Nanoelectrospray Ionization Source Research Articles

Pim-1 Ligand-bound Structures Reveal the Mechanism of Serine/Threonine Kinase Inhibition by LY294002

Pim-1 is an oncogene-encoded serine/threonine kinase primarily expressed in hematopoietic and germ cell lines. Pim-1 kinase was originally identified in Maloney murine leukemia virus-induced T-cell lymphomas and is associated with multiple cellular functions such as proliferation, survival, differentiation, apoptosis, and tumorigenesis (Wang, Z., Bhattacharya, N., Weaver, M., Petersen, K., Meyer, M., Gapter, L., and Magnuson, N. S. (2001) J. Vet. Sci. 2, 167-179). The crystal structures of Pim-1 complexed with staurosporine and adenosine were determined. Although a typical two-domain serine/threonine protein kinase fold is observed, the inter-domain hinge region is unusual in both sequence and conformation; a two-residue insertion causes the hinge to bulge away from the ATP-binding pocket, and a proline residue in the hinge removes a conserved main chain hydrogen bond donor. Without this hydrogen bond, van der Waals interactions with the hinge serve to position the ligand. The hinge region of Pim-1 resembles that of phosphatidylinositol 3-kinase more closely than it does other protein kinases. Although the phosphatidylinositol 3-kinase inhibitor LY294002 also inhibits Pim-1, the structure of the LY294002.Pim-1 complex reveals a new binding mode that may be general for Ser/Thr kinases.

Light-independent Phosphorylation of WHITE COLLAR-1 Regulates Its Function in the Neurospora Circadian Negative Feedback Loop

Phosphorylation is a major regulatory mechanism controlling circadian clocks. In the Neurospora circadian clock, the PER-ARNT-SIM (PAS) domain-containing transcription factor, WHITE COLLAR (WC)-1, acts both as the blue light photoreceptor of the clock and as a positive element in the circadian negative feedback loop in constant darkness, by activating the transcription of the frequency (frq) gene. To understand the role of WC-1 phosphorylation, five in vivo WC-1 phosphorylation sites, located immediately downstream of the WC-1 zinc finger DNA binding domain, were identified by tandem mass spectrometry using biochemically purified endogenous WC-1 protein. Mutations of these phosphorylation sites suggest that they are major WC-1 phosphorylation sites under constant conditions but are not responsible for the light-induced hyperphosphorylation of WC-1. Although phosphorylation of these sites does not affect the light function of WC-1, strains carrying mutations of these sites show short period, low amplitude, or arrhythmic conidiation rhythms in constant darkness. Furthermore, normal or slightly higher levels of frq mRNA and FRQ proteins were observed in a mutant strain containing mutations of all five sites despite its low WC-1 levels. Together, these data suggest that phosphorylation of these sites negatively regulates the function of WC-1 in the circadian negative feedback loop and is important for the function of the Neurospora circadian clock.

Parkin Phosphorylation and Modulation of Its E3 Ubiquitin Ligase Activity

Mutations in the PARKIN gene are the most common cause of hereditary parkinsonism. The parkin protein comprises an N-terminal ubiquitin-like domain, a linker region containing caspase cleavage sites, a unique domain in the central portion, and a special zinc finger configuration termed RING-IBR-RING. Parkin has E3 ubiquitin-protein ligase activity and is believed to mediate proteasomal degradation of aggregation-prone proteins. Whereas the effects of mutations on the structure and function of parkin have been intensely studied, post-translational modifications of parkin and the regulation of its enzymatic activity are poorly understood. Here we report that parkin is phosphorylated both in human embryonic kidney HEK293 cells and human neuroblastoma SH-SY5Y cells. The turnover of parkin phosphorylation was rapid, because inhibition of phosphatases with okadaic acid was necessary to stabilize phosphoparkin. Phosphoamino acid analysis revealed that phosphorylation occurred mainly on serine residues under these conditions. At least five phosphorylation sites were identified, including Ser101, Ser131, and Ser136 (located in the linker region) as well as Ser296 and Ser378 (located in the RING-IBR-RING motif). Casein kinase-1, protein kinase A, and protein kinase C phosphorylated parkin in vitro, and inhibition of casein kinase-1 caused a dramatic reduction of parkin phosphorylation in cell lysates. Induction of protein folding stress in cells reduced parkin phosphorylation, and unphosphorylated parkin had slightly but significantly elevated autoubiquitination activity. Thus, complex regulation of the phosphorylation state of parkin may contribute to the unfolded protein response in stressed cells.

