Separation of proteins using hydrophobic interaction membrane chromatography

Membrane chromatography can overcome some of the problems associated with packed bed chromatography. In most membrane chromatographic studies reported so far, ion-exchange and affinity interactions have been utilised. In this paper the use of hydrophobic interactions for chromatographic separation is described. A polyvinylidene fluoride membrane was identified which could bind specific proteins in the presence of high ammonium sulphate concentration. The separation of CAMPATH-IG monoclonal antibody and bovine serum albumin using this membrane is discussed.     

Selective incorporation of isotopically labeled amino acids for identification of intact proteins on a proteome-wide level

The post-genomic era and increased demands for broad proteome measurements have greatly increased the needs for protein identification. We describe a strategy that uses accurate mass measurements and partial amino acid content information to unambiguously identify intact proteins, and show its initial application to the proteomes of Escherichia coli and Saccharomyces cerevisiae. Proteins were extracted from the organisms grown in minimal medium or minimal medium to which isotopically labeled leucine (Leu-D(10)) had been added. The two protein extracts were mixed and analyzed by capillary isoelectric focusing (CIEF) coupled with Fourier transform ion cyclotron resonance mass spectrometry (FTICR). The incorporation of the isotopically labeled residue has no effect on the CIEF separation of proteins, and both isotopically labeled and unlabeled versions of specific proteins are observed within the same mass spectrum. The difference in the mass of the unlabeled and labeled proteins is used to determine the number of Leu residues present in a particular protein. Proteins can then often be unambiguously identified based on their accurately determined molecular mass and the additional constraint provided by number of Leu residues. The identities of proteins were further confirmed by repeating CIEF/FTICR measurements with samples that contain other isotopically labeled amino acid residues (e.g. His, Arg, Ile, Phe, Lys). A theoretical study of the amino acid composition (for a difference in the amino acid sequence) showed the constraints needed in order to identify the protein unambiguously. Additionally, the mass differences between the predicted and the experimental accurate mass measurement provide insights into the nature of simple post-translational modifications.     

High-performance capillary electrophoresis of hydrophobic membrane proteins

Hydrophobic membrane proteins, extrinsic and intrinsic ones, were separated by high-performance capillary zone electrophoresis (HPCZE) and high-performance capillary isotachophoresis (HPCITP). In the case of HPCZE with both coated and uncoated quartz capillaries the addition of 7 M urea to the separation buffers was necessary to achieve reproducible results. In the HPCITP experiments PTFE capillaries were used. When spacers were used, e.g., ampholytes, additional splitting of peaks was observed. The splitting was caused by the microheterogeneity of the investigated proteins, which are differently glycosylated and/or phosphorylated.     

Selective turn-on fluorescence detection of cyanide in water using hydrophobic CdSe quantum dots

The ability of 2,2'-bipyridine-bound copper(ii) ions to quench the photoluminescence of hydrophobic CdSe quantum dots is used to create a novel, selective turn-on fluorescence cyanide sensor.     

Towards the total chemical synthesis of integral membrane proteins: a general method for the synthesis of hydrophobic peptide-thioester building blocks

Modification of a peptide-^αthioester with a sequence of six arginines on the thioester leaving group can render soluble all peptides derived from a polytopic integral membrane protein. This strategy greatly simplifies the synthesis of peptide-^αthioester building blocks for the total chemical synthesis of integral membrane proteins by native chemical ligation.     

A fluorescence-based assay for nanogram quantification of proteins using a protein binding ligand

Fluorescence emission has been investigated in the context of estimation of proteins at nanogram levels. A Schiff base ligand with donor-acceptor substituents has been utilized as a fluorescent probe. The potency of this ligand is that it possesses the binding sites for both hydrophobic as well as hydrophilic groups in the proteins. The fluorescence emission of the probe was enhanced in the presence of nanogram levels of protein, which clearly signifies that even the least concentration of the protein is sufficient to perturb the environment around the probe. We demonstrate here that the fluorescence characteristic of the probe can be utilized to estimate even nanogram levels (66 ng-1 microgram mL(-1)) of protein. The major limitation of the currently available standard methods is the range of protein estimation, which terminates at microgram level and the interference due to the specificity of the amino acids, which vary from proteins to proteins. This fluorescence emission-based method is free from interference from any type of buffers, ionic strength of the medium and any specific amino acid residue and is a simple, rapid, single-step, sensitive method of estimation which can be applied to different classes of proteins.     

