Dynamic imaging of single DNA-protein interactions using atomic force microscopy

Atomic force microscopy (AFM) imaging of static DNA-protein complexes, in air and in liquid, can be used to directly obtain quantitative and qualitative information on the structure of different complexes. For example, DNA length, the location of preferential binding sites for proteins and bending of DNA as a result of the complexation can all be measured. Recording consecutive AFM images of DNA and protein molecules under conditions that they are still able to move and interact, or dynamic AFM imaging, however, can reveal information on the dynamic aspects of the interactions between these molecules. Here, an overview is given of the technical challenges that need to be considered for successful dynamic AFM imaging studies of individual DNA-protein interactions. Necessary technical improvements to the AFM set-up and the development of new sample preparation methods are described in this paper.     

What to Learn from a Comparative Genomic Sequence Analysis of <Emphasis Type="Italic">L</Emphasis>-Carnitine Dehydrogenase

Summary. In contrast to eukaryotic cells certain eubacterial strains have acquired the ability to utilize L-carnitine (R-(–)-3-hydroxy-4-(trimethylamino)butyrate) as sole source of energy, carbon and nitrogen. The first step of the L-carnitine degradation to glycine betaine is catalysed by L-carnitine dehydrogenase (L-CDH, EC 1.1.1.108) and results in the formation of the dehydrocarnitine. During the oxidation of L-carnitine a simultaneous conversion of the cofactor NAD⁺ to NADH takes place. This catabolic reaction has always been of keen interest, because it can be exploited for spectroscopic L-carnitine determination in biological fluids – a quantification method, which is developed in our lab – as well as L-carnitine production.Based on a cloned L-CDH sequence an expedition through the currently available prokaryotic genomic sequence space began to mine relevant information about bacterial L-carnitine metabolism hidden in the enormous amount of data stored in public sequence databases. Thus by means of homology-based and context-based protein function prediction is revealed that L-CDH exists in certain eubacterial genomes either as a protein of approximately 35 kDa or as a homologous fusion protein of approximately 54 kDa with an additional putative domain, which is predicted to possess a thioesterase activity. These two variants of the enzyme are found on one hand in the genome sequence of bacterial species, which were previously reported to decompose L-carnitine, and on the other hand in gram-positive bacteria, which were not known to express L-CDH. Furthermore we could not only discover that L-CDH is located in a conserved genetic entity, which genes are very likely involved in this L-carnitine catabolic pathway, but also pinpoint the exact genomic sequence position of several other enzymes, which play an essential role in the bacterial metabolism of L-carnitine precursors.     

Short range photoinduced electron transfer in proteins: QM-MM simulations of tryptophan and flavin fluorescence quenching in proteins

Hybrid quantum mechanical-molecular mechanics (dynamics) were performed on flavin reductase (Fre) and flavodoxin reductase (Fdr), both from Escherichia coli. Each was complexed with riboflavin (Rbf) or flavin mononucleotide (FMN). During 50 ps trajectories, the relative energies of the fluorescing state (S₁) of the isoalloxazine ring and the lowest charge transfer state (CT) were assessed to aid prediction of fluorescence lifetimes that are shortened due to quenching by electron transfer from tyrosine. The simulations for the four cases display a wide range in CT–S₁ energy gap caused by the presence of phosphate, other charged and polar residues, water, and by intermolecular separation between donor and acceptor. This suggests that the Gibbs energy change (ΔG₀) and reorganization energy (λ) for the electron transfer may differ in different flavoproteins.     

Bioimprinted protein exhibits glutathione peroxidase activity

A strategy for design of bioimprinted proteins with glutathione peroxidase (GPX) activity has been proposed. The proteins imprinted with a glutathione derivative were converted into selenium-containing proteins by chemical modifying the reactive hydroxyl groups of serines followed by sodium hydrogen selenide displacement. These selenium-containing proteins exhibited remarkable GPX activities and the GPX activities of reduction of H₂O₂ by glutathione (GSH) were found to be 101-817 U μmol⁻¹, which approaches the activity of a selenium-containing catalytic antibody elicited by a hapten similar to our template. The steady state kinetic study for imprinted protein catalysis revealed Michaelis-Menten kinetics for both H₂O₂ and GSH, e.g. the pesudo-first-order rate constant k_cat (H₂O₂) and the apparent Michaelis constant K_m (H₂O₂) at 1 mM GSH were calculated to be 784 min⁻¹ and 1.24×10⁻³ M, respectively, and the apparent second-order rate constant k_cat (H₂O₂)/K_m (H₂O₂) was determined to be 6.33×10⁵ (M min)⁻¹. The kinetics and the template inhibition showed that the strategy might be a remarkably efficient one for generating artificial enzyme with GPX activity.     

Synthesis, characterization and thermal studies on cellulose acetate membranes with additive

Cellulose acetate (CA) membranes are used in ultrafiltration applications, although they show low chemical, mechanical and thermal resistance. In order to prepare membranes with improved properties, modification of cellulose acetate with polyethelene glycol (PEG 600) has been attempted. In this study, CA has been mixed with PEG 600 as an additive in a polar solvent. The effects of CA composition and additive concentration given by a mixture design of experiments on membrane compaction, pure water flux, water content and membrane hydraulic resistance have been studied and discussed. The efficiency of protein separation by the developed CA membranes have been quantified using model proteins such as pepsin, egg albumin (EA) and bovine serum albumin (BSA). The thermal stability of the developed membranes prepared with PEG 600 additive has also been investigated using thermogravimetric analysis and differential scanning calorimetry.     

