Polyamine Pathway Inhibitor DENSPM Suppresses Lipid Metabolism in Pheochromocytoma Cell Line.

Pheochromocytomas (PCCs) are tumors arising from chromaffin cells in the adrenal medulla, and paragangliomas (PGLs) are tumors derived from extra-adrenal sympathetic or parasympathetic paraganglia; these tumors are collectively referred to as PPGL cancer. Treatment for PPGL primarily involves surgical removal of the tumor, and only limited options are available for treatment of the disease once it becomes metastatic. Human carriers of the heterozygous mutations in the succinate dehydrogenase subunit B () gene are susceptible to the development of PPGL.

Temperature Dependence of the Air/Water Interface Revealed by Polarization Sensitive Sum-Frequency Generation Spectroscopy.

The temperature dependence of the vibrational sum-frequency generation (vSFG) spectra of the air/water interface is investigated using many-body molecular dynamics (MB-MD) simulations performed with the MB-pol potential energy function. The vSFG spectra calculated for different polarization combinations are then analyzed in terms of molecular autocorrelation and cross-correlation contributions. To provide molecular-level insights into interfacial hydrogen-bonding topologies, which give rise to specific spectroscopic features, the vSFG spectra are further investigated by separating contributions associated with water molecules donating zero, one, or two hydrogen bonds to neighboring water molecules.

Temperature-dependent vibrational spectra and structure of liquid water from classical and quantum simulations with the MB-pol potential energy function.

The structure of liquid water as a function of temperature is investigated through the modeling of infrared and Raman spectra along with structural order parameters calculated from classical and quantum molecular dynamics simulations with the MB-pol many-body potential energy function. The magnitude of nuclear quantum effects is also monitored by comparing the vibrational spectra obtained from classical and centroid molecular dynamics, both in intensities and peak positions. The observed changes in spectral activities are shown to reflect changes in the underlying structure of the hydrogen-bond network and are found to be particularly sensitive to many-body effects in the representation of the electrostatic interactions.

Molecular Origin of the Vibrational Structure of Ice I.

An unambiguous assignment of the vibrational spectra of ice I remains a matter of debate. This study demonstrates that an accurate representation of many-body interactions between water molecules, combined with an explicit treatment of nuclear quantum effects through many-body molecular dynamics (MB-MD), leads to a unified interpretation of the vibrational spectra of ice I in terms of the structure and dynamics of the underlying hydrogen-bond network. All features of the infrared and Raman spectra in the OH stretching region can be unambiguously assigned by taking into account both the symmetry and the delocalized nature of the lattice vibrations as well as the local electrostatic environment experienced by each water molecule within the crystal.

On the accuracy of the MB-pol many-body potential for water: Interaction energies, vibrational frequencies, and classical thermodynamic and dynamical properties from clusters to liquid water and ice.

The MB-pol many-body potential has recently emerged as an accurate molecular model for water simulations from the gas to the condensed phase. In this study, the accuracy of MB-pol is systematically assessed across the three phases of water through extensive comparisons with experimental data and high-level ab initio calculations. Individual many-body contributions to the interaction energies as well as vibrational spectra of water clusters calculated with MB-pol are in excellent agreement with reference data obtained at the coupled cluster level.

Exploring Electrostatic Effects on the Hydrogen Bond Network of Liquid Water through Many-Body Molecular Dynamics.

To probe the dynamic nature of the hydrogen bond network in water, linear and nonlinear infrared spectra of dilute HOD in H2O are computed from many-body molecular dynamics simulations with the MB-pol potential, which have been shown to accurately predict the properties of water from the gas to the condensed phase. The effects of various approximations to the many-body expansion of the dipole moment surface on the OD-stretch absorption line shapes are analyzed at different levels of theory. The interplay between effects associated with the variation of the HOD dipole moment and instantaneous nuclear configurations causes qualitative differences in the absorption profiles, which are traced back to how induction contributions are treated within the many-body formalism.

Troponins, intrinsic disorder, and cardiomyopathy.

