NMR solution conformation of gramicidin A double helix

AbstractThe conformation of species 3 of Val-gramicidin A in dioxane has been determined by two-dimensional NMR spectroscopy. It is presented by the left handed ⇅ππ5.6LD double helix, a suitable model of an ion permeable pore across the membrane matrix

Two-dimensional 1H-NMR study of bacterioopsin-(34–65)-polypeptide conformation

AbstractConformation of the synthetic 32-residue polypeptide, an analog of membrane spanning segment B (residues 34–65) of the Halobacterium halobium bacteriorhodopsin in the membrane mimetic system, methanol/chloroform (1:1), was investigated by 1H-NMR spectroscopy. Previously it was shown by 19F-NMR spectroscopy that this medium retains the native conformation of membrane bound BR and its fragments. The spectrum resonance was assigned by means of the sequential signal assignment porcedure using phase-sensitive DQF-COSY, MLEV17 HOHAHA and NOESY techniques. Interproton nuclear Overhauser effects, spin-spin coupling constant of vicinal H-NCα-H protons and deuterium exchange rates of individual NH groups were derived from two-dimensional NMR spectra. The data unequivocally define the peptide conformation as the right-handed α-helix, extremely rigid in the central region from Phe 42 to Nle 60 and flexible in the N- and C-terminal parts

Local piezoresponse and polarization switching in nucleobase thymine microcrystals

Thymine (2-oxy-4-oxy-5 methyl pyrimidine) is one of the four nucleobases of deoxyribonucleic acid (DNA). In the DNA molecule, thymine binds to adenine via two hydrogen bonds, thus stabilizing the nucleic acid structure and is involved in pairing and replication. Here, we show that synthetic thymine microcrystals grown from the solution exhibit local piezoelectricity and apparent ferroelectricity, as evidenced by nanoscale electromechanical measurements via Piezoresponse Force Microscopy. Our experimental results demonstrate significant electromechanical activity and polarization switchability of thymine, thus opening a pathway for piezoelectric and ferroelectric-based applications of thymine and, perhaps, of other DNA nucleobase materials. The results are supported by molecular modeling of polarization switching under an external electric field. (C) 2015 AIP Publishing LLC

Conductance Simulation of the Purinergic P2X(2), P2X(4), and P2X(7) Ionic Channels Using a Combined Brownian Dynamics and Molecular Dynamics Approach

This paper investigates the application of an original combined approach of molecular and Brownian dynamic methods with quantum chemistry calculations for modeling the process of conductance of ion channels using purinergic P2X family receptors P2X(2), P2X(4), and P2X(7) as a case study. A simplified model of the ionic channel in the lipid bilayer has been developed. A high level of conductance (30 pS) of P2X(2) ionic channel together with the key role of Asp(349) in forming the selectivity filter of P2X(2) has been shown by using this approach. Calculated P2X(2) permeability to monovalent cations Li+, Na+, and K+ conforms to the free diffusion coefficient of these ions, which shows the low selectivity of P2X(2) ionic channel

First Principles Studies of Hydroxyapatite Structure and Properties

Results of first principles calculations of Hydroxyapatite (HAP) nanostructures in combination with computational molecular modeling by various methods are presented. The detailed explorations of the bulk and surface HAP properties are analyzed in this review. HAP structures and properties were studied from first principles approaches using ab initio Local Density Approximation (LDA) method in combination with various quantum-chemical (QM), including semi-empirical (PM3, etc.), Density Functional Theory (DFT) and molecular mechanical (MM+, OPLS, BIO CHARM) methods from HypemChem 7.5/8.0 package. The optimizations of lattice parameters and atoms positions were performed for hexagonal and monoclinic HAP structures with different orientation of hydroxyl group in HAP OH-channels

Structural Features of Oxyapatite

One of the most widely known representatives of the apatite family is hydroxyapatite, Ca10(PO4)6(OH)2. This mineral is a part of the human dental and bone tissues, and, therefore, is widely used in medicine. Less known is oxyapatite, Ca10(PO4)6O, which has the same biocompatibility as hydroxyapatite. In this work, it is shown that oxyapatite can be obtained by heating hydroxyapatite powder at 1000 °C in vacuum. IR and NMR spectroscopy proved the absence of the hydroxyl groups in the apatite obtained. In the IR spectrum, the presence of new absorption bands of phosphate groups, indicating a symmetry disorder, was observed. Density functional theory modeling confirmed lowering of symmetry for the oxyapatite structure. Modeling the IR spectrum of oxyapatite made it possible to identify the experimentally observed new absorption bands. According to the modeling, the presence of a vacancy in a hydroxyl channel of the apatite structure lowered the symmetry. Powder X-ray diffraction data confirmed that full dehydroxylation of hydroxyapatite led to a decrease in symmetry to triclinic phase. Comparison of the formation energies showed that formation of the hydroxyapatite phase was more preferable than that of oxyapatite, which explains apatite’s tendency to rehydroxylation. It was shown that the solubility of oxyapatite in water was comparable to that of hydroxyapatite

Growth and Nonlinear Optical Properties of β-Glycine Crystals Grown on Pt Substrates

Glycine is the simplest amino acid and one of the basic and important elements in biology, as it serves as a building block for proteins. The interest in this material has recently arisen from its useful functional properties, such as its high value of nonlinear optical susceptibility and ferroelectricity. Three polymorphic forms with different physical properties are possible in glycine, the most useful β-polymorph being much less stable than the other two. In this work, we could grow stable microcrystals of β-glycine using a (111)Pt/SiO2/Si substrate as a template. The effects of the solution concentration and Pt-assisted nucleation on the crystal growth and phase evolution were evaluated using X-ray diffraction analysis and Raman spectroscopy. A second harmonic generation (SHG) method confirmed that the 2-fold symmetry is preserved in as-grown crystals, thus reflecting the expected P21 symmetry of the β-phase. Spontaneous polarization direction is found to be parallel to the monoclinic [010] axis and directed along the crystal length. These data are confirmed by computational molecular modeling. Optical measurements revealed also relatively high values of the nonlinear optical susceptibility (50% greater than in the z-cut quartz). The potential use of stable β-glycine crystals in nonlinear optical applications is discussed