Signal transduction in the photoactive yellow protein. II. Proton transfer initiates conformational changes

Molecular dynamics simulation techniques, together with semiempirical PM3 calculations, have been used to investigate the effect of photoisomerization of the 4-hydroxy-cinnamic acid chromophore on the structural properties of the photoactive yellow protein (PYP) from Ectothiorodospira halophila. In this bacteria, exposure to blue light leads to a negative photoactic response. The calculations suggest that the isomerization does not directly destabilize the protein. However, because of the isomerization, a proton transfer from a glutamic acid residue (Glu46) to the phenolate oxygen atom of the chromophore becomes energetically favorable. The proton transfer initiates conformational changes within the protein, which are in turn believed to lead to signaling.     

ProteinVolume: calculating molecular van der Waals and void volumes in proteins

Background

Voids and cavities in the native protein structure determine the pressure unfolding of proteins. In addition, the volume changes due to the interaction of newly exposed atoms with solvent upon protein unfolding also contribute to the pressure unfolding of proteins. Quantitative understanding of these effects is important for predicting and designing proteins with predefined response to changes in hydrostatic pressure using computational approaches. The molecular surface volume is a useful metric that describes contribution of geometrical volume, which includes van der Waals volume and volume of the voids, to the total volume of a protein in solution, thus isolating the effects of hydration for separate calculations.

Results

We developed ProteinVolume, a highly robust and easy-to-use tool to compute geometric volumes of proteins. ProteinVolume generates the molecular surface of a protein and uses an innovative flood-fill algorithm to calculate the individual components of the molecular surface volume, van der Waals and intramolecular void volumes. ProteinVolume is user friendly and is available as a web-server or a platform-independent command-line version.

Conclusions

ProteinVolume is a highly accurate and fast application to interrogate geometric volumes of proteins. ProteinVolume is a free web server available on http://gmlab.bio.rpi.edu. Free-standing platform-independent Java-based ProteinVolume executable is also freely available at this web site.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-015-0531-2) contains supplementary material, which is available to authorized users.     

Phytochemicals with NO inhibitory effects and interactions with iNOS protein from Trigonostemon howii

A phytochemical investigation to obtain new NO inhibitors led to the isolation of nine compounds including one new guaiane-type sesquiterpenoid (1) and two new cleistanthane diterpenoids (2 and 3) from the stems of Trigonostemon howii. Their structures were elucidated on the basis of extensive 1D and 2D NMR spectroscopic data analysis, and the absolute configurations of new compounds 1–3 were established via comparison of experimental and calculated electronic circular dichroism (ECD) spectra. Compounds 2 and 3 possess a rare 3,4-seco-cleistanthane diterpenoid skeleton. All of the compounds showed inhibitory effects on lipopolysaccharide-induced NO production in murine microglial BV-2 cells. The further molecular docking studies indicated the strong interactions between some bioactive compounds with the iNOS protein, which revealed the possible and potential mechanism of NO inhibition of bioactive compounds.     

The enzyme 3-hydroxykynurenine transaminase as potential target for 1,2,4-oxadiazoles with larvicide activity against the dengue vector Aedes aegypti

The mosquito Aedes aegypti is the vector agent responsible for the transmission of yellow fever and dengue fever viruses to over 80 million people in tropical and subtropical regions of the world. Exhaustive efforts have lead to a vaccine candidate with only 30% effectiveness against the dengue virus and failure to protect patients against the serotype 2. Hence, vector control remains the most viable route to dengue fever control programs. We have synthesized a class of 1,2,4-oxadiazole derivatives whose most biologically active compounds exhibit potent activity against Aedes aegypti larvae (ca. of 15 ppm) and low toxicity in mammals. Exposure to these larvicides results in larvae pigmentation in a manner correlated with the LC₅₀ measurements. Structural comparisons of the 1,2,4-oxadiazole nucleus against known inhibitors of insect enzymes allowed the identification of 3-hydroxykynurenine transaminase as a potential target for these synthetic larvicides. Molecular docking calculations indicate that 1,2,4-oxadiazole compounds can bind to 3-hydroxykynurenine transaminase with similar conformation and binding energies as its crystallographic inhibitor 4-(2-aminophenyl)-4-oxobutanoic acid.     

Monensin A methyl ester complexes with Li+, Na+, and K+ cations studied by ESI-MS, 1H- and 13C-NMR, FTIR, as well as PM5 semiempirical method

Monensin A methyl ester (MON1) was synthesized by a new method and its ability to form complexes with Li+, Na+, and K+ cations was studied by electrospray ionization-mass spectroscopy (ESI-MS), 1H and 13C nuclear magnetic resonance (NMR), Fourier transform infrared (FTIR), and PM5 semiempirical methods. It is shown that MON1 with monovalent metal cations forms stable complexes of 1:1 stoichiometry. The structures of the complexes are stabilized by intramolecular hydrogen bonds in which the OH groups are always involved. In the structure of MON1, the oxygen atom of the C=O ester group is involved in very weak bifurcated intramolecular hydrogen bonds with two hydroxyl groups, whereas in the complexes of MON1 with monovalent metal cations the C=O ester group is not engaged in any intramolecular hydrogen bonds. Furthermore, it is demonstrated that the strongest intramolecular hydrogen bonds are formed within the MON1-Li+ complex structure. The structures of the MON1 and its complexes with Li+, Na+, and K+ cations are visualized and discussed in detail.     

