cells...
March 16, 2018: Journal of Physics. Condensed Matter: An Institute of Physics Journal
Natalia Papadopoulos, Johan Lennartsson, Carl-Henrik Heldin
Translocation of full-length or fragments of receptors to the nucleus has been reported for several tyrosine kinase receptors. In this paper, we show that a fraction of full-length cell surface platelet-derived growth factor (PDGF) receptor β (PDGFRβ) accumulates in the nucleus at the chromatin and the nuclear matrix after ligand stimulation. Nuclear translocation of PDGFRβ was dependent on PDGF-BB-induced receptor dimerization, clathrin-mediated endocytosis, β-importin, and intact Golgi, occurring in both normal and cancer cells...
March 15, 2018: Journal of Cell Biology
Hisao Tsukamoto, Masahiro Higashi, Hideyoshi Motoki, Hiroki Watanabe, Christian Ganser, Koichi Nakajo, Yoshihiro Kubo, Takayuki Uchihashi, Yuji Furutani
Canonical K+ channels are tetrameric and highly K+ selective, whereas two-pore domain K+ (K2P) channels form dimers, but with a similar pore architecture. A two-pore domain potassium channel TWIK1 (KCNK1 or K2P1) allows permeation of Na+ and other monovalent ions, resulting mainly from the presence of Thr118 in the P1 domain. However, the mechanistic basis for this reduced selectivity is unclear. Using ion-exchange-induced difference infrared spectroscopy, we analyzed WT TWIK1 and T118I (highly K+ selective) and L228F (substitution in the P2 domain) TWIK1 variants and found that in the presence of K+ ions, WT and both variants exhibit an amide-I band at 1680 cm-1 This band corresponds to interactions of the backbone carbonyls in the selectivity filter with K+ , a feature very similar to that of the canonical K+ channel KcsA...
March 15, 2018: Journal of Biological Chemistry
Pushp Bajaj, Xiao-Gang Wang, Tucker Carrington, Francesco Paesani
Full-dimensional vibrational spectra are calculated for both X- (H2 O) and X- (D2 O) dimers (X = F, Cl, Br, I) at the quantum-mechanical level. The calculations are carried out on two sets of recently developed potential energy functions (PEFs), namely, Thole-type model energy (TTM-nrg) and many-body energy (MB-nrg), using the symmetry-adapted Lanczos algorithm with a product basis set including all six vibrational coordinates. Although both TTM-nrg and MB-nrg PEFs are derived from coupled-cluster single double triple-F12 data obtained in the complete basis set limit, they differ in how many-body effects are represented at short range...
March 14, 2018: Journal of Chemical Physics
Zelig Chernia, Yoav Tsori
Phase separation in substituted pyridines in water is usually described as an interplay between temperature-driven breakage of hydrogen bonds and the associating interaction of the van der Waals force. In previous quantum-chemical studies, the strength of hydrogen bonding between one water and one pyridine molecules (the 1:1 complex) was assigned a pivotal role. It was accepted that the disassembly of the 1:1 complex at a critical temperature leads to phase separation and formation of the miscibility gap. Yet, for over two decades, notable empirical data and theoretical arguments were presented against that view, thus revealing the need in a revised quantum-mechanical description...
March 14, 2018: Journal of Chemical Physics
Kaili Jiang, Jonathan Nafziger, Adam Wasserman
Approximations of the non-additive non-interacting kinetic energy (NAKE) as an explicit functional of the density are the basis of several electronic structure methods that provide improved computational efficiency over standard Kohn-Sham calculations. However, within most fragment-based formalisms, there is no unique exact NAKE, making it difficult to develop general, robust approximations for it. When adjustments are made to the embedding formalisms to guarantee uniqueness, approximate functionals may be more meaningfully compared to the exact unique NAKE...
March 14, 2018: Journal of Chemical Physics
Philip T M Carlsson, Thomas Zeuch
We have developed a new model utilizing our existing kinetic gas phase models to simulate experimental particle size distributions emerging in dry supersaturated H2 SO4 vapor homogeneously produced by rapid oxidation of SO2 through stabilized Criegee-Intermediates from 2-butene ozonolysis. We use a sectional method for simulating the particle dynamics. The particle treatment in the model is based on first principles and takes into account the transition from the kinetic to the diffusion-limited regime. It captures the temporal evolution of size distributions at the end of the ozonolysis experiment well, noting a slight underrepresentation of coagulation effects for larger particle sizes...
