Simple and rapid identification of phosphorylated peptides from bovine brain myelin basic protein by reversed-phase high-performance liquid chromatography

The phosphorylation sites of the myelin basic protein from bovine brain were determined after phosphorylation with a cyclic 3':5'-phosphate-dependent protein kinase from the same source. Three phosphorylated peptides were selectively and rapidly separated, before and after dephosphorylation, by reversed-phase high-performance liquid chromatography on a styrene 250 column under alkaline conditions. Partial sequencing of the peptides by automated Edman degradation revealed that the serine-115 residue located in the main encephalitogenic determinant of the protein was a phosphorylation site, in addition to the two phosphorylation sites established (threonine-34 and serine-55).     

Piperazines for peptide carboxyl group derivatization: effect of derivatization reagents and properties of peptides on signal enhancement in matrix-assisted laser desorption/ionization mass spectrometry

Piperazine-based derivatives, including 1-(2-pyridyl)piperazine (2-PP), 1-(2-pyrimidyl)piperazine (2-PMP), 1-(4-pyridyl)piperazine (4-PP), and 1-(1-methyl-4-piperidinyl)piperazine (M-PP), were used for the derivatization of carboxyl groups on peptides with 1-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride (EDC) and 1-hydroxy-7-azabenzotriazole (HOAt) as coupling reagents, and trifluoroacetic acid (TFA) as activator. Taking synthetic peptides RVYVHPI (RI-7) and APGDRIYVHPF (AF-11) as samples, the yields of derivatized peptides by 2-PP, 2-PMP and 4-PP were higher than 94%. The effect of piperazine derivatives on the signals of tryptic digests of α-transferrin and bovine serum albumin (BSA) was investigated, and it was found that peptides derivatized by 2-PP and 2-PMP exhibited obviously improved ionization efficiency. Furthermore, comparison of identified peptides before and after derivatization showed that peptides with low molecular weight (MW) and high pI value were preferably detected after derivatization. In addition, after derivatization with 2-PP and 2-PMP, protein myelin basic protein S, 20 kDa protein, and histone H were confidently identified from the tryptic digests of two fractions of rat brain protein separated by reversed-phase high-performance liquid chromatography (HPLC), indicating the potential application of 2-PP and 2-PMP for the highly sensitive determination of peptides in comprehensive proteome analysis.     

A 2D NMR method to study peptide phosphorylation

We demonstrate a 2D NMR method which distinguishes between phosphorylated and non-phosphorylated amino acids. The method is capable of monitoring the amino acid and site-specific enzymatic phosphorylation and dephosphorylation of peptides. The method was developed using O-phosphorylated amino acids and its potential is shown with a peptide fragment of the myelin basic protein (MBP).     

Direct profiling of myelinated and demyelinated regions in mouse brain by imaging mass spectrometry

One of the newly developed imaging mass spectrometry (IMS) technologies utilizes matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to map proteins in thin tissue sections. In this study, we evaluated the power of MALDI IMS as we developed it in our (Bruker) MALDI TOF (Reflex IV) and TOF-TOF (Ultraflex II) systems to study myelin patterns in the mouse central nervous system under normal and pathological conditions. MALDI IMS was applied to assess myelin basic protein (MBP) isoform-specific profiles in different regions throughout the mouse brain. The distribution of ions of m/z 14,144 and 18,447 displayed a striking resemblance with white matter histology and were identified as MBP isoform 8 and 5, respectively. In addition, we demonstrated a significant reduction of the MBP-8 peak intensity upon MALDI IMS analysis of focal ethidium bromide-induced demyelinated brain areas. Our MS images were validated by immunohistochemistry using MBP antibodies. This study underscores the potential of MALDI IMS to study the contribution of MBP to demyelinating diseases.     

Comparison of reversed-phase and weak anion-exchange high-performance liquid chromatographic methods for peptide separations

Weak anion-exchange and reversed-phase high-performance liquid chromatographic methods for peptide separations were compared using a tryptic digest of "rat small myelin basic protein". In these experiments, a number of tryptic peptides that were not resolved on the reversed-phase column could be separated on the weak anion-exchange column, and in other instances, as might be expected, reversed-phase chromatography provided better resolution of certain peptides than did the weak anion-exchange method. The results obtained strongly suggest that the combined use of these two methods of separation, which utilize different selectivities, can provide an excellent improvement in resolving power for a number of peptide separations.     

