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Molecular Environment (molecular + environment)
Selected AbstractsThe Effect of Molecular Environment on the Photoisomerization of Urocanic Acid,PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 2 2004Richard A. Wallis ABSTRACT Urocanic acid, imidazole propenoic acid, is a metabolic product of histidine, which accumulates in skin and is excreted in sweat. It absorbs UV radiation at wavelengths shorter than 340 nm, and its principal photochemical reaction is a trans-cis isomerization about the propenyl double bond. This isomerization to the biologically active cis isomer is implicated in the photo-induced suppression of the immune system of skin. The kinetics of the trans,cis photoisomerization of urocanic acid has been determined in a number of solvents, spanning a range of polarities. The initial rates of isomerization and the photostationary trans-cis compositions, in all solvents except water, correlate linearly with solvent polarity. This indicates that the isomerization proceeds through a polar intermediate that is stabilized by coulombic interactions with the molecular environment. [source] The embedded ion method: A new approach to the electrostatic description of crystal lattice effects in chemical shielding calculationsCONCEPTS IN MAGNETIC RESONANCE, Issue 5 2006Dirk Stueber Abstract The nuclear magnetic shielding anisotropy of NMR active nuclei is highly sensitive to the nuclear electronic environment. Hence, measurements of the nuclear magnetic shielding anisotropy represent a powerful tool in the elucidation of molecular structure for a wide variety of materials. Quantum mechanical ab initio nuclear magnetic shielding calculations effectively complement the experimental NMR data by revealing additional structural information. The accuracy and capacity of these calculations has been improved considerably in recent years. However, the inherent problem of the limitation in the size of the systems that may be studied due to the relatively demanding computational requirements largely remains. Accordingly, ab initio shielding calculations have been performed predominantly on isolated molecules, neglecting the molecular environment. This approach is sufficient for neutral nonpolar systems, but leads to serious errors in the shielding calculations on polar and ionic systems. Conducting ab initio shielding calculations on clusters of molecules (i.e., including the nearest neighbor interactions) has improved the accuracy of the calculations in many cases. Other methods of simulating crystal lattice effects in shielding calculations that have been developed include the electrostatic representation of the crystal lattice using point charge arrays, full ab initio methods, ab initio methods under periodic boundary conditions, and hybrid ab initio/molecular dynamics methods. The embedded ion method (EIM) discussed here follows the electrostatic approach. The method mimics the intermolecular and interionic interactions experienced by a subject molecule or cluster in a given crystal in quantum mechanical shielding calculations with a large finite, periodic, and self-consistent array of point charges. The point charge arrays in the EIM are generated using the Ewald summation method and embed the molecule or ion of interest for which the ab initio shielding calculations are performed. The accuracy with which the EIM reproduces experimental nuclear magnetic shift tensor principal values, the sensitivity of the EIM to the parameters defining the point charge arrays, as well as the strengths and limitations of the EIM in comparison with other methods that include crystal lattice effects in chemical shielding calculations, are presented. © 2006 Wiley Periodicals, Inc. Concepts Magn Reson Part A 28A: 347,368, 2006 [source] Expression, stability and performance of the three-component alkane mono-oxygenase of Pseudomonas oleovorans in Escherichia coliFEBS JOURNAL, Issue 7 2000Ivo E. Staijen We tested the synthesis and in vivo function of the inducible alkane hydroxylase of Pseudomonas oleovorans GPo1 in several Escherichia coli recombinants. The enzyme components (AlkB, AlkG and AlkT) were synthesized at various rates in different E. coli hosts, which after induction produced between twofold and tenfold more of the Alk components than did P. oleovorans. The enzyme components were less stable in recombinant E. coli hosts than in P. oleovorans. In addition, the specific activity of the alkane mono-oxygenase component AlkB was five or six times lower in E. coli than in P. oleovorans. Evidently, optimal functioning of the hydroxylase system requires factors or a molecular environment that are available in Pseudomonas but not in E. coli. These factors are likely to include correct interactions of AlkB with the membrane and incorporation of iron into the AlkG and AlkB apoproteins. [source] Electronic Structure and Geminate Pair Energetics at Organic,Organic Interfaces: The Case of Pentacene/C60 HeterojunctionsADVANCED FUNCTIONAL MATERIALS, Issue 23 2009Stijn Verlaak Abstract Organic semiconductors are characterized by localized states whose energies are predominantly determined by electrostatic interactions with their immediate molecular environment. As a result, the details of the energy landscape at heterojunctions between different organic semiconductors cannot simply be deduced from those of the individual semiconductors, and they have so far remained largely unexplored. Here, microelectrostatic computations are performed to clarify the nature of the electronic structure and geminate pair energetics at the pentacene/C60 interface, as archetype