Correlation between Li Plating Behavior and Surface Characteristics of Carbon Matrix toward Stable Li Metal Anodes

Carbonaceous materials are widely employed to host Li for stable and safe Li metal batteries while relatively little effort is devoted to tailoring the surface properties of carbon to facilitate uniform Li plating. Herein, the correlation between Li plating behavior and the surface characteristics of electrospun porous carbon nanofibers (PCNFs) is systemically elucidated through experiments and theoretical calculations. It is revealed that the neat carbon surface suffers from severe lattice mismatch with Li metal, hindering uniform Li plating. In contrast, open pores created on the PCNF surface serve as active sites for controlled initial nucleation of Li. The introduction of oxygenated functional groups further facilitates the nucleation of Li on PCNFs through the largely reduced nucleation energy barrier. The Li film uniformly deposited on PCNFs enables efficient use of the whole carbon surface, giving rise to enhanced cyclic stability of the electrode. When used as an anode in lithium–sulfur batteries, the modified electrode delivers an excellent energy density of 385 Wh kg^?1 after 100 cycles. The fundamental correlation established in this study is universal to all types of carbonaceous materials and sheds new light on the rational design of high‐performance Li metal anodes by controlling the initial Li nucleation.     

Ab initio double-ζ (D95) valence bond calculations for the ground states of NO2, O3, and ClO2

The results of some double-ζ D95 valence-bond (VB) calculations are reported for the ground states of nitrogen dioxide, NO₂ (17 valence electrons), ozone, O₃ (18 valence electrons), and chlorine dioxide, ClO₂ (19 valence electrons). The Mulliken, Löwdin and Hiberty structural weights are reported for nine (NO₂), six (O₃), and three (ClO₂) Lewis structures that differ in the locations of the π electrons. The most important Lewis structures for NO₂ are the uncharged spin-paired diradical structure VII and the two equivalent structures that carry no formal charges (II and V). For O₃ and ClO₂, the primary Lewis structures are, respectively, the uncharged singlet diradical structure III, and I with the odd electron located in the chlorine 3pπ atomic orbital.For ClO₂, the results of some STO-6G calculations, with 16 canonical Lewis type structures included, give a much smaller value for the chlorine odd-electron charge than does the D95 vb2000 calculation with a Hartree-Fock core. However, the structural weights obtained from the STO-6G calculations do reflect the expectation that small atomic formal charge separations, together with some Cl-O covalent σ-bonding, are associated with large structural weights.     

Eremophilane Sesquiterpenes and Benzene Derivatives from the Endophyte Microdiplodia sp. WGHS5

Three new eremophilane sesquiterpenes phomadecalins G−I ( 1 – 3 ) and two new benzene derivatives microdiplzenes A and B ( 12 and 13 ), together with nine known eremophilane sesquiterpenes ( 4 – 11 and 14 ) were isolated from an endophytic fungus, Microdiplodia sp. WGHS5. Their structures were elucidated by the interpretation of HR-ESI-MS and NMR data; meanwhile, the absolute configurations of new compounds were determined on the base of ECD calculations. All compounds were evaluated for the antimicrobial activities and antiproliferative effect on human gastric cancer cell lines (BGC-823).     

Mechanistic investigation of platinum-catalysed hydroformylation of propene: A density functional study

The mechanism of hydroformylation of propene in the presence of both cis-PtH(SnCl₃)(PH₃)₂ and trans-PtH(SnCl₃)(PH₃)₂ catalysts has been investigated. A density functional study has been carried out for all of the elementary steps of the catalytic cycle, i.e. for the alkene coordination, for its insertion into the Pt-H bond, carbon monoxide activation and its subsequent insertion into the Pt-alkyl bond. Finally, the product forming step, the dihydrogen activation and aldehyde elimination have been investigated.It has been found that the regioselectivity of hydroformylation is determined in the olefin insertion step. The computed ratio of the linear regioisomer, n-butanal is predicted to be 83% when solvation corrections were employed, being in very good agreement with the experimental result. Among the elementary steps the hydrogenolysis has been found to be the slowest followed by the migratory carbon monoxide insertion step. Due to the crucial role of the trichlorostannato ligand the electronic effects of SnCl₃ has been analysed employing the charge decomposition analysis (CDA), the natural bond orbital (NBO) and the atoms in molecules (AIM) methods.     