Isoelectric focusing of membrane proteins: high resolution separation of myelin proteins

A mixture of the nonionic detergent Triton X-100, the zwitterionic detergent 3-[(cholamidopropyl)dimethylammonio]-1-propanesulphonate (CHAPS), 9M urea and carrier ampholytes was found comparable to media containing sodium dodecyl sulfate in the capacity for solubilization of myelin proteins, including the highly hydrophobic proteolipid protein. The solubilized sample was incorporated into the polymerization mixture before moulding an ultrathin gel, with heat convection characteristics allowing a high wattage to be applied, thus allowing fast separation with high resolving power. Since the most basic protein in myelin focuses at a pH greater than 10, fast separation is essential in order to minimize decay of the cathodic end of the pH gradient.     

The Myelin Membrane of the Central Nervous System—Essential Macromolecular Structure and Function

The neural sheaths that surround the nerve fibers (axons) are composed of myelin-specific complex lipids and are assembled during the myelination phase either by the oligodendrocytes in the central nervous system (CNS) or by the Schwann cells in the peripheral nervous system. These multilayered myelin membranes insulate the axons and permit a rapid, saltatory conduction of excitation and a reduced axon diameter in comparison with noninsulated axons. Myelination was hence the decisive evolutionary event in miniaturization of the central nervous system (brain and spinal cord). The morphology of the myelin membrane has been studied in detail mainly by electron microscopy. Most of its biochemistry has been elucidated in recent years by molecular-level analysis of both the lipid components (cholesterol, phospholipids and sphingolipids) and the constituent proteins. The multilamellar system is distinguished by a characteristic periodicity due to the 5-nm-thick bilayer formed by the myelin-specific lipids. The bilayer interacts with the myelin basic protein (MBP) on the cytosolic side of the plasma membrane process, while the integral membrane protein proteolipid protein (PLP) has hydrophilic domains exposed on both the cytosolic and extracytosolic faces of the bilayer. Numerous protein-chemical and -immunotopochemical findings have been summarized in a model of the myelin membrane. Through molecular biological studies, the genetic structure and chromosomal location of the myelin proteins have been determined. By employing techniques of molecular and cell biology together, it is now possible to analyze the process of myelinogenesis, the time- and location-specific expression of myelin-specific genes in the brain. Gene-technological methods have been used to define the mutations in the models jimpy mouse and myelin-deficient rat. These are animal models that correspond to genetically determined myelin defects (dysmyelinoses) in humans. Using them, it will be possible to study the cell death of oligodendrocytes on a molecular level; this process is the result of expression of mutant myelin proteins and is incompatible with life. Oligodendrocytes and the myelin structures they synthesize are the target structures of cytotoxic lymphocytes (T_c). In the course of the demyelination process in multiple sclerosis, these cause the breakdown of the myelin sheaths, in gradually appearing inflammations. T_c lymphocytes recognize myelin structures as epitopes and destroy them. The picture of the myelin membrane's molecular composition, which we are now perfecting, will also lead to a better understanding of demyelination on a molecular level, and hence to new therapeutic possibilities.     

Laminar order within Langmuir-Blodgett multilayers from phospholipid and myelin basic protein: a neutron reflectivity study

Multilayers consisting of negatively charged phospholipid DMPA and myelin basic protein (MBP) were assembled by Langmuir-Blodgett deposition of floating Langmuir monolayers from the air/water interface to solid substrates. Protein/lipid samples were obtained by binding MBP from the aqueous subphase to the phospholipid monolayers before deposition. The vertical organization of these model membranes (i.e., with organization perpendicular to the substrate surface) was investigated in detail by neutron reflectivity measurements, and the internal distribution of water molecules was determined from the change of contrast after in-situ H2O/D2O exchange. The multilayers were well ordered, with repeating lipid bilayers as fundamental structural unit. MBP was inserted in between adjacent lipid headgroups, such as in the natural myelin membrane. Water molecules in the multilayers were present mainly in the lipid headgroup and protein slab. On exposition of the pure lipid multilayers to a dry atmosphere, a reduction of the bilayer spacing was determined, whereas the global lamellar order was not affected. In contrast, drying of the protein/lipid multilayers induced degradation of the laminar order. The data demonstrate that ordered Langmuir-Blodgett multilayers are versatile model systems for studying how competing interactions between lipid, protein, water, and ions affect the global organization of such multilamellar lipid/protein assemblies. Here, the water molecules were found to be a necessary mediator to maintain the laminar order in a multilayer from DMPA and myelin basic protein.     

