Assembly of transmembrane helices of simple polytopic membrane proteins from sequence conservation patterns

The transmembrane (TM) domains of most membrane proteins consist of helix bundles. The seemingly simple task of TM helix bundle assembly has turned out to be extremely difficult. This is true even for simple TM helix bundle proteins, i.e., those that have the simple form of compact TM helix bundles. Herein, we present a computational method that is capable of generating native-like structural models for simple TM helix bundle proteins having modest numbers of TM helices based on sequence conservation patterns. Thus, the only requirement for our method is the presence of more than 30 homologous sequences for an accurate extraction of sequence conservation patterns. The prediction method first computes a number of representative well-packed conformations for each pair of contacting TM helices, and then a library of tertiary folds is generated by overlaying overlapping TM helices of the representative conformations. This library is scored using sequence conservation patterns, and a subsequent clustering analysis yields five final models. Assuming that neighboring TM helices in the sequence contact each other (but not that TM helices A and G contact each other), the method produced structural models of Calpha atom root-mean-square deviation (CA RMSD) of 3-5 A from corresponding crystal structures for bacteriorhodopsin, halorhodopsin, sensory rhodopsin II, and rhodopsin. In blind predictions, this type of contact knowledge is not available. Mimicking this, predictions were made for the rotor of the V-type Na(+)-adenosine triphosphatase without such knowledge. The CA RMSD between the best model and its crystal structure is only 3.4 A, and its contact accuracy reaches 55%. Furthermore, the model correctly identifies the binding pocket for sodium ion. These results demonstrate that the method can be readily applied to ab initio structure prediction of simple TM helix bundle proteins having modest numbers of TM helices.     

Assembly of light-harvesting bacteriochlorophyll in a model transmembrane helix in its natural environment

The transmembrane, bacteriochlorophyll-binding region of a bacterial light-harvesting complex, (LH2-alpha from the photosynthetic bacterium Rhodobacter sphaeroides) was redesigned and overexpressed in a mutant of Rb. sphaeroides lacking LH2. Bacteriochlorophyll served as internal probe for the fitness of this new region for the assembly and energy transfer function of the LH2 complex. The ability to absorb and transfer light energy is practically undisturbed by the exchange of the transmembrane segment, valine -7 to threonine +6, of LH2-alpha with a 14 residue Ala-Leu sequence. This stretch makes up the residues of the transmembrane helix that are in close contact (< or =4.5 A) with the bacteriochlorophyll molecules that are coordinated through His of both the alpha and beta-subunits. In this Ala-Leu stretch, neither alpha-His0, which binds the bacteriochlorophyll, nor the adjacent alpha-Ile-1, were replaced. Novel LH2 complexes composed of LH2-alpha with a model transmembrane sequence and a normal LH2-beta are assembled in vivo into a complex, the biochemical and spectroscopic properties of which closely resemble the native one. In contrast, the additional insertion of four residues just outside the C-terminal end of the model transmembrane helix leads to complete loss of functional antenna complex. The results suggest that light energy can be harvested and transferred efficiently by bacteriochlorophyll molecules attached to only few key residues distributed over the polypeptide, while residues at the bacteriochlorophyll-helix interface seem to be largely dispensable for the functional assembly of this membrane protein complex. This novel antenna with a simplified transmembrane domain and a built-in probe for assembly and function provides a powerful model system for investigation of the factors that contribute to the assembly of chromophores in membrane-embedded proteins.     

The role of the transmembrane domain in determining the targeting of membrane proteins to either the inner envelope or thylakoid membrane

Chloroplastic membrane proteins can be targeted to any of three distinct membrane systems, i.e., the outer envelope membrane (OEM), inner envelope membrane (IEM), and thylakoid membrane. This complex structure of chloroplasts adds significantly to the challenge of studying protein targeting to various membrane sub-compartments within a chloroplast. In this investigation, we examined the role played by the transmembrane domain (TMD) in directing membrane proteins to either the IEM or thylakoid membrane. Using the IEM protein, Arc6 (Accumulation and Replication of Chloroplasts 6), we exchanged the stop-transfer TMD of Arc6 with various TMDs derived from different IEM and thylakoid membrane proteins and monitored the subcellular localization of these Arc6-hybrid proteins. We showed that when the Arc6 TMD was replaced with a TMD derived from various thylakoid membrane proteins, these Arc6(thylTMD) hybrid proteins could be directed to the thylakoid membrane rather than to the IEM. Conversely, when the TMD of the thylakoid membrane proteins, STN8 (State Transition protein kinase 8) or Plsp1 (Plastidic type I signal peptidase 1), was replaced with the stop-transfer TMD of Arc6, STN8 and Plsp1 were halted at the IEM. From our investigation, we conclude that the TMD plays a critical role in targeting integral membrane proteins to either the IEM or thylakoid membrane.     

