cAMP-dependent protein kinase (PKA) complexes probed by complementary differential scanning fluorimetry and ion mobility-mass spectrometry.

cAMP-dependent protein kinase (PKA) is an archetypal biological signaling module and a model for understanding the regulation of protein kinases. In the present study, we combine biochemistry with differential scanning fluorimetry (DSF) and ion mobility-mass spectrometry (IM-MS) to evaluate effects of phosphorylation and structure on the ligand binding, dynamics and stability of components of heteromeric PKA protein complexes in vitro We uncover dynamic, conformationally distinct populations of the PKA catalytic subunit with distinct structural stability and susceptibility to the physiological protein inhibitor PKI. Native MS of reconstituted PKA R2C2 holoenzymes reveals variable subunit stoichiometry and holoenzyme ablation by PKI binding. Finally, we find that although a 'kinase-dead' PKA catalytic domain cannot bind to ATP in solution, it interacts with several prominent chemical kinase inhibitors. These data demonstrate the combined power of IM-MS and DSF to probe PKA dynamics and regulation, techniques that can be employed to evaluate other protein-ligand complexes, with broad implications for cellular signaling.

Time-resolved photoelectron spectroscopy of a dinuclear Pt(II) complex: Tunneling autodetachment from both singlet and triplet excited states of a molecular dianion.

Time-resolved pump-probe photoelectron spectroscopy has been used to study the relaxation dynamics of gaseous [Pt2(µ-P2O5H2)4 + 2H](2-) after population of its first singlet excited state by 388 nm femtosecond laser irradiation. In contrast to the fluorescence and phosphorescence observed in condensed phase, a significant fraction of the photoexcited isolated dianions decays by electron loss to form the corresponding monoanions. Our transient photoelectron data reveal an ultrafast decay of the initially excited singlet (1)A2u state and concomitant rise in population of the triplet (3)A2u state, via sub-picosecond intersystem crossing (ISC). We find that both of the electronically excited states are metastably bound behind a repulsive Coulomb barrier and can decay via delayed autodetachment to yield electrons with characteristic kinetic energies. While excited state tunneling detachment (ESETD) from the singlet (1)A2u state takes only a few picoseconds, ESETD from the triplet (3)A2u state is much slower and proceeds on a time scale of hundreds of nanoseconds. The ISC rate in the gas phase is significantly higher than in solution, which can be rationalized in terms of changes to the energy dissipation mechanism in the absence of solvent molecules. [Pt2(µ-P2O5H2)4 + 2H](2-) is the first example of a photoexcited multianion for which ESETD has been observed following ISC.

Conformer-selective photoelectron spectroscopy of α-lactalbumin derived multianions in the gas phase.

We have recorded conformer-selective, gas-phase photoelectron spectra of α-lactalbumin derived multianions generated by electrospraying solutions of both the native protein and its denatured form (as prepared by breaking the sulfur-sulfur bonds by chemical reduction). Three different groups of gas-phase multianion conformers have been observed and characterized. Highly-folded and partially-unfolded structures are obtained from solutions of the native protein. Only highly-elongated conformers are observed upon electrospraying the denatured protein. Adiabatic detachment energies were determined at several negative charge states for each conformer group. In comparison to highly-elongated conformations, highly-folded structures show a steeper decrease of electron binding energy with increasing negative charge. By comparing experimental detachment energies for highly-elongated structures with the predictions of a simple electrostatic model calculation, we have determined the effective dielectric shielding constant.

Cu(II)- and Mn(III)-porphyrin-derived oligomeric multianions: structures and photoelectron spectra.

We present structures and photoelectron spectra of Mn(III) and Cu(II) meso-tetra(4-sulfonatophenyl)porphyrin (TPPS) multianions, as well as of homomolecular dimers and trimers thereof. The structural assignments are based on a combination of mass spectrometry, ion mobility measurements, and semiempirical as well as density functional theory (DFT) calculations. Depending on the type of central metal atom, two completely different dimer structural motifs are found. With a central Mn(III), the monomeric units are connected via sulfonic-acid-manganese bonds resulting in a tilted stack arrangement of porphyrin rings. With Cu(II) as the central atom, the sulfonic acid groups preferentially bind to the sodium counterions, resulting in a flat dimer structure with coplanar porphyrins. Photoelectron spectra were recorded for monomers, dimers, and trimers, each in a number of different negative charge states as determined by protonation degree (+nH). In some cases, e.g., [Cu(II)TPPS](4-), [(Mn(III)TPPS)2 + H](5-), and [(Mn(III)TPPS)3 + 3H](6-), we observe electron detachment energies close to zero, or even slightly negative. In all cases, we find a large repulsive Coulomb barrier. The observed trends in detachment energies can be interpreted in terms of a simple electrostatic model.

