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. We oxidized a 32 base pair (bp) double-stranded (ds) oligonucleotide representing exon 7 of the p53 gene. Oxidized oligonucleotides were cut by a restriction endonuclease to provide small strands and enable positions and amounts of 8-oxodG to be determined directly by LC-MS/MS. Oxidation sites on the oligonucleotide generated by two oxidants, catechol/Cu2+/NADPH and Fenton's reagent, were located and compared. Guanines in codons 243, 244, 245, and 248 were most frequently oxidized by catechol/Cu2+/NADPH with relative oxidation of 5.6, 7.2, 2.6, and 10.7%, respectively. Fenton's reagent oxidations were more specific for guanines in codons 243 (20.3%) and 248 (10.4%). Modeling of docking of oxidizing species on the ds-oligonucleotide were consistent with the experimental codon oxidation sites. Significantly, codons 244 and 248 are mutational "hotspots" in nonsmall cell and small cell lung cancers, supporting a possible role of oxidation in p53 mutations leading to lung cancer.

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. This method allows direct kinetic measurements by LC-MS/MS sequencing for oligonucleotides longer than 20 base pairs (bp). We used MeC and non-MeC (C) versions of a 32 bp exon 7 fragment of the p53 gene. Methylation of 19 cytosines increased the rate constant 3-fold for adduction on G at the major reactive CpG in codon 248 vs. the non-MeC fragment. Rate constants for non-CpG codons 244 and 243 were not influenced significantly by MeC. Conformational and hydrophobicity changes in the MeC-p53 exon 7 fragment revealed by CD spectra and molecular modeling increase the BPDE binding constant to G in codon 248 consistent with a pathway in which preceding reactant binding greatly facilitates the rate of covalent SN2 coupling.

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. Herein, we describe LC-MS/MS methodology to reveal codons with metabolite-adducted nucleobases by LC-MS/MS for oligonucleotides longer than 20 base pairs. Specifically, we used a known carcinogen, benzo[a]pyrene-7,8-dihydrodiol-9,10-epoxide (BPDE) to determine the most frequently adducted nucleobases within codons. We used a known sequence of 32 base pairs (bp) representing part of p53 exon 7 with 5 possible reactive hot spots. This is the first nucleobase reactivity study of a double stranded DNA p53 fragment featuring more than 20 base pairs with multiple reactive sites. We reacted the 32 bp fragment with benzo[a]pyrene metabolite BPDE that undergoes nucleophilic substitution by DNA bases. Liquid chromatography-mass spectrometry (LC-MS/MS) was used for sequencing of oligonucleotide products from the reacted 32 bp fragment after fragmentation by a restriction endonuclease. Analysis of the adducted p53 fragment compared with unreacted fragment revealed guanines of codons 248 and 244 as most frequently targeted, which are also mutated with high frequency in human tumors. Codon 248 is mutated in non-small cell and small cell lung, head and neck, colorectal and skin cancer, while codon 244 is mutated in small cell lung cancer, all of which involve possible BDPE exposure. Results suggest the utility of this approach for screening of adducted p53 gene by drugs and environmental chemicals to predict risks for organ specific cancers.

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. We also found that Nrbf2-Beclin 1 interaction required the N terminus of Nrbf2. We next used the human retinal pigment epithelial cell line RPE-1 as a model system and showed that transiently knocking down Nrbf2 by siRNA increased autophagic flux under both nutrient-rich and starvation conditions. To investigate the mechanism by which Nrbf2 regulates autophagy, we demonstrated that Nrbf2 interacted and colocalized with Atg14L, suggesting that Nrbf2 is a component of the Atg14L-containing Beclin 1-Vps34 complex. Moreover, ectopically expressed Nrbf2 formed cytosolic puncta that were positive for isolation membrane markers. These results suggest that Nrbf2 is involved in autophagosome biogenesis. Furthermore, we showed that Nrbf2 deficiency led to increased intracellular phosphatidylinositol-3 phosphate levels and diminished Atg14L-Vps34/Vps15 interactions, suggesting that Nrbf2-mediated Atg14L-Vps34/Vps15 interactions likely inhibit Vps34 activity. Therefore, we propose that Nrbf2 may interact with the Atg14L-containing Beclin 1-Vps34 protein complex to modulate protein-protein interactions within the complex, leading to suppression of Vps34 activity, autophagosome biogenesis, and autophagic flux. This work reveals a novel aspect of the intricate mechanism for the Beclin 1-Vps34 protein-protein interaction network to achieve precise control of autophagy.

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. Specifically, at young ages (3 and 6 months), Na(+)/K(+) ATPase and several signal transduction proteins exhibited elevated levels, but dropped dramatically at 12 months. In contrast, components of the oxidative phosporylation pathway (OXPHOS), the mitochondrial permeability transition pore (MPTP), and energy metabolism proteins remained unchanged at 3 months but significantly increased with age. We propose that alterations in calcium homeostasis induced by the PS-1 mutation have a major impact in young animals by inhibiting the function of relevant proteins and inducing compensatory changes. However, in older mice combination of the PS-1 mutation and accumulated oxidative damage results in a functional suppression of OXPHOS and MPTP proteins requiring a compensatory increase in expression levels. In contrast, signal transduction proteins showed decreased levels due to a break down in the compensatory mechanisms. The dysfunction of Na(+)/K(+) ATPase and signal transduction proteins may induce impaired cognition and memory before neurodegeneration occurs.

