Regulating the Supramolecular Polymerization of Fibrous Crystalline Structures in Aqueous Solution.

Inspired by protein polymerizations, much progress has been made in making "polymer-like" supramolecular structures from small synthetic subunits through non-covalent bonds. A few regulation mechanisms have also been explored in synthetic platforms to create supramolecular polymers and materials with dynamic properties. Herein, a type of reactive regulator that facilitates the dimerization of the monomer precursors through dynamic bonds to trigger the supramolecular assembly from small molecules in an aqueous solution is described.

Binding and backbone dynamics of protein under topological constraint: calmodulin as a model system.

Herein we present the effect of artificially imposed topological constraint on calmodulin (CaM) backbone dynamics and its molecular recognition behavior. While backbone dynamics of CaM remain largely unperturbed, the thermodynamic profile of CaM binding to the smooth-muscle myosin light-chain kinase (smMLCK) peptide is modulated significantly.

Direct LC-MS/MS Detection of Guanine Oxidations in Exon 7 of the p53 Tumor Suppressor Gene.

Oxidation of DNA by reactive oxygen species (ROS) yields 8-oxo-7,8-dihydroguanosine (8-oxodG) as primary oxidation product, which can lead to downstream G to T transversion mutations. DNA mutations are nonrandom, and mutations at specific codons are associated with specific cancers, as widely documented for the p53 tumor suppressor gene. Here, we present the first direct LC-MS/MS study (without isotopic labeling or hydrolysis) of primary oxidation sites of p53 exon 7.

Single Chain Polymeric Nanoparticles to Promote Selective Hydroxylation Reactions of Phenol Catalyzed by Copper.

Metal-containing single chain polymeric nanoparticles (SCPNs) can be used as synthetic mimics of metalloenzymes. Currently, the role of the folded polymer backbones on the activity and selectivity of metal sites is not clear. Herein, we report our findings on how polymeric frameworks modulate the coordination of Cu sites and the catalytic activity/selectivity of Cu-containing SCPNs mimicking monophenol hydroxylation reactions.

Methyl-Cytosine-Driven Structural Changes Enhance Adduction Kinetics of an Exon 7 fragment of the p53 Gene.

Methylation of cytosine (C) at C-phosphate-guanine (CpG) sites enhances reactivity of DNA towards electrophiles. Mutations at CpG sites on the p53 tumor suppressor gene that can result from these adductions are in turn correlated with specific cancers. Here we describe the first restriction-enzyme-assisted LC-MS/MS sequencing study of the influence of methyl cytosines (MeC) on kinetics of p53 gene adduction by model metabolite benzo[a]pyrene-7,8-dihydrodiol-9,10-epoxide (BPDE), using methodology applicable to correlate gene damage sites for drug and pollutant metabolites with mutation sites.

A Biocompatible and Biodegradable Protein Hydrogel with Green and Red Autofluorescence: Preparation, Characterization and In Vivo Biodegradation Tracking and Modeling.

Because of its good biocompatibility and biodegradability, albumins such as bovine serum albumin (BSA) and human serum albumin (HSA) have found a wide range of biomedical applications. Herein, we report that glutaraldehyde cross-linked BSA (or HSA) forms a novel fluorescent biological hydrogel, exhibiting new green and red autofluorescence in vitro and in vivo without the use of any additional fluorescent labels. UV-vis spectra studies, in conjunction with the fluorescence spectra studies including emission, excitation and synchronous scans, indicated that three classes of fluorescent compounds are presumably formed during the gelation process.

CHEMICAL SELECTIVITY OF NUCLEOBASE ADDUCTION RELATIVE TO IN VIVO MUTATION SITES ON EXON 7 FRAGMENT OF P53 TUMOR SUPPRESSOR GENE.

Damage to p53 tumor suppressor gene is found in half of all human cancers. Databases integrating studies of large numbers of tumors and cancer cell cultures show that mutation sites of specific p53 codons are correlated with specific types of cancers. If the most frequently damaged p53 codons in vivo correlate with the most frequent chemical damage sites in vitro, predictions of organ-specific cancer risks might result.

