Fluorescence detection and quantitation of recombinant proteins containing oligohistidine tag sequences directly in sodium dodecyl sulfate-polyacrylamide gels

Two fluorophore-nitrilotriacetic acid conjugates, Pro-Q Sapphire 365 and Pro-Q Sapphire 488 oligohistidine gel stains, have been developed for the fluorescence detection of fusion proteins containing oligohistidine tags directly in sodium dodecyl sulfate polyacrylamide gels, without the requirement for electroblotting, reporter enzymes or secondary detection reagents. Pro-Q Sapphire 365 oligohistidine gel stain exhibits bright-blue fluorescence (emission maximum = 450 nm) when illuminated with UV-A or UV-B light from a standard ultraviolet transilluminator. Pro-Q Sapphire 488 oligohistidine gel stain exhibits bright-green fluorescence (emission maximum = 515 nm) when illuminated with visible light from a laser-based gel scanner equipped with a 470 nm second-harmonic generation (SHG) or 488 nm argon-ion laser source. Typically, 25-65 ng of oligohistidine-tagged fusion protein in whole cell lysates is detectable using either stain. After documenting the fluorescence signal from the Pro-Q Sapphire dyes, gels may be post-stained with the red-fluorescent SYPRO Ruby protein gel stain in order to reveal the total protein pattern.     

A sequence and structural study of transmembrane helices

A comparison is made between the distribution of residue preferences, three dimensional nearest neighbour contacts, preferred rotamers, helix-helix crossover angles and peptide bond angles in three sets of proteins: a non-redundant set of accurately determined globular protein structures, a set of four-helix bundle structures and a set of membrane protein structures. Residue preferences for the latter two sets may reflect overall helix stabilising propensities but may also highlight differences arising out of the contrasting nature of the solvent environments in these two cases. The results bear out the expectation that there may be differences between residue type preferences in membrane proteins and in water soluble globular proteins. For example, the -branched residue types valine and isoleucine are considerably more frequently encountered in membrane helices. Likewise, glycine and proline, residue types normally associated with `helix-breaking' propensity are found to be relatively more common in membrane helices. Three dimensional nearest neighbour contacts along the helix, preferred rotamers, and peptide bond angles are very similar in the three sets of proteins as far as can be ascertained within the limits of the relatively low resolution of the membrane proteins dataset. Crossing angles for helices in the membrane protein set resemble the four helix bundle set more than the general non-redundant set, but in contrast to both sets they have smaller crossing angles consistent with the dual requirements for the helices to form a compact structure while having to span the membrane. In addition to the pairwise packing of helices we investigate their global packing and consider the question of helix supercoiling in helix bundle proteins.     

The temperature-induced denaturation of small globular proteins as a first-order phase transition of ‘crystal molecules’

A general feature of temperature-induced reversible denaturation of small globular proteins is its all-or-none character. This strong cooperativity leads to think that protein molecules, possessing only two accessible thermodynamic states, the native and the denatured one, resemble ‘crystal molecules’ that melt at raising temperature. An analysis, grounded on mean field theory, allows to conclude that the two-state transition is a first-order phase transition. The implication of this conclusion are briefly discussed.     

Probing the water coordination of protein-targeted MRI contrast agents by pulsed ENDOR spectroscopy.

A novel methodology based on electron-nuclear double resonance (ENDOR) spectroscopy is used for the direct determination of the water coordination number (q) of gadolinium-based magnetic resonance imaging (MRI) contrast agents. Proton ENDOR spectra can be obtained at approximately physiological concentrations for metal complexes in frozen aqueous solutions either in the presence or absence of protein targets. It is shown that, depending on the structure of the co-ligand, the water hydration number of a complex in aqueous solution can be significantly different to when the complex is noncovalently bound to a protein. From the ENDOR spectra of the exchangeable protons, precise information on the metal-proton distance can be derived as well. These essential parameters directly correlate with the efficacy of MRI contrast agents and should therefore aid the development of novel, highly efficient compounds targeted to various proteins.     

Dynamically coating the capillary with 1-alkyl-3-methylimidazolium-based ionic liquids for separation of basic proteins by capillary electrophoresis

Ionic substances with melting points close to room temperature are referred to as ionic liquids. Because ionic liquids are environmentally benign and are good solvents for a wide range of both organic and inorganic materials, interest for their potential uses in different chemical processes is increasing. In this paper, a capillary electrophoretic method for the analysis of basic proteins including lysozyme, cytochrome c, trypsinoge, and α-chymotyypsinogen A is reported. The method, in which 1-alkyl-3-methylimidazolium-based ionic liquids are used as the running electrolytes, leads to a surface charge reversal on the capillary wall. The effects of the alkyl group, imidazolium counterion, and the concentration of the ionic liquids were discussed. The optimum buffer system was a 90 mM 1-ethyl-3-methylimidazolium tetrafluoroborate (1E-3MI-TFB) solution. The applied voltage was −15 kV and detection was performed by monitoring absorbance at 240 nm. Baseline separation, high efficiencies, and symmetrical peaks of four proteins were obtained. The R.S.D. values of migration times and peak areas were <0.68 and <3.0%, respectively. The separation mechanism seems to involve association between the imidazolium cations and the proteins.     

