Identification of post-translationally modified proteins in proteome studies.

Proteome studies are powerful tools to solve many different problems in metabolism, signal transduction, drug discovery, and other areas of interest in life sciences. Up to now, high-sensitive methods for protein identification after two-dimensional gel electrophoresis using mass spectrometry are available. However, the identification of post-translational modifications after two-dimensional gel electrophoresis is still an unsolved problem. In this paper, we want to give several examples for the successful identification of post-translational modifications and point mutations.     

Capillary electrophoresis of histone H1 variants at neutral pH in dynamically modified fused- silica tubing

Existing methods for the analysis of histone H1 by capillary electrophoresis (CE) employ acidic buffers (pH <3.0) to suppress silanol ionization and minimize the loss of these extremely basic proteins by adsorption to capillary walls. Here we describe the use of Polybrene (PB) as a dynamic modification reagent in a simple procedure that facilitates the analysis of chicken H1 at neutral pH. PB is adsorbed to the inner surfaces of capillaries to render them cationic prior to use and a low concentration of PB is included in the electrolyte to replenish the coating during use. Inclusion of ethylenediaminetetraacetic acid (EDTA) in the electrolyte results in the assembly of a dynamic cation-exchange layer upon the immobilized PB that influences the relative mobilities of H1 variants. The six nonallelic variants of H1 known in this species as well as certain allelic variants are resolved. Because the procedure is effective in preventing the adsorption of proteins as basic as H1 at neutral pH, this strategy should facilitate CE analyses of many basic proteins under conditions that maintain their native conformation.     

Thermal stability of organosilica and their forms modified by ions of copper(II)

Thermal stability of two-component organosilica sorbents – silico-polymethylsiloxanes with the ratio of hydrophilic and hydrophobic components of 50:50 and 70:30 mass%, and their forms, modified by copper(II), was investigated using thermal analysis (DTG, DTA, TG). The influence of the composition of modified organosilica sorbents and copper(II) content on the endothermic (removal of adsorbed water) and exothermic (decomposition by oxidation of methyl groups, possible hydration of surface) peak temperatures and on mass loss is shown. It was found that thermal stability of organosilica modified by copper(II) was lower than that of initial sorbents and depends on the content of modifying component and ratio of silanol and methylsilil groups in organosilica composition.     

Analysis of trace elements and their physico-chemical forms in natural waters

Trace elements in natural waters can be present in different physico-chemical forms, varying in size, charge and density properties. Knowledge of speciation is essential for understanding the transport, distribution, and biological uptake of trace elements in the environment. The development of techniques to provide reliable information on physico-chemical forms has, therefore, become a challenge within Analytical Chemistry.When selecting analytical methods for the determination of total concentrations or fractions of trace elements in natural waters, no exclusion of species should occur, or at least it must be accounted for. Furthermore, the determination limits must be sufficiently low to allow the actual concentrations to be determined with reasonable precision and accuracy. For very low concentrations, preconcentration techniques are applicable, provided the chemical yield of the spike represents that of the original species present. For methods meeting these criteria, the suitability for routine analysis should be considered.When the physico-chemical forms of trace elements are to be determined, the fractionation should take placein situ or shortly after sampling. As the concentrations involved in speciation studies may be extremely low, there is an increasing awareness of potential sources of errors influencing analytical results. Sample collection and separation/fractionation/concentration procedures prior to analysis are, therefore, essential within Analytical Chemistry, and the whole procedure must be taken into account when interpreting the results. There are, however, several requirements which should be met by techniques applicable for speciation purposes. In general, size fractionation techniques (e.g.in situ hollow fibre ultrafiltration) should be applied prior to the addition of any chemical reagents (charge fractionation techniques).     

IR-spectroscopic examination of polytetrafluoroethylene and its modified forms

The results of IR-spectroscopic examinations of the molecular and supramolecular structure of polytetrafluoroethylene and polymer materials thereof were summarized. It was shown that, upon heat, mechanical, and other treatment, as well as under radiation exposure, polytetrafluoroethylene preserves its chain-helical conformation, and the resulting modified forms consist of crystalline and amorphous phases in a ratio depending on the history of the sample. The degree of the structural ordering in the polymer decreases with increasing temperature and pressure. The formation of branched moieties and short macromolecules with double bonds (?CF=CF₂) in the terminal groups is specific for the process caused by thermal and radiation-induced degradation. The oxidation of the polymer macromolecules requires applying high irradiation doses and heating samples in an oxygen or air atmosphere.     