On the identification of ionic species of neutral halogen dimers, monomers and pincer type palladacycles in solution by electrospray mass and tandem mass spectrometry

Electrospray (ESI) mass spectra analysis of acetonitrile solutions of a series of neutral chloro dimers, pincer type, and monomeric palladacycles has enabled the detection of several of their derived ionic species. The monometallic cationic complexes Pd[κ¹-C,κ¹-N,κ¹-S-C(CH₃S-2-C₆H₄)C(Cl)CH₂N(CH₃)₂]⁺ (1a) and [Pd[κ¹-C,κ¹-N,κ¹-S-C(CH₃S-2-C₆H₄)C(Cl)CH₂N(CH₃)₂](CH₃CN)]⁺ (1b) and the bimetallic cationic complex [κ¹-C,κ¹-N,κ¹-S-C(CH₃S-2-C₆H₄)C(Cl)CH₂N(CH₃)₂]Pd-Cl-Pd[κ¹-C,κ¹-N,κ¹-S-C(CH₃S-2-C₆H₄)C(Cl)CH₂N(CH₃)₂]⁺ (1c) were detected from an acetonitrile solution of the pincer palladacycles Pd[κ¹-C,κ¹-N,κ¹-S-C(CH₃S-2-C₆H₄)C(Cl)CH₂N(CH₃)₂](Cl) 1. For the dimeric compounds {Pd[κ¹-C,κ¹-N-C(Y-2-C₆H₄)C(Cl)CH₂N(CH₃)₂](μ-Cl)}₂ (2, Y=H and 3, CF₃), highly electronically unsaturated palladacycles [Pd[κ¹-C,κ¹-N-C(Y-2-C₆H₄)C(Cl)CH₂N(CH₃)₂]⁺ (2d, 3d) and their mono and di-acetonitrile adducts, namely, [Pd[κ¹-C,κ¹-N-C(Y-2-C₆H₄)C(Cl)CH₂N(CH₃)₂](CH₃CN)]⁺ (2e, 3e) and [Pd[κ¹-C,κ¹-N-C(Y-2-C₆H₄)C(Cl)CH₂N(CH₃)₂](CH₃CN)₂]⁺ (2f and 3f) were detected together with the bimetallic complex [Pd[κ¹-C,κ¹-N-C(Y-2-C₆H₄)C(Cl)CH₂N(CH₃)₂]-Cl-Pd[κ¹-C,κ¹-N-C(Y-2-C₆H₄)C(Cl)CH₂N](CH₃)₂]⁺ (2a, 3a) and its acetonitrile adducts [κ¹-C,κ¹-N-C(Y-2-C₆H₄)C(Cl)CH₂N(CH₃)₂](CH₃CN)Pd-Cl-Pd[ κ¹-C,κ¹-N-C(Y-2-C₆H₄)C(Cl)CH₂N(CH₃)₂]⁺ (2b, 3b) and [κ¹-C,κ¹-N-C(Y-2-C₆H₄)C(Cl)CH₂N(CH₃)₂](CH₃CN)Pd-Cl-Pd[κ¹-C, κ¹-N-C(Y-2-C₆H₄)C(Cl)CH₂N(CH₃)₂(CH₃CN)]⁺ (2c, 3c). The dimeric palladacycle {Pd[κ¹-C,κ¹-N-C(CH₃O-2-C₆H₄)C(Cl)CH₂N(CH₃)₂](μ-Cl)}₂ (4) is unique as it behaves as a pincer type compound with the OCH₃ substituent acting as an intramolecular coordinating group which prevents acetonitrile full coordination, thus forming the cationic complexes [(C₆H₄(o-CH₃O)CC(Cl)CH₂N(CH₃)₂-κO,κC,κN)Pd]⁺ (4b), [(C₆H₄(o-CH₃O)CC(Cl)CH₂N(CH₃)₂- κO,κC,κN)Pd(CH₃CN)]⁺ (4c) and [(C₆H₄ (o-MeO)CC(Cl)CH₂N(CH₃)₂-κO, κC,κN)Pd-Cl-Pd(C₆H₄(o-CH₃O)CC(Cl)CH₂N(CH₃)₂-κO,κC,κN)]⁺ (4a). ESI-MS spectra analysis of acetonitrile solutions of the monomeric palladacycles Pd[κ¹-C,κ¹-N-C(Y-2-C₆H₄)C(Cl)CH₂N(CH₃)₂](Cl)(Py) (5, Y=H and 6, Y=CF₃) allows the detection of some of the same species observed in the spectra of the dimeric palladacycles, i.e., monometallic cationic 2d-3d, 2e-3e and {Pd[κ¹-C,κ¹-N-C(Y-2-C₆H₄)C(Cl)CH₂N(CH₃)₂](Py)}⁺ (5a, 6a) and {Pd[κ¹-C,κ¹-N-C(Y-2-C₆H₄)C(Cl)CH₂N(CH₃)₂](CH₃CN)(Py)}⁺ (5b, 6b) and the bimetallic 2a, 3a, 2b, 3b, 2c and 3c. In all cationic complexes detected by ESI-MS, the cyclometallated moiety was intact indicating the high stability of the four or six electron anionic chelate ligands. The anionic (chloride) or neutral (pyridine) ligands are, however, easily replaced by the acetonitrile solvent.