Structural biology of membrane-acting peptides: Conformational plasticity of anticoccidial peptide PW2 probed by solution NMR

The bottleneck for the complete understanding of the structure-function relationship of flexible membrane-acting peptides is its dynamics. At the same time, not only the structure but also the dynamics are the key points for their mechanism of action. Our model is PW2, a TRP-rich, cationic peptide selected from phage display libraries that shows anticoccidial activity against Eimeria acervulina. In this manuscript we used a combination of several NMR techniques to tackle these difficulties. The structural features of the membrane-acting peptide PW2 was studied in several membrane mimetic environments: we compared the structural features of PW2 in SDS and DPC micelles, that were reported earlier, with the structure properties in different lipid vesicles and the peptide free in water. We were able to unify the structural information obtained in each of these systems. The structural constraints of the peptide free in water were fundamental for the understanding of plasticity necessary for the membrane interaction. Our data suggested that the WWR sequence is the region responsible for anchoring the peptide to the interfaces, and that this same region displays some degree of conformational order in solution. For PW2, we found that affinity is related to the aromatic region, by anchoring the peptide to the membrane, and specificity is related to the N- and C-termini, which are able to accommodate in the membrane due to its plasticity. (C) 2007 Elsevier B.V. All rights reserved.

Structural studies of NaPO3-WO3 glasses by solid state NMR and Raman spectroscopy

Vitreous samples were prepared in the (100 2 x) NaPO3-x WO3 (0 <= x <= 70) glass forming system using conventional melting-quenching methods. The structural evolution of the vitreous network was monitored as a function of composition by thermal analysis, Raman spectroscopy and high resolution one- and two-dimensional P-31 solid state NMR. Addition of WO3 to the NaPO3 glass melt leads to a pronounced increase in the glass transition temperatures, suggesting a significant increase in network connectivity. At the same time Raman spectra indicate that up to about 30 mol% WO3 the tungsten atoms are linked to some non-bridging oxygen atoms (W-O- or W=O bonded species), suggesting that the network modifier sodium oxide is shared to some extent between both network formers. W-O- W bond formation occurs only at WO3 contents exceeding 30 mol%. P-31 magic angle spinning (MAS)-NMR spectra, supported by two-dimensional J-resolved spectroscopy, allow a clear distinction between species having two, one, and zero P-O-P linkages. The possible formation of some anionic tungsten sites suggested from the Raman data implies an average increase in the degree of polymerization for the phosphorus species, which would result in diminished P-31/Na-23 interactions. This prediction is indeed confirmed by P-31{Na-23} and Na-23{P-31} rotational echo double resonance (REDOR) NMR results, which indicate that successive addition of WO3 to NaPO3 glass significantly diminishes the strength of phosphorus-sodium dipole-dipole couplings.

Motional heterogeneities in siloxane/poly(ethylene glycol) ormolyte nanocomposites studied by C-13 solid-state exchange NMR

C-13 exchange solid-state NMR methods were used to study two families of siloxane/poly-(ethylene glycol) hybrid materials: Types I and II, where the polymer chains interact with the inorganic phase through physical (hydrogen bonds or van der Waals forces) or chemical (covalent bonds) interactions, respectively. These methods were employed to analyze the effects of the interactions between the organic and inorganic phases on the polymer dynamics in the milliseconds to seconds time scale, which occurs at temperatures below the motional narrowing of the NMR line width and around the polymer glass transition. Motional heterogeneities associated with these interactions and evidence of both small and large amplitude motions were directly observed for both types of hybrids. The results revealed that the hindrance to the slow molecular motions of the polymer chains due to the siloxane structures depends on the chain length and the nature of the interaction between the organic and inorganic phases.

Automatic identification by C-13 NMR of substituent groups bonded in natural product skeletons

The aim of this paper is to present a procedure that utilizes C-13 NMR for identification of substituent groups which are bonded to carbon skeletons of natural products. For so much was developed a new version of the program (MACRONO), that presents a database with 161 substituent types found in the most varied terpenoids. This new version was widely tested in the identification of the substituents of 60 compounds that, after removal of the signals that did not belong to the carbon skeleton, served to test the prediction of skeletons by using other programs of the expert system (SISTEMAT). (C) 2002 Elsevier B.V. Ltd. All rights reserved.

