Viscoelastic characteristics of protein solutions and micromechanics of their motion in porous carriers

The interactions of model proteins with the templates of porous carriers in biosensors were analyzed in terms of events occurring during the molecular contact of biopolymers with a solid. The viscoelastic properties of casein and albumin at small widths of the layer of the solution applied to the crystal were estimated using the dynamic method of piezoqartz resonator. The experimental data on the viscoelastic characteristics of protein solutions of different concentrations were compared with the characteristics of their tangential motion in porous carriers from cellulose nitrate. It was found that the parameters of dynamic viscosity correlate with the time of motion of protein solution in a porous polymeric carrier.     

Exploiting Leishmania tarentolae cell-free extracts for the synthesis of human solute carriers

Abstract

Cell-free protein production offers a versatile alternative to complement in vivo expression systems. However, usage of prokaryotic cell-free systems often leads to non-functional proteins. We modified a previously designed cell-free system based on the protozoan Leishmania tarentolae, a parasite of the Moorish gecko Tarentola mauritanica, together with a species-independent translational sequences-based plasmid to produce human membrane proteins in 2 hours reaction time. We successfully established all four commonly used expression modes for cell-free synthesis of membrane proteins with a human organic anion transporter, SLC17A3, as a model membrane protein: (i) As precipitates without the addition of any hydrophobic environment, (ii) in the presence of detergents, (iii) with the addition of liposomes, and (iv) supplemented with nanodiscs. We utilized this adapted system to synthesize 22 human solute carriers from 20 different families. Our results demonstrate the capability of the Leishmania tarentolae cell-free system for the production of a huge variety of human solute carriers in the precipitate mode. Furthermore, purified SLC17A3 shows the formation of an oligomeric state.     

Lipid-based colloidal carriers for peptide and protein delivery--liposomes versus lipid nanoparticles

This paper highlights the importance of lipid-based colloidal carriers and their pharmaceutical implications in the delivery of peptides and proteins for oral and parenteral administration. There are several examples of biomacromolecules used nowadays in the therapeutics, which are promising candidates to be delivered by means of liposomes and lipid nanoparticles, such as solid lipid nanoparticles (SLN) and nanostructured lipid carriers (NLC). Several production procedures can be applied to achieve a high association efficiency between the bioactives and the carrier, depending on the physicochemical properties of both, as well as on the production procedure applied. Generally, this can lead to improved bioavailability, or in case of oral administration a more consistent temporal profile of absorption from the gastrointestinal tract. Advantages and drawbacks of such colloidal carriers are also pointed out. This article describes strategies used for formulation of peptides and proteins, methods used for assessment of association efficiency and practical considerations regarding the toxicological concerns.     

Spatial development of the cultivation of a bone marrow stromal cell line in porous carriers

The spatial development of the cultivation of a bone marrow stromal cell line (SR-4987) in porous carriers was investigated in order to construct a three-dimensional hematopoietic culture system. Low-rate continuous agitation, 20 rpm, was an appropriate method to achieve initial adhesion of cells onto a cellulose porous beads (CPB, 100 μm pore diameter) in a spinner bottle, compared with other methods such as centrifugation and intermittent agitation. Cell growth with continuous agitation at 70 rpm after initial cell adhesion was not inferior to that at 20 rpm. A 2- and 10-fold increase in the inoculum cell concentration for CPB and another type of porous cellulose beads (Micro-cube (MC), 500 μm pore diameter) resulted in a 1.2- and 2-fold increase in final cell concentrationm, respectively. Cells attached to the MC beads and a polyester nonwoven dic (Fibra-cell (FC)) could grow and spread well on the carriers and a fibroblast-like shape was observed under scanning electron microscopy while the cells on CPB were globular. The flatness and inner surface area of these carriers may be the reason for the differences in cell morphology. This revised version was published online in July 2006 with corrections to the Cover Date.     

