Fine-tuning the topology of a polytopic membrane protein: role of positively and negatively charged amino acids

The effects of positively and negatively charged residues on the membrane topology of a model E. coli protein with two transmembrane segments have been studied. We show that addition or removal of as little as a single positively charged lysine residue in one of two critical regions can be sufficient to reverse the transmembrane topology of the molecule from Nout-Cout to Nin-Cin. Negatively charged residues are much less potent and significantly affect the topology only if present in high numbers. Finally, we provide data to suggest that sec-independent and sec-dependent translocation mechanisms differ in their sensitivity to positively charged amino acids.     

Integration of charged membrane into perstraction system for separation of amino acid derivatives

The integration of a charged membrane into a perstraction system for high selective separation is reported. A mixture of N-(benzyloxycarbonyl)-L-aspartic acid (ZA), L-phenylalanine methyl ester (PM), and N-(benzyloxycarbonyl)-L-aspartyl-L-phenylalanine methyl ester (ZAPM) was used as the model solution. The aqueous phase containing ZA, PM, and ZAPM was adjusted to pH 6 and was contacted with tert-amyl alcohol through a charged membrane. Seven different ion-exchange membranes and two different microfiltration membranes were tested for the separation system. Only ZAPM could permeate into the organic phase through SELEMION AMV and ASV. The separations between ZA and ZAPM and between PM and ZAPM were performed by biphasic extraction and electrostatic rejection, respectively. The permeabilities of ZAPM were higher than those of PM for all experiments using the ion-exchange membranes, although the molecular weight of ZAPM is larger than that of PM. The membrane that had a smaller pore size showed higher ZAPM selectivity. (c) 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 56: 162-167, 1997.     

Brownian dynamic model of the glycine receptor chloride channel: effect of the position of charged amino acids on ion membrane currents

Glycine is the major inhibitory neurotransmitter in the brainstem and spinal cord, where it participates in a variety of motor and sensory functions. It activates a special type of ligand-gated membrane receptor, which provides for Cl- ion conductance of the neuronal membrane. Computer simulations of a single-channel current through this receptor have been carried out on the basis of Brownian (Langevin) dynamics. The dependence of the currents on pore diameter and the location of the charged amino acid residues have been obtained. It has been shown that the presence and the symmetry of the filter-forming residues determined not only the ion-selectivity of the channel but also increased transmembrane anion current.     

A liquid emulsion membrane process for the separation of amino acids

The method of using liquid emulsion membranes featuring the cation carrier D2EHPA [di-(2-ethylhexyl) phosphoric acid] for the separation of L-phenylalanine is examined. Results from experiments performed under various conditions are discussed and an optimal condition for separation is determined. The selectivity of the liquid emulsion membrane system is discussed. The effects of impurities such as sodium chloride, glucose, lactic acid, and L-tryptophan on the transport of L-phenylalanine are evaluated. It is shown that the liquid emulsion membrane system is a potential operation not only to separate L-phenylalanine but also concentrate it with great efficiency.     

Trypanosoma gambiense: membrane transport of amino acids.

Trypanosoma gambiense absorbed ¹⁴C-labeled lysine, arginine, glutamate, phenylalanine, methionine, threonine, glycine, and alanine by mediated transport systems. The interactions of these compounds as inhibitors or stimulators formed complex patterns of uptake which suggested the presence of five binding and/or transport loci: Locus A bound glutamate, arginine, and lysine, and the binding of glutamate or arginine stimulated the transport of lysine. Locus B transported threonine, glycine, and alanine and appeared to be partially sensitive to ouabain and Na⁺. Locus C transported glutamate, locus D transported phenylalanine and methionine, and locus E transported lysine and arginine.     

Selective constraints on amino acids estimated by a mechanistic codon substitution model with multiple nucleotide changes

Background

Empirical substitution matrices represent the average tendencies of substitutions over various protein families by sacrificing gene-level resolution. We develop a codon-based model, in which mutational tendencies of codon, a genetic code, and the strength of selective constraints against amino acid replacements can be tailored to a given gene. First, selective constraints averaged over proteins are estimated by maximizing the likelihood of each 1-PAM matrix of empirical amino acid (JTT, WAG, and LG) and codon (KHG) substitution matrices. Then, selective constraints specific to given proteins are approximated as a linear function of those estimated from the empirical substitution matrices.

Results

Akaike information criterion (AIC) values indicate that a model allowing multiple nucleotide changes fits the empirical substitution matrices significantly better. Also, the ML estimates of transition-transversion bias obtained from these empirical matrices are not so large as previously estimated. The selective constraints are characteristic of proteins rather than species. However, their relative strengths among amino acid pairs can be approximated not to depend very much on protein families but amino acid pairs, because the present model, in which selective constraints are approximated to be a linear function of those estimated from the JTT/WAG/LG/KHG matrices, can provide a good fit to other empirical substitution matrices including cpREV for chloroplast proteins and mtREV for vertebrate mitochondrial proteins.