化学与酶促相结合合成并克隆核糖体失活蛋白Gelonin基因

利用已知Gelonin的氨基酸序，逆向推算出整个基因的碱基序列，根据E.coli的密码子偏爱性和后续基因克隆的需要，通过沉默突变设计相应的酶切位点和碱基序列，将整个基因分为四段，每个片段约175－220pb，每一个片段中的互补链从5′末端用化学合成100－120的碱基单链，其中两个链的3′末端有20个互补碱基。利用T4DNA聚合酶酶促添补成双链DNA，用分子克隆技术，分别构建重组子，然后再构建成含整个Gelonin基因的表达载体pET-gel进行表面，经诱导后，获得了一个28000的重组蛋白，并主要以可溶形式存在。     

The effect of ph and gas composition on the bubble fractionation of proteins

Studies were conducted to establish the effect of the variation of environmental factors on the separation occurring in protein systems, resulting from bubble fractionation in a bioreactor. The measure of separation was selected to be the separation ratio. This is defined to be the ratio of either the top or the middle position concentration in the vessel to the bottom concentration of the vessel. Invertase and α-amylase were the two “model” enzymes considered. It was observed that, under certain conditions, i.e., a combination of the nature of the sparging gas and the medium pH, varying degrees of protein separation were achieved. The pH of the system dramatically influenced the separation. It was found that the best separation occurred at a certain pH, assumed to be at or close to thepI of the protein in question. Furthermore, it was observed that systems sparged with CO₂ exhibited greater separation than systems sparged with air. In fact, in the case of invertase, almost threefold separation was observed at the top port when the solution was sparged with CO₂.     

Characterization and properties of the copper(II/I) complexes of macrocyclic hexathiaether ligand [21]aneS6

The copper(II/I) complexes of hexathiaether macrocyclic ligand, 1,4,8,11,15,18-hexathiacyclohenicosane ([21]aneS₆), were synthesized, and characterized by electrochemical and spectroscopic techniques. Cyclic voltammetric studies indicate that Cu([21]aneS₆)^2+/+ forms a reversible one-electron redox couple. The electrochemical potential obtained for Cu([21]aneS₆)^2+/+ (E^f = 0.89 V, against SHE) was found to be the highest potential reported to date for a Cu^2+/+ macrocyclic system in aqueous solution. By employing the Nernst equation, we can infer that the practical upper limit for formal potential of Cu(II/I)L systems maybe close to this high value. Stability constant data obtained for these complexes indicate that Cu([21]aneS₆)⁺is 12 orders of magnitude greater in stability than that of Cu([21]aneS₆)²⁺ indicating the favorable nature of this large macrocyclic ligand towards formation of Cu(I) complexes over Cu(II) complexes. Crystal structure of Cu([21]aneS₆)⁺ ( Fig. 2) shows that four sulfurs adjacent to one another are coordinated to Cu⁺ ion in this complex. Bond angles and distances calculated for the crystal indicate that it is a distorted tetrahedron, a geometry commonly encountered by Cu(I) complexes. This is the first report of synthesis and characterization of a metal coordinated [21]aneS₆ complex.     

以交联聚乙烯醇为载体的离子交换剂对蛋白质的分离性能

本文对阴离子交换剂ＤＥＡ—ＰＶＴ常压液相离子交换色谱分离蛋白质的性能、分离条件进行了探讨。结果表明其对蛋白质的分离性能良好，容易洗脱。与载体交联聚乙烯醇相比，ＤＥＡ—ＰＶＴ对蛋白质的非特异性吸附明显降低。     

Combinatorial Synthesis and Multidimensional NMR Spectroscopy: An Approach to Understanding Protein–Ligand Interactions

Combinatorial chemistry is a laboratory emulation of natural recombination and selection processes. Strategies in this developing discipline involve the generation of diverse, molecular libraries through combinatorial synthesis and the selection of compounds that possess a desired property. Such approaches can facilitate the identification of ligands that bind to biological receptors, promoting our chemical understanding of cellular processes. This article illustrates that the coupling of combinatorial synthesis, multidimensional NMR spectroscopy, and biochemical methods has enhanced our understanding of a protein receptor used commonly in signal transduction, the Src Homology 3 (SH3) domain. This novel approach to studying molecular recognition has revealed a set of rules that govern SH3–ligand interactions, allowing models of receptor–ligand complexes to be constructed with only a knowledge of the polypeptide sequences. Combining combinatorial synthesis with structural methods provides a powerful new approach to understanding how proteins bind their ligands in general.