for an interface between a donor molecule and a fullerene electron acceptor. The size and orientation of the molecular quadrupole moments, determined by material choice, crystal orientation, and thermodynamic growth parameters of the semiconductors, dominate the interface energetics. Not only do quadrupoles produce direct electrostatic interactions with charge carriers, but, in addition, the discontinuity of the quadrupole field at the interface induces permanent interface dipoles. That discontinuity is particularly striking for an interface with C60 molecules, which by virtue of their symmetry possess no quadrupole. Consequently, at a pentacene/C60 interface, both the vacuum-level shift and geminate pair dissociation critically depend on the orientation of the pentacene ,-system relative to the adjacent C60. [source] Femtosecond dynamics of electron transfer, localization, and solvation processes at the ice,metal interfaceISRAEL JOURNAL OF CHEMISTRY, Issue 1-2 2005Uwe Bovensiepen The ultrafast dynamics of excess electrons in amorphous ice layers on single-crystal metal surfaces are investigated by femtosecond time- and angle-resolved two-photon-photoemission spectroscopy. Photoexcited electrons are injected from the metal substrate into delocalized states of the conduction band of ice and localize in the ice layer within 100 fs. Subsequently, energetic stabilization of this localized species is observed on a time scale of ,1 ps, which is attributed to electron solvation by nonadiabatic coupling to nuclear degrees of freedom of the surrounding polar molecular environment. Concomitant with this stabilization process, residual wave function overlap of the solvated electron with the metal substrate results in back-transfer by tunneling through the solvation shell. At such interfaces the correlation of electronic and molecular structure with the resulting solvation dynamics can be explored using different substrates as a template. Here we compare data on molecularly thin D2O ice layers grown on Cu(111) and Ru(001). On Ru(001) both the stabilization and back-transfer proceed about three times faster compared to Cu(111), which is attributed to different interfacial structures and the role of d-states, and projected band gaps in the electron transfer process. [source] Investigation of penetratin peptides Part 1.JOURNAL OF PEPTIDE SCIENCE, Issue 4 2002The environment dependent conformational properties of penetratin, two of its derivatives Abstract The homeodomain, the DNA-binding domain of Antennapedia homeoprotein, is composed of three ,-helices and one ,-turn between helices II and III. Its third helix from the N -terminal (helix III) can translocate through the cell membrane into the nucleus and can be used as an intracellular vehicle for the delivery of oligopeptides and oligonucleotides. To the best of our knowledge, this helix III, called penetratin, which consists of 16 amino acids, is internalized by cells in a specific, non-receptor-mediated manner. For a better understanding of the mechanism of the transfer, the structure of penetratin was examined in both extracellular matrix-mimetic and membrane-mimetic environments; 1H-NMR and CD spectroscopic measurements were performed in mixtures of TFE/water with different ratios. The molecular conformations of two analogue peptides [(6,14-Phe)-penetratin and a 12 amino acid penetratin derivative (peptide 3)] were also studied. An atomic level comprehensive analysis of penetratin and its two analogues was performed. In a membrane-mimetic solvent system (TFEd2/water = 9 : 1), on the basis of 553 distance restraints, the 4,12 region of penetratin exhibits a bent, irregular helical structure on NMR examination. Interactions between hydrophobic amino acid residues in conjunction with H-bonds stabilize the secondary structure of the molecule. Thus, both derivatives adopt a helix-like conformation. However, while (6,14-Phe)-penetratin displays both ,-helical and 310 -helical features, the structure of peptide 3 is predominantly a 310 -helix. Of the three peptides, surprisingly (6,14-Phe)-penetratin has the largest helical content. An increase in the polarity of the molecular environment gradually disintegrates these helix-like secondary structures. In a highly aqueous molecular system (TFEd2/water = 1 : 9), the fast exchange of multiple conformers leads to too few distance restraints being extracted, therefore the NMR structures can no longer be determined. The NMR data show that only short-range order can be traced in these peptides. Under these conditions, the molecules adopt nascent helix-like structures. On the other hand, CD spectra could be recorded at any TFE/water ratio and the conformational interconversion could therefore be monitored as a function of the polarity of the molecular environment. The CD data were analysed comprehensively by the quantitative deconvolution method (CCA+). All three penetratin peptides display helical conformational features in a low dielectric medium, with significant differences as a function of their amino acid composition. However, these conformational features are gradually lost during the shift from an apolar to a polar molecular environment. Copyright © 2002 European Peptide Society and John Wiley & Sons, Ltd. [source] Counterintuitive influence of microscopic chirality on helical order in polymersJOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 9 2004Kap Soo Cheon Abstract Studies of copolymers of chiral and achiral units forming a helical array correlate to statistical physical predictions of the influence of the chiral units on the helical sense taken by the array. In the absence of conflict