March 14, 2018: Journal of Chemical Physics
Kevin P Bishop, Pierre-Nicholas Roy
Free energy calculations are a crucial part of understanding chemical systems but are often computationally expensive for all but the simplest of systems. Various enhanced sampling techniques have been developed to improve the efficiency of these calculations in numerical simulations. However, the majority of these approaches have been applied using classical molecular dynamics. There are many situations where nuclear quantum effects impact the system of interest and a classical description fails to capture these details...
March 14, 2018: Journal of Chemical Physics
Christoph Schran, Felix Uhl, Jörg Behler, Dominik Marx
The design of accurate helium-solute interaction potentials for the simulation of chemically complex molecules solvated in superfluid helium has long been a cumbersome task due to the rather weak but strongly anisotropic nature of the interactions. We show that this challenge can be met by using a combination of an effective pair potential for the He-He interactions and a flexible high-dimensional neural network potential (NNP) for describing the complex interaction between helium and the solute in a pairwise additive manner...
March 14, 2018: Journal of Chemical Physics
Sebastian Trippel, Joss Wiese, Terry Mullins, Jochen Küpper
Strong quasi-adiabatic laser alignment of the indole-water-dimer clusters, an amino-acid chromophore bound to a single water molecule through a hydrogen bond, was experimentally realized. The alignment was visualized through ion and electron imaging following strong-field ionization. Molecular-frame photoelectron angular distributions showed a clear suppression of the electron yield in the plane of the ionizing laser's polarization, which was analyzed as strong alignment of the molecular cluster with ⟨cos2 θ2D ⟩ ≥ 0...
March 14, 2018: Journal of Chemical Physics
Giovanni Di Liberto, Riccardo Conte, Michele Ceotto
We present an investigation of vibrational features in water clusters performed by means of our recently established divide-and-conquer semiclassical approach [M. Ceotto, G. Di Liberto, and R. Conte, Phys. Rev. Lett. 119, 010401 (2017)]. This technique allows us to simulate quantum vibrational spectra of high-dimensional systems starting from full-dimensional classical trajectories and projection of the semiclassical propagator onto a set of lower dimensional subspaces. The potential energy surface employed is a many-body representation up to three-body terms, in which monomers and two-body interactions are described by the high level Wang-Huang-Braams-Bowman (WHBB) water potential, while, for three-body interactions, calculations adopt a fast permutationally invariant ab initio surface at the same level of theory of the WHBB 3-body potential...
March 14, 2018: Journal of Chemical Physics
Hong-Hua Wu, Xu Deng, Hu Zhang, Ying-Peng Chen, Shu-Song Ying, Yi-Jing Wu, Yan-Ting Liu, Yan Zhu, Xiu-Mei Gao, Yan-Tong Xu, Li Li
Dinardokanshones C-E, three sesquiterpenoid dimers comprising an unusual nornardosinane-type sesquiterpenoid core and an aristolane-type sesquiterpenoid unit conjugated by an extra pyran or furan ring, together with monomeric sesquiterpenoids isonardoeudesmols A-D and nardoeudesmol D, were isolated from the underground parts of Nardostachys jatamansi DC. Structures of the eight compounds were elucidated by analysis of the extensive spectroscopic data, and their absolute configurations were established by analysis of NOESY and X-ray diffraction data, combined with computational electronic circular dichroism (ECD) calculations...
March 12, 2018: Phytochemistry
Qingzhong Li, Hui-Li Xu, Steve Scheiner
HOX (X = Cl, Br, I, and At) can engage in either a H-bond (HB) or halogen bond (XB) with a base like HCN, NH3, and imidazole. While the former is energetically preferred for X=Cl and Br, it is the XB that is more stable for At, with I showing little preference. MgY2 forms a Mg-bond with the O atom of HOX, which grows stronger in the order X= Cl < Br < I < At and Y= F< Cl < Br. When all three molecules are combined together, both the Mg and the H/X bonds are cooperatively strengthened to a large degree...