Ion mobility spectrometry, infrared dissociation spectroscopy, and ab initio computations toward structural characterization of the deprotonated leucine-enkephalin peptide anion in the gas phase.

Although the sequencing of protonated proteins and peptides with tandem mass spectrometry has blossomed into a powerful means of characterizing the proteome, much less effort has been directed at their deprotonated analogues, which can offer complementary sequence information. We present a unified approach to characterize the structure and intermolecular interactions present in the gas-phase pentapeptide leucine-enkephalin anion by several vibrational spectroscopy schemes as well as by ion-mobility spectrometry, all of which are analyzed with the help of quantum-chemical computations. The picture emerging from this study is that deprotonation takes place at the C terminus. In this configuration, the excess charge is stabilized by strong intramolecular hydrogen bonds to two backbone amide groups and thus provides a detailed picture of a potentially common charge accommodation motif in peptide anions.

Heterobimetallic cuprates consisting of a redox-switchable, silicon-based metalloligand: synthesis, structures, and electronic properties.

A series of bimetallic silyl halido cuprates consisting of the new tripodal silicon-based metalloligand [κ(3)N-Si(3,5-Me2pz)3Mo(CO)3](-) is presented (pz = pyrazolyl). This metalloligand is straightforwardly accessible by reacting the ambidentate ligand tris(3,5-dimethylpyrazolyl)silanide ({Si(3,5-Me2pz)3}(-)) with [Mo(CO)3(η(6)-toluene)]. The compound features a fac-coordinated tripodal chelating ligand and an outward pointing, "free" pyramidal silyl donor, which is easily accessible for a secondary coordination to other metal centers. Several bimetallic silyl halido cuprates of the general formula [CuX{µ-κ(1)Si:κ(3)N-Si(3,5-Me2pz)3Mo(CO)3}](-) (X = Cl, Br, I) have been synthesized. The electronic and structural properties of these complexes were probed in detail by X-ray diffraction analysis, electrospray mass spectrometry, infrared-induced multiphoton dissociation studies, cyclic voltammetry, spectroelectrochemistry, gas-phase photoelectron spectroscopy, as well as UV/Vis and fluorescence spectroscopy. The heterobimetallic complexes contain linear two-coordinate copper(I) entities with the shortest silicon-copper distances reported so far. Oxidation of the anionic complexes in methylene chloride and acetonitrile solutions at E(1/2)(0( = -0.60 and -0.44 V (vs. ferrocene/ferrocenium (Fc/Fc(+))), respectively, shows substantial reversibility. Based on various results obtained from different characterization methods, as well as density functional theory calculations, these oxidation events were attributed to the Mo(0)/Mo(I) redox couple.

Spectroscopic and theoretical investigations of adenosine 5'-diphosphate and adenosine 5'-triphosphate dianions in the gas phase.

Doubly deprotonated adenosine 5'-diphosphate ([ADP-2H](2-)) and adenosine 5'-triphosphate ([ATP-2H](2-)) dianions were investigated using infrared multiple photon dissociation (IR-MPD) and photoelectron spectroscopy. Vibrational spectra acquired in the X-H stretch region (X = C, N, O) and augmented by isotope-labelling were compared to density functional theory (DFT) calculations at the B3LYP/TZVPP level. This suggests that in [ATP-2H](2-) the two phosphate groups adjacent to the ribose ring are preferentially deprotonated. Photoelectron spectra recorded at 4.66 and 6.42 eV photon energies revealed adiabatic detachment energies of 1.35 eV for [ADP-2H](2-) and 3.35 eV for [ATP-2H](2-). Repulsive Coulomb barriers were estimated at ~2.2 eV for [ADP-2H](2-) and ~1.9 eV for [ATP-2H](2-). Time-dependent DFT calculations have been used to simulate the photoelectron spectra. Photodetachment occurs primarily from lone pair orbitals on oxygen atoms within the phosphate chain.

Isomer-selected photoelectron spectroscopy of isolated DNA oligonucleotides: phosphate and nucleobase deprotonation at high negative charge states.