among the chiral units for helical sense control, the sergeants and soldiers experiment, a larger chiral bias leads to increased control. However, when conflict exists among the chiral units for helical sense control, the majority rule experiment, a larger chiral bias leads to decreased control of the helical sense and therefore a smaller optical activity. Changing the achiral units in the majority rule experiment can change the nature of the statistical physics between statistical and thermal randomness. In general, the experiments quantitatively demonstrate that the effect of chirality is not an intrinsic property of the chiral moiety but rather depends on the molecular environment. Copyright © 2004 John Wiley & Sons, Ltd. [source] Optical probing and imaging of live cells using SERS labelsJOURNAL OF RAMAN SPECTROSCOPY, Issue 1 2009Janina Kneipp Abstract During surface-enhanced Raman scattering (SERS), molecules exhibit a significant increase in their Raman signals when attached, or in very close vicinity, to gold or silver nanostructures. This effect is exploited as the basis of a new class of optical labels. Here we demonstrate robust and sensitive SERS labels as probes for imaging live cells. These hybrid labels consist of gold nanoparticles with Rose Bengal or Crystal Violet attached as reporter molecules. These new labels are stable and nontoxic, do not suffer from photobleaching, and can be excited at any excitation wavelength, even in the near infrared. SERS labels can be detected and imaged through the specific Raman signatures of the reporters. In addition, surface-enhanced Raman spectroscopy in the local optical fields of the gold nanoparticles also provides sensitive information on the immediate molecular environment of the label in the cell and allows imaging of the native constituents of the cell. This is demonstrated by images based on a characteristic Raman line of the reporter as well as by displaying lipids based on the SERS signal of the CH deformation/bending modes at ,1470 cm,1. Copyright © 2008 John Wiley & Sons, Ltd. [source] A clash to conquer: the malaria parasite liver infectionMOLECULAR MICROBIOLOGY, Issue 6 2006Sebastian A. Mikolajczak Summary All mammalian malaria parasite species have an initial tissue stage in liver cells. The liver stage produces new parasite forms that can enter and live inside red blood cells. Accordingly, the first place of residence provides parasites with a radically different cellular and molecular environment from their subsequent red blood cell home. Liver stages have remained refractory to reveal their secrets, yet the last few years have seen several advances in elucidating their biology. This review looks at the more recent findings concerning the liver stage,host hepatocyte association, some of which may become powerful weapons in the prevention of malaria infection. We also outline areas of liver stage research and technological development that provide promising foci to accelerate a better understanding of this most elusive of the parasites many life cycle stages. [source] The Effect of Molecular Environment on the Photoisomerization of Urocanic Acid,PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 2 2004Richard A. Wallis ABSTRACT Urocanic acid, imidazole propenoic acid, is a metabolic product of histidine, which accumulates in skin and is excreted in sweat. It absorbs UV radiation at wavelengths shorter than 340 nm, and its principal photochemical reaction is a trans-cis isomerization about the propenyl double bond. This isomerization to the biologically active cis isomer is implicated in the photo-induced suppression of the immune system of skin. The kinetics of the trans,cis photoisomerization of urocanic acid has been determined in a number of solvents, spanning a range of polarities. The initial rates of isomerization and the photostationary trans-cis compositions, in all solvents except water, correlate linearly with solvent polarity. This indicates that the isomerization proceeds through a polar intermediate that is stabilized by coulombic interactions with the molecular environment. [source] Preferential regeneration of the NADPH: protochlorophyllide oxidoreductase oligomer complexes in pea epicotyls after bleachingPHYSIOLOGIA PLANTARUM, Issue 1 2010Andrea Szenzenstein The regeneration and stability of the NADPH:protochlorophyllide oxidoreductase (POR, EC 1.3.1.33) enzyme complexes were studied in bleached epicotyls of 9-day-old dark-germinated pea (Pisum sativum L. cv. Zsuzsi) seedlings. Middle segments were illuminated with 1300 µmol m,2 s,1photon flux density (PFD) white light and subsequently incubated in total darkness for 4,24 h at 24°C. Almost the full amount of protochlorophyllide (Pchlide) was degraded after 60 min illumination. The preferential regeneration of the 655 nm emitting Pchlide form was observed after 4 h dark incubation; the accumulation of the short-wavelength Pchlide form,dominating in epicotyls of dark-grown seedling,required 18,24 h dark. The Pchlide content of bleached samples was around 2.5% of that of the etiolated samples; after 4 h of dark incubation this value increased to 4,7%. Polyacrylamide gel electrophoresis and western blot showed that the amount of the POR protein decreased to about 50% during bleaching; after 4 h regeneration it reached almost the same level as that of dark-grown samples. We concluded that much more POR protein compared with Pchlide pigment remained stable during bleaching and the non-destroyed POR units were able to form preferentially oligomers during the dark-regeneration which could collect de novo synthesized Pchlide into 655 nm emitting