The construction of an in vitro three-dimensional hematopoietic microenvironment for mouse bone marrow cells employing porous carriers

Spatial development of mouse bone marrow cellsemploying porous carriers was investigated in order todesign a bioreactor with a three-dimensionalhematopoietic microenvironment. Three types of porouscarriers were used for examining the spatialdevelopment of anchorage-dependent primary stromalcells as feeder cells. Stromal cells were found tospread well at a high density on a polyester nonwovendisc carrier (Fibra cel (FC)) under a scanningelectron microscope, while cells on porous cellulosebeads (Microcube (MC), 500 m pore diameter)spread at a low density; cells on another type ofcellulose porous beads (CPB, 100 m pore diameter)were globular. Mouse bone marrow cells wereinoculated to dishes containing three types of porouscarriers which shared more than 30% of the bottomsurface in a dish. The concentration of stromal cellsin the well containing FC was lower than that on theother two carriers. However, the weekly output oftotal hematopoietic cell (suspension cells) increasedbetween day 21 and 28 in the culture using FC while itdecreased monotonously in the cultures by use of theother two carriers. The proportion of progenitorcells (BFU-E, CFU-GM) in the total hematopoietic cellpopulation, after showing an initial decrease,increased after 1 week in the culture using FC whilethe proportion decreased monotonously to zero in thecultures using MC and CPB.     

Involvement of mitochondrial inner membrane anion carriers in the uncoupling effect of fatty acids

This paper considers stages of the search (initiated by V. P. Skulachev) for a receptor protein for fatty acids that is involved in their uncoupling effect. Based on these studies, mechanism of the ADP/ATP antiporter involvement in the uncoupling induced by fatty acids was proposed (Skulachev, V. P. (1991) FEBS Lett., 294, 158– 162). New data (suppression by carboxyatractylate of the SDS-induced uncoupling, pH-dependence of the ADP/ATP and the glutamate/aspartate antiporter contributions to the uncoupling, etc.) led to modification of this hypothesis. During discussion of the uncoupling effect of fatty acids caused by opening of the Ca²⁺-dependent pore, special attention is given to the effects of carboxyatractylate added in the presence of ADP. The functioning of the uncoupling protein UCP2 in kidney mitochondria is considered, as well as the diversity observed by us in effects of 200 µM GDP on decrease in under the influence of oleic acid added after H₂O₂ (in the presence of succinate, oligomycin, malonate). A speculative explanation of the findings is as follows: 1) products of lipid and/or fatty acid peroxidation (PPO)modify the ADP/ATP antiporter in such a way that its involvement in the fatty acid-induced uncoupling is suppressed by GDP; 2) GDP increases the PPO concentration in the matrix by suppression of efflux of fatty acid hydroperoxide anions through the UCP (Goglia, F., and Skulachev, V. P. (2003) FASEB, 17, 1585–1591)and/or of efflux of PPO anions with involvement of the GDP-sensitive ADP/ATP antiporter; 3) PPO can potentiate the oleate-induced decrease in due to inhibition of succinate oxidation.Translated from Biokhimiya, Vol. 70, No. 2, 2005, pp. 197–202.Original Russian Text Copyright © 2005 by Mokhova, Khailova.This revised version was published online in April 2005 with corrections to the post codes.     

The complexation between holothurian triterpene glycosides and Chl as the basis for lipid-saponin carriers of subunit protein antigens