Characterizing protein modifications by reactive metabolites using magnetic bead bioreactors and LC-MS/MS.

We report here label-free metabolite-protein adduct detection and identification employing magnetic beads coated with metabolic enzymes as bioreactors to generate metabolites and possible metabolite-protein adducts for analysis by liquid chromatography-tandem mass spectrometry.

Nrbf2 protein suppresses autophagy by modulating Atg14L protein-containing Beclin 1-Vps34 complex architecture and reducing intracellular phosphatidylinositol-3 phosphate levels.

Autophagy is a tightly regulated lysosomal degradation pathway for maintaining cellular homeostasis and responding to stresses. Beclin 1 and its interacting proteins, including the class III phosphatidylinositol-3 kinase Vps34, play crucial roles in autophagy regulation in mammals. We identified nuclear receptor binding factor 2 (Nrbf2) as a Beclin 1-interacting protein from Becn1(-/-);Becn1-EGFP/+ mouse liver and brain.

Quantitative proteomic analysis of mitochondria in aging PS-1 transgenic mice.

Accumulating evidence suggests mitochondrial alterations are intimately associated with the pathogenesis of Alzheimer's disease (AD). In order to determine if mutations of presenilin-1 (PS-1) affect levels of mitochondrial proteins at different ages we enriched mitochondrial fractions from 3-, 6-, 12-month-old knock-in mice expressing the M146V PS-1 mutation and identified, and quantified proteins using cleavable isotope-coded affinity tag labeling and two-dimensional liquid chromatography/tandem mass spectrometry (2D-LC/MS/MS). Using this approach, 165 non-redundant proteins were identified with 80 of them present in all three age groups.

Inhibition of MITF and tyrosinase by paeonol-stimulated JNK/SAPK to reduction of phosphorylated CREB.

Tyrosinase and its transcriptional regulator microphthalmia-associated transcription factor (MITF) play critical roles in regulation of melanogenesis, and are required for environmental cues or agents in modulation of melanin synthesis. Identifying the signals regulating tyrosinase and MITF is crucial to understanding how pigmentation responds to extracellular stimuli. In this report, we discovered that paeonol down-regulated melanin production via decreasing MITF expression and consequent mRNA and protein levels of tyrosinase.

Interior and interfacial aqueous solvation of benzene dicarboxylate dianions and their methylated analogues: A combined molecular dynamics and photoelectron spectroscopy study.

Aqueous solvation of benzene dicarboxylate dianions (BCD(2-)) was studied by means of photoelectron spectroscopy and molecular dynamics simulations. Photoelectron spectra of hydrated o- and p-BCD(2-) with up to 25 water molecules were obtained. An even-odd effect was observed for the p-BCD(2-) system as a result of the alternate solvation of the two negative charges.

Probing the electronic structure of [2Fe-2S] clusters with three coordinate iron sites by use of photoelectron spectroscopy.

Five series of [2Fe-2S] complexes, [Fe(2)S(2)Cl(2)(-)(x)(CN)(x)](-), [Fe(2)S(2)(SEt)(2)(-)(x)Cl(x)](-), [Fe(2)S(2)(SEt)(2)(-)(x)(CN)(x)](-), [Fe(2)S(2)Cl(2)(-)(x)(OAc)(x)](-) (OAc = acetate), and [Fe(2)S(2)(SEt)(2)(-)(x)(OPr)(x)](-) (OPr = propionate) (x = 0-2), were produced by collision-induced dissociation of the corresponding [4Fe-4S] complexes, and their electronic structures were studied by photoelectron spectroscopy. All the [2Fe-2S] complexes contain a [Fe(2)S(2)](+) core similar to that in reduced [2Fe] ferredoxins but with different coordination geometries. For the first three series, which only involve tricoordinated Fe sites, a linear relationship between the measured binding energies and the substitution number (x) was observed, revealing the independent ligand contributions to the total electron binding energies.

Electronic structure and intrinsic redox properties of [2Fe-2S]+ clusters with tri- and tetracoordinate iron sites.