complexes. These data indicate the high stability of the POR protein in pea epicotyls and the importance of the molecular environment in stimulating the aggregation of POR units. [source] The structure of short-lived excited states of molecular complexes by time-resolved X-ray diffractionACTA CRYSTALLOGRAPHICA SECTION A, Issue 2 2005Philip Coppens Experimental and computational methods for time-resolved (TR) diffraction now allow the determination of geometry changes on molecular excitation. The first results indicate significant changes in the interatomic distances and molecular shape on photo-excitation, but also a dependence of the induced changes on the molecular environment. Though the use of high-brightness synchrotron sources is essential, it limits the time resolution to the width of the synchrotron pulse which is currently 70,100,ps. The experiments discussed fall into two categories: (i) picosecond powder diffraction experiments on the molecular excitation to a singlet state, and (ii) microsecond experiments on the excited states of inorganic complexes. Both involve reversible processes for which a stroboscopic technique can be applied. [source] Viral interactions with the cytoskeleton: a hitchhiker's guide to the cellCELLULAR MICROBIOLOGY, Issue 3 2006Kerstin Radtke Summary The actin and microtubule cytoskeleton play important roles in the life cycle of every virus. During attachment, internalization, endocytosis, nuclear targeting, transcription, replication, transport of progeny subviral particles, assembly, exocytosis, or cell-to-cell spread, viruses make use of different cellular cues and signals to enlist the cytoskeleton for their mission. Viruses induce rearrangements of cytoskeletal filaments so that they can utilize them as tracks or shove them aside when they represent barriers. Viral particles recruit molecular motors in order to hitchhike rides to different subcellular sites which provide the proper molecular environment for uncoating, replicating and packaging viral genomes. Interactions between subviral components and cytoskeletal tracks also help to orchestrate virus assembly, release and efficient cell-to-cell spread. There is probably not a single virus that does not use cytoskeletal and motor functions in its life cycle. Being well informed intracellular passengers, viruses provide us with unique tools to decipher how a particular cargo recruits one or several motors, how these are activated or tuned down depending on transport needs, and how cargoes switch from actin tracks to microtubules to nuclear pores and back. [source] Cooperative activity of multiple upper layer proteins for thalamocortical axon growthDEVELOPMENTAL NEUROBIOLOGY, Issue 3 2008Takuro Maruyama Abstract During development, sensory thalamocortical (TC) axons grow into the neocortex and terminate primarily in layer 4. To study the molecular mechanism that underlies lamina-specific TC axon termination, we investigated the responsiveness of TC axons to ephrin-A5, semaphorin-7A (Sema7A) and kit ligand (KL), which are expressed in the upper layers of the developing cortex. Dissociated cells of the dorsal thalamus from embryonic rat brain were cultured on dishes that were coated with preclustered Fc-tagged extracellular domains of these molecules. Each protein was found to promote TC axon growth in a dose-dependent fashion of a bell-shaped curve. Any combination of the three proteins showed a cooperative effect in lower concentrations but not in higher concentrations, suggesting that their growth-promoting activities act in a common pathway. The effect of spatial distributions of these proteins was further tested on a filter membrane, in which these proteins were printed at a size that recapitulates the scale of laminar thickness in vivo, using a novel protein-printing technique, Simple-To-mAke Micropore Protein-Printing (STAMP2) method. The results demonstrated that TC axons grew massively on the laminin-coated region but were prevented from invading the adjacent ephrin-A5-printed region, suggesting that TC axons detect relative differences in the growth effect between these regions. Moreover, the inhibitory action of ephrin-A5 was enhanced by copresence with KL and Sema7A. Together, these results suggest that the lamina-specific TC axon targeting mechanism involves growth-inhibitory activity by multiple molecules in the upper layers and detection in the molecular environments between the upper and deep layers. © 2007 Wiley Periodicals, Inc. Develop Neurobiol, 2008 [source] Relativistic correlating basis sets for actinide atoms from 90Th to 103LrJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 16 2007Takeshi Noro Abstract For 14 actinide atoms from 90Th to 103Lr, contracted Gaussian-type function sets are developed for the description of correlations of the 5f, 6d, and 7s electrons. Basis sets for the 6d orbitals are also prepared, since the orbitals are important in molecular environments despite their vacancy in the ground state of some actinides. A segmented contraction scheme is employed for the compactness and efficiency. Contraction coefficients and exponents are so determined as to minimize the deviation from accurate natural orbitals of the lowest term arising from the 5fn,16d17s2 configuration. The spin-free relativistic effects are considered through the third-order Douglas-Kroll approximation. To test the present correlating sets, all-electron calculations are performed on the ground state of 90ThO molecule. The calculated spectroscopic constants are in excellent agreement with experimental values. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007 [source] | |||||||||||||