Interaction of bovine myelin basic protein with triphosphoinositide

Despite the essential role played by myelin basic protein (MBP) in stabilizing the multilamellar structure of the myelin membrane, attempts at deciphering the structure of MPB have so far failed. Given that MBP is known to specifically interact with the membrane's lipid components, this study was designed to explore the effects of these lipids on the conformation of the protein by examining its interaction with the lipid triphosphoinositide (TPI). MBP was identified by high-performance liquid chromatography (HPLC) in myelin extracted from cow's brain and its molecular weight determined. In aqueous solution, MBP showed a random coil structure confirmed by its circular dichroism (CD) spectra. Possible structural changes to the protein induced by different proportions of TPI were also explored. The CD spectra of these mixtures indicated that this lipid fails to induce the adoption of a secondary structure by MBP. We then performed monolayer experiments to evaluate the type of interaction that occurs between MBP and TPI. First, the molecular weight of the protein sample was established to determine the state of the MBP within the monolayer by applying the equation for gases to the so-called gaseous zone of the monolayer for the conditions under which the expression holds. The similar molecular weights yielded by HPLC performed on dissolved samples and by the monolayers suggests that, as in solution, in the membrane the protein exists as a monomer. Monolayer data suggest forces of attraction between the two components and, through thermodynamic calculations, it was established that this interaction is spontaneous and the interaction is of the electrostatic type.     

Construction of a protein-detection system using a loop peptide library with a fluorescence label

Construction of a novel protein-detection system was carried out using a designed peptide library with fluorescent labels based on loop structures. As a basic model study, detection of alpha-amylase using fluorescent-labeled peptides derived from an active loop of tendamistat was examined. The detection methods for proteins with immobilized peptides as well as peptides in solution have been successfully established. Based on these results, a loop peptide library that has various turn sequences grafted on a stable loop structure has been constructed. Various proteins with recognition patterns corresponding, for instance, to "protein fingerprints" could be detected using an immobilized peptide library. The present results suggest that the system can be applied to the development of a peptide microarray that behaves as a protein chip.     

Western blot detection of brain material in heated meat products using myelin basic protein and neuron-specific enolase as biomarkers

An assay based on Western blotting and detection of central nervous system (CNS)-specific antigens was developed to detect brain tissue in processed (heated) meat products. Bands of antigen-bound primary antibodies were visualised through secondary anti-antibodies labelled with peroxidase, which generated chemiluminescence documented by a photographic film. Ponceau-S staining before antibody incubation and molecular mass information on detected antigens after immunoreactions added information supporting correct identification of brain tissue in the meat products. In this approach B50/growth-associated protein (B50), glial fibrillary acidic protein (GFAP), myelin basic protein (MBP), neurofilament (NF), neuron-specific enolase (NSE) and synaptophysin (Syn) proteins were detected in raw luncheon meat and a liver product enriched with brain tissue at a level of 5% (m/m). Only MBP and NSE were considered suitable biomarkers for detection of 1% (m/m) brain tissue in meat products pasteurised at 70 °C or sterilised at 115 °C. The use of an anti-monkey MBP instead of anti-human MBP enabled speciation of the CNS material whether from bovine and ovine brains or from porcine brain tissue. This immunoblot assay potentiates the analysis of approximately 70 samples within 8 h, including sample preparation and the simultaneous probing of NSE and MBP target antigens.     

