Hiroki Kuyama

A simple and highly successful C‐terminal sequence analysis of proteins by mass spectrometry

A simple and efficient method for C‐terminal sequencing of proteins has long been pursued because it would provide substantial information for identifying the covalent structure, including post‐translational modifications. However, there are still significant impediments to both direct sequencing from C termini of proteins and specific isolation of C‐terminal peptides from proteins. We describe here a highly successful, de novo C‐terminal sequencing method of proteins by employing succinimidyloxycarbonylmethyl tris (2,4,6‐trimethoxyphenyl) phosphonium bromide and mass spectrometry.

A method for N-terminal de novo sequence analysis of proteins by matrix-assisted laser desorption/ionization mass spectrometry.

A novel method for isolation and de novo sequencing of N-terminal peptides from proteins is described. The method presented here combines selective chemical tagging using succinimidyloxycarbonylmethyl tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP-Ac-OSu) at the N(alpha)-amino group of peptides after digestion by metalloendopeptidase (from Grifola frondosa) and selective capture procedures using p-phenylenediisothiocyanate resin, by which the N-terminal peptide can be isolated, whether or not it is N-terminally blocked. The isolated N-terminal peptide modified N-terminally with TMPP-Ac-OSu reagent produces a simple fragmentation pattern under tandem mass spectrometric analysis to significantly facilitate sequencing.

Sensitive detection of phosphopeptides by matrix‐assisted laser desorption/ionization mass spectrometry: use of alkylphosphonic acids as matrix additives

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has been one of the most powerful tools for analyzing protein phosphorylation. However, it is frequently difficult to detect phosphopeptides with high sensitivity by MALDI-MS. In our investigation of matrix/matrix-additive substances for improving the phosphopeptide ion response in MALDI-MS, we found that the addition of low-concentration alkylphosphonic acid to the matrix/analyte solution significantly enhanced the signal of phosphopeptides. In this study, the combination of methanediphosphonic acid and 2,5-dihydroxybenzoic acid gave the best results. In addition to enhancing the signal of the phosphopeptides, alkylphosphonic acid almost completely eliminated the signals of sodium and potassium ion adducts. We report herein sensitive detection of phosphopeptides by MALDI-MS with the use of alkylphosphonic acids as matrix additives.

Laser-induced propagation and destruction of amyloid β fibrils

The amyloid deposition of amyloid β (Aβ) peptides is a critical pathological event in Alzheimer disease (AD). Preventing the formation of amyloid deposits and removing preformed fibrils in tissues are important therapeutic strategies against AD. Previously, we reported the destruction of amyloid fibrils of β2-microglobulin K3 fragments by laser irradiation coupled with the binding of amyloid-specific thioflavin T. Here, we studied the effects of a laser beam on Aβ fibrils. As was the case for K3 fibrils, extensive irradiation destroyed the preformed Aβ fibrils. However, irradiation during spontaneous fibril formation resulted in only the partial destruction of growing fibrils and a subsequent explosive propagation of fibrils. The explosive propagation was caused by an increase in the number of active ends due to breakage. The results not only reveal a case of fragmentation-induced propagation of fibrils but also provide insights into therapeutic strategies for AD.

A novel type of prophenoloxidase from the kuruma prawn Marsupenaeus japonicus contributes to the melanization of plasma in crustaceans

Melanization is one of the major immune responses in arthropods. Prophenoloxidases (proPOs) catalyze the oxidation of mono- or o-diphenols, a reaction that is the key initial step of melanin formation. Well-characterized proPOs from crustaceans are synthesized in haemocytes and are released into plasma in response to microbial attack. However, PO activity does exist in the plasma of haemolymph without pathogenic infections. Here, we demonstrate that a novel type of proPO contributes to such PO activity in the plasma fraction of haemolymph of crustaceans. The novel enzyme, which was purified from the plasma of the kuruma prawn (Marsupenaeus japonicus), possessed strong and specific monophenol and o-diphenol oxidation activity compared with that of known haemocyte-type proPO. Amino acid sequence analyses indicated that this enzyme was distinct from the known proPO. The cDNA sequence and deduced amino acid sequence of this enzyme has a putative binuclear copper center, and showed approximately 30% and 20% identity with the primary structures of reported proPO and haemocyanin sequences of the kuruma prawn, respectively. Reverse transcription PCR analysis showed that this enzyme was synthesized in the hepatopancreas rather than in haemocytes. Although the primary structure and enzymatic properties of this novel enzyme suggested that it is a phenoloxidase, its biogenesis, tissue distribution, and oligomeric state resemble those of haemocyanin, which belongs to the same protein family (type III copper protein). This novel proPO enzyme may share a role with the already characterized version, itself a major component of the innate immune system in crustaceans.

