Lauren J. Webb

Multitargeting by curcumin as revealed by molecular interaction studies.

Curcumin (diferuloylmethane), the active ingredient in turmeric (Curcuma longa), is a highly pleiotropic molecule with anti-inflammatory, anti-oxidant, chemopreventive, chemosensitization, and radiosensitization activities. The pleiotropic activities attributed to curcumin come from its complex molecular structure and chemistry, as well as its ability to influence multiple signaling molecules. Curcumin has been shown to bind by multiple forces directly to numerous signaling molecules, such as inflammatory molecules, cell survival proteins, protein kinases, protein reductases, histone acetyltransferase, histone deacetylase, glyoxalase I, xanthine oxidase, proteasome, HIV1 integrase, HIV1 protease, sarco (endo) plasmic reticulum Ca(2+) ATPase, DNA methyltransferases 1, FtsZ protofilaments, carrier proteins, and metal ions. Curcumin can also bind directly to DNA and RNA. Owing to its β-diketone moiety, curcumin undergoes keto-enol tautomerism that has been reported as a favorable state for direct binding. The functional groups on curcumin found suitable for interaction with other macromolecules include the α, β-unsaturated β-diketone moiety, carbonyl and enolic groups of the β-diketone moiety, methoxy and phenolic hydroxyl groups, and the phenyl rings. Various biophysical tools have been used to monitor direct interaction of curcumin with other proteins, including absorption, fluorescence, Fourier transform infrared (FTIR) and circular dichroism (CD) spectroscopy, surface plasmon resonance, competitive ligand binding, Forster type fluorescence resonance energy transfer (FRET), radiolabeling, site-directed mutagenesis, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), immunoprecipitation, phage display biopanning, electron microscopy, 1-anilino-8-naphthalene-sulfonate (ANS) displacement, and co-localization. Molecular docking, the most commonly employed computational tool for calculating binding affinities and predicting binding sites, has also been used to further characterize curcumins binding sites. Furthermore, the ability of curcumin to bind directly to carrier proteins improves its solubility and bioavailability. In this review, we focus on how curcumin directly targets signaling molecules, as well as the different forces that bind the curcumin-protein complex and how this interaction affects the biological properties of proteins. We will also discuss various analogues of curcumin designed to bind selective targets with increased affinity.

Cancer drug discovery by repurposing: teaching new tricks to old dogs

Progressively increasing failure rates, high cost, poor bioavailability, poor safety, limited efficacy, and a lengthy design and testing process associated with cancer drug development have necessitated alternative approaches to drug discovery. Exploring established non-cancer drugs for anticancer activity provides an opportunity rapidly to advance therapeutic strategies into clinical trials. The impetus for development of cancer therapeutics from non-cancer drugs stems from the fact that different diseases share common molecular pathways and targets in the cell. Common molecular origins of diverse diseases have been discovered through advancements in genomics, proteomics, and informatics technologies, as well as through the development of analytical tools that allow researchers simultaneously to screen large numbers of existing drugs against a particular disease target. Thus, drugs originally identified as antitussive, sedative, analgesic, antipyretic, antiarthritic, anesthetic, antidiabetic, muscle relaxant, immunosuppressant, antibiotic, antiepileptic, cardioprotective, antihypertensive, erectile function enhancing, or angina relieving are being repurposed for cancer. This review describes the repurposing of these drugs for cancer treatment.

Electrostatic Fields Near the Active Site of Human Aldose Reductase: 1. New Inhibitors and Vibrational Stark Effect Measurements†

Vibrational Stark effect spectroscopy was used to measure electrostatic fields in the hydrophobic region of the active site of human aldose reductase (hALR2). A new hALR2 inhibitor was designed and synthesized that contains a nitrile probe with a Stark tuning rate of 0.77 cm-1/(MV/cm). Mutations to amino acid residues in the vicinity of the nitrile functional group were selected based on electrostatics calculations, possible complications from hydrogen bonds near the nitrile, and comparison with the active site of human aldehyde reductase, whose structure is very similar. Changes in the absorption energy of the nitrile probe when bound to those mutated proteins were then used to quantify perturbations to the proteins electrostatic field. Electrostatic field changes as large as -10 MV/cm were observed. Measured electrostatic fields were compared to predictions based on continuum electrostatics calculations, revealing that substantial modifications to the calculation strategy are necessary. The effects of hydrogen bonding of amino acid side chains to the nitrile probe are considered, and applications of vibrational Stark effect spectroscopy to investigations of ligand binding and biological function are discussed.