Mechanistic insights into the reaction between VO2+ and propene based on a DFT study

Calculations based on density functional theory have been carried out to investigate the free energy profiles at singlet and triplet electronic states associated with the gas-phase ion/molecule reactions of VO2++ ((1)A(1)/(3)A) with propene. The complex potential energy Surfaces, including Six reaction pathways (three dehydrogenation and three oxygen transfer processes), have been explored and analyzed. Along dehydrogenation reactive channels, three final products can be obtained: V(OH)(2)(+) ((1)Sigma(+)/(3)Sigma(-)) and allene (path Dehl), being the most kinetically and thermodynamically favorable reaction pathway, V(OH)(2)(+) ((1)Sigma(+)/(3)Sigma(-)) and propyne (path Deh2),and VO2+ ((1)A(1)/(3)A) and H-2 plus allene (path Deh3). The oxyoenation processes can yield its final products Vo(+) ((1)Delta/(3)Sigma) and acetone (path Ox1), VO+ ((1)Delta/(3)Sigma 2) and propanaldehyde (path Ox2), and VO+ ((1)Delta/(3)Sigma) and H-2 and propenaldehyde (path Ox3). Both paths Deh1 and Deh2 are associated with two consecutive hydrogen transfer processes from carbon atoms of the propene fragment to vanadyl oxygen atoms, while in path Deh3 the second hydrogen migration takes place to the vanadiurn atorn followed by the formation ola hydrogen molecule. Both paths Ox1 and Ox2 comprise an intramolecular hydrogen transfer between the ethylenic moiety of the propene fragment, while two consecutive hydrogen transfer processes take place from the propene fragment to oxygen and vanadium atoms of the vanadyl moiety along path Ox3. Three crossing points between both electronic states take place along path Deh1 (CP-Deh1) and path Deh2 (CP-Deh2) and in the entrance channel of oxidation processes (CP-Ox). A comparison with previous works on related reactions VO2+ + C2H4, VO2 + C2H6, and VO2+ + C3H8 allows us to rationalize the different reactivity patterns.

DFT study on the water-assisted mechanism for the reaction between VO+ and NH3 to yield VNH+ and H2O

On the basis of DFT calculations, an understanding on the catalytic effect of water in the dehydration reaction between VO+ and NH3 to yield VNH+ and H2O has been obtained. The Gibbs free energy profiles point out that the global process involves two consecutive hydrogen shifts from the nitrogen to the oxygen atom. The catalytic role is achieved by a water assisted mechanism in which water acts as proton donor and acceptor, via transition structures corresponding to a six-membered rings. The corresponding stationary points lie below both the entrance VO+ + NH3, and VNH+ + H2O, channels. (c) 2006 Elsevier B... All rights reserved.

NMR structural study on the As-P-S glassy system

Glasses having the composition As2S3(1-x)-P2S5(x) with x ranging from 0 to 0.7 have been investigated to determine the compositional effect on properties and local structure. Glass transition temperature (T,) decreases and molar volume (V,,) increases with an increase in P content. Using P-31 NMR, we measured the strength of the P-31-P-31 magnetic dipolar interaction in the glass samples and the AsPS4 crystallized phase. Based on these data, we observed the formation of the As2P2S8 network, which reflects an increase in the average coordination number and a decrease in the degree of rigidity.

NMR study of ion-conducting organic-inorganic nanocomposites poly(ethylene glycol) - Silica - LiClO4

Hybrid organic-inorganic ionic conductors, also called ormolytes, were obtained by dissolution of LiClO4 into silica/poly(ethylene glycol) matrices. Solid-state nuclear magnetic resonance (NMR) was used to probe the inorganic phase structure (Si-29) and the effects of the temperature and composition on the dynamic behavior of the ionic species (Li-7) and the polymer chains (H-1 and C-13). The NMR results between -100 and +90 degrees C show a strong correlation with ionic conductivity and differential scanning calorimetry experiments. The results also demonstrate that the cation mobility is assisted by segmental motion of the polymer, which is in agreement with the results previously reported for pure poly(ethylene oxide), PEG, electrolytes.

Study of the effect of the peptide loading and solvent system in SPPS by HRMAS-NMR

The SPPS methodology has continuously been investigated as a valuable model to monitor the solvation properties of polymeric materials. In this connection, the present work applied HRMAS-NMR spectroscopy to examine the dynamics of an aggregating peptide sequence attached to a resin core with varying peptide loading (up to 80%) and solvent system. Low and high substituted BHAR were used for assembling the VQAAIDYING sequence and some of its minor fragments. The HRMAS-NMR results were in agreement with the swelling of each resin, i.e. there was an improved resolution of resonance peaks in the better solvated conditions. Moreover, the peptide loading and the attached peptide sequence also affected the spectra. Strong peptide chain aggregation was observed mainly in highly peptide loaded resins when solvated in CDCl3. Conversely, due to the better swelling of these highly loaded resins in DMSO, improved NMR spectra were acquired in this polar aprotic solvent, thus enabling the detection of relevant sequence-dependent conformational alterations. The more prominent aggregation was displayed by the VQAAIDYING segment and not by any of its intermediary fragments and these findings were also corroborated by EPR studies of these peptide-resins labelled properly with an amino acid-type spin probe. Copyright (c) 2005 European Peptide Society and John Wiley & Sons, Ltd.