Observations on transmembrane structures of surface immunoglobulin in the plasma membrane of B lymphocytes

We have investigated the possible role of intramembraneous particles as revealed by freeze-fracture electron microscopy in the plasma membrane of B lymphocytes from rabbits and mice as reflections of transmembrane structures of surface immunoglobulin receptor molecules. This was achieved by aggregation of the surface receptors using fluorochrome-conjugated antibodies, fixation and freezing of the cells in 35% glycerol. This procedure resulted in replicas of lymphocytes with well-preserved morphology (no ice-crystals), enabling the study of both protoplasmic and external fracture face in combination with surface receptor markers. It appeared that very small intramembraneous particles (3–6 nm diameter) were selectively clustered under patches of surface receptor label. This phenomenon was found on the external fracture face exclusively and not on the protoplasmic fracture face. ‘Classical’ intramembraneous particles (6–12 nm diameter) were not involved. We suggest that these small, clustered particles should be interpreted as transmembrane structures of surface immunoglobulin molecules.     

转基因植物表达药用蛋白的研究进展

基因工程技术的进步使得转基因植物广泛应用于工业、农业各个领域,尤其在医药制造领域。研究成果表明,转基因植物作为生物反应器在制备药用蛋白,如重组疫苗、重组动物抗体、细胞因子等方面较其他表达系统,如微生物及动物表达系统具有成本低、应用安全等优势,但在工业化技术方面仍存在障碍。     

The hexose transporters at the plasma membrane and the tonoplast of higher plants

The uptake of hexoses in higher plant cells is thought to be catalyzed by an H⁺/hexose contrasporter in the plasma membrane. Transport studies with isolated plant vacuoles indicate that, at the tonoplast, a second hexose transporter is located with properties different from the plasma membrane transporter. Recently membrane vesicles of high purity and defined orientation have been used for a more rigorous individual characterization of these two carriers. Concomitantly, a cDNA for the inducible H⁺/hexose cotransporter of the green alga Chlorella has been sequenced and shown to exhibit homology to a group of hexose transporters (for facilitated diffusion) of other eukaryotic and prokaryotic organisms. With a probe derived from the Chlorella sequence, the first plant gene for an H⁺/hexose contransporter ( Arabidopsis thaliana ) has been isolated, opening the route to molecular studies of structure, function and evolution of the hexose transporters of higher plants. The present review discusses recent work on the kinetic characterization and identification of the higher plant plasma membrane and tonoplast hexose transporters as well as their respective cellular functions. Furthermore, perspectives for future research on the plant hexose transporters are outlined.     

Molecular principles of membrane microdomain targeting in plants

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Purification and characterization of the apical plasma membrane of the rat pancreatic acinar cell

Summary A method is described for the rapid purification of the apical plasma membrane from the rat pancreatic acinar cell. It makes use of wheat germ agglutinin affinity chromatography to selectively bind vesicles with N-acetyl glucosamine present at their surface. Particular conditions (150 mm NaCl) had then to be used to keep membrane vesicles in the coveted orientation, i.e. as right-side-out vesicles. Due to its specific apical location in many epithelial cells, -glutamyltranspeptidase was chosen to monitor the purification procedure. The final fraction was enriched in -glutamyltranspeptidase by a factor of 75 relative to the homogenate. Na,K-ATPase, a strict basolateral membrane marker, was not detectable in the fraction. No membranes originating from other compartments, more particularly expected from zymogen granules, or from other cell types, did contaminate the preparation. As expected for an epithelial cell apical plasmalemma, lipid composition showed a very high ratio of glycolipids (37.5%). The absence of membrane-bound GP-2, and the exceptionally high specific activity of -glutamyltranspeptidase suggest that the apical membrane would not be made up by the exocytosis of secretory granule, but instead by the fusion of specialized secretory vesicles very likely originating from the constitutive secretory pathway. In conclusion, this report describes a method of obtaining a fraction highly enriched in the secretory apex of the pancreatic exocrine cell that would be directly involved in exocytosis with zymogen granules and also in local anion transport.The authors would like to thank Dr. Andrew W. Shyjan (Yale University, New Haven, CT) for his kind gift of anti-Na,K-ATPase 1 subunit, Dr. Yannick Laperche (INSERM, Hôpital Mondor, Paris) for his gift of anti--GT, and finally Mr. Gilles P. Grondin for the production of antibodies against amylase. D.L. is supported by NSERC of Canada, FCAR of Québec, and the Canadian Cystic Fibrosis Foundation.     