Studies of natural kaolinite and its modified forms

Modified forms of the natural and annealed at 700°C kaolinite have been fabricated by treatment using hydrochloric acid of different concentrations. The resulting samples were investigated using X-ray fluorescence spectroscopy, X-ray diffraction analysis, IR spectroscopy, and positron annihilation spectroscopy, scanning electron microscopy, etc. The dependencies of elements contents, dye adsorption, specific surface area, and specific internal volume on the concentration of hydrochloric acid have been determined. It has been demonstrated that the changes in the structure of annealed kaolinite were significantly increased by the increase of the concentration of acid, and also there were proportional changes in the values of specific surface area, internal volume, and dye adsorption. Changes in the structural parameters of natural kaolinite depend on the acid concentration in a less degree. Modification with acid results in obtaining solutions that contain metal chlorides. Precipitation of these metals in the form of oxides on the surface of kaolinite particles results in fabrication of new sorbents, whose yield is close to the quantitative one, whereas the kaolinite sorption characteristics become improved. Further kaolinite modification by cellulose under similar conditions results in fabrication of a new, more efficient sorbent. It has been demonstrated that natural kaolinite treated with 12% hydrochloric acid had lower friction coefficient than the annealed one.     

尺寸排阻-反相液相色谱-质谱联用技术在大鼠肾脏翻译后修饰蛋白质鉴定中的应用

LC-MS联用技术在蛋白质组学研究中具有重要的作用,但是在复杂的生物体系中,由于样品的高度复杂性和其中蛋白质含量的巨大差异,执行全面且无倾向的蛋白质组分析是一项挑战。因此,在液相色谱分离中采用基于不同原理的色谱分离方法来降低蛋白质样本的复杂度,并对微量蛋白质进行富集,对后续采用质谱方法进行信息的采集和深入分析至关重要。在这里我们开发了一种基于尺寸排阻色谱(SEC)与反相液相色谱(RPLC)结合的新方法来进行复杂体系蛋白质的分离和鉴定,特别是对于微量蛋白质的分析。首先使用SEC对蛋白质进行分离和富集,并酶解成多肽,再通过RPLC-MS联用的方法对酶解后的多肽进行分离和鉴定。结果显示使用上述方法可以有效降低蛋白质样本的复杂度,并有效提高微量蛋白质的鉴定能力,可从大鼠肾脏鉴定出23621个肽段及1345个蛋白质,比常规的二维强阳离子交换-反相液相色谱法(2D SCX-RPLC)鉴定到的肽段及蛋白质分别多出69%及27%。此外,该方法对肾脏翻译后修饰(PTM)蛋白质的鉴定显示出更多的优势,翻译后修饰的多肽鉴定率显著增加,特别是磷酸化肽段的鉴定效率可达到靶向富集策略的水平。在此展示的SEC-RPLC-MS可以更好地了解蛋白质翻译后修饰对肾脏的影响,最终将有助于增加我们对正常的生理性肾功能以及病理过程机制的理解。     

Separation of phosphorylated histone H1 variants by high-performance capillary electrophoresis.

High-performance capillary electrophoresis (HPCE) was used to separate successfully distinct phosphorylated derivatives of individual histone H1 variants. With an untreated capillary (50 cm x 75 microns I.D.) the electrophoresis was performed in about 15 min. Inconvenient interactions of these highly basic proteins with the capillary wall were eliminated by using 0.1 M sodium phosphate buffer (pH 2.0) containing 0.03% hydroxypropylmethylcellulose. Under these experimental conditions the histone H1 variants H1b and H1c obtained from mitotic enriched NIH 3T3 fibroblasts and isolated by reversed-phase high-performance liquid chromatography were clearly separated in their non-phosphorylated and different phosphorylated forms. This result was confirmed by acid-urea gel electrophoresis, comparison with non-phosphorylated histones H1b and H1c, isolated from quiescent NIH 3T3 cells, and incubation of multi-phosphorylated histone H1b with alkaline phosphatase and subsequent acid-urea and capillary electrophoresis. The results illustrate that the application of HPCE to the analysis of histone modifications provides a new alternative to traditional gel electrophoresis.     