Selective isolation of N-terminal peptides from proteins and their de novo sequencing by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry without regard to unblocking or blocking of N-terminal amino acids

We have developed a new method to determine the N-terminal amino acid sequences of proteins, regardless of whether their N-termini are modified. This method consists of the following five steps: (1) reduction, S-alkylation and guanidination for targeted proteins; (2) coupling of sulfo-NHS-SS-biotin to N(alpha)-amino groups of proteins; (3) digestion of the modified proteins by an appropriate protease followed by oxidation with performic acid; (4) specific isolation of N-terminal peptides from digests using DITC resins; (5) de novo sequence analysis of the N-terminal peptides by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) using the CAF (chemically assisted fragmentation) method or tandem mass spectrometric (MS/MS) analysis according to unblocked or blocked peptides, respectively. By employing DITC resins instead of avidin resins used in our previous method (Yamaguchi et al., Rapid Commun. Mass Spectrom. 2007; 21: 3329), it has been possible to isolate selectively N-terminal peptides from proteins regardless of modification of N-terminal amino acids. Here we propose a universal method for N-terminal sequence analysis of proteins.

A new approach for detecting C-terminal amidation of proteins and peptides by mass spectrometry in conjunction with chemical derivatization

We describe a mass spectrometric method for distinguishing between free and modified forms of the C‐terminal carboxyl group of peptides and proteins, in combination with chemical approaches for the isolation of C‐terminal peptides and site‐specific derivatization of the C‐terminal carboxyl group. This method could most advantageously be exploited to discriminate between peptides having C‐terminal carboxyl groups in the free (COOH) and amide (CONH2) forms by increasing their mass difference from 1 to 14 Da by selectively converting the free carboxyl group into methylamide (CONHCH3). This method has been proven to be applicable to peptides containing aspartic and glutamic acids, because all the carboxyl groups except the C‐terminal one are inert to derivatization, according to oxazolone chemistry. The efficiency of the method is illustrated by a comparison of the peaks of processed peptides obtained from a mixture of adrenomedullin, calcitonin, and BSA. Among these components of the mixture, only the C‐terminal peptide of BSA exhibited the mass shift of 13 Da upon treatment, eventually unambiguously validating the C‐terminal amide structures of adrenomedullin and calcitonin. The possibility of extending this method for the analysis of C‐terminal PTMs is also discussed.

Control of aqueous droplets using magnetic and electrostatic forces

Basic control operations were successfully performed on an aqueous droplet using both magnetic and electrostatic forces. In our droplet-based microfluidics, magnetic beads were incorporated in an aqueous droplet as a force mediator. This report describes droplet anchoring and separation of the beads from the droplet using a combination of magnetic and electrostatic forces. When an aqueous droplet is placed in an oil-filled reservoir, the droplet sinks to the bottom, under which an electrode had been placed. The droplet was adsorbed (or anchored) to the bottom surface on the electrode when a DC voltage was applied to the electrode. The magnetic beads were removed with magnetic force after the droplet had been anchored. Surfactant addition into droplet solution was very effective for the elimination of electric charge, which resulted in the stable adsorption of a droplet to hydrophobic substrate under an applied voltage of DC 0.5-3 kV. In a sequential process, small volume of aqueous liquid was successfully transferred using both magnetic and electrostatic forces.

An improved method for de novo sequencing of arginine-containing, Nα-tris(2,4,6-trimethoxyphenyl)phosphonium-acetylated peptides

An improved method for de novo sequencing of arginine-containing peptides modified with succinimidyloxycarbonylmethyl tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP-Ac-OSu) is reported. A tagging reagent, TMPP-Ac-OSu, was introduced to improve the sequence analysis of peptides owing to the simplified fragmentation pattern. However, peptides containing arginine residues did not fragment efficiently even after TMPP-Ac modification at their N-termini. This report describes how fragmentation efficiency of TMPP-Ac-modified arginine-containing peptides was significantly improved by modifying the guanidino group on the side chain of arginine with acetylacetone.

Field-inversion electrophoresis on a microchip device

We have proposed a field‐inversion electrophoresis on a microchip for a shorter effective length, and investigated the external frequency for the DNA analysis based on the field‐inversion electrophoresis device. By using the optimized frequency, we demonstrated that the field‐inversion electrophoresis has great potentials for the separation of DNA fragments with shorter effective length.