The ability of holothurian triterpene glycosides (cucumarioside A₂-2 from Cucumaria japonica, cucumarioside G₁ from C. fraudatrix, frondoside A from C. frondosa, and holotoxin A₁ from Apostichopus japonicus) to form supramolecular lipid-saponin complexes was studied. TEM demonstrated that all the studied compounds form supramolecular cholesterol-saponin complexes (nanoparticles) in aqueous medium. The complexes formed by cucumarioside A₂-2, holotoxin A₁, and frondoside A had a tubular structure and fundamentally differed in the structure from the particles produced by cucumarioside G₁. The morphology of the nanoparticles formed by cucumarioside A₂-2, holotoxin A₁, and cucumarioside G₁ changed depending on the fraction of cholesterol in the lipid-saponin system; however, this pattern was not observed for frondoside A. At the same molar fraction of cholesterol in the lipid-saponin system, cucumarioside A₂-2 formed the particles with the most pronounced tubular structure; the cholesterol-saponin complexes of holotoxin A₁ had a less pronounced tubular structure, whereas the structure of frondoside A particles was extremely heterogeneous. Comparative analysis of the morphology of the described supramolecular complexes and specific structural features of the glycosides demonstrated that the structure of the corresponding nanoparticles depended on the degree of branching of the carbohydrate moiety in the glycoside molecule and the complexation with cholesterol was determined by the specific features of aglycone structure. Thus, the feasibility of producing new generation antigen carriers using the complexes in question was proved.     

E-type delayed fluorescence depolarization, technique to probe rotational motion in the microsecond range.

E (eosin)-type delayed fluorescence depolarization studies extend the time range for the measurement of rotational diffusion to microseconds and ms, thereby allowing investigation of slow rotational movement of macromolecules like membrane proteins. An apparatus is described for the determination of time-dependent anisotropy in this interesting time range. The method has been tested on eosin-labelled cytochrome P-450 incorporated into phospholipid membrane vesicles.     

Dynamics of transfer of charge carriers in DNA molecule

An equivalent electrical circuit of DNA molecule is suggested and used to model the charge transfer dynamics in the molecule. Its switching time is shown to be in the femtosecond time range and to depend on the frequency of input electric signal. Raising the input signal frequency from 1 GHz to 4 THz and lowering the temperature decrease the current through DNA. The switching rate of DNA molecule is determined by the processes of delocalization and localization of holes, which is achieved by variation in the base sequence and length.     

Time-resolved fluorescence spectroscopy and molecular dynamics simulations point out the effects of pressure on the stability and dynamics of the porcine odorant-binding protein

The effects of hydrostatic pressure on the structure and stability of porcine odorant-binding protein (pOBP) in the presence and absence of the odorant molecule 2-isobutyl-3-methoxypyrazine (IBMP) were studied by steady-state and time-resolved fluorescence spectroscopy as well as by molecular dynamics simulation. The authors found that the application of moderate values of hydrostatic pressure to pOBP solutions perturbed the microenvironment of Trp(16) and disrupted its highly quenched complex with Met(39). In addition, compared with the protein in the absence of IBMP, the MD simulations experiments carried out at different pressures highlighted the role of this ligand in stabilizing the Trp(16)/Met(39) interaction even at 2000 bar. The obtained results will assist for the tailoring of this protein as specific sensing element in a new class of fluorescence-based biosensors for the detection of explosives.     

Effects of G-protein probes on interactions between auxin efflux carriers and phytotropin receptors in zucchini (Cucurbita pepo L.) microsomal membranes

Microsomal vesicles prepared from etiolated hypocotyl tissue of zucchini (Cucurbita pepo L. cv. All Green Bush) exhibited saturable N-1-naphthylphthalamic acid ([³H]NPA) binding, NPA-stimulated association of indol-3yl-acetic acid ([³H]IAA), and saturable binding of guanosine 5-O-[3-thiotriphosphate] (GTP--[³⁵S]). These vesicles were used to test the possibility that NPA receptors might interact with IAA-anion efflux carriers by coupling through a GTP-binding protein (G-protein). Unlabelled GTP--S or guanosine 5-O-[2-thiodiphosphate] (GDP--S) had no effect on saturable NPA binding or on the NPA-stimulated association of IAA with microsomes. NPA did not affect saturable binding of GTP--[³⁵S] to microsomes, either in the presence or absence of saturating concentrations of unlabelled GTP--S or GDP. It is concluded that the occupancy of phytotropin receptors is not transduced to auxin efflux carriers by a GTP-binding protein.     