Separation of tonoplast and plasma membrane potential and resistance in cells of oat coleoptiles

Summary Membrane potential and resistance were recorded from parenchymal cells of oat (Avena) coleoptiles, using one and two intracellular electrodes. Membrane potential is largest (–100 mV) in impalements with low input resistance (2–4 M), and is less negative (–50 mV) in penetrations with high input resistance (> 20 m). The interpretation is that the electrode lodges in the vacuole which is positive to the cytoplasm (but still negative to the external solution), and that measurements of net membrane potential are compromised to varying degrees by leakage shunts introduced across the high resistance vacuolar membrane by the electrode. This conclusion is supported by several additional lines of evidence. (1) It is possible to convert large-R/small-V impalements into small-R/large-V penetrations by passing excess current through the electrode or by briefly ringing the capacitance neutralization circuit in the amplifier. The cells usually recover their resistance in a few minutes, with a concomitant decrease in the negativity of the membrane potential. (2) Changes in external [K] affect the measuree potential by an amount that is independent of the input resistance of the impalement. This is consistent with an effect of [K] _o on the potential of the plasma membrane and the occurrence of leakage shunts primarily at the tonoplast. (3) Quantitatively, the effects of a change in [K] _o on resistance indicate that nearly 90 percent of the input resistance of unshunted cells resides in the tonoplast. (4) The effects of metabolic inhibitors (DNP, CN^–) on potential are smaller in large-R than in small-R impalements. This observation suggests there are electrogenic pumps contributing to the membrane potential at both the plasmalemma and tonoplast. Finally, we conclude that with an electrode in the vacuole it is possible to record potentials that are dominated by the contribution of the plasma membrane, provided care is taken to select impalements combining both large, negative potential and low input resistance.     

The stability of transmembrane helix interactions measured in a biological membrane

Despite some promising progress in the understanding of membrane protein folding and assembly, there is little experimental information regarding the thermodynamic stability of transmembrane helix interactions and even less on the stability of transmembrane helix-helix interactions in a biological membrane. Here we describe an approach that allows quantitative measurement of transmembrane helix interactions in a biological membrane, and calculation of changes in the interaction free energy resulting from substitution of single amino acids. Dimerization of several variants of the glycophorin A transmembrane domain are characterized and compared to the wild-type (wt) glycophorin A transmembrane helix dimerization. The calculated DeltaDeltaG(app) values are further compared with values found in the literature. In addition, we compare interactions between the wt glycophorin A transmembrane domain and helices in which critical glycine residues are replaced by alanine or serine, respectively. The data demonstrate that replacement of the glycine residues by serine is less destabilizing than replacement by alanine with a DeltaDeltaG(app) value of about 0.4 kcal/mol. Our study comprises the first measurement of a transmembrane helix interaction in a biological membrane, and we are optimistic that it can be further developed and applied.     

An improved method for the detection and quantification of recombinant protein in transgenic plants

A sensitive method has been developed for the detection of recombinant protein produced as a result of gene transfer into plants. This method is based upon antibody binding, which is then visualized using enhanced chemiluminescence and recorded on x-ray film for long-term storage. The technique is simple, rapid and reliable and can be used to screen large numbers of transgenic plants. Several plant species have been successfully tested in this way for a range of recombinant proteins.     

Inhibition of plasma membrane and mitochondrial transmembrane potentials by ethanol

The actions of ethanol and its primary oxidative metabolite, acetaldehyde, on plasma membrane and mitochondrial transmembrane potentials were examined in rat brain using fluorescence techniques. Subchronic treatment of adult rats with ethanol resulted in a significant depolarization of both the plasma and mitochondrial membranes when the mean blood ethanol level of the rats was 59±11 mM (mean±SEM, n=6). Acute dosing of animals (4.5 g/kg, i.p.) failed to show any significant alterations. Various concentrations of ethanol, added in vitro to a crude synaptosomal preparation isolated from the rat cerebrocortex (P₂) from untreated animals, depolarized both the plasma and mitochondrial transmembrane potentials in a dose-related manner. Addition of acetaldehyde in vitro did not reveal any significant effects on plasma or mitochondrial transmembrane potential.     

