An ionic liquid-assisted sample preparation method for sensitive integral-membrane proteome analysis.

Many ion channels and receptor proteins are potential targets for new drugs. However, standard methods for profiling these integral membrane proteins (IMPs) have not been fully established, especially when applied to rare and quantity-limited biological samples. We previously demonstrated that a mixture containing 1-butyl-3-methylimidazolium cyanate, an ionic liquid (IL), and NaOH (termed i-soln) is an excellent solubilizer for insoluble aggregates. In this study, we present a combined i-soln-assisted proteomic sample preparation platform (termed pTRUST), which is compatible with starting materials in the sub-microgram range, using our previously reported i-soln-based sample preparation strategy (iBOPs) and an in-StageTip technique. This novel and straightforward approach allows for the rapid solubilization and processing of a variety of IMPs from human samples to support highly sensitive mass spectrometry analysis. We also demonstrated that the performance of this technology surpasses that of conventional methods such as filter-aided sample preparation methods, FASP and i-FASP. The convenience and availability of pTRUST technology using the IL system have great potential for proteomic identification and characterization of novel drug targets and disease biology in research and clinical settings.

Formation of α-synuclein aggregates in aqueous ethylammonium nitrate solutions.

The effect of adding ethylammonium nitrate (EAN), which is an ionic liquid (IL), on the aggregate formation of α-synuclein (α-Syn) in aqueous solution has been investigated. FTIR and Raman spectroscopy were used to investigate changes in the secondary structure of α-Syn and in the states of water molecules and EAN. The results presented here show that the addition of EAN to α-Syn causes the formation of an intermolecular ß-sheet structure in the following manner: native disordered state → polyproline II (PPII)-helix → intermolecular ß-sheet (α-Syn amyloid-like aggregates: α-SynA). Although cations and anions of EAN play roles in masking the charged side chains and PPII-helix-forming ability involved in the formation of α-SynA, water molecules are not directly related to its formation. We conclude that EAN-induced α-Syn amyloid-like aggregates form at hydrophobic associations in the middle of the molecules after masking the charged side chains at the N- and C-terminals of α-Syn.

An Ionic Liquid-Based Sample Preparation Method for Next-Stage Aggregate Proteomic Analysis.

A wide variety of proteomic methods have been applied for protein profiling of insoluble aggregates or inclusion bodies deposited in various cells or tissues. However, these are essentially optimized or modified classical protein chemistry techniques using conventional denaturing agents such as formic acid, urea, and sodium dodecyl sulfate (SDS). The use of these denaturants has several shortcomings, including limited solubilization, contamination, and restrictions on absolute sample quantity and throughput. Here, we describe an alternative proteomic sample preparation platform for widespread aggregation analysis. This approach combines two techniques, (1) the use of ionic liquid for protein solubilization and (2) the recently published microbead-based and organic-media-assisted proteolysis strategy (BOPs), into a single-tube workflow. We demonstrate that the combined approach (iBOPs) enabled the successful solubilization of heat-aggregated hen egg whites within 10 min and supported sensitive mass spectrometry (MS) analysis. The performance of the iBOPs system surpassed those of conventional detergents and chaotropes. Moreover, this technology enabled ultrasensitive proteomic characterization of protein aggregates deposited in individual Caenorhabditis elegans nematodes. We identified ubiquitin and other molecules as candidate stochastic factors whose accumulation levels varied among aging nematode individuals. The sensitivity and applicability of the present iBOPs make it especially attractive for next-stage aggregate proteomic analysis of various biological processes.

How does the flexibility of pyrrolidinium cations affect the phase behaviour of 1-alkyl-1-methylpyrrolidinium bis(trifluoromethanesulfonyl)imide homologues under stressful conditions?

We conducted high-pressure Raman spectroscopy measurements on a series of 1-alkyl-1-methylpyrrolidinium bis(trifluoromethanesulfonyl)imide ([Pyr1n][TFSI], n = 3, 4, 6 and 8) homologues that have different alkyl chain lengths, n, at room temperature. The results showed that all [Pyr1n][TFSI] samples formed a glassy state in which the glass transition pressure (pg) slightly increased with an increase in n. This tendency is similar to prior results of high-pressure glass formation of [Cnmim][TFSI], although the pgs for [Pyr1n][TFSI] are larger than those for [Cnmim][TFSI] with corresponding n by ∼0.5 GPa. We discuss the local structural changes occurring in [Pyr1n][TFSI] in view of the conformational changes of the Pyr+1n cation and TFSI- anion.