Conclusions/Significance

The present codon-based model with the ML estimates of selective constraints and with adjustable mutation rates of nucleotide would be useful as a simple substitution model in ML and Bayesian inferences of molecular phylogenetic trees, and enables us to obtain biologically meaningful information at both nucleotide and amino acid levels from codon and protein sequences.     

Scaling up a microbore separation for semipreparative analysis: differential recoveries of radiolabeled amino acids

Application of a high-sensitivity microbore system designed to separate and quantify nonderivatized amino acids by anion exchange chromatography and amperometric detection for determination of amino acid-specific activities in biological samples requires high capacity to recover sufficient labeled material for adequate count statistics. Scale up from a low (25-1000 pmol) to a high (500-15,000 pmol) working range was achieved by use of a thick working electrode gasket to reduce sensitivity and eliminate peak splitting and tailing and by modification of the wash procedure to eliminate carryover. Analysis of recoveries of labeled amino acids revealed that specific amino acids are either selectively retained on the column or partially degraded during analysis and that assessment of purities of labeled compounds and metabolic labeling patterns requires careful analysis of recoveries of labeled compounds in the appropriate eluate fraction.     

Characterization and effect of biofouling on polyamide reverse osmosis and nanofiltration membrane surfaces

Biofouling is a major reason for flux decline in the performance of membrane-based water and wastewater treatment plants. Initial biochemical characterization of biofilm formation potential and biofouling on two commercially available membrane surfaces from FilmTec Corporation were investigated without filtration in laboratory rotating disc reactor systems. These surfaces were polyamide aromatic thin-film reverse osmosis (RO) (BW30) and semi-aromatic nanofiltration (NF270) membranes. Membrane swatches were fixed on removable coupons and exposed to water with indigenous microorganisms supplemented with 1.5 mg l(-1) organic carbon under continuous flow. After biofilms formed, the membrane swatches were removed for analyses. Staining and epifluorescence microscopy revealed more cells on the RO than on the NF surface. Based on image analyses of 5-μm thick cryo-sections, the accumulation of hydrated biofoulants on the RO and NF surfaces exceeded 0.74 and 0.64 μm day(-1), respectively. As determined by contact angle the biofoulants increased the hydrophobicity up to 30° for RO and 4° for NF surfaces. The initial difference between virgin RO and NO hydrophobicities was ～5°, which increased up to 25° after biofoulant formation. The initial roughness of RO and NF virgin surfaces (75.3 nm and 8.2 nm, respectively) increased to 48 nm and 39 nm after fouling. A wide range of changes of the chemical element mass percentages on membrane surfaces was observed with X-ray photoelectron spectroscopy. The initial chemical signature on the NF surface was better restored after cleaning than the RO membrane. All the data suggest that the semi-aromatic NF surface was more biofilm resistant than the aromatic RO surface. The morphology of the biofilm and the location of active and dead cell zones could be related to the membrane surface properties and general biofouling accumulation was associated with changes in the surface chemistry of the membranes, suggesting the validity of the combination of these novel approaches for initial assessment of membrane performance.     

WRF-TMH: predicting transmembrane helix by fusing composition index and physicochemical properties of amino acids

Membrane protein is the prime constituent of a cell, which performs a role of mediator between intra and extracellular processes. The prediction of transmembrane (TM) helix and its topology provides essential information regarding the function and structure of membrane proteins. However, prediction of TM helix and its topology is a challenging issue in bioinformatics and computational biology due to experimental complexities and lack of its established structures. Therefore, the location and orientation of TM helix segments are predicted from topogenic sequences. In this regard, we propose WRF-TMH model for effectively predicting TM helix segments. In this model, information is extracted from membrane protein sequences using compositional index and physicochemical properties. The redundant and irrelevant features are eliminated through singular value decomposition. The selected features provided by these feature extraction strategies are then fused to develop a hybrid model. Weighted random forest is adopted as a classification approach. We have used two benchmark datasets including low and high-resolution datasets. tenfold cross validation is employed to assess the performance of WRF-TMH model at different levels including per protein, per segment, and per residue. The success rates of WRF-TMH model are quite promising and are the best reported so far on the same datasets. It is observed that WRF-TMH model might play a substantial role, and will provide essential information for further structural and functional studies on membrane proteins. The accompanied web predictor is accessible at http://111.68.99.218/WRF-TMH/.     

Effects of N-phosphorylated amino acids on membrane phospholipid of human erythrocytes

Abtract Raman spectra were used to study the effects of the phosphorylated amino acids on the erythrocyte membrane. It was found that some phosphorylated amino acids might cause the polar part of the membrane phospholipid to become less ordered, the packing of the chains to become looser, and the end of the chain more ordered. Some of the phosphoamino acids cause the phospholipids' all-trans/gauche ratio to increase and some cause them to decrease. This could give some clues to the function of phosphorylated proteins in the biological process concerning the change in membrane mobility.