Prediction of integral membrane protein type by collocated hydrophobic amino acid pairs

A computational model, IMP-TYPE, is proposed for the classification of five types of integral membrane proteins from protein sequence. The proposed model aims not only at providing accurate predictions but most importantly it incorporates interesting and transparent biological patterns. When contrasted with the best-performing existing models, IMP-TYPE reduces the error rates of these methods by 19 and 34% for two out-of-sample tests performed on benchmark datasets. Our empirical evaluations also show that the proposed method provides even bigger improvements, i.e., 29 and 45% error rate reductions, when predictions are performed for sequences that share low (40%) identity with sequences from the training dataset. We also show that IMP-TYPE can be used in a standalone mode, i.e., it duplicates significant majority of correct predictions provided by other leading methods, while providing additional correct predictions which are incorrectly classified by the other methods. Our method computes predictions using a Support Vector Machine classifier that takes feature-based encoded sequence as its input. The input feature set includes hydrophobic AA pairs, which were selected by utilizing a consensus of three feature selection algorithms. The hydrophobic residues that build up the AA pairs used by our method are shown to be associated with the formation of transmembrane helices in a few recent studies concerning integral membrane proteins. Our study also indicates that Met and Phe display a certain degree of hydrophobicity, which may be more crucial than their polarity or aromaticity when they occur in the transmembrane segments. This conclusion is supported by a recent study on potential of mean force for membrane protein folding and a study of scales for membrane propensity of amino acids.     

Synthesis and lyotropic phase behavior of novel nonionic surfactants for the crystallization of integral membrane proteins

A series of new sugar-based nonionic surfactants have been synthesized and their lyotropic liquid crystalline properties characterized. When in contact with water, these surfactants formed a range of lyotropic liquid crystalline phases, including cubic, hexagonal, and lamellar, as well as a separate micellar phase. These are features that have promise for the crystallization of integral membrane proteins.     

Selective interface detection: mapping binding site contacts in membrane proteins by NMR spectroscopy

Intermolecular contact surfaces are important regions where specific interactions mediate biological function. We introduce a new magic angle spinning solid state NMR technique, dubbed "selective interface detection spectroscopy" (SIDY). In this technique, 13C-attached protons (1Hlig) are dephased by 1H-13C REDOR. A spin diffusion period is then used to enhance long distance 1H-1H correlations, and the results are detected by a short period of cross polarization to the 13C isotope labels. This SIDY approach allows selective observation of the interface between 13C-labeled and unlabeled moieties. We have used SIDY to probe the ligand-protein binding surface between a uniformly isotopically labeled ligand cofactor, U-13C20-11-cis-retinal, and its binding site in rhodopsin (Rho), an unlabeled, membrane-embedded G-protein coupled receptor (GPCR). The observed 1HGPCR-13Clig correlations indicate multiple close contacts between the protein and the ionone ring of the ligand, in agreement with binding studies. The polyene tail of the ligand displays fewer strong correlations in the SIDY spectrum. Some correlations can be assigned to the protein side chains lining the ligand binding site, in agreement with the crystal structure.     

Fractionation of human plasma proteins by hydrophobic interaction membrane chromatography

This paper discusses the fractionation of human plasma proteins HSA and HIgG by hydrophobic interaction membrane chromatography. A type of microporous polyvinylidine fluoride (PVDF) membrane having 0.1 μm pore size was identified as being suitable for carrying out this separation. This membrane bound HIgG at 1.5 M ammonium sulphate concentration, a condition at which HSA did not. Based on this selective binding resulting from the selective pressure induced by the high anti-chaotropic salt concentration, these human plasma proteins were fractionated. The HIgG binding capacity of the PVDF membrane examined in this study was 42.8 mg/ml at a feed concentration of 0.45 mg/ml. Separation of simulated HSA/HIgG mixtures were carried out in the pulse and step input modes and the HSA and HIgG fractions thus obtained were analysed for purity using affinity chromatography and SDS-PAGE. HSA and HIgG purities were typically in excess of 97–98%.     