Force field parameters for the simulation of modified histone tails

We describe the development of force field parameters for methylated lysines and arginines, and acetylated lysine for the CHARMM all‐atom force field. We also describe a CHARMM united‐atom force field for modified sidechains suitable for use with fragment‐based docking methods. The development of these parameters is based on results of ab initio quantum mechanics calculations of model compounds with subsequent refinement and validation by molecular mechanics and molecular dynamics simulations. The united‐atom parameters are tested by fragment docking to target proteins using the MCSS procedure. The all‐atom force field is validated by molecular dynamics simulations of multiple experimental structures. In both sets of calculations, the computational predictions using the force field were compared to the corresponding experimental structures. We show that the parameters yield an accurate reproduction of experimental structures. Together with the existing CHARMM force field, these parameters will enable the general modeling of post‐translational modifications of histone tails. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Study of phenol adsorption on modified forms of zeolite

Analcime samples were studied with the aim of cleaning air from phenol.     

Cu-assisted two dimensional charge-mass double focusing gel electrophoresis and mass spectrometric analysis of histone variants

Abundant isoforms and dynamic posttranslational modifications cause the separation and identification of histone variants to be experimentally challenging. To meet this need, we employ two-dimensional electrophoretic gel separation followed by mass spectrometric detection which takes advantage of the chelation of Cu²⁺ with amino acid residues exposed on the surfaces of the histone proteins. Acid-extracted rat liver histones were first mixed with CuSO₄ solution and then separated in one dimension with triton–acid–urea (TAU) gel electrophoresis and in a second dimension using sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). The separations result from both the changes in charge and mass upon Cu²⁺ chelation. Identities of each separated gel bands were obtained by using matrix-assisted laser desorption-ionization mass spectrometry (MALDI-MS). It was found that the migration of H3 histone isoforms of rat liver is markedly affected by the use of Cu²⁺ ions.     

Studying of phenol adsorption on modified forms of bentonite

The modified forms of bentonite are formed by treating it with salts of various metals. Their nature, force and molecule number per 1 cm² are investigated. Also quantity of basic centers on their surface was determined by phenol adsorption.     

Convergent chemoenzymatic synthesis of O-GalNAc rare cores 5, 7, 8 and their sialylated forms

All O-GalNAc glycans are derived from 8 cores with 2 or 3 monosaccharides linked via α- or β-glycosidic bonds. While chemical and chemoenzymatic syntheses of β-linked cores 1–4 and 6 and derived glycans have been well developed, the preparation of α-linked rare cores 5, 7, and 8 is challenging due to the presence of this 1,2-cis linkage. Meanwhile, the biosynthesis and functional roles of these structures are poorly understood. Herein, we synthesize 3 α-linked rare cores with exclusive α-configuration from a versatile precursor through multifaceted chemical modulations. Efficient regioselective α2-6sialylion of the rare cores was then achieved by Photobacterium damselae α2-6sialyltransferase-catalyzed reactions. These structures, together with β-linked cores 1–4 and 6, and their sialylated forms, were fabricated into a comprehensive O-GalNAc core microarray to profile the binding of clinically important GalNAc-specific lectins. It is found that only Tn, (sialyl-)core 5, and core 7 are the binders of WFL, VVL, and SBA, while DBA only recognized (sialyl-)core 5, and Jacalin is the only lectin that binds core 8. In addition, activity assays of human α-N-acetylgalactosaminide α2-6sialyltransferases (ST6GalNAcTs) towards the cores suggested that ST6GalNAc1 may be involved in the biosynthesis of previously identified sialyl-core 5 and sialyl-core 8 glycans. In conclusion, we provide efficient routes to access α-linked O-GalNAc rare cores and derived structures, which are valuable tools for functional glycomics studies of mucin O-glycans.

Mucin rare cores 5, 7, and 8 with 1,2-cis glycosidic bonds were prepared with exclusive stereo-selectivity from a versatile precursor. Enzyme-catalyzed regio-selective sialylation was then achieved, yielding natural sialylated rare cores.     

