Mixed-ligand complex formation of mercury (II) ethylenediaminetetraacetate with cysteine and methionine in aqueous solution

The mixed-ligand complex formation in the systems Hg²⁺-Edta⁴⁻-L (L = Cys²⁻, Met⁻) has been studied by means of calorimetry, pH-potentiometry and NMR spectroscopy in aqueous solution at 298.15 K and the ionic strength of I = 0.5 (KNO₃). The thermodynamic parameters of formation of the HgEdtaL, HgEdtaHL and (HgEdta)₂L complexes have been determined. The most probable coordination mode for the complexone and the amino acid in the mixed-ligand complexes is discussed.     

A convenient solid phase approach to obtain lipophilic 5′-phosphoramidate derivatives of DNA and RNA oligonucleotides

This paper explores the potential of a modified phosphotriester approach to the synthesis of 5′-phosphoramidate derivatives of DNA and RNA oligonucleotides. The modification of 5′-deprotected support-bound oligonucleotides is done in two steps: i) conversion of the 5′-OH group of an oligonucleotide into an activated phosphodiester, and ii) treatment of the activated phosphodiester with an aminocompound. The approach is efficient and compatible with conventional solid phase oligonucleotide synthesis. It can be used for the conjugation of therapeutically relevant oligonucleotides with functional moieties or carrier constructions, which are to be removed after endocytosis.     

The NISTmAb tryptic peptide spectral library for monoclonal antibody characterization

We describe the creation of a mass spectral library composed of all identifiable spectra derived from the tryptic digest of the NISTmAb IgG1κ. The library is a unique reference spectral collection developed from over six million peptide-spectrum matches acquired by liquid chromatography-mass spectrometry (LC-MS) over a wide range of collision energy. Conventional one-dimensional (1D) LC-MS was used for various digestion conditions and 20- and 24-fraction two-dimensional (2D) LC-MS studies permitted in-depth analyses of single digests. Computer methods were developed for automated analysis of LC-MS isotopic clusters to determine the attributes for all ions detected in the 1D and 2D studies. The library contains a selection of over 12,600 high-quality tandem spectra of more than 3,300 peptide ions identified and validated by accurate mass, differential elution pattern, and expected peptide classes in peptide map experiments. These include a variety of biologically modified peptide spectra involving glycosylated, oxidized, deamidated, glycated, and N/C-terminal modified peptides, as well as artifacts. A complete glycation profile was obtained for the NISTmAb with spectra for 58% and 100% of all possible glycation sites in the heavy and light chains, respectively. The site-specific quantification of methionine oxidation in the protein is described. The utility of this reference library is demonstrated by the analysis of a commercial monoclonal antibody (adalimumab, Humira®), where 691 peptide ion spectra are identifiable in the constant regions, accounting for 60% coverage for both heavy and light chains. The NIST reference library platform may be used as a tool for facile identification of the primary sequence and post-translational modifications, as well as the recognition of LC-MS method-induced artifacts for human and recombinant IgG antibodies. Its development also provides a general method for creating comprehensive peptide libraries of individual proteins.     

Spatial-temporal characteristics of intercellular junctions in early zebrafish and loach embryos before and during gastrulation

 Injections of lucifer yellow and fluorescein dyes into loach (Misgurnus fossilis) and zebrafish (Danio rerio) embryos were used to analyse the intercellular communication via gap junctions (GJs) and their role in morphogenetic processes during the period from early blastula to late gastrula. It is shown that the efficiency of dye transfer between the superficial blastomeres increases by the late blastula stage. Blastomeres of the basal layer, on the other hand, become gradually uncoupled from the yolk cell (YC). This process is spatially uneven and finishes by the late gastrula stage. Prior to it, at the early epiboly stage, a local increase in dye transfer is observed in the circular zone of the blastoderm margin. During gastrulation, GJ communication between blastomeres and the YC in this zone and also in the newly-formed germ ring region (the prospective mesoderm domain) persists for a longer period of time (up to the stage of 60–70% epiboly) than in the remaining part of the basal layer (the prospective ectoderm domain). Taking into account the data on changes in the adhesive properties of blastomeres during normal development and observations on embryos with retarded epiboly, we hypothesize that changes in GJ communication between superficial blastomeres, on one hand, and between basal blastomeres and the YC, on the other, are the consequences of the same, more general morphogenetic process of compaction occurring within the blastoderm, which supports epiboly and is probably responsible for the distinction between mesodermal and ectodermal fates of cells differently located within the forming epithelioid sheet. Received: 18 October 1996 / Accepted: 4 April 1997     

DNA B to D transition can be explained in terms of hydration economy of the minor groove atoms

Adjacent phosphate oxygen atoms in A and Z-DNA are located much closer together than in the B form and can be hydrated more economically due to the formation of water bridges between them, whereas in the B form phosphates are hydrated individually. This principle of hydration economy of phosphate groups discovered by Saenger and colleagues could not be applied to the B-D transition, which, like the B-A and B-Z transitions, occurs in a situation of water deficiency, because the distances between adjacent phosphates of individual polynucleotide chains in the D form are not much different from B-DNA. It follows from our calculations of B and D-DNA accessibility to solvent performed by the method of Lee & Richards, and from a simulation of solvent structure near DNA, that there is an economy of hydration only for the minor groove atoms. This feature and some experimental data can explain why only a limited range of sequences consisting of A.T or I.C pairs undergo the transition to the D form. The conformational transition in DNAs with such sequences to a poly[d(A]).poly[d(T])-like conformation (Bh-DNA), which is accompanied by a narrowing of the minor groove, can be explained in the same way. Calculations suggest that in the D-form minor groove of different A-T or I-C DNAs there is a double-layer hydration spine similar to that observed by Drew & Dickerson in the A-T tract of the d(C-G-C-G-A-A-T-T-C-G-C-G) dodecamer. The B-D and B-Bh transitions in A + T-rich DNAs can have biological implications, e.g. they can facilitate DNA bending upon the interaction with proteins.     

Architecture of Microcin B17 Synthetase: An Octameric Protein Complex Converting a Ribosomally Synthesized Peptide into a DNA Gyrase Poison

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Mechanism of thermal aggregation of rabbit muscle glyceraldehyde-3-phosphate dehydrogenase

Thermal denaturation and aggregation of rabbit muscle glyceraldehyde-3-phosphate dehydrogenase (GAPDH) have been studied using differential scanning calorimetry (DSC), dynamic light scattering (DLS), and analytical ultracentrifugation. The maximum of the protein thermal transition (T(m)) increased with increasing the protein concentration, suggesting that the denaturation process involves the stage of reversible dissociation of the enzyme tetramer into the oligomeric forms of lesser size. The dissociation of the enzyme tetramer was shown by sedimentation velocity at 45 degrees C. The DLS data support the mechanism of protein aggregation that involves a stage of the formation of the start aggregates followed by their sticking together. The hydrodynamic radius of the start aggregates remained constant in the temperature interval from 37 to 55 degrees C and was independent of the protein concentration (R(h,0) approximately 21 nm; 10 mM sodium phosphate, pH 7.5). A strict correlation between thermal aggregation of GAPDH registered by the increase in the light scattering intensity and protein denaturation characterized by DSC has been proved.