Long Periodic Structure of a Room-Temperature Ionic Liquid by High-Pressure Small-Angle X-Ray Scattering and Wide-Angle X-Ray Scattering: 1-Decyl-3-Methylimidazolium Chloride.

The Bragg reflections of 1-decyl-3-methylimidazolium chloride ([C10 mim][Cl]), a room-temperature ionic liquid, are observed in a lowly scattered wavevector (q) region using high-pressure (HP) small-angle X-ray scattering methods. The HP crystal of [C10 mim][Cl] was characterized by an extremely long periodic structure. The peak position at the lowest q (1.4 nm-1 ) was different from that of the prepeak observed in the liquid state (2.3 nm-1 ). Simultaneously, Bragg reflections at high-q were detected using HP wide-angle X-ray scattering. The longest lattice constant was estimated to be 4.3 nm using structural analysis. The crystal structure of HP differed from that of the low-temperature (LT) crystal and the LT liquid crystal. With increasing pressure, Bragg reflections in the high-q component became much broader, and were accompanied by phase transition, although those in the low-q component were observed to be relatively sharp.

Optical absorption and photoconductivity in iodine-excess ionic liquids: the case of 1-alkyl-3-methyl imidazolium iodides.

We investigated the optical absorption and photoconductivity of iodine-excess ionic liquids (ILs) based on 1-alkyl-3-methyl imidazolium iodide ([Cnmim][I]; n = 3, 4, and 6). The iodide concentration m was 2 ≦ m ≦ 8, which was determined by the molar fraction [Cnmim]+ : [Im]- = 1 : m. By adding iodine, an absorption edge shifted from 282 nm in the UV region to around 600 nm in the visible-light region. The optical bandgaps Eo decreased gradually from 2.3 eV to 1.9 eV with increasing m from 2 to 8. The alkyl-side chain lengths of the cations have little effect on the Eo. This experimental result was confirmed by ab initio molecular orbital calculations. The effects were reflected in the photoconductivity of the ILs, as expected. [C4mim][Im] exhibited greater photo-induced electron generation compared with [C3mim][Im] and [C6mim][Im]. The photoconductivity in both [C3mim][Im] and [C6mim][Im] increased slightly with increasing m. The trend of photoconductivity in [C4mim][Im] exhibited an N-shaped form. The highest photoconductivity 1.6 was observed in [C4mim][I8].

High-pressure glass formation of a series of 1-alkyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide homologues.

We investigated the stability of the liquid phase of a series of 1-alkyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide ([Cnmim][TFSI]) homologues with different alkyl chain lengths for 3 ≤ n ≤ 10 at room temperature. We found that all [Cnmim][TFSI] samples (n = 3-10) formed a glassy state when pressure was applied. Intriguingly, the glass transition pressure (pg) slightly increases up to n = 5, reaches a plateau at n ≧ 8, and increases again at n = 10. This is completely different from the high-pressure glass formation of [Cnmim][BF4], where the pg decreases as n increases. We discussed the local structural changes occurring in [Cnmim][TFSI] in view of the conformational changes of the cation and anion, and small-angle X-ray scattering data. It seems that [Cnmim][TFSI] is resistant to external pressure and retains its local liquid structure by conformational adjustments of the cation and anion.

Anomalous Freezing of Nano-Confined Water in Room-Temperature Ionic Liquid 1-Butyl-3-Methylimidazolium Nitrate.

Non-crystal formation of ice is investigated by simultaneous X-ray diffraction and differential scanning calorimetry measurements upon cooling to -100 °C. At room temperature, size-tunable water confinement (≈20 Šsize) in a room-temperature ionic liquid (RTIL, 1-butyl-3-methylimidazolium nitrate, [C4 mim][NO3 ]) exists in a water-rich region (70-90 mol % D2 O). The confined water (water pocket) is characterized by almost monodispersive size distribution. In [C4 mim][NO3 ]-x mol % D2 O (70

Conformational adjustment for high-pressure glass formation of 1-alkyl-3-methylimidazolium tetrafluoroborate.