Catalytic applications of hydrotalcite-like materials and their derived forms

Hydrotalcite-like (HT-like) materials have been studied extensively in the last three decades. Although these materials initially perceived as potential anion exchangers, unrelenting efforts have also been attempted to use them as catalytic materials or as catalytic supports. There are varied ways by which one can use them for catalysis viz.; 1. Use them in as-synthesized form 2. Use them after calcining where the structural integrity of layered lattice is lost 3. Use the interlayer as functional spaces with moieties of catalytic interest 4. Use them after destruction or delamination and restructuring and 5. Use them as support or matrix. In this review, we are reporting the catalytic applications of HT-like materials and their derived forms carried out in our research group for the last 15 years in these various ways, covering reactions such as nitrous oxide decomposition, selective oxidation of organic compounds of industrial relevance and base-catalyzed isomerization of chemicals of perfumery interest. Although this review primarily focuses on our work, wherever applicable, related or relevant works from other groups are also presented to bestow comprehensiveness.     

Ab initio calculations of methionines and their protonated forms

Ab initio calculations of molecular and electronic structures of neutral molecules and protonated forms of methionine and its derivatives in the gaseous phase were carried out by the Hartree-Fock method using the 6–31G^* basis set with full geometry optimization. Proton affinities of methionine (1), methionine sulfoxide (2), and methionine sulfone (3) were calculated for different modes of coordination of the proton. The results of calculations demonstrated that in protonated forms of 1 and 3, bonding between the proton and the N atom is most favorable, while in protonated form of 2, bonding between the proton and the O atom of the SO group is most favorable. The proton affinities of the amino acids are as follows: 223.2 (1), 241.2 (2), and 221.5 (3) kcal mol⁻¹,i.e., methionine sulfoxide 2 exhibits the highest proton affinity in the series of the amino acids under consideration. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 8, pp. 1487–1490, August, 1998.     

Electronic absorption spectra for free hydrazyl radicals,their ionic forms and initial hydrazines

The results of the calculations of π–π^* transition energies of some free hydrazyl radicals, their ionic forms and initial hydrazines by the SCF –MO –LCAO method with restricted configuration interaction are presented. The comparison of the data obtained with the electronic spectra experimentally found, revealed that the absorption of radical solutions in the visible area was due to the electronic structure of radical molecules, the contribution of ionic forms to the absorption being negligible.     

Mercury forms and their transformation in pyrite under weathering

Pyrite is considered to be the major carrier of mercury in coal. Here, the chemical characteristics of two natural pyrite samples of different weathering degrees were characterized by time-of-flight secondary ion mass spectrometry (TOF-SIMS). Thermal stability of Hg was also analyzed via temperature programmed desorption experiment (TPD). Characteristic ions such as S⁻, Fe⁺, FeS⁻, and FeS₂⁻ were detected on the surface of fresh pyrite. The release temperature of Hg ranged between 180°C and 300°C, and the characteristic peak of black HgS was recorded. In addition, abundant Fe₂O₃⁻, FeSO⁻, SO₄⁻, and HSO₄⁻ were detected on the surface of weathered pyrite, and the release temperature of Hg therein was mainly distributed at 260°C to 380°C and 520°C to 600°C, corresponding to the characteristic peaks of red HgS and HgSO₄, respectively. The results show that pyrite is acidified during weathering and that Hg forms in pyrite are transformed from the original state (HgS) to HgSO₄.     

Colloidal forms of radionuclides and their separation from water solution

Colloidal properties of¹⁴⁴Ce(III),¹⁴⁷Pm(III),⁹¹Y(III), and other, radionuclides were determined from the course of their self-diffusion. A reduced self-diffusion indicated the formation of colloidal radionuclides. The decrease in the self-diffusion coefficient began from a certain value of pH, and a pH region of slowest self-diffusion existed for each of the radionuclides studies. The maximum formation of colloidal radionuclides may be assumed to lie in the range of these pH values. An increase in the rate of self-diffusion was observed with radionuclides in colloidal forms under the effect of gamma-radiation. The possibility of mutual interaction between radionuclides was also inferred from the course their self-diffusion. High effective sorption of¹⁴⁷Pm(III) was attained on hydrated ferric oxide in the pH range were hydrolytic products and colloidal forms of¹⁴⁷Pm(III) were formad to a large extent.