Mechanistic Roles of Ser-114, Tyr-155, and Lys-159 in 3α-Hydroxysteroid Dehydrogenase/Carbonyl Reductase from Comamonas testosteroni

3alpha-hydroxysteroid dehydrogenase/carbonyl reductase (3alpha-HSD/CR) from Comamonas testosteroni, a short chain dehydrogenase/reductase, catalyzes the oxidation of androsterone with NAD+ to form androstanedione and NADH. A catalytic triad of Ser-114, Tyr-155, and Lys-159 in 3alpha-HSD/CR has been proposed based on structural analysis and sequence alignment of the short chain dehydrogenase/reductase family. The 3alpha-HSD/CR-catalyzed reaction has not been kinetically analyzed in detail, however. In this study, we combined steady-state kinetics, site-directed mutagenesis, and pH profile to explore the function of Ser-114, Tyr-155, and Lys-159 in 3alpha-HSD/CR-catalyzed reaction. The catalytic efficiency of wild-type and mutants S114A, Y155F, K159A, and Y155F/K159A is 4.3 x 10(7), 7.3 x 10(4), 1.7 x 10(4), 2.4 x 10(5), and 71 m(-1)s(-1), respectively. The values of pKa on kcat/Km for the wild-type, S114A, Y155F, K159A, and Y155F/K159A are 7.2, 7.4, 8.4, 9.1, and 10.2, respectively. Mutant S114A/Y155F exhibits a pH-independent profile with 10(-5) times of wild-type activity at pH 10.5. The activity decreases as the pH lowers, which indicates that a functional group with an apparent pKa of 7.2 is involved in the general base catalysis for wild-type 3alpha-HSD/CR. The pKa shift to 9.1 for mutant K159A suggests the role of Lys-159 is to lower the pKa of the residues involved in the general base catalysis. Because pH dependence is observed for both S114A and Y155F mutants and pH independence is observed in S114A/Y155F, Tyr-155 may be important as a general base catalysis in the wild-type, whereas Ser-114 may act as a general base on mutant Y155F to catalyze the reaction.

Mapping the Topology and Determination of a Low-Resolution Three-Dimensional Structure of the Calmodulin−Melittin Complex by Chemical Cross-Linking and High-Resolution FTICRMS: Direct Demonstration of Multiple Binding Modes

Calmodulin serves as a calcium-dependent regulator in many metabolic pathways and is known to bind with high affinity to various target proteins and peptides. One such target is the small peptide melittin, the principal component of honeybee venom. The calmodulin-melittin system was used as a model system to gain further insight into target recognition of calmodulin. Using chemical cross-linking in combination with high-resolution Fourier transform ion cyclotron resonance mass spectrometry (FTICRMS), we have determined the interacting regions within the calcium-dependent calmodulin-melittin complex and thus the orientation of bound melittin. Using ambiguous distance restraints derived from the chemical cross-linking data in combination with recently developed computational methods of conjoined rigid body/torsion angle simulated annealing, we were able to generate low-resolution three-dimensional structure models of the calmodulin-melittin complex, for which no high-resolution structure exists to date. Our data provide evidence for the first time that calmodulin can recognize target peptides in two opposing orientations simultaneously. The general procedure for mapping interacting regions within the complex involves conjugation of calmodulin and melittin with several cross-linking reagents possessing different specificities and spacer lengths, followed by enzymatic proteolysis of the cross-linked complex. The highly complex peptide mixtures were subsequently analyzed by nano-HPLC, which was online coupled to a FTICR mass spectrometer equipped with a nano-electrospray ionization source. The mass spectra obtained in this manner were screened for possible cross-linking products using customized software programs. This integrated approach, exemplified for mapping the topology of the calmodulin-melittin complex, is likely to have wide-ranging implications for structural studies on protein-protein interactions.

A glassy carbon microfluidic device for electrospray mass spectrometry.

Due to the broad impact of microfabrication technology on chemistry and biology, new methods to pattern and etch a variety of materials are being explored in a number of laboratories. Here, we report the design, fabrication, and operation of a glassy carbon (GC) microchip interfaced to a nanoelectrospray ionization source and a quadrupole mass spectrometer. The method involves standard photolithographic pattern transfer to a photoresist layer and anodization of the exposed GC substrate in basic electrolyte to produce a series of channels with well-defined wall structure. The performance of the microchip was evaluated with standard polymer and peptide samples.