Properties and one-step synthesis of (2-acetylpyridine)tetraammineruthenium(II), [Ru-II(2-acpy)(NH3)(4)](2+) and tetraammine(2-benzoylpyridine)ruthenium(II), [Ru-II(NH3)(4)(2-bzpy)](2+) Redox potentials, UV-Vis and NMR spectra

A more direct and efficient route to the syntheses of [Ru(NH3)(4)(X-Y)](BF4)(2), where X-Y can be 2-acetylpyridine (2-acpy) or 2-benzoylpyridine (2-bzpy), based on the reactions of [RuCl(NH3)(5)]Cl-2 with these ortho-substituted azines is described. The [Ru(2-acpy)(NH3)(4)](BF4)(2) and [Ru(NH3)(5)(2-bzpy)](BF4)(2) complexes have a molar conductance of 328 and 292 Ohm(-1) cm(2) mol(-1), respectively, corresponding to a 1:2 species in solution. These complexes showed two intense absorption bands around 620-650 and 380 nm, the energies of which are solvent dependent, decreasing with the increase of the Gutman's donor number of the solvent, and were assigned as metal-to-ligand charge transfer (MLCT). The complexes have oxidation potentials (Ru-II/III) of +0.380 V vs. Ag/AgCl (2-acpy) and +0.400 V vs. Ag/AgCl (2-bzpy), and reduction potentials (X-Y0/-) of -1.10 V vs. Ag/AgCl (2-acpy) and -0.950 V vs. Ag/AgCl (2-bzpy) on CF3COOH/NaCF3COO at pH=3.0, scan rate 100 mV s(-1), [Ru]=1.0x10(-3) mol l(-1). Both processes show a coupled chemical reaction. Upon oxidation of the metal center, the MLCT absorption bands are bleached and restored upon subsequent reduction. In order to confirm the structure of the complexes a detailed LH NMR investigation was performed in d(6)-acetone. Further confirmation of the structure was obtained by recording the N-15 NMR spectrum of [Ru(NH3)(4)(2-bzpy)](2+) in d(6)-DMSO using the INEPT pulse sequence improving the sensitivity of N-15 by polarization transfer from the protons to the N-15. The Nuclear Overhauser Effect (NOE) experiments were made qualitatively for [Ru(NH3)(4)(2-acpy)](2+), and showed that H-6 of the pyridine is close to a NH3 proton, which should then be in a cis position, and, hence, confirming that acpy is acting as a bidentate ligand. (C) 1999 Elsevier B.V. Ltd. All rights reserved.

Structural and electronic properties of PbTiO3 slabs: a DFT periodic study

Structural and electronic properties of the bulk and relaxed surfaces (TiO2 and PbO terminated) of cubic PbTiO3 are investigated by means of periodic quantum-mechanical calculations based on density functional theory. It is observed that the difference in surface energies is small and relaxations effects are most prominent for Ti and Ph surface atoms. The electronic structure shows a splitting of the lowest conduction bands for the TiO2 terminated surface and of the highest valence bands for the PbO terminated slab. The calculated indirect band gap is: 3.18, 2.99 and 3.03 eV for bulk, TiO2 and PbO terminations, respectively. The electron density maps show that the Ti-O bond has a partial covalent character, whereas the Pb-O bonds present a very low covalency. (C) 2004 Elsevier B.V. All rights reserved.

Automated NMR structure determination and disulfide bond identification of the myotoxin crotamine from Crotalus durissus terrificus

Crotamine is one of four major components of the venom of the South American rattlesnake Crotalus durissus terrificus. Similar to its counterparts in the family of the myotoxins, it induces myonecrosis of skeletal muscle cells. This paper describes a new NMR structure determination of crotamine in aqueous solution at pH 5.8 and 20 degrees C, using standard homonuclear (1)H NMR spectroscopy at 900 MHz and the automated structure calculation software ATNOS/CANDID/DYANA. The automatic NOESY spectral analysis included the identification of a most likely combination of the six cysteines into three disulfide bonds, i.e. Cys4-Cys36, Cys11-Cys30 and Cys18-Cys37; thereby a generally applicable new computational protocol is introduced to determine unknown disulfide bond connectivities in globular proteins. A previous NMR structure determination was thus confirmed and the structure refined. Crotamine contains an alpha-helix with residues 1-7 and a two-stranded anti-parallel beta-sheet with residues 9-13 and 34-38 as the only regular secondary structures. These are connected with each other and the remainder of the polypeptide chain by the three disulfide bonds, which also form part of a central hydrophobic core. A single conformation was observed, with Pro13 and Pro21 in the trans and Pro20 in the cis-form. The global fold and the cysteine-pairing pattern of crotamine are similar to the beta-defensin fold, although the two proteins have low sequence homology, and display different biological activities. (c) 2005 Elsevier Ltd. All rights reserved.