Specific biotinylation and sensitive enrichment of citrullinated peptides

Protein citrullination is a posttranslational modification where peptidylarginine is enzymatically deiminated to form peptidylcitrulline. Although the role of protein citrullination in both health and disease is being increasingly recognised, techniques available to identify citrullinated proteins and to map their citrullination site(s) are rare and often show poor sensitivity. Here, we present a sensitive technique for specific modification and selective enrichment of citrullinated peptides from complex biological samples. The technique is based on highly specific in-solution biotinylation of citrulline residues followed by selective enrichment of modified peptides using streptavidin beads. We demonstrate that a synthetic citrulline-containing peptide can be selectively enriched when less than 0.5 pmol is spiked into a highly heterogeneous peptide mixture. After enrichment, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) analysis of an aliquot of the streptavidin eluate corresponding to theoretically 50 fmol of the spiked-in peptide showed a prominent signal. We further demonstrate the sensitivity of our technique by enrichment of citrullinated peptides from enzymatically deiminated myelin basic protein (MBP), when 10 pmol was spiked into a heterogeneous biological digest. In MALDI-TOF MS analysis, six MBP-derived citrullinated peptides were observed, showing the efficiency of this enrichment strategy. The high sensitivity combined with the remarkable specificity of the described technique makes it a valuable tool for elucidating citrullination in various biological processes.

Three-dimensional visualization of protein expression in mouse brain structures using imaging mass spectrometry

We have developed a method to visualize matrix-assisted laser desorption ionization imaging mass spectrometry (MALDI IMS) data aligned with optically determinable tissue structures in three dimensions. Details of the methodology are exemplified using the 3-D reconstruction of myelin basic protein (MBP) in the corpus callosum of a mouse brain. In this procedure, optical images obtained from serial coronal sections are first aligned to each other to reconstruct a surface of the corpus callosum from segmented contours of the aligned images. The MALDI IMS data are then coregistered to the optical images and superimposed into the surface to create the final 3-D visualization. Correlating proteomic data with anatomical structures provides a more comprehensive understanding of healthy and pathological brain functions, and holds promise to be utilized in more complex anatomical arrangements.     

Analysis of arginine and lysine methylation utilizing peptide separations at neutral pH and electron transfer dissociation mass spectrometry

Arginine and lysine methylation are widespread protein post-translational modifications. Peptides containing these modifications are difficult to retain using traditional reversed-phase liquid chromatography because they are intrinsically basic/hydrophilic and often fragment poorly during collision induced fragmentation (CID). Therefore, they are difficult to analyze using standard proteomic workflows. To overcome these caveats, we performed peptide separations at neutral pH, resulting in increased retention of the hydrophilic/basic methylated peptides before identification using MS/MS. Alternatively trifluoroacetic acid (TFA) was used for increased trapping of methylated peptides. Electron-transfer dissociation (ETD) mass spectrometry was then used to identify and characterize methylated residues. In contrast to previous reports utilizing ETD for arginine methylation, we observed significant amount of side-chain fragmentation. Using heavy methyl stable isotope labeling with amino acids in cell culture it was shown that, similar to CID, a loss of monomethylamine or dimethylamine from the arginine methylated side-chain during ETD can be used as a diagnostic to determine the type of arginine methylation. CID of lysine methylated peptides does not lead to significant neutral losses, but ETD is still beneficial because of the high charge states of such peptides. The developed LC MS/MS methods were successfully applied to tryptic digests of a number of methylated proteins, including splicing factor proline-glutamine-rich protein (SFPQ), RNA and export factor-binding protein 2 (REF2-I) and Sul7D, demonstrating significant advantages over traditional LC MS/MS approaches.     

Electrophoretic mobility for peptides with post-translational modifications in capillary electrophoresis

Several semiempirical models for peptide electrophoretic mobility have been tested for capillary electrophoresis (CE) separation with a positively charged capillary using on-line CE combined with electrospray ionization-mass spectrometry (ESI-MS). In the current system with pH 2.7, the expression q/M(0.56) provided the best correlation with the electrophoretic mobility in the analysis of a set of 18 standard samples, where q is the calculated net charge and M is the molecular weight. The peptides resulting from various digests of horse heart myoglobin or bovine hemoglobin were used to demonstrate the validity of this correlation. Post-translationally modified peptides from tryptic digest of human myelin basic protein were also investigated and were found to provide excellent correlation with the linear plot when the total charge of the peptide was correctly calculated. If the total charge was not properly calculated then the post-translationally modified peptides fell off the linear plot. Using this method five arginine residues (residues 5, 49, 54, 97 and 130) were found to be partially citrullinated, four glutamine residues (residues 8, 103, 121 and 147) were found to be partially deamidated and both methionines at residues 21 and 167 were found to be partially oxidized. Three peptides were found with phosphorylation; TPPPSQGK (residue 98 to 105), FSWGAEGQR (residue 114 to 122), and SGSPMAR (residue 163 to 169) and Arginine at 107 was found to be partially monomethylated or dimethylated. The method may provide an excellent means of identifying the presence of peptides with post-translational modifications in conjunction with MS.     