Fractionation according to ion mobility and mass-to-charge ratio has been used to select individual isomers of deprotonated DNA oligonucleotide multianions for subsequent isomer-resolved photoelectron spectroscopy (PES) in the gas phase. Isomer-resolved PE spectra have been recorded for tetranucleotides, pentanucleotides, and hexanucleotides. These were studied primarily in their highest accessible negative charge states (3-, 4-, and 5-, respectively), as provided by electrospraying from room temperature solutions. In particular, the PE spectra obtained for pentanucleotide tetraanions show evidence for two coexisting classes of gas-phase isomeric structures. We suggest that these two classes comprise: (i) species with excess electrons localized exclusively at deprotonated phosphate backbone sites and (ii) species with at least one deprotonated base (in addition to several deprotonated phosphates). By permuting the sequence of bases in various [A(5-x)T(x)](4-) and [GT(4)](4-) pentanucleotides, we have established that the second type of isomer is most likely to occur if the deprotonated base is located at the first or last position in the sequence. We have used a combination of molecular mechanics and semiempirical calculations together with a simple electrostatic model to explore the photodetachment mechanism underlying our photoelectron spectra. Comparison of predicted to measured photoelectron spectra suggests that a significant fraction of the detected electrons originates from the DNA bases (both deprotonated and neutral).

Combining ion mobility spectrometry, mass spectrometry, and photoelectron spectroscopy in a high-transmission instrument.

We have developed a novel instrument that combines ion mobility spectrometry, mass spectro-metry, and photoelectron spectroscopy. The instrument couples an electrospray ion source, a high-transmission ion mobility cell based on ion funnels, a quadrupole mass filter, and a time-of-flight (magnetic bottle) photoelectron spectrometer operated with a pulsed detachment laser. We show that the instrument can resolve highly structured anion arrival time distributions and at the same time provide corresponding photoelectron spectra-using the DNA oligonucleotide ion [dC(6) - 5H](5-) as a test case. For this multianion we find at least four different, noninterconverting isomers (conformers) simultaneously present in the gas phase at room temperature. For each of these we record well-resolved and remarkably different photoelectron spectra at each of three different detachment laser wavelengths. Two-dimensional ion mobility/electron binding energy plots can be acquired with an automated data collection procedure. We expect that this kind of instrument will significantly improve the capabilities for structure determination of (bio)molecular anions in the gas phase.

Heating a bowl of single-molecule-soup: structure and desorption energetics of water-encapsulated open-cage [60] fullerenoid anions in the gas-phase.

The gas-phase unimolecular decay kinetics of an anionic, open-cage [60] fullerene derivative encapsulating one water molecule is studied by means of black-body IR radiation induced dissociation (BIRD) in the temperature programmable ion trap of a Fourier-transform ion cyclotron resonance (FT-ICR) mass spectrometer. The primary reaction channel observed is escape of the water molecule from the fullerenoid bowl. The rate constants for this water loss as a function of temperature are evaluated using the Arrhenius equation to yield an activation energy of 104 ± 4 kJ mol(-1). A complementary ion mobility spectrometry study contrasting the water-encapsulated and the empty fullerene cages finds identical collision cross sections to within experimental error-supporting the structural assignment of this gas-phase anion as an endohedral (i.e. encapsulated) species. Both experiments were compared with quantum-chemical computations which well-describe the transition state for water desorption and the concomitant binding and activation energies.

Probing electrostatic interactions and structural changes in highly charged protein polyanions by conformer-selective photoelectron spectroscopy.

We have recorded the first conformer-selective photoelectron spectra of a protein polyanion in the gas-phase. Bovine cytochrome c protein was studied in 8 different negative charge states ranging from 5- to 12-. Electron binding energies were extracted for all charge states and used as a direct probe of intramolecular Coulomb repulsion. Comparison of experimental results with simulations shows that the experimental outcome can be reproduced with a simple electrostatic model. Energetics are consistent with a structural transition from a folded to an unfolded conformational state of the protein as the number of charges increases. Furthermore, the additional ion-mobility data show that the onset of unfolding can be assigned to charge state 6- where three conformers can be distinguished.

Covalent Aurora A regulation by the metabolic integrator coenzyme A.