The conformational stability of 1-alkyl-3-methylimidazolium tetrafluoroborate ([Cnmim][BF4], n = 3-8) under high pressure was investigated using Raman spectroscopy to reveal the preferential role of the alkyl-chain length (n) in high-pressure glass transition. To evaluate this, we determined the intensity ratio (r) and differences in the partial molar volume (ΔVtrans→gauche) between the whole trans and gauche conformers of the [Cnmim] cation using Raman intensities. Interestingly, both values were classified into a two alkyl-chain length region at the border of n = 5. The coulombic interaction (cation-anion interaction) for the conformational stability is the predominant factor below n = 5 (the cation-head portion: alkyl carbon number C < 5), and the alkyl-chain packing effect (cation-cation interaction) is the predominant factor above n = 5 (the cation-tail portion: C > 5). In combination with the conformational preference of the [Cnmim] cation under a high-pressure glassy state, the alkyl chain displays a preferential role, i.e., an increase in the gauche conformer of [Cnmim][BF4] adjusts to avoid crystallization (the conformational adjustment effect). In the presence of the coulombic interaction, the preferential role of the flexible alkyl chain is an important key to elucidate the mechanism of the complicated high-pressure phase transition behavior of ionic liquids.

Effect of exercise therapy on muscle mass and physical functioning in patients undergoing allogeneic hematopoietic stem cell transplantation.

PURPOSE: Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is associated with transplant-related toxicities, which may have a profound impact on a patient's physical functioning and body composition. In order to analyze the effect of exercise therapy on muscle mass and physical functioning in patients receiving allo-HSCT, we measured muscle mass and physical functioning before and after allo-HSCT. METHODS: Eighty-six patients who had undergone allo-HSCT between February 2010 and September 2013 at Imamura Bun-in Hospital participated in this study. Physical therapists performed exercise therapy with patients 5 days a week, starting 2 weeks before allo-HSCT. Body composition, 6-min walk test (6MWT) scores, and handgrip strength were evaluated 2 weeks before allo-HSCT and 6 weeks after allo-HSCT. RESULTS: Thirty-five patients were available for evaluation 2 weeks before and 6 weeks after allo-HSCT. The 6MWT (p = 0.005) and handgrip strength (p < 0.001) significantly decreased after allo-HSCT. Although upper extremity muscle mass (p = 0.001) and trunk muscle mass (p < 0.001) significantly decreased after allo-HSCT, lower extremity muscle mass remained unchanged. CONCLUSIONS: In this study, it is suggested that exercise therapy may be effective for maintaining lower extremity muscle mass in patients undergoing allo-HSCT.

Protein Cryoprotectant Ability of the Aqueous Zwitterionic Solution.

Protein cryopreservation is important for the long-term storage of unstable proteins. Recently, we found that N-acetylglucosaminyltransferase-V (GnT-V) can be cryopreserved in a deep freezer without temperature control using a dilute binary aqueous solution of 3-(1-(2-(2-methoxyethoxy)ethyl)imidazol-3-io)butane-1-carboxylate (OE2imC3C) [10 wt %, mole fraction of solute (x) = 7.75 × 10-3], an artificial zwitterion. However, it is unclear which solvent properties are required in these media to preserve unstable proteins, such as GnT-V. In this study, we investigated the melting phenomena and solution structure of dilute binary aqueous OE2imC3C solutions [x = 0-2.96 × 10-2 (0-30 wt %)] using differential scanning calorimetry (DSC) and Raman and Fourier transform infrared (FTIR) spectroscopies combined with molecular dynamics (MD) simulation to compare the cryoprotectant ability of OE2imC3C with two general cryoprotectants (CPAs), glycerol and dimethyl sulfoxide. DSC results indicated that aqueous OE2imC3C solutions can be melted at lower temperatures with less energy than the control CPA solution, with increasing x, primarily due to OE2imC3C having a higher content of unfrozen water molecules. Moreover, Raman and FTIR results showed that the high content of unfrozen water molecules in aqueous OE2imC3C solutions was due to the hydration around the ionic parts (the COO- group and imidazolium ring) and the OCH2CH2O segment. In addition, the MD simulation results showed that there were fewer structured water molecules around the OCH2CH2O segment than the hydration water molecules around the ionic parts. These solvent properties suggest that dilute aqueous OE2imC3C solutions are effective in preventing freezing, even in a deep freezer. Therefore, this medium has the potential to act as a novel cryoprotectant for proteins in biotechnology and biomedical fields.

Effect of rehabilitation in patients undergoing hematopoietic stem cell transplantation.

