Supramolecular chirogenesis in zinc porphyrins: equilibria, binding properties, and thermodynamics

Complexation mechanism, binding properties and thermodynamic parameters of supramolecular chirality induction in the achiral host molecule, syn (face-to-face conformation) ethane-bridged bis(zinc porphyrin), upon interaction with chiral monoamine and monoalcohol guests have been studied by means of the UV-vis, CD, (1)H NMR, and ESI MS techniques. It was found that the chirogenesis process includes three major equilibria steps: the first guest ligation to a zinc porphyrin subunit of the host (K(1)), syn to anti conformational switching (K(S)), and further ligation by a second guest molecule to the remaining ligand-free zinc porphyrin subunit (K(2)), thus forming the final bis-ligated species possessing supramolecular chirality. The validity of this equilibria model is confirmed by the excellent match between the calculated and experimentally observed spectral parameters of the bis-ligated species. The second ligation proceeds in a cooperative manner as K(2) > K(1) for all supramolecular systems studied, regardless of the structure of the chiral ligand used. The binding properties are highly dependent on the nature of the functional group (amines are stronger binders than alcohols) and on the structure of the chiral guests (primary and aliphatic amines have overall binding constant values greater than those of secondary and aromatic amines, respectively).     

Molecular dynamics simulations for human CAR inverse agonists

Constitutive androstane receptor (CAR), along with pregnane x receptor (PXR), is an important metabolic sensor in the hepatocytes. Like all other nuclear receptors (NRs), CAR works in concert with coregulator proteins, coactivators, and corepressors which bind to the NRs. The main basis for the receptor to distinguish between coactivators and corepressors is the position of the C-terminal helix 12 (H12), which is determined by the bound NR ligand. CAR, having constitutive activity, can be repressed or further activated by its ligands. Crystal structure of human CAR bound to an agonist and a coactivator peptide is available, but no structural information on an inverse agonist-bound human CAR and a corepressor exists. In our previous molecular dynamics (MD) studies, no corepressor peptide was included. Therefore, probably due to the strong interactions which keep the relatively short H12 of CAR in the active position, the structural changes elicited by inverse agonists were very subtle, and H12 of CAR seemed to more or less retain its active conformation. Here, we have run a series of MD simulations to study the movement of H12 in the presence of both activating and repressing ligands as well as a corepressor peptide. The presence of the corepressor on the coregulator surface of CAR induced a clear shift of H12 of the inverse agonists-bound CAR. In general, H12 moved toward H10 and not away from the ligand binding domain, as seen in some other NRs. However, H12 of CAR is short enough that this movement seems to be adequate to accommodate the binding of the corepressor.     

Gauge invariance,charge conservation,and variational principles

We present new results on the correspondence between symmetries, conservation laws and variational principles for field equations in general non-abelian gauge theories. Our main result states that second order field equations possessing translational and gauge symmetries and the corresponding conservation laws are always derivable from a variational principle. We also show by the way of examples that the above result fails in general for third order field equations.     

A semisynthetic Eph receptor tyrosine kinase provides insight into ligand-induced kinase activation

We have developed a methodology for generating milligram amounts of functional Eph tyrosine kinase receptor using the protein engineering approach of expressed protein ligation. Stimulation with ligand induces efficient autophosphorylation of the semisynthetic Eph construct. The in vitro phosphorylation of key Eph tyrosine residues upon ligand-induced activation was monitored via time-resolved, quantitative phosphoproteomics, suggesting a precise and unique order of phosphorylation of the Eph tyrosines in the kinase activation process. To our knowledge, this work represents the first reported semisynthesis of a receptor tyrosine kinase and provides a potentially general method for producing single-pass membrane proteins for structural and biochemical characterization.     

Synthesis, characterization, and saccharide binding studies of bile acid-porphyrin conjugates

Synthesis and characterization of bile acid-porphyrin conjugates (BAPs) are reported. Binding of saccharides with BAPs in aqueous methanol was studied by monitoring changes in the visible absorption spectral of the porphyrin-moieties. Although these studies clearly showed absorbance changes, suggesting quite high if non-selective binding, the mass spectral studies do not unambiguously support these results.     

The equivalence between pointwise Hardy inequalities and uniform fatness

We prove an equivalence result between the validity of a pointwise Hardy inequality in a domain and uniform capacity density of the complement. This result is new even in Euclidean spaces, but our methods apply in general metric spaces as well. We also present a new transparent proof for the fact that uniform capacity density implies the classical integral version of the Hardy inequality in the setting of metric spaces. In addition, we consider the relations between the above concepts and certain Hausdorff content conditions.     

Pulsating instability of a Bose-Einstein condensate in an optical lattice

We find numerically that in the limit of weak atom-atom interactions a Bose-Einstein condensate in an optical lattice may develop a pulsating dynamical instability in which the atoms nearly periodically form a peak in the occupation numbers of the lattice sites, and then return to the unstable initial state. Multiple peaks behaving similarly are also found. Simple arguments show that the pulsating instability is a remnant of integrability, and give a handle on the relevant physical scales.     

Principles and calibration of collinear photofragmentation and atomic absorption spectroscopy

The kinetics of signal formation in collinear photofragmentation and atomic absorption spectroscopy (CPFAAS) are discussed, and theoretical equations describing the relation between the concentration of the target molecule and the detected atomic absorption in case of pure and impure samples are derived. The validity of the equation for pure samples is studied experimentally by comparing measured target molecule concentrations to concentrations determined using two other independent techniques. Our study shows that CPFAAS is capable of measuring target molecule concentrations from parts per billion (ppb) to hundreds of parts per million (ppm) in microsecond timescale. Moreover, the possibility to extend the dynamic range to cover eight orders of magnitude with a proper selection of fragmentation light source is discussed. The maximum deviation between the CPFAAS technique and a reference measurement technique is found to be less than 5 %. In this study, potassium chloride vapor and atomic potassium are used as a target molecule and a probed atom, respectively.     

Nuclear magnetic resonance chemical shifts and quadrupole couplings for different hydrogen-bonding cases occurring in liquid water: a computational study

Nuclear magnetic resonance (NMR) parameters are determined theoretically for the oxygen and hydrogen/deuterium nuclei of differently hydrogen-bonded water molecules in liquid water at 300 K. The parameters are the chemical shift, the shielding anisotropy, the asymmetry parameter of shielding, the nuclear quadrupole coupling constant, and the asymmetry parameter of the nuclear quadrupole coupling. We sample instantaneous configurations from a Car-Parrinello molecular dynamics simulation and feed nuclear coordinates into a quantum chemical program for the calculation of NMR parameters using density-functional theory with the three-parameter hybrid exchange-correlation (B3LYP) functional. In the subsequent analysis, molecules are divided into groups according to the number of hydrogen bonds they possess, and the full average NMR tensors are calculated separately for each group. The classification of the hydrogen-bonding cases is performed using a simple distance-based criterion. The analysis reveals in detail how the NMR tensors evolve as the environment changes gradually from gas to liquid upon increasing the number of hydrogen bonds to the molecule of interest. Liquid-state distributions of the instantaneous values of the NMR properties show a wide range of values for each hydrogen-bonding species with significant overlap between the different cases. Our study shows how local changes in the environment, along with classical thermal averaging, affect the NMR parameters in liquid water. For example, a broken or alternatively extra hydrogen bond induces major changes in the NMR tensors, and the effect is more pronounced for hydrogen or deuterium than for oxygen. The data sheds light on the usefulness of NMR experiments in investigating the local coordination of liquid water.