Selective aggregation of membrane proteins by membrane-mediated interactions

There are different types of membrane proteins in a cellular membrane,and most of them must correctly assemble into appropriate clusters for their cellular functions.In this work,we suggest a physical mechanism for selective aggregation of different membrane proteins without specific protein-protein attraction by dissipative particle dynamics method.A membrane-mediated interaction may result in different protein clusters with ideal mixing,nonideal mixing and demixing of different types of membrane proteins,depending on the extent of the similarity of membrane deformations by those proteins.     

Organic solvent extraction as a versatile procedure to identify hydrophobic chloroplast membrane proteins

As a complementary approach to genome projects, proteomic analyses have been set up to identify new gene products. One of the major challenges in proteomics concerns membrane proteins, especially the minor ones. A procedure based on the differential extraction of membrane proteins in chloroform/methanol mixtures, was tested on the two different chloroplast membrane systems: envolope and thylakoid membranes. Combining the use of classical sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and mass spectrometry analyses, this procedure enabled identification of hydrophobic proteins. The propensity of hydrophobic proteins to partition in chloroform/methanol mixtures was directly correlated with the number of amino acid residues/number of putative transmembrane regions (Res/TM ratio). Regardless of the particular case of some lipid-interacting proteins, chloroform/methanol extractions allowed enrichment of hydrophobic proteins and exclusion of hydrophilic proteins from both membrane systems, thus demonstrating the versatility of the procedure.     

Molecular dynamics simulations of hydrophobic and amphiphatic proteins interacting with a lipid bilayer membrane

Molecular dynamics simulations of polypeptides at high dilution near a fully hydrated bilayer membrane have been performed. In contrast to previous theoretical predictions, Monte Carlo simulations and conclusions from experiments a spontaneous insertion of amphiphatic or hydrophobic proteins into a membrane is not observed. Rather it is found that an amphiphatic chain has the tendency to remain in proximity to the membrane surface, whereas the location of a hydrophobic chain is more unbound. This is shown using two proteins, melittin and polyleucine. The conformation of the proteins and their orientation with respect to the membrane surface are discussed.     

Selective potentiometric determination of nitrite ion using a novel (4-sulphophenylazo-)1-naphthylamine membrane sensor

A novel polymeric membrane sensor sensitive to (4-sulphophenylazo-)1-naphthylamine (SPAN) based on the use of tris(bathophenanthroline) Ni(II)–SPAN ion pair as an ion exchanger in plasticised PVC membrane is described. The sensor exhibits a linear calibration plot with near-Nernstian anionic slope of −55.0±0.3 mV log[SPAN]⁻¹ over the concentration range 10⁻⁶–10⁻² mol l⁻¹ at pH 7. The sensor shows working range over the pH 6–8, response time of 20 s for 10⁻⁵ mol l⁻¹ and operational lifetime of 8 weeks. The sensor is used for quantification of micro quantities of nitrite ion by a prior conversion into the more lipophilic SPAN ion, which is measured with adequate sensitivity, and high selectivity using SPAN sensor. Validation of the method according to the quality assurance standards shows good performance characteristics. The sensor is satisfactory utilised for potentiometric determination of nitrite ion in wastewater samples and meat products. The results are favourably compared with data obtained using the standard spectrophotometric procedure involving the same reaction.     

Molecular dynamics simulations of large integral membrane proteins with an implicit membrane model

The heterogeneous dielectric generalized Born (HDGB) methodology is an the extension of the GBMV model for the simulation of integral membrane proteins with an implicit membrane environment. Three large integral membrane proteins, the bacteriorhodopsin monomer and trimer and the BtuCD protein, were simulated with the HDGB model in order to evaluate how well thermodynamic and dynamic properties are reproduced. Effects of the truncation of electrostatic interactions were examined. For all proteins, the HDGB model was able to generate stable trajectories that remained close to the starting experimental structures, in excellent agreement with explicit membrane simulations. Dynamic properties evaluated through a comparison of B-factors are also in good agreement with experiment and explicit membrane simulations. However, overall flexibility was slightly underestimated with the HDGB model unless a very large electrostatic cutoff is employed. Results with the HDGB model are further compared with equivalent simulations in implicit aqueous solvent, demonstrating that the membrane environment leads to more realistic simulations.     