Structure characterization of molecular complexes for non-linear optical materials. II. 1 : 1 complexes of 4-methyl-morpholine-N-oxide (1) and 3-picoline-N-oxide (2) with 2,4,6-trinitrophenol, studied by X-ray, AM1 and DFT calculations

(1) C6H2N3O7- center dot C5H12NO2+, Mr = 346.26, P2(1)/c, a = 7.2356(6), b = 10.5765(9), c = 19.593(2) angstrom, 3 beta=95.101(6)degrees, V = 1493.5(2) angstrom(3), Z = 4, R-1 = 0.0414; (2) C6H2N3O7- center dot C6H8NO+, Mr = 38.24, P2(1)/n, a = 7.8713(5), b = 6.1979(7), c = 28.697(3) angstrom, beta = 90.028(7)degrees, V = 1400.0(2) angstrom(3), Z = 4, R-1 = 0.0416. The packing units in both compounds consist of hydrogen bonded cation-anion pairs. The (hyper)polarizabilities have been calculated for the crystallographic and optimized molecules, by AM1 and at the DFT/B3LYP(6-31G**) level.

Conductivity and F-19 NMR in PbGeO3-PbF2-CdF2 glasses and glass-ceramics

The temperature dependence of the electrical conductivity and the F-19 nuclear magnetic resonance (NMR) of PbGeO3-PbF2CdF, glasses and glass ceramics are investigated. The measured conductivity values of the glasses are above 10(-5) Skin at 500 K, and increase with increasing lead fluoride content. Activation energies extracted from the conductivity data are in the range 0.59-0.73 eV. Results are consistent with the hypothesis that in these oxyfluoride glasses lead fluoride rich clusters are dispersed in a metagermanate based matrix providing increasing mobility pathways for conducting ions. The conductivity of a sample of the glass ceramic of composition (mol%) 60PbGeO(3-)20PbF(2)-20CdF(2) was found to be smaller than that in the corresponding glass, suggesting that there are poor ionic conducting regions in the interface between the nanometer sized crystals. The temperature dependence of the F-19 relaxation times, measured in the range 100-800 K, exhibit the qualitative features associated with high fluorine mobility in both, glass and glass ceramics materials. We suggest that de-convolution of the spin-lattice relaxation rates observed in the glass ceramics shows that the observed high temperature rate maximum is associated with the diffusional motions of the fluorine ions in beta-PbF2 crystals. (c) 2005 Elsevier B.V. All rights reserved.

DFT study of the reaction between VO2+ and C2H6

The molecular mechanisms of the reaction VO2+ ((1)A(1)/(3)A'') + C2H6 ((1)A(g)) to yield V(OH)(2)(+) ((1)Sigma(+)/(3)Sigma(-)) + C2H4 ((1)A(g)) and/or VO+ ((1)Delta/(3)Sigma) + H2O ((1)A(1)) + C2H4 (Ag-1) have been investigated with density functional theory (DFT) at the B3LYP/6-311G(2d,p) level. Calculations including geometry optimization, vibrational analysis, and Gibbs free energy for the stationary points on the reactive potential energy surfaces at both the singlet (s) and first excited triplet (t) electronic states have been carried out. The most thermodynamically and kinetically favorable pathway is the formation of t-V(OH)(2)(+) + C2H4 along a four-step molecular mechanism (insertion, two consecutive hydrogen transfers, and elimination). A crossing point between s and t electronic states has been characterized. A comparison with previous works on VO2+ + C2H4 (Gracia et al. J. Phys. Chem. A 2003, 107, 3107-3120) and VO2+ + C3H8 (Engeser et al. Organometallics 2003, 22, 3933-3943) reactions allows us a rationalization of the different reactivity patterns. The catalytic role of water molecules in the tautomerization process between hydrated oxide cation, VO(H2O)(+,) and dihydroxide cation, V(OH)(2)(+), is achieved by a water-assisted mechanism.