Cardiac troponin is a dynamic complex of troponin C, troponin I, and troponin T (TnC, TnI, and TnT, respectively) found in the myocyte thin filament where it plays an essential role in cardiac muscle contraction. Mutations in troponin subunits are found in inherited cardiomyopathies, such as hypertrophic cardiomyopathy (HCM) and dilated cardiomyopathy (DCM). The highly dynamic nature of human cardiac troponin and presence of numerous flexible linkers in its subunits suggest that understanding of structural and functional properties of this important complex can benefit from the consideration of the protein intrinsic disorder phenomenon.

PKC ε Phosphorylates and Mediates the Cell Membrane Localization of RhoA.

Protein kinase C ε (PKC ε ) signals through RhoA to modulate cell invasion and motility. In this study, the multifaceted interaction between PKC ε and RhoA was defined. Phosphopeptide mapping revealed that PKC ε phosphorylates RhoA at T127 and S188.

Multicellular bacteria deploy the type VI secretion system to preemptively strike neighboring cells.

The Type VI Secretion System (T6SS) functions in bacteria as a contractile nanomachine that punctures and delivers lethal effectors to a target cell. Virtually nothing is known about the lifestyle or physiology that dictates when bacteria normally produce their T6SS, which prevents a clear understanding of how bacteria benefit from its action in their natural habitat. Proteus mirabilis undergoes a characteristic developmental process to coordinate a multicellular swarming behavior and will discriminate itself from another Proteus isolate during swarming, resulting in a visible boundary termed a Dienes line.

N-way FRET microscopy of multiple protein-protein interactions in live cells.

Fluorescence Resonance Energy Transfer (FRET) microscopy has emerged as a powerful tool to visualize nanoscale protein-protein interactions while capturing their microscale organization and millisecond dynamics. Recently, FRET microscopy was extended to imaging of multiple donor-acceptor pairs, thereby enabling visualization of multiple biochemical events within a single living cell. These methods require numerous equations that must be defined on a case-by-case basis.

Photonic modulation of electron transfer with switchable phase inversion.

Photochromes may be reversibly photoisomerized between two metastable states and their properties can influence, and be influenced by, other chromophores in the same molecule through energy or electron transfer. In the photochemically active molecular tetrad described here, a porphyrin has been covalently linked to a fullerene electron acceptor, a quinoline-derived dihydroindolizine photochrome, and a dithienylethene photochrome. The porphyrin first excited singlet state undergoes photoinduced electron transfer to the fullerene to generate a charge-separated state.

Pulse-shaping multiphoton FRET microscopy.

Fluorescence Resonance Energy Transfer (FRET) microscopy is a commonly-used technique to study problems in biophysics that range from uncovering cellular signaling pathways to detecting conformational changes in single biomolecules. Unfortunately, excitation and emission spectral overlap between the fluorophores create challenges in quantitative FRET studies. It has been shown previously that quantitative FRET stoichiometry can be performed by selective excitation of donor and acceptor fluorophores.

A systematic method for the targeted discovery of chemical attribution signatures: application to isopropyl bicyclophosphate production.

Potential attribution signatures for the synthesis of a highly toxic bicyclophosphate, 4-isopropyl-2,6,7-trioxa-1-phosphabicyclo[2.2.2]octane 1-oxide (Isopropyl Bicyclophosphate or IPBCP) were discovered using a trilateral synthetic, analytical, and statistical approach.

Coordination of the Rab5 cycle on macropinosomes.

The GTPase Rab5a regulates the homotypic and heterotypic fusion of membranous organelles during the early stages of endocytosis. Many of the molecules which regulate the Rab5a cycle of association with membranes, activation, deactivation and dissociation are known. However, the extent to which these molecular scale activities are coordinated on membranes to affect the behavior of individual organelles has not been determined.

All-photonic multifunctional molecular logic device.

Photochromes are photoswitchable, bistable chromophores which, like transistors, can implement binary logic operations. When several photochromes are combined in one molecule, interactions between them such as energy and electron transfer allow design of simple Boolean logic gates and more complex logic devices with all-photonic inputs and outputs. Selective isomerization of individual photochromes can be achieved using light of different wavelengths, and logic outputs can employ absorption and emission properties at different wavelengths, thus allowing a single molecular species to perform several different functions, even simultaneously.

Transient increase in cyclic AMP localized to macrophage phagosomes.