Targeted analysis of protein citrullination using chemical modification and tandem mass spectrometry

Protein citrullination originates from enzymatic deimination of polypeptide‐bound arginine and is involved in various biological processes during health and disease. However, tools required for a detailed and targeted proteomic analysis of citrullinated proteins in situ, including their citrullination sites, are limited. A widely used technique for detection of citrullinated proteins relies on antibody staining after specific derivatization of citrulline residues by 2,3‐butanedione and antipyrine. We have recently reported on the details of this reaction. Here, we show that this chemical modification can be utilized to specifically detect and identify citrullinated peptides and their citrullination sites by liquid chromatography/tandem mass spectrometry (LC/MS/MS) analysis. Using model compounds, we demonstrate that in collision‐induced dissociation (CID) a specific, modification‐derived fragment ion appears as the dominating signal at m/z 201.1 in the MS/MS spectra. When applying electron transfer dissociation (ETD), however, the chemical modification of citrulline remained intact and extensive sequence coverage allowed identification of peptides and their citrullination sites. Therefore, LC/MS/MS analysis with alternating CID and ETD has been performed, using CID for specific, signature ion‐based detection of derivatized citrullinated peptides and ETD for sequence determination. The usefulness of this targeted analysis was demonstrated by identifying citrullination sites in myelin basic protein deiminated in vitro. Combining antibody‐based enrichment of chemically modified citrulline‐containing peptides with specific mass spectrometric detection will increase the potential of such a targeted analysis of protein citrullination in the future. Copyright © 2009 John Wiley & Sons, Ltd.     

Analysis of the performance of antibody capture methods using fluorescent peptides with capillary zone electrophoresis with laser-induced fluorescence

A method to analyze the performance of an antibody capture method using fluorescent peptides by capillary zone electrophoresis using laser-induced fluorescence (CZE-LIF) for detection has been developed. Fluorescent peptides from the prion protein were synthesized and the corresponding antibodies were produced in rabbits against these peptides. The antibodies were used to capture the fluorescent peptides. The antibodies were then bound to protein A Sepharose. After elution, the amount of fluorescent peptide that was captured vs. the total amount placed in the assay was evaluated by CZE-LIF. Of the three peptides used in this evaluation, it was found that the recovery was approximately 25-35%. When the abnormal prion protein was prepared from scrapie-infected brain samples from hamsters and a sheep using the previously described extraction method and this method, the amount of abnormal prion protein that was measured in the fluorescence immunoassay correlated with amounts estimated from Western blot. We conclude that this method can be used to detect abnormal prion protein in a tissue sample.     

Selective N-terminal modification of peptides and proteins: Recent progresses and applications

Numerous strategies for linking desired chemical probes with target peptides and proteins have been developed and applied in the field of biological chemistry. Approaches for site-specific modification of native amino acid residues in test tubes and biological contexts represent novel biological tools for understanding the role of peptides and proteins. Selective N-terminal modification strategies have been broadly studied especially in the last 10 years, as N-terminal positions are typically so...     

High-performance liquid chromatography of acid-stable and acid-labile phosphoamino acids

A high-performance liquid chromatographic system has been developed which permits the separation of both acid-stable and acid-labile phosphoamino acids. An anion-exchange resin and two buffers of different ionic strength and near neutral pH are used. A low-ionic-strength buffer is used for the separation of N-omega-phosphoarginine and N-epsilon-phospholysine, while the higher-ionic-strength buffer permits the clear separation of tau-phosphohistidine, omicron-phosphoserine and omicron-phosphothreonine. An in-stream fluorometric detection system using omicron-phthalaldehyde permits the rapid analysis of samples containing as little as 25 pmoles of phosphoamino acid. This method has been applied to the detection of tau-phosphohistidine from alkaline digests of chemically phosphorylated calf thymus histone 4 and bovine myelin basic protein.