Patients undergoing hematopoietic stem cell transplantation (HSCT) tend to experience decline in physical function, mental function, and quality of life (QOL) after HSCT due to low activity caused by adverse reactions to chemotherapy used in pre-transplantation treatment and post-transplant complications. Rehabilitation for HSCT patients is effective in preventing decline in physical function, reducing fatigue, and improving QOL. A combination of aerobic exercise and strength training is recommended for exercise therapy. Risk management is also important in the implementation of exercise therapy, and the exercise intensity should be determined according to the presence of anemia, low platelet counts, or post-transplant complications. On the other hand, post-transplant complications can decrease the patient's motivation and daily activity level. A multidisciplinary approach, which includes physicians and nurses, is important to achieve early discharge from the hospital and as quick a return to society as possible.

Anomalous conformational change in 1-butyl-3-methylimidazolium tetrafluoroborate-D2O mixtures.

We have investigated the effect of deuterated water on the conformational equilibrium between the gauche and trans conformers of the [bmim] cation in mixtures of water and 1-butyl-3-methylimidazolium tetrafluoroborate ([bmim][BF(4)]), an ionic liquid, at room temperature. A comparison of the results obtained from solutions made with H(2)O and with D(2)O highlights an anomalous conformational change in the D(2)O solution showing an extended N-shaped behavior. The gauche conformer of the [bmim] cation in D(2)O increased up to x = ~50 (D(2)O mol %); however, it decreased up to higher water concentrations of x = ~85 before again increasing drastically toward x = ~100. We provide spectroscopic evidence that the anomalous conformational dynamics of the [bmim] cation in D(2)O is directly related to the H/D exchange reaction of the C-H group at position 2 of the imidazolium ring.

Cryostorage of unstable N-acetylglucosaminyltransferase-V by synthetic zwitterions.

We report biocompatible materials for cryostorage of unstable proteins such as cancer-related enzyme, N-acetylglucosaminyltransferase-V (GnT-V). GnT-V activity and the amount of protein after freezing were better retained in synthetic zwitterion solutions than in the glycerol solution. This study highlights the potential utility of synthetic zwitterions as novel cryoprotectants.

Effect of pressure on the secondary structure of coiled coil peptide GCN4-p1.

It has recently been demonstrated that pressure induces folding of the alpha-helix of an alanine-based peptide (AK20), which is a monomer in water (Imamura and Kato, Proteins 2009;76:911-918). The present study focused on a coiled coil peptide GCN4-p1, the alpha-helices of which associate via a hydrophobic core, to examine whether the pressure stability of the alpha-helices depends on the hydrophobic core. Fourier transform infrared spectroscopy was used to investigate the effect of pressure on the secondary structures of GCN4-p1. The infrared spectra of GCN4-p1 shows the two amide I' peaks at approximately 1650 and approximately 1630 cm(-1) stemming from the solvent-inaccessible alpha-helix and the solvent-accessible alpha-helix, respectively. The intensities of both the peaks increase with increasing pressure, whereas they decrease with increasing temperature. This indicates that pressure induces both the alpha-helices of GCN4-p1 to fold. The present result suggests that the positive volume change upon unfolding of an alpha-helix is a common characteristic of peptides. The pressure-induced stabilization of the alpha-helices is discussed in comparison with the pressure denaturation of proteins.

Geometry and efficacy of cross-strand Trp/Trp, Trp/Tyr, and Tyr/Tyr aromatic interaction in a beta-hairpin peptide.

The Trpzip2 peptide (WTWENGKWTWK-NH(2)), designed by Cochran and co-workers, contains two pairs of Trp's having cross-strand interaction and forms a stable antiparallel beta-hairpin. In order to study the geometries and effects on the structure and stability of different aromatic interactions, selected tryptophan residues were substituted with Tyr to get three Trpzip2 mutants with different Trp/Trp, Trp/Tyr, and Tyr/Tyr interacting pairs. Their native-state structures were determined using two-dimensional (2D) NMR and shown to have the same cross-strand edge-to-face Trp/Trp interaction as that in Trpzip2 for the Trp/Trp pair. The analogous Trp/Tyr and Tyr/Tyr pairs also tended to have an edge-to-face geometry. The effects of specific Trp/Trp, Trp/Tyr, and Tyr/Tyr interactions on hairpin stability were studied by varying temperature and monitoring structure with electronic circular dichroism (CD) and infrared (IR) absorption spectra. IR and CD temperature variations were fit to a two-state model that yielded lower T(m) values for Tyr containing mutants, indicating that Trp/Tyr and Tyr/Tyr interactions have less contribution to hairpin stability than the Trp/Trp interaction. Trp/Tyr interactions can provide significant stabilization, much greater than the Trp/aliphatic interaction, but Tyr/Tyr interactions are not as significant. Cross-strand interacting residues involving Trp with an edge-to-face orientation with Trp or Tyr had the strongest impact on hairpin stability.