ＬＣ／ＭＳを用いた糖鎖プロファイリングによるグライコーム解析

Liquid chromatography/mass spectrometry equipped with a graphitized carbon column is useful for the simultaneous analysis of oligosaccharides. By using capillary column and nanoelectrospray ion source, the method can be used for the oligosaccharide profiling of sub microgram quantities of glycoproteins. This oligosaccharide profiling is expected to be a powerful tool for the glycome analysis. We demonstrate a potential application of oligosaccharide profiling in glycomics with two examples, the structural analysis of N-linked oligosaccharides from a gel-separated glycoprotein, and the differential analysis of N-linked oligosaccharides in cells.

Design and development of an interchangeable nanomicroelectrospray source for a quadrupole mass spectrometer

An interchangeable microelectrospray and nanoelectrospray ionization source has been designed and constructed for use on a triple-quadrupole mass spectrometer. This new source is specially designed to conduct nanoelectrospray experiments utilizing pulled borosilicate glass emitters, as well as various ionization modes utilizing silica capillaries. The source design facilitates the easy exchange between a microelectrospray source and nanoelectrospray source. The microionspray assembly can be quickly replaced by the nanoelectrospray adaptation in order to conduct nanoelectrospray experiments. Furthermore, this source design allows for the coupling of low flow separation techniques, like microliquid chromatography or capillary electrophoresis.

Quantitative determination of noncovalent binding interactions using automated nanoelectrospray mass spectrometry.

Electrospray ionization mass spectrometry (ESI-MS) has proven to be an extremely powerful tool for studying biomolecular structures and noncovalent interactions. Here we report a method using a fully automated, chip-based nanoESI-MS system to determine the dissociation constants (Kd) for the complexes of two different proteins with their ligands. The automated nanoelectrospray system, consisting of the NanoMate and ESI chip, serves functionally as a combination of autosampler and nanoelectrospray ionization source. This system provides all the advantages of conventional nanoelectrospray plus automated, high-throughput analyses without carryover. The automated nanoESI system was used to investigate quantitative noncovalent interactions between ribonuclease A (RNase A) and cytidylic acid ligands (2'-CMP, CTP), a well-characterized model protein-ligand complex, and between an inactive endocellulase mutant (Thermobifida fusca Cel6A D117Acd) and four oligosaccharide ligands (cellotriose, cellotetraose, cellopentaose, cellohexaose). Both titration and competitive binding approaches were performed prior to automated nanoESI-MS analysis with a Q-TOF mass spectrometer. Dissociation constants for each complex were calculated from the sum of ion peak areas of free and complexed proteins during the titration and competition experiments. The measured Kd values for the RNase A-CMP and Cel6A D117Acd-G3 complexes were found to be in excellent agreement with the available published values obtained by standard spectroscopic titration techniques. To our knowledge, this is the first report of using an ESI-MS approach to study the interactions between a cellulase and oligosaccharides. The results provide new insights for understanding the nature of cellulase-cellulose interactions.

Noise filtering techniques for electrospray quadrupole time of flight mass spectra

The sensitivity of protein identification by peptide sequencing using a nanoelectrospray ion source is limited by our ability to identify peptide ions in the mass spectrum. Their intensity must be higher than the chemical noise level to allow a rapid localization in the spectrum. Multiply-charged peptide ions on or below this level can only be found because their isotopic pattern is denser than that of the mostly singly-charged chemical background ions. However, to find peptides by looking for multiply-charged isotope clusters can be very timeconsuming and may lead to misassignments of the first isotope. Here we present a software-based method to increase the signal to noise ratio of ion signals in an electrospray spectrum. The software has two elements, one to reduce the noise level and a second to increase the intensity of ion peaks. Both methods together generate a spectrum in which the signal to noise ratio of ion signals is considerably improved. Peptide ions previously hidden in the chemical background are dismantled and can now be localized and selected for fragmentation. The method has been used successfully to identify low level proteins separated by one dimensional gel electrophoresis.

Nanoelectrospray-based detection and sequencing of substoichiometric amounts of phosphopeptides in complex mixtures.

A novel immobilized metal affinity chromatography (IMAC)-based protocol was successfully used for sample preparation prior to nanoelectrospray-based sequencing of phosphopeptides. In a first step, phosphorylated peptides are detected in an unseparated peptide mixture using precursor ion scanning in the negative ion mode on a triple-quadrupole mass spectrometer. Then the phosphorylated peptides are enriched by passing the sample over an IMAC column and sequenced in the positive ion mode. The IMAC-based enrichment allows the sequencing of phosphorylated peptides even if other, much more abundant, peptides are present at the same m/z value in the original mixture. Using this two-step approach, we are able to combine the simplicity, sensitivity and specificity of precursor ion scanning-based detection of phosphopeptides using the nanoelectrospray ion source with the ability to sequence phosphorylated peptides even if they are present in substoichiometric amounts.