Chlorination of hydrogen-terminated silicon (111) surfaces

Infrared absorption spectroscopy was used to investigate the chlorination of hydrogen-terminated Si(111) surfaces by three different methods: (a) exposure to a saturated solution of phosphorus pentachloride (PCl5) in chlorobenzene; (b) exposure to chlorine gas, Cl2(g), and (c) exposure to Cl2(g) under UV illumination. X-ray photoelectron spectroscopy and first principles model (clusters) calculations were used to explore the structure and dynamics of these surfaces. The infrared spectra exhibited sharp chlorine-related vibrations at 586 and 527 cm^–1. The narrow full width at half maximum of these vibrations for all three preparation methods indicated that all functionalization schemes produced a nearly complete monolayer of Cl with little surface roughening or introduction of step edges. The 527 cm^–1 mode was at a much higher frequency than might be expected for the bending vibration of Si monochloride. Theoretical calculations show, however, that this vibration involves the displacement of the top Si atom parallel to the surface, subject to a relatively stiff potential, shifting its frequency to a value fairly close to that of the Si–Cl stretching mode on a Si(111) surface.

Vibrational Stark Effect Spectroscopy at the Interface of Ras and Rap1A Bound to the Ras Binding Domain of RalGDS Reveals an Electrostatic Mechanism for Protein−Protein Interaction

Electrostatic fields at the interface of the Ras binding domain of the protein Ral guanine nucleotide dissociation stimulator (RalGDS) with the structurally analogous GTPases Ras and Rap1A were measured with vibrational Stark effect (VSE) spectroscopy. Eleven residues on the surface of RalGDS that participate in this protein-protein interaction were systematically mutated to cysteine and subsequently converted to cyanocysteine in order to introduce a nitrile VSE probe in the form of the thiocyanate (SCN) functional group. The measured SCN absorption energy on the monomeric protein was compared with solvent-accessible surface area (SASA) calculations and solutions to the Poisson-Boltzmann equation using Boltzmann-weighted structural snapshots from molecular dynamics simulations. We found a weak negative correlation between SASA and measured absorption energy, indicating that water exposure of protein surface amino acids can be estimated from experimental measurement of the magnitude of the thiocyanate absorption energy. We found no correlation between calculated field and measured absorption energy. These results highlight the complex structural and electrostatic nature of the protein-water interface. The SCN-labeled RalGDS was incubated with either wild-type Ras or wild-type Rap1A, and the formation of the docked complex was confirmed by measurement of the dissociation constant of the interaction. The change in absorption energy of the thiocyanate functional group due to complex formation was related to the change in electrostatic field experienced by the nitrile functional group when the protein-protein interface forms. At some locations, the nitrile experiences the same shift in field when bound to Ras and Rap1A, but at others, the change in field is dramatically different. These differences identify residues on the surface of RalGDS that direct the specificity of RalGDS binding to its in vivo binding partner, Rap1A, through an electrostatic mechanism.

Electrochemical Detection of Single Phospholipid Vesicle Collisions at a Pt Ultramicroelectrode

We report the collision behavior of single unilamellar vesicles, composed of a bilayer lipid membrane (BLM), on a platinum (Pt) ultramicroelectrode (UME) by two electrochemical detection methods. In the first method, the blocking of a solution redox reaction, induced by the single vesicle adsorption on the Pt UME, can be observed in the amperometric i-t response as current steps during the electrochemical oxidation of ferrocyanide. In the second technique, the ferrocyanide redox probe is directly encapsulated inside vesicles and can be oxidized during the vesicle collision on the UME if the potential is poised positive enough for ferrocyanide oxidation to occur. In the amperometric i-t response for the latter experiment, a current spike is observed. Here, we report the vesicle blocking (VB) method as a relevant technique for determining the vesicle solution concentration from the collisional frequency and also for observing the vesicle adhesion on the Pt surface. In addition, vesicle reactor (VR) experiments show clear evidence that the lipid bilayer membrane does not collapse or break open at the Pt UME during the vesicle collision. Because the bilayer is too thick for electron tunneling to occur readily, an appropriate concentration of a surfactant, such as Triton X-100 (TX100), was added in the VR solution to induce loosening of the bilayer (transfection conditions), allowing the electrode to oxidize the contents of the vesicle. With this technique, the TX100 effect on the vesicle lipid bilayer permeability can be evaluated through the current spike charge and frequency corresponding to redox vesicle collisions.