Cyclic AMP (cAMP) regulates many biological processes and cellular functions. The importance of spatially localized intracellular gradients of cAMP is increasingly appreciated. Previous work in macrophages has shown that cAMP is produced during phagocytosis and that elevated cAMP levels suppress host defense functions, including generation of proinflammatory mediators, phagocytosis and killing.

Photochemical "triode" molecular signal transducer.

A molecular "hexad" in which five bis(phenylethynyl)anthracene (BPEA) fluorophores and a dithienylethene photochrome are organized by a central hexaphenylbenzene unit has been prepared. Singlet-singlet energy transfer among the BPEA units occurs on the 0.4 and 60 ps time scales, and when the dithienylethene is in the open form, the BPEA units fluoresce in the 515 nm region with a quantum yield near unity.

An all-photonic molecular keypad lock.

Off and on: A molecular triad, consisting of a porphyrin linked to two different, independently addressable photochromic moieties, functions as a molecular keypad lock with all-photonic inputs and output. The porphyrin correlates the responses of the two inputs to light of different wavelengths and provides an appropriate output as fluorescence, which results only when one of eight possible input combinations has been applied (see figure).

Molecular all-photonic encoder-decoder.

In data processing, an encoder can compress digital information for transmission or storage, whereas a decoder recovers the information in its original form. We report a molecular triad consisting of a dithienylethene covalently linked to two fulgimide photochromes that performs as an all-photonic single-bit 4-to-2 encoder and 2-to-4 decoder. The encoder compresses the information contained in the four inputs into two outputs.

Self-regulation of photoinduced electron transfer by a molecular nonlinear transducer.

Organisms must adapt to survive, necessitating regulation of molecular and subcellular processes. Green plant photosynthesis responds to potentially damaging light levels by downregulating the fraction of excitation energy that drives electron transfer. Achieving adaptive, self-regulating behaviour in synthetic molecules is a critical challenge that must be met if the promises of nanotechnology are to be realized.

All-photonic molecular half-adder.

One molecule acts as both an AND and an XOR Boolean logic gate that share the same two photonic inputs. The molecule comprises a half-adder, adding two binary digits with only light as inputs and outputs, and consists of three covalently linked photochromic moieties, a spiropyran and two quinoline-derived dihydroindolizines. The AND function is based on the absorption properties of the molecule, whereas the XOR function is based on an off-on-off response of the fluorescence to the inputs that results from interchromophore excited-state quenching interactions.

Mammalian lin-7 stabilizes polarity protein complexes.

Mammalian Lin-7 forms a complex with several proteins, including PALS1, that have a role in polarity determination in epithelial cells. In this study we have found that loss of Lin-7 protein from the polarized epithelial cell line Madin-Darby canine kidney II by small hairpin RNA results in defects in tight junction formation as indicated by lowered transepithelial electrical resistance and mislocalization of the tight junction protein ZO-1 after calcium switch. The knock down of Lin-7 also resulted in the loss of expression of several Lin-7 binding partners, including PALS1 and the polarity protein PATJ.

Molecular AND and INHIBIT gates based on control of porphyrin fluorescence by photochromes.

A molecular triad consisting of a porphyrin (P) covalently linked to two photochromes-one from the dihydroindolizine family (DHI) and one from the dihydropyrene family (DHP)-has been synthesized and found to act as either a molecular AND logic gate or an INHIBIT gate, depending on the inputs and initial state of the photochromes. The basis of these functions is quenching of porphyrin fluorescence (output of the gates) by the photochromes. The spiro form of DHI does not quench porphyrin fluorescence, whereas its betaine isomer strongly quenches by photoinduced electron transfer.

PATJ regulates tight junction formation and polarity in mammalian epithelial cells.

Recent studies have revealed an important role for tight junction protein complexes in epithelial cell polarity. One of these complexes contains the apical transmembrane protein, Crumbs, and two PSD95/discs large/zonula occludens domain proteins, protein associated with Lin seven 1 (PALS1)/Stardust and PALS1-associated tight junction protein (PATJ). Although Crumbs and PALS1/Stardust are known to be important for cell polarization, recent studies have suggested that Drosophila PATJ is not essential and its function is unclear.