A Transmembrane Tight Junction Protein Selectively Expressed on Endothelial Cells and Platelets

Searching for cell surface proteins expressed at interendothelial cell contacts, we have raised monoclonal antibodies against intact mouse endothelial cells. We obtained two monoclonal antibodies, 1G8 and 4C10, that stain endothelial cell contacts and recognize a protein of 55 kDa. Purification and identification by mass spectrometry of this protein revealed that it contains two extracellular Ig domains, reminiscent of the JAM family, but a much longer 120-amino acid cytoplasmic domain. The antigen is exclusively expressed on endothelial cells of various organs as was analyzed by immunohistochemistry. Immunogold labeling of ultrathin sections of brain as well as skeletal muscle revealed that the antigen strictly colocalizes in capillaries with the tight junction markers occludin, claudin-5, and ZO-1. Upon transfection into MDCK cells, the antigen was restricted to the most apical tip of the lateral cell surface, where it colocalized with ZO-1 but not with beta-catenin. In contrast to JAM-1, however, the 1G8 antigen does not associate with the PDZ domain proteins ZO-1, AF-6, or ASIP/PAR-3, despite the presence of a PDZ-binding motif. The 1G8 antigen was not detected on peripheral blood mouse leukocytes, whereas similar to JAM-1 it was strongly expressed on platelets and megakaryocytes. The 1G8 antigen supports homophilic interactions on transfected Chinese hamster ovary cells. Based on the similarity to the JAM molecules, it is plausible that the 1G8 antigen might be involved in interendothelial cell adhesion.

"De novo" sequencing of peptides recovered from in-gel digested proteins by nanoelectrospray tandem mass spectrometry.

Proteins separated by one-dimensional or two-dimensional gel electrophoresis can be digested in-gel with trypsin and the recovered peptides can be sequenced de novo using triple quadrupole or hybrid quadrupole time-of-flight instruments equipped with a nanoelectrospray ion source. The peptide sequences determined provide useful information for identification of proteins by homology searching for cloning of the cognate genes by PCR based approaches.

Interfacing a polymer-based micromachined device to a nanoelectrospray ionization Fourier transform ion cyclotron resonance mass spectrometer.

Here we report the design, fabrication, and operation of a polymer-based microchip device interfaced to a nanoelectrospray ionization source and a Fourier transform ion cyclotron resonance mass spectrometer. The poly(methyl methacrylate) micromachined device was fabricated using X-ray lithography to produce a network of channels with high aspect ratios. Fabrication of high aspect ratio channels allows for zero dead volume interfaces between the microchip platform and the nanoelectrospray capillary interface. The performance of this device was evaluated with standard peptide and protein samples. High-quality mass spectral data from peptide and proteins (and mixtures thereof) were obtained without any interfering chemical noise from the polymer or the developers and plasticizers used in the fabrication process. Sample cross-contamination is not a problem using this polymer-based microchip device as demonstrated by the sequential analysis of several proteins. The nanoelectrospray source was operated at flow rates from 20 to 100 nL/min using pressure-driven flow, and uninterrupted operation for several hours is demonstrated without any noticeable signal degradation. The ability to fabricate multiple devices using injection molding or hot-embossing techniques of polymers provides a lower cost alternative to silica-based devices currently utilized with mass spectrometry.

Capillary electrophoresis–mass spectrometry, liquid chromatography–mass spectrometry and nanoelectrospray-mass spectrometry of praziquantel metabolites

Capillary electrophoresis–mass spectrometry (CE–MS) and liquid chromatography–mass spectrometry (LC–MS) coupling was used for the investigation of metabolites of the anthelmintic drug praziquantel. Human urine samples and microsomal incubation mixtures were investigated after preparation by solid-phase extraction. CE– and LC–MS coupling was performed using an electrospray ionization interface. An ion trap mass spectrometer equipped with a laboratory-made nanoelectrospray ion source was used for the investigation of the glucuronide conjugates by consecutive fragmentations. The nanoelectrospray interface offers the opportunity to perform complicated MS n spectrometric investigations. Different phase I metabolites of praziquantel and their glucuronidated and sulfated conjugates were detected.