Role of Surface Oxides in the Formation of Solid-Electrolyte Interphases at Silicon Electrodes for Lithium-Ion Batteries

Nonaqueous solvents in modern battery technologies undergo electroreduction at negative electrodes, leading to the formation of a solid-electrolyte interphase (SEI). The mechanisms and reactions leading to a stable SEI on silicon electrodes in lithium-ion batteries are still poorly understood. This lack of understanding inhibits the rational design of electrolyte additives, active material coatings, and the prediction of Li-ion battery life in general. We prepared SEI with a common nonaqueous solvent (LiPF6 in PC and in EC/DEC 1:1 by wt %) on silicon oxide and etched silicon (001) surfaces in various states of lithiation to understand the role of surface chemistry on the SEI formation mechanism and SEI structure. Anhydrous and anoxic techniques were used to prevent air and moisture contamination of prepared SEI films, allowing for more accurate characterization of SEI chemical stratification and composition by X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (TOF-SIMS) depth profiling. Additionally, multivariate statistical methods were used to better understand TOF-SIMS depth profiling studies. We conclude that the absence of native-oxide layer on silicon has a significant impact on the formation, composition, structure, and thickness of the SEI.

Apyrase Suppression Raises Extracellular ATP Levels and Induces Gene Expression and Cell Wall Changes Characteristic of Stress Responses

Suppressing the expression of two apyrase genes raises extracellular ATP levels and induces gene expression, growth, and cell wall changes characteristic of stress responses, thus implicating extracellular nucleotides as early signals linking biotic and abiotic stresses to growth inhibition. Plant cells release ATP into their extracellular matrix as they grow, and extracellular ATP (eATP) can modulate the rate of cell growth in diverse tissues. Two closely related apyrases (APYs) in Arabidopsis (Arabidopsis thaliana), APY1 and APY2, function, in part, to control the concentration of eATP. The expression of APY1/APY2 can be inhibited by RNA interference, and this suppression leads to an increase in the concentration of eATP in the extracellular medium and severely reduces growth. To clarify how the suppression of APY1 and APY2 is linked to growth inhibition, the gene expression changes that occur in seedlings when apyrase expression is suppressed were assayed by microarray and quantitative real-time-PCR analyses. The most significant gene expression changes induced by APY suppression were in genes involved in biotic stress responses, which include those genes regulating wall composition and extensibility. These expression changes predicted specific chemical changes in the walls of mutant seedlings, and two of these changes, wall lignification and decreased methyl ester bonds, were verified by direct analyses. Taken together, the results are consistent with the hypothesis that APY1, APY2, and eATP play important roles in the signaling steps that link biotic stresses to plant defense responses and growth changes.

Scanning tunneling spectroscopy of methyl- and ethyl-terminated Si(111) surfaces

Methyl- and ethyl-terminated Si(111) surfaces prepared by a two-step chlorination/alkylation method were characterized by low temperature scanning tunneling spectroscopy (STS). The STS data showed remarkably low levels of midgap states on the CH3- and C2H5-terminated Si surfaces. A large conductance gap relative to the Si band gap was observed for both surfaces as well as for the hydrogen-terminated Si(111) surface. This large gap is ascribed to scanning tunneling microscope tip-induced band bending resulting from a low density of midgap states which avoid pinning of the Fermi levels on these passivated surfaces.

Review: recent advances and current challenges in scanning probe microscopy of biomolecular surfaces and interfaces.

The introduction of scanning probe microscopy (SPM) techniques revolutionized the field of condensed matter science by allowing researchers to probe the structure and composition of materials on an atomic scale. Although these methods have been used to make molecular- and atomic-scale measurements on biological systems with some success, the biophysical sciences remain on the cusp of a breakthrough with SPM technologies similar in magnitude to that experienced by fields related to solid-state surfaces and interfaces. Numerous challenges arise when attempting to connect biological molecules that are often delicate, dynamic, and complex with the experimental requirements of SPM techniques. However, there are a growing number of studies in which SPM has been successfully used to achieve subnanometer resolution measurements in biological systems where carefully designed and prepared samples have been paired with appropriate SPM techniques. We review significant recent innovations in applying SPM techniques to biological molecules, and highlight challenges that face researchers attempting to gain atomic- and molecular-level information of complex biomolecular structures.