Modeling of protein and phenolic compound removal from aqueous solutions by electrocoagulation

Electrocoagulation is a technique basically applied in water and wastewater treatment, but which has a number of potential applications in polymer, protein, drug, and vaccine delivery. In this work, we correlate the current applied between the electrodes to the removal of phenolic compounds or protein from aqueous solutions, but the principle can also be applied to other biological compounds such as plant pigments and sugars. Simple and time‐dependent models were developed based on the complex formation between these biological substances and the aluminium hydroxide gel phase. The models developed represent a good agreement with experimental data (R² as high as 0.992). Besides construction of the models, the effect of pH on the efficiency of removal of proteins and phenolic compounds was evaluated. It was found that this parameter has significant effect on the efficiency of the electrocoagulation and the maximal removal efficiency for bovine serum albumin and phenolic compound catechin was observed at pH 8.0. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2010     

Numerical and series solutions of the peristaltic motion of an Oldroyd 8-constant fluid in an endoscope

In the present article, we have presented the peristaltic flow of an Oldroyd 8-constant fluid in an endoscope. The governing equations for the flow problem are simplified using long wavelength and low Reynold's number approximations. The solutions of the simplified problem are calculated using (i) Homotopy analysis method and (ii) Shooting method. The comparison of both the solutions shows a very good agreement between the results. The graphical results for the velocity field and stresses are presented to show the physical behaviour of all the parameters appearing in the problem.     

The use of protein characteristics to assess the retrievability of ancient DNA from ancient bones

The ability to retrieve DNA from ancient specimens has been one of the greatest achievements of the past decade, and has opened a totally new field of research with applications in seemingly distant domains such as archeobotany, the molecular phylogeny of extinct genomes, human paleopathology and the genetic of ancient human populations. However, extraction of ancient DNA has often a very low rate of success, prompting researchers to develop screening methods for the selection of promising specimens. With this goal in mind, we studied the amino acid content of nine human bones of ancient origin. We demonstrate that a single HPLC chromatogram is indicative of the integrity of ancient bone proteins. Among five specimens containing amplifiable DNA, four exhibited a protein content similar to that of contemporary bone protein content. Three of the four specimens, from which we were unable to extract any amplifiable DNA, had an amino acid content strikingly different from that of contem-porary bone. A non-parametric statistical test, Kendall's tau, was used to show that protein content and PCR products, are probably correlated (at a 95% confidence level). In addition, the D/L Asp and D/L Glu racemization ratios obtained are indicative of the presence of ancient organic compounds. We propose that protein analysis should be systematically performed in studies where there are many samples in order to select the specimens that are most likely to contain retrievable ancient DNA.     

Functional comparison of hemoglobin purified by different methods and their biophysical implications

Hemoglobin (Hb) that is purified from red blood cells (RBCs) is commonly subjected to harsh processing conditions, such as high temperatures and extensive column separation, which may damage the Hb by altering the heme prosthetic group and/or the Hb protein structure. In this study, bovine and human Hb purified by tangential flow filtration (TFF) was compared to commercial preparations of human Hb (Hemosol, Inc., Toronto, Canada) and bovine Hb (Biopure, Inc., Cambridge, MA). Purified Hbs were characterized by measuring their overall purity (SDS–PAGE, SEC, and ESI‐MS), susceptibility to oxidation (k_ox), responses to physiological conditions (pH, [Cl^?], [IHP], and T), and ligand binding kinetics (O₂, NO, and CO). All Hbs evaluated possessed comparable biophysical properties, however, a small amount of catalase was detected in the TFF‐purified Hbs that reduced the rate of autoxidation. Mass changes observed by mass spectrometry suggest that structural alterations may be introduced into Hbs that are purified by extensive chromatographic separations. These results demonstrate that TFF is a suitable process for the purification of Hb from RBCs with a quality equivalent to that of commercial Hb preparations that employ more extensive purification strategies. This work also shows that TFF can yield highly pure Hb which can be used for Hb‐based O₂ carrier synthesis. Biotechnol. Bioeng. 2010; 106: 76–85. © 2010 Wiley Periodicals, Inc.     