Platelet-activating Factor (PAF)-dependent Transacetylase and Its Relationship with PAF Acetylhydrolases

Platelet-activating Factor (PAF)-dependent Transacetylase and Its Relationship with PAF Acetylhydrolases

Design and construction of a nanoelectrospray ion source for a triple quadrupole mass spectrometer

The design and construction of a nanoelectrospray ion source for a triple quadrupole mass spectrometer that is used for identification and analysis of minimum peptide amounts is described. This interface exhibits several improvements over commercially available devices: a new capillary holder that allows very simple loading and placement of the spray capillary, and a rotary stage that enables reproducible adjustment of the capillary’s angle at the orifice of the mass spectrometer. We also introduced a pressure-regulating system for fast and reproducible adjustment of the static backing air pressure onto the sample solution in the spray capillary. Furthermore, an electric safety circuit increases handling and operation safety of the nanoelectrospray interface.

Fourier transform ion cyclotron resonance study of multiply charged aggregates of small singly charged peptides formed by electrospray ionization

Aggregates of singly protonated peptides formed with a nanoelectrospray ion source have been observed in the gas phase using Fourier transform ion cyclotron resonance (FT-ICR). Employment of “soft” ion sampling conditions in the source, which were developed previously to generate water clusters of biomolecules, provides significant yields of aggregates of singly protonated GGDPG ([2GGDPG + 2H] 2+), GGEPG ([2GGEPG + 2H] 2+), and VEPIPY (2VEPIPY + 2H] 2+). With peptide mixtures, heteroaggregates, e.g., [GGDPG + GGEPG + 2H] 2+ have also been observed along with the homoaggregates. These weakly bound noncovalent complexes undergo facile exothermic dissociation into the corresponding singly protonated monomer species with normal operation of the electrospray ion source. For example, the aggregates were not observed in FT-ICR experiments utilizing a conventional electrospray ionization (ESI) or fast atom bombardment source or with a quadrupolar ion trap mass spectrometer equipped with a conventional ESI source. The formation and metastability of these aggregates are dependent on highly specific intermolecular hydrogen bonding between the monomers. The amino acid sequence (DPG) of GGDPG mimics the well-known β reverse turn of proteins and semiempirical calculations show that it provides excellent hydrogen bonding sites for a protonated N-terminus amino group. Support for this conjecture is provided by the failure to observe aggregate formation of singly protonated peptides with several larger peptides, including hexaglycine and hexaalanine.

Rapid 'de novo' peptide sequencing by a combination of nanoelectrospray, isotopic labeling and a quadrupole/time-of-flight mass spectrometer.

Protein microanalysis usually involves the sequencing of gel-separated proteins available in very small amounts. While mass spectrometry has become the method of choice for identifying proteins in databases, in almost all laboratories 'de novo' protein sequencing is still performed by Edman degradation. Here we show that a combination of the nanoelectrospray ion source, isotopic end labeling of peptides and a quadrupole/ time-of-flight instrument allows facile read-out of the sequences of tryptic peptides. Isotopic labeling was performed by enzymatic digestion of proteins in 1:1 16O/18O water, eliminating the need for peptide derivatization. A quadrupole/time-of-flight mass spectrometer was constructed from a triple quadrupole and an electrospray time-of-flight instrument. Tandem mass spectra of peptides were obtained with better than 50 ppm mass accuracy and resolution routinely in excess of 5000. Unique and error tolerant identification of yeast proteins as well as the sequencing of a novel protein illustrate the potential of the approach. The high data quality in tandem mass spectra and the additional information provided by the isotopic end labeling of peptides enabled automated interpretation of the spectra via simple software algorithms. The technique demonstrated here removes one of the last obstacles to routine and high throughput protein sequencing by mass spectrometry.

Parent ion scans of unseparated peptide mixtures.

The nanoelectrospray ion source (NanoES) developed recently has proven to be an excellent tool for the sequencing of peptides out of unseparated mixtures. At lower levels of analyte, however, it is increasingly difficult to distinguish the peptide ions in the spectrum, limiting the overall sensitivity of the procedure. Scans for the parents of common fragmentation products of peptides such as immonium ions allow determination of peptide ion masses even when these ions have signal-to-noise ratios of < 1 in the mass spectrum. With this technique, concentration limits for sequencing peptides could be improved to < 5 fmol/microL in favorable cases. Parent ions scan were used to identify posttranslational modifications of peptides in mixtures, with phosphorylation and glycosylation as examples. Detecting phosphorylation by parent scans increased sensitivity by 1-2 orders of magnitude. Modified peptides can be subjected to tandem mass spectrometry in the same experiment to localize the modification. The present approach expands the range of application of nanoelectrospray and complements established liquid chromatography/mass spectrometry methods.