Peculiar High-Pressure Phase Behavior of 1-Butyl-3-methylimidazolium Iodide.

We investigated the stability of the liquid phase of 1-butyl-3-methylimidazolium iodide (hereafter abbreviated as [C4mim][I]) up to 16.7 GPa at room temperature. We observed a peculiar phase transition behavior in the [C4mim][I] sample. In particular, a glassy state was formed at ∼1.3 GPa; however, the reddish-brown precipitate was formed probably due to concentrated I3- or I2- species that were formed above 12 GPa; [C4mim][I] showed a pressure-induced partial crystallization from the glassy state. We concluded that the conformation of [C4mim]+ is essential in iterative modulation to control the environmental formation of iodide precipitate.

High-Pressure Raman Study of n-Octane up to 15 GPa.

The high-pressure (HP) phase transition and conformational change of n-octane (hereafter abbreviation as n-C8) up to 15.3 GPa were studied using Raman spectroscopy to investigate the relationship between the HP phase state and the alkyl chain length of n-alkanes. The Raman spectral analysis of n-C8 indicated that the liquid-solid transition (solidification) occurs at ∼0.9 GPa and that the corresponding transition pressure of n-alkanes depends on their density. Further pressurization at ∼4 GPa increased the population of the gauche conformer, while the solid (order)-amorphous transition occurred at ∼6 GPa along with a change in the full width at half maximum of the ruby R1 fluorescence line. The comparison of our findings with previously reported results suggested that the even-odd effect in the HP phase transition after solidification of n-alkanes appears between n-C7 and n-C8 as their HP phase transition up to ∼15 GPa was different.

Relationship between hydrophobic interactions and secondary structure stability for Trpzip beta-hairpin peptides.

The temperature-induced beta-hairpin stabilities of selected mutations of the Trpzip1 peptide, SWTWEGNKWTWK (WWWW), have been investigated by electronic circular dichroism (CD), Raman, and FT-IR spectroscopies. The tryptophan (Trp) residues in the original Trpzip1 sequence were systematically substituted with tyrosine (Tyr) in different positions to test the impact of Trp interactions on the beta-hairpin structure and stability. The CD intensity at approximately 228 nm, which arises from Trp-Trp interactions (tertiary structure), and the amide I' IR absorbance at approximately 1635 cm(-1) (secondary structure) have been measured over a range of temperatures to investigate the impact of Tyr substitution on beta-hairpin thermal stability in Trpzip peptides. Mutation from Trp to Tyr in the Trpzip1 sequence reduces the extent of beta-hairpin structure and monotonically decreases the beta-hairpin stability of Trpzip1 mutant peptides with an increasing number of Tyr substitutions. Substituted Trpzip peptides with just one pair of Trp-Trp interactions close to either the terminal residues (WYYW) or the turn (YWWY) have similar stabilities. Comparison of conformational transitions monitored by CD and IR reveals them to have multistate behavior in which the temperature-induced disruption of the Trp-Trp interaction (tertiary structure) occurs at a lower temperature than the unfolding of the secondary structure.

Raman spectroscopic study on the coordination behavior of rare earth ions in N-methylacetamide.

The coordination behavior of rare earth (Ln (3+)) ions in N-methylacetamide (NMA) solution has been investigated at room temperature by Raman spectroscopy. The behavior of the symmetric Raman Ln-Cl stretching (nu Ln-Cl) band, and amide I (nu AI), and III (nu AIII) bands of NMA with the rare earth series is discussed in conjunction with the change in the coordination structure occurring in the middle of the rare earth series. A competition for a coordination equilibria between a Cl (-) ion and an NMA molecule from the rare earth chloride-NMA complex might occur in the middle rare earth region. It is demonstrated that the change in the coordination structure of Ln (3+) ions in NMA is due to an elimination of an NMA molecule.