Transmembrane topology,genes, and biogenesis of the mitochondrial phosphate and oxoglutarate carriers

Phosphate and oxoglutarate carriers transport phosphate and oxoglutarate across the inner membranes of mitochondria in exchange for OH^– and malate, respectively. Both carriers belong to the mitochondrial carrier protein family, characterized by a tripartite structure made up of related sequences about 100 amino acids in length. The results obtained on the topology of the phosphate and oxoglutarate carriers are consistent with the six -helix model proposed by Saraste and Walker. In both carriers the N- and C-terminal regions are exposed toward the cytosol. In addition, the oxoglutarate carrier has been shown to be a dimer by means of cross-linking studies. The bovine and human genes coding for the oxoglutarate carrier are split into eight and six exons, respectively, and five introns are found in the same position in both genes. The bovine and human phosphate carrier genes have the same organization with nine exons separated by eight introns at exactly the same positions. The phosphate carrier of mammalian mitochondria is synthesized with a cleavable presequence, in contrast to the oxoglutarate carrier and the other members of the mitochondrial carrier family. The precursor of the phosphate carrier is efficiently imported, proteolytically processed, and correctly assembled in isolated mitochondria. The presequence-deficient phosphate carrier is imported with an efficiency of about 50% as compared with the precursor of the phosphate carrier and is correctly assembled, demonstrating that the mature portion of the phosphate carrier contains sufficient information for import and assembly into mitochondria.     

Novel, rapid purification of the membrane protein photosystem I by high-performance liquid chromatography on porous materials

New porous materials have been tested for their potential to speed up purification of membrane proteins. As an example the purification of photosystem I, a light-driven electron pump from the cyanobacterium Synechocystis PCC6803, was optimized. The combination of two HPLC steps (an anion-exchange chromatography followed by a hydrophobic interaction chromatography) yields homogeneous monomeric or trimeric photosystem I as determined by gel filtration and gel electrophoresis. In comparison to traditional purification schemes our method is at least three-times faster and allows for easy scale-up.     

Thermodynamic stability of proteins in salt solutions: A comparison of the effectiveness of protein stabilizers

The denaturation of proteins by guanidine hydrochloride was studied in the presence of different concentrations of stabilizing salts, namely potassium phosphate, ammonium sulfate, and potassium acetate. The denaturation transition was followed by observing changes in the peptide circular dichroism atpH 7.0 and 25°C. From these results the free energy of stabilization for the process native denatured was determined. It was found that the stabilizing power of the anions increased in the order acetate < sulfate < phosphate, in agreement with the anionic lyotropic series. Ribonuclease A, which is known to have a site that can bind either a phosphate or a sulfate ion, showed a larger stabilization by these anions than that for lysozyme, pepsinogen, and myoglobin.     

Direct analysis of protein sedimentation equilibrium in detergent solutions without density matching

Characterizing membrane proteins by sedimentation equilibrium is challenging because detergents and/or lipid molecules, usually required for solubilization, form a complex with the protein. The most common way to overcome this problem is Tanford and Reynolds' density matching method, which eliminates the buoyant mass contributions of detergents/lipids by adjusting the solvent density with D2O/H2O mixtures to render either detergent or lipid molecules neutrally buoyant. Unfortunately, the method is practical only for detergent densities between 1.0 (H2O) and 1.1 (D2O) g ml(-1), excluding many of the more commonly used detergents for membrane protein studies. Here, we present a modern variant of Tanford and Reynolds' method that (1) is applicable to any detergent regardless of its specific density, (2) does not compromise accuracy and precision, and (3) provides additional information about the number of detergent molecules that are bound to each protein. The new method was applied successfully to Delta(1-43)A-I, an amino-terminal deletion mutant of human apolipoprotein A-I. Interestingly, we observed a significantly lower Delta(1-43)A-I/octyl-glucoside complex partial specific volume than that expected from volume additivity rules, indicative of specific protein-detergent interactions.