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. We also found that paeonol reduced phosphorylation of a cAMP responsive element binding protein (phospho-CREB), which binds and activates MITF. A selective inhibitor of c-jun N-terminal or stress-activated protein kinases (JNK/SAPK)-SP600125 significantly reversed paeonol-induced down-regulation of melanogenesis. Inhibition of cAMP/PKA pathway intensified the hypopigmentation response to paeonol. These results identify a mechanism in which paeonol induces the down-regulation of melanogenesis through inhibition of CREB phosphorylation, leading to the expression reduction of MITF and subsequently tyrosinase. The key kinase mediating the effects of paeonol on melanogenesis in B16F10 cells is JNK/SAPK. Additionally, the cAMP/PKA pathway may take part in this process.

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. It was found that tetracoordination significantly decreases the electron binding energies of the [2Fe] complexes, thus increasing the reducing capability of the [2Fe-2S]+ clusters.

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. The effect of the ligand increases in the order SEt --> Cl --> CN, conforming to their electron-withdrawing ability in the same order. The carboxylate ligands in the [Fe(2)S(2)Cl(2)(-)(x)(OAc)(x)](-) and [Fe(2)S(2)(SEt)(2)(-)(x)(OPr)(x)](-) complexes were observed to act as bidentate ligands, giving rise to tetracoordinated iron sites. This is different from their monodentate coordination behavior in the [4Fe-4S] cubane complexes, reflecting the high reactivity of the unsatisfied three-coordinate iron site in the [2Fe-2S] complexes. The [2Fe-2S] complexes with tetracoordinated iron sites exhibit lower electron binding energies, that is, higher reductive activity than the all tricoordinate planar clusters. The electronic structures of all the [2Fe-2S] complexes were shown to conform to the "inverted energy level scheme".

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. However, the high polarizability of the benzene ring makes the two carboxylate groups interact with each other in p-BCD(2-), suppressing the strength of this even-odd effect compared with the linear dicarboxylate dianions linked by an aliphatic chain. No even-odd effect was observed for the o-BCD(2-) system, because each solvent molecule can interact with the two carboxylate groups at the same time due to their proximity. For large solvated clusters, the spectral features of the solute decreased while the solvent features became dominant, suggesting that both o- and p-BCD(2-) are situated in the center of the solvated clusters. Molecular dynamics simulations with both nonpolarizable and polarizable force fields confirmed that all three isomers (o-, m-, and p-BCD(2-)) solvate in the aqueous bulk. However, upon methylation the hydrophobic forces overwhelm electrostatic interactions and, as a result, the calculations predict that the tetramethyl-o-BCD(2-) is located at the water surface with the carboxylate groups anchored in the liquid and the methylated benzene ring tilted away from the aqueous phase.

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. The competition between hydrophilic interactions of the charged carboxylate groups and hydrophobic interactions of the aliphatic chain leads to conformation changes in large water clusters containing dicarboxylates bigger than adipate. It also leads to a transition from bulk aqueous solvation of small dicarboxylates to solvation at the water/vapor interface of the larger ones. Whereas oxalate and adipate solvate in the inner parts of the aqueous slab, suberate and longer dicarboxylate dianions have a strong propensity to the surface. This transition also has consequences for the folding of the flexible aliphatic chain and for the structure of aqueous solvation shells around the dianions.

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 5.6, 6.46, 6.3, and 7.0 eV, for x=1-4, respectively. Our ab initio gradient embedded genetic algorithm program detected the linear global minima for NaCl(2) (-) and Na(2)Cl(3) (-) and three-dimensional structures for the larger species. Na(3)Cl(4) (-) was found to have C(3v) symmetry, which can be viewed as a Na(4)Cl(4) cube missing a corner Na(+) cation, whereas Na(4)Cl(5) (-) was found to have C(4v) symmetry, close to a 3x3 planar structure. Excellent agreement between the theoretically calculated and the experimental spectra was observed, confirming the obtained structures and demonstrating the power of the developed genetic algorithm technique.

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. The photoelectron data revealed that each extra S atom in Fe(4)S(5)(-) and Fe(4)S(6)(-) removes two minority-spin Fe 3d electrons from the [4Fe--4S] cubane core and each halogen ligand removes one Fe 3d electron from the cubane core in the Fe(4)S(4)L(n)(-) complexes, clearly revealing a behavior of sequential oxidation of the cubane over five formal oxidation states: [4Fe--4S](-) --> [4Fe--4S](0) --> [4Fe--4S](+) --> [4Fe-4S](2+) --> [4Fe-4S](3+). The current work shows the electron-storage capability of the [4Fe--4S] cubane, contributes to the understanding of its electronic structure, and further demonstrates the robustness of the cubane as a structural unit and electron-transfer center.

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(-). A linear relationship between the electron binding energies and the substitution number x was observed for each series, indicating that each ligand contributes independently and additively to the total binding energy. The electron binding energies of the gaseous complexes represent their intrinsic oxidation energies; the observed linear dependence on x is consistent with similar observations on the redox potentials of mixed-ligand cubane complexes in solution. The current study reveals the electrostatic nature of the interaction between the [4Fe-4S] cubane core and its coordination environment and provides further evidence for the electronic and structural stability of the cubane core and its robustness as a structural and functional unit in Fe-S proteins.

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. This conformation change, revealed both from the experiment and from the simulation, is a manifestation of the hydrophilic and hydrophobic forces at the molecular level.