Using potentially bidentate ligands (-SC2H4NH2), we produced [2Fe-2S]+ species of different coordination geometries by fission of [4Fe-4S]2+ complexes. Even though the ligands are monodentate in the cubane complexes, both mono- and bidentate complexes were observed in the [2Fe] fission products through self-assembly because of the high reactivity of the tricoordinate iron sites. The electronic structure of the [2Fe] species was probed using photoelectron spectroscopy and density functional calculations.

Structure of the Na(x)Cl(x+1) (-) (x=1-4) clusters via ab initio genetic algorithm and photoelectron spectroscopy.

The application of the ab initio genetic algorithm with an embedded gradient has been carried out for the elucidation of global minimum structures of a series of anionic sodium chloride clusters, Na(x)Cl(x+1) (-) (x=1-4), produced in the gas phase using electrospray ionization and studied by photoelectron spectroscopy. These are all superhalogen species with extremely high electron binding energies. The vertical electron detachment energies for Na(x)Cl(x+1) (-) were measured to be 5.

Bulk versus interfacial aqueous solvation of dicarboxylate dianions.

Solvation of dicarboxylate dianions of varying length of the aliphatic chain in water clusters and in extended aqueous slabs was investigated using photoelectron spectroscopy and molecular dynamics simulations. Photoelectron spectra of hydrated succinate, adipate, and tetradecandioic dianions with up to 20 water molecules were obtained. Even-odd effects were observed as a result of the alternate solvation mode of the two negative charges with increasing solvent numbers.

Sequential oxidation of the cubane [4Fe--4S] cluster from [4Fe--4S](-) to [4Fe--4S](3+) in Fe(4)S(4)L(n)(-) complexes.

Gaseous Fe(4)S(n)(-) (n = 4-6) clusters and synthetic analogue complexes, Fe(4)S(4)L(n)(-) (L = Cl, Br, I; n = 1-4), were produced by laser vaporization of a solid Fe/S target and electrospray from solution samples, respectively, and their electronic structures were probed by photoelectron spectroscopy. Low binding energy features derived from minority-spin Fe 3d electrons were clearly distinguished from S-derived bands. We showed that the electronic structure of the simplest Fe(4)S(4)(-) cubane cluster can be described by the two-layer spin-coupling model previously developed for the [4Fe] cubane analogues.

Terminal ligand influence on the electronic structure and intrinsic redox properties of the [Fe4S4]2+ cubane clusters.

We used photoelectron spectroscopy (PES) to study how the terminal ligands influence the electronic structure and redox properties of the [4Fe-4S] cubane in several series of ligand-substituted analogue complexes: [Fe(4)S(4)Cl(4-x)(CN)(x)](2-), [Fe(4)S(4)Cl(4-x)(SCN)(x)](2-), [Fe(4)S(4)Cl(4-x)(OAc)(x)](2-), [Fe(4)S(4)(SC(2)H(5))(4-x)(OPr)(x)](2-), and [Fe(4)S(4)(SC(2)H(5))(4-x)Cl(x)](2-) (x = 0-4). All the ligand-substituted complexes gave similar PES spectral features as the parents, suggesting that the mixed-ligand coordination does not perturb the electronic structure of the cubane core significantly. The terminal ligands, however, have profound effects on the electron binding energies of the cubane and induce significant shifts of the PES spectra, increasing in the order SC(2)H(5)(-) --> Cl(-) --> OAc(-)/OPr(-) --> CN(-) --> SCN(-).

Solvent-mediated folding of a doubly charged anion.

The microsolvation of the suberate dianion, -O2C(CH2)6CO2-, with two separate charge centers was studied by photoelectron spectroscopy and molecular dynamics simulation one solvent molecule at a time for up to 20 waters. It is shown that the two negative charges are solvated in the linear suberate alternately. As the solvent number increases, the negative charges are screened and a conformation change occurs at 16 waters, where the cooperative hydrogen bonding of water is large enough to overcome the Coulomb repulsion and pull the two negative charges closer through a water bridge.