March 15, 2018: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
Artur Lik, Sangeth Jenthra, Lars Fritze, Lars Müller, Khai-Nghi Truong, Holger Helten
The application of our newly developed B-C coupling method by catalytic Si/B exchange is demonstrated for the synthesis of a series of triarylboranes (1), monodisperse thienyl- and furylborane dimers (2) and trimers (9), extended oligomers (3) and polymers (3'), as well as mixed (oligo)thienyl-/furylboranes. The structures of 1aaTip, 1bbTip, and 2bbbMes*, determined by X-ray crystallography, reveal largely coplanar hetarene rings and BR3 environments, being most pronounced in the furylborane species. Photophysical investigations, supported by TD-DFT calculations, revealed pronounced pi-electron delocalization over the hetarene backbones including the boron centers...
March 15, 2018: Chemistry: a European Journal
F Nici, G Oliviero, A P Falanga, S D'Errico, M Marzano, D Musumeci, D Montesarchio, S Noppen, C Pannecouque, G Piccialli, N Borbone
By combining the ability of short G-rich oligodeoxyribonucleotides (ODNs) containing the sequence 5'CGGA3' to form higher order G-quadruplex (G4) complexes with the tetra-end-linked (TEL) concept to produce aptamers targeting the HIV envelope glycoprotein 120 (gp120), three new TEL-ODNs (1-3) having the sequence 5'CGGAGG3' were synthesized with the aim of studying the effect of G4 dimerization on their anti-HIV activity. Furthermore, in order to investigate the effect of the groups at the 5' position, the 5' ends of 1-3 were left uncapped (1) or capped with either the lipophilic dimethoxytrityl (DMT) (2) or the hydrophilic glucosyl-4-phosphate (3) moieties...
March 15, 2018: Organic & Biomolecular Chemistry
Hiroki Yokoi, Satoru Hiroto, Hiroshi Shinokubo
The reversible formation of σ-bonds between organic radicals has been widely investigated. However, reports on the formation of σ-dimers from delocalized π-radical cations are scarce. Herein, we report the reversible σ-dimerization behavior of a bowl-shaped π-radical cation generated from a nitrogen-embedded buckybowl, both in the crystalline state and in solution. The detailed structure of the σ-dimer in the crystalline state was determined by a single-crystal X-ray diffraction analysis. The monomeric radical cation exists predominantly in solution at room temperature, while dimerization of the radical cations occurs through carbon-carbon σ-bond formation upon reducing the temperature...
March 15, 2018: Journal of the American Chemical Society
M R Kholghy, G A Kelesidis, S E Pratsinis
Nucleation is an important, yet poorly understood step in soot formation. Here, the importance of reactive PAH dimerization in reducing soot nucleation reversibility is investigated by simulating soot formation in a so-called "nucleation" flame (P. Desgroux et al., Combust. Flame, 2017, 184, 153-166). There, inception of soot particles is prolonged at minimal subsequent growth. With only reversible PAH dimerization, the simulated soot concentration is negligible. Accounting however for PAH chemical bond formation after physical dimerization, stabilizes dimers by covalent bonds and increases the soot concentration by four orders of magnitude, in good agreement with Laser Induced Incandescence measurements...
March 15, 2018: Physical Chemistry Chemical Physics: PCCP
Rehan M Hussain, Ninel Z Gregori, Thomas A Ciulla, Byron L Lam
Pharmacotherapy with visual cycle modulators (VCMs) is under investigation for retinitis pigmentosa (RP), Leber congenital amaurosis (LCA), Stargardt macular dystrophy (SMD) and nonexudative age-related macular degeneration (AMD), all blinding diseases that lack effective treatment options. Areas covered: The authors review investigational VCMs, including oral retinoids, 9-cis-retinyl-acetate (zuretinol) and 9-cis-β-carotene, which restore 11-cis-retinal levels in RP and LCA caused by LRAT and RPE65 gene mutations, and may improve visual acuity and visual fields...
March 15, 2018: Expert Opinion on Pharmacotherapy
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