Selective gas-chromatographic detection using an ion-selective electrode-II Selective detection of fluorine compounds

Components in samples are separated on a gas chromatography column using hydrogen as carrier gas. The individual components from the column are passed through a platinum tube heated at 1000 degrees , where they undergo hydrogenolysis, and fluorine compounds are converted into hydrogen fluoride. The hydrogen fluoride is dissolved in a slow stream of an absorption solution, and the fluoride ion concentration in the resulting solution is monitored in a flow-cell with a fluoride ion electrode. The potentiometric output of the cell is converted into a signal, which is proportional to the concentration of fluoride ion, by an antilogarithmic converter, and recorded. The response of the detector to fluorine compounds was about 10,000 times that to an equal quantity of other organic compounds, and 5 x 10(-11) mole of fluorobenzene could be detected.     

Selective transport of zinc and copper ions by synthetic ionophores using liquid membrane technology

This work highlights the role of synthetic carrier (ionophore) in the separation of heavy metal ions. A new series of ionophores; 4,4′-nitrophenyl-azo-O,O′-phenyl-3,6,9-trioxaundecane-1,10-dioate (R₁), bis[4,4′nitro-phenylazo-naphthyl-(2,2-dioxydiethylether)] (R₂) 1,8-bis-(2-naphthyloxy)-3,6-dioxaoctane (R₃), 1,11-bis-(2-naphthyloxy)-3,6,9-trioxaunde-cane (R₄), 1,5-bis-(2-naphthyloxy)-3-oxa-pentane (R₅) have been synthesized and used as extractant as well as carrier for the transport of various metal ions (Na⁺, K⁺, Mg²⁺, Ni²⁺, Cu²⁺ and Zn²⁺) through liquid membranes. Effect of various parameters such as metal ion concentration, ionophore concentration, liquid–liquid extraction, back extraction, comparison of transport efficiency of BLM and SLM and different membrane support (hen’s egg shell and PTFE) have been studied. In BLM ionophores (R₂–R₅) transport Zn⁺ at greater extent and the observed trend for the transport of Zn²⁺ is R₂?>?R₄?>?R₃?>?R₅ respectively. Further transport efficiency is increased in SLM. In egg shell membrane ionophores (R₂–R₅) transport Zn⁺ due to their non-cyclic structure and pseudo cavity formation while ionophore R₁ transports Cu²⁺ ions at greater extent due to its cyclic structure and cavity size. Among the membrane support used egg shell membrane is found best for the transport of zinc ions because of its hydrophobic nature and exhibits electrostatic interactions between positively charged zinc ions and –COOH group of egg shell membrane. Thus structure of ionophores, hydrophobicity and porosity of the membrane support plays important role in separation of metal ions.     

MALDI tissue profiling of integral membrane proteins from ocular tissues

MALDI tissue profiling and imaging have become valuable tools for rapid, direct analysis of tissues to investigate spatial distributions of proteins, potentially leading to an enhanced understanding of the molecular basis of disease. Sample preparation methods developed to date for these techniques produce protein expression profiles from predominantly hydrophilic, soluble proteins. The ability to obtain information about the spatial distribution of integral membrane proteins is critical to more fully understand their role in physiological processes, including transport, adhesion, and signaling. In this article, a sample preparation method for direct tissue profiling of integral membrane proteins is presented. Spatially resolved profiles for the abundant lens membrane proteins aquaporin 0 (AQP0) and MP20, and the retinal membrane protein opsin, were obtained using this method. MALDI tissue profiling results were validated by analysis of dissected tissue prepared by traditional membrane protein processing methods. Furthermore, direct tissue profiling of lens membrane proteins revealed age related post-translational modifications, as well as a novel modification that had not been detected using conventional tissue homogenization methods.