Aurora A kinase is a master mitotic regulator whose functions are controlled by several regulatory interactions and post-translational modifications. It is frequently dysregulated in cancer, making Aurora A inhibition a very attractive antitumor target. However, recently uncovered links between Aurora A, cellular metabolism and redox regulation are not well understood. In this study, we report a novel mechanism of Aurora A regulation in the cellular response to oxidative stress through CoAlation. A combination of biochemical, biophysical, crystallographic and cell biology approaches revealed a new and, to our knowledge, unique mode of Aurora A inhibition by CoA, involving selective binding of the ADP moiety of CoA to the ATP binding pocket and covalent modification of Cys290 in the activation loop by the thiol group of the pantetheine tail. We provide evidence that covalent CoA modification (CoAlation) of Aurora A is specific, and that it can be induced by oxidative stress in human cells. Oxidising agents, such as diamide, hydrogen peroxide and menadione were found to induce Thr 288 phosphorylation and DTT-dependent dimerization of Aurora A. Moreover, microinjection of CoA into fertilized mouse embryos disrupts bipolar spindle formation and the alignment of chromosomes, consistent with Aurora A inhibition. Altogether, our data reveal CoA as a new, rather selective, inhibitor of Aurora A, which locks this kinase in an inactive state via a "dual anchor" mechanism of inhibition that might also operate in cellular response to oxidative stress. Finally and most importantly, we believe that these novel findings provide a new rationale for developing effective and irreversible inhibitors of Aurora A, and perhaps other protein kinases containing appropriately conserved Cys residues.

DNA Binding and Phosphorylation Regulate the Core Structure of the NF-κB p50 Transcription Factor.

The NF-κB transcription factors are known to be extensively phosphorylated, with dynamic site-specific modification regulating their ability to dimerize and interact with DNA. p50, the proteolytic product of p105 (NF-κB1), forms homodimers that bind DNA but lack intrinsic transactivation function, functioning as repressors of transcription from κB promoters. Here, we examine the roles of specific phosphorylation events catalysed by either protein kinase A (PKAc) or Chk1, in regulating the functions of p50 homodimers. LC-MS/MS analysis of proteolysed p50 following in vitro phosphorylation allows us to define Ser328 and Ser337 as PKAc- and Chk1-mediated modifications, and pinpoint an additional four Chk1 phosphosites: Ser65, Thr152, Ser242 and Ser248. Native mass spectrometry (MS) reveals Chk1- and PKAc-regulated disruption of p50 homodimer formation through Ser337. Additionally, we characterise the Chk1-mediated phosphosite, Ser242, as a regulator of DNA binding, with a S242D p50 phosphomimetic exhibiting a > 10-fold reduction in DNA binding affinity. Conformational dynamics of phosphomimetic p50 variants, including S242D, are further explored using ion-mobility MS (IM-MS). Finally, comparative theoretical modelling with experimentally observed p50 conformers, in the absence and presence of DNA, reveals that the p50 homodimer undergoes conformational contraction during electrospray ionisation that is stabilised by complex formation with κB DNA. Graphical Abstract ᅟ.

Understanding protein-drug interactions using ion mobility-mass spectrometry.

Ion mobility-mass spectrometry (IM-MS) is an important addition to the analytical toolbox for the structural evaluation of proteins, and is enhancing many areas of biophysical analysis. Disease-associated proteins, including enzymes such as protein kinases, transcription factors exemplified by p53, and intrinsically disordered proteins, including those prone to aggregation, are all amenable to structural analysis by IM-MS. In this review we discuss how this powerful technique can be used to understand protein conformational dynamics and aggregation pathways, and in particular, the effect that small molecules, including clinically-relevant drugs, play in these processes. We also present examples of how IM-MS can be used as a relatively rapid screening strategy to evaluate the mechanisms and conformation-driven aspects of protein:ligand interactions.

Local protein kinase A action proceeds through intact holoenzymes.

Hormones can transmit signals through adenosine 3',5'-monophosphate (cAMP) to precise intracellular locations. The fidelity of these responses relies on the activation of localized protein kinase A (PKA) holoenzymes. Association of PKA regulatory type II (RII) subunits with A-kinase-anchoring proteins (AKAPs) confers location, and catalytic (C) subunits phosphorylate substrates. Single-particle electron microscopy demonstrated that AKAP79 constrains RII-C subassemblies within 150 to 250 angstroms of its targets. Native mass spectrometry established that these macromolecular assemblies incorporated stoichiometric amounts of cAMP. Chemical-biology- and live cell-imaging techniques revealed that catalytically active PKA holoenzymes remained intact within the cytoplasm. These findings indicate that the parameters of anchored PKA holoenzyme action are much more restricted than originally anticipated.