Affinity enrichment of plasma membrane for proteomics analysis

Proteomics analysis of plasma membranes from cells exposed to different extracellular environments is potentially a powerful approach for the identification of membrane-associated proteins responding to these environments. Preparation of high concentration plasma membrane fractions with low contamination from cellular organelles is essential for such studies. Here, we describe an affinity enrichment method, which combines cell surface biotinylation with affinity enrichment by immobilized streptavidin beads, for the isolation of plasma membranes. This method results in a 400-fold enrichment of plasma membrane relative to endoplasmic reticulum, a major contaminant in standard plasma membrane preparations, and dramatically reduces contamination from other cellular organelles. The biotinylation reaction did not interfere with ligand-dependent activation of receptor tyrosine kinases or G-protein coupled receptors, suggesting cell-surface signal transduction machinery remains functional. Membrane fractions prepared by this method should provide excellent starting materials for membrane proteomics analysis such as studies of dynamic trafficking and regulation of signaling molecules or identification of disease-specific membrane markers.     

Spectroscopic and Electrochemical Characterization of Cytochrome P450st‐DDAB Films on a Plastic‐Formed Carbon Electrode

We have studied the characterization of thermophilic cytochrome P450 (P450st)‐didodecyldimethylammonium bromide (DDAB) films by using UV‐vis absorption, resonance Raman spectroscopy, and electrochemical methods. The observed Raman spectrum indicated near‐native conformation of the heme iron in DDAB film on the surface of a glass slide, while on the surface of a plastic‐formed carbon (PFC) electrode, the conformation of P450st‐DDAB was very similar to that of heme‐DDAB film, suggesting the release of heme from P450st in DDAB films on PFC electrodes. When NaBr was added as salt to the casting solution, the result of Raman spectrum indicated near‐native conformation of P450st in DDAB film even on the PFC electrode, but no redox potential of P450st which has near native structure was observed. This study suggests the essential experimental conditions when working with heme protein‐DDAB films as, in some cases, heme iron from proteins is released on the surface of the electrode.     

Development and characterisation of a new interface for coupling capillary LC with collision-cell ICP–MS and its application for phosphorylation profiling of tryptic protein digests

A comparison of different nebulisers for direct hyphenation of capillary and nano liquid chromatography (Cap-LC, Nano-LC) and quadrupole-based collision cell inductively coupled plasma mass spectrometry (CC-ICP–MS) for phosphorylation profiling of tryptic protein digests is described. Helium was used as cell gas and specially tuned instrumental conditions were used to achieve background minimisation at the mass of phosphorus, because of kinetic energy discrimination of the interfering polyatomic ions. The proposed set-up is based on a modified capillary electrophoresis interface and a home-made 4 mL spray chamber. It enables the use of gradient conditions with a highly concentrated organic mobile phase as often used in protein phosphorylation analysis, without the need to apply membrane desolvation for removal of the organic phase or further background minimisation. No significant signal suppression or other negative effects caused by the organic mobile phase occur, because of the low flow rates used in Cap-LC and the robust plasma conditions of the CC-ICP–MS instrument. A tryptic digest of beta-casein was investigated as model compound to demonstrate the applicability of the proposed set-up for phosphorylation profiling in protein analysis using quadrupole based collision-cell ICP–MS as phosphorus-specific detector. Detection limits for phosphorylated peptides down to the sub picomole level were obtained. As a complementary technique, electrospray ionisation tandem mass spectrometry (ESI–MS–MS) with data base searching was used for further characterisation of the phosphorylated peptides detected.     

Screening of antagonists based on induced dissociation of a calmodulin-melittin interaction entrapped in a sol-gel derived matrix

Sol-gel derived materials offer a unique advantage for the development of sensing and screening platforms in that they allow for the entrapment of multiple species within a confined space. In this work, we show that it is possible to entrap an intact protein-peptide interaction, consisting of bovine calmodulin (bCaM) and melittin, into a sol-gel derived silicate material. Fluorescence emission data demonstrate that the entrapped complex behaves similarly to the complex in solution, and can undergo reversible dissociation upon introduction of the denaturant guanidine hydrochloride. Screening of antagonists of the bCaM-melittin complex was accomplished based on induced dissociation of the entrapped complex, which was followed by measuring the loss of sensitization of Tb(III) luminescence originating from energy transfer from the Trp of melittin to Tb(III) bound in the loops of bCaM. This study shows that entrapped protein-peptide complexes can be used as targets for drug screening or for fluorescence-based biosensing.     

Bound water measurements for aqueous protein solutions and food gels

The role of aqueous media in the stabilization of globular proteins and formation of gels was studied by absorption millimeter spectroscopy. This method allowed to measure bound water, the fraction of water which had decreased rotational mobility owing to the presence of solute. Hydration data for globular proteins were compared with data obtained previously for low-weight molecules and groups. It was found that rotational mobility of water molecules in the hydration shells of various kinds of solutes (groups) decreased in the following order: water structure breaking compounds>polar groups>unfolded proteins>globular proteins>non-polar groups. Time courses of the storage modulus were determined for the chemical acidification by glucono-δ-lactone (GDL) of milk samples prepared from skimmed milk powder (SMP). Gelation of unheated milk was a monotonous process that started at pH 4.9. Heat-treated milk from SMP (16 and 14 g per 100 ml) acidified by GDL (3 g per 100 ml) at 43 °C gave non-monotonous kinetics of gelation with two phases corresponding to the mechanisms induced by denatured whey proteins at pH>5 and by casein–casein interactions at pH 4.8–4.9. For heat-treated milk, measurement of bound water gave two stages of decrease in water mobility. Additional hydration of SMP during acidification gave 0.15–0.2 g and 0.8 g bound H₂O per gram of SMP for unheated and heat-treated milk, respectively.