A murine monoclonal antibody produced in transgenic plants with plant-specific glycans is not immunogenic in mice

Previous studies have shown that the production of recombinant antibodies in plants is highly efficient and presents numerous therapeutic applications. It is, however, known that plant glycoproteins display different glycosylation patterns to those exhibited by mammalian glycoproteins. Thus, it is important to know if these plant recombinant antibodies could induce undesirable immune responses in mammal; and to date no report has documented the potential immunogenicity of parenterally administered plant recombinant antibodies in animals. In order to answer this question, mice were immunised subcutaneously with a recombinant mouse monoclonal antibody produced in tobacco plants, together with alum as adjuvant. Two control groups were immunised in the same way with either the original murine monoclonal antibody or horseradish peroxidase (a plant glycoprotein). Analyses by direct immunoassay, competition immunoassay and real-time surface plasmon resonance, showed undetectable levels of antibody directed against both the protein and the glycan part of the plant recombinant antibody. These results have a direct relevance for the application of plant recombinant proteins as therapeutic agents and vaccines in humans.     

Application of recombinant DNA technology to plant protection: molecular approaches to engineering virus resistance in crop plants

Developments in plant tissue culture, plant transformation and regeneration, and improvements in techniques to isolate and manipulate viral genes have led to the exploitation of the concept of cross protection: turning the virus onto itself and controlling it with its own genes. By introducing and expressing genes of viral origin in crop plants, scientists have engineered resistance to several plant viruses. Some of the approaches, used singly or in combination, include expression of viral-coat protein, untranslatable sense or antisense RNA, satellite RNA, virusspecific neutralizing antibody genes, plant viral replicase, protease or movement proteins and defective, interfering RNA. All of these approaches have resulted in manifestation of virus resistance to varying degrees in several commercially important crop plants. This review summarizes the recent advances in engineering virus resistance using the above approaches, and lists specific examples of their use in cultivated crop plants of economic importance.H.R. Pappu and C.L. Niblett are with the Plant Pathology Department, University of Florida. Gainesville, FL 32611-0680, USA; R.F. Lee is with the Citrus Research and Education Center, University of Florida, Lake Alfred, FL 33850, USA. Florida Agricultural Experiment Station Journal Series No. R-04558.     

Prediction of the transmembrane regions of beta-barrel membrane proteins with a neural network-based predictor

A method based on neural networks is trained and tested on a nonredundant set of beta-barrel membrane proteins known at atomic resolution with a jackknife procedure. The method predicts the topography of transmembrane beta strands with residue accuracy as high as 78% when evolutionary information is used as input to the network. Of the transmembrane beta-strands included in the training set, 93% are correctly assigned. The predictor includes an algorithm of model optimization, based on dynamic programming, that correctly models eight out of the 11 proteins present in the training/testing set. In addition, protein topology is assigned on the basis of the location of the longest loops in the models. We propose this as a general method to fill the gap of the prediction of beta-barrel membrane proteins.     

Expression and long-term stability of a recombinant single-chain Fv antibody fragment in transgenic Nicotiana tabacum seeds

A functionally active anti-hepatitis B surface antigen single-chain Fv antibody fragment (scFv) was expressed in seeds of transgenic tobacco plants using genetic constructs for expression in the vacuole or the apoplastic fluid. Antibody levels close to 0.2% of the total soluble protein were found. After storage of the transgenic tobacco seeds for one year and a half a year at room temperature, the scFv maintained its antigen-binding activity in full.     

Effects of 3,4-dihydroxybenzoic acid on root membrane potential in micropropagated tobacco plants

In order to understand the mechanism of action of the phenolic compound 3,4-dihydroxybenzoic acid, we tested its effect on tobacco root membrane potential. Tobacco root segments, excised from micropropagated plants grown in liquid media, were perfused with 0.1–5 mM 3,4-dihydroxybenzoic acid. Activity on the plasma membrane potential was compared with that obtained after perfusion with 0.05 mM indole-3-acetic acid, 0.05 mM kinetin and 0.05 mM gibberellic acid. Possible interactions between 3,4-dihydroxybenzoic acid and plant growth regulators were evaluated by the means of successive applications. When applied to tobacco root segments, 3,4-dihydroxybenzoic acid elicited a transient membrane depolarization. The membrane depolarization induced by 3,4-dihydroxybenzoic acid was followed by a repolarization phase, as for auxin applications. In roots preconditioned with the other growth regulators, the activity of 3,4-dihydroxybenzoic acid on membrane potential was non-specifically affected. In roots preconditioned with 3,4-dihydroxybenzoic acid, indole-3-acetic acid activity on cell membrane was altered, suggesting a specific reciprocal interaction. This revised version was published online in June 2006 with corrections to the Cover Date.     

Differentiation between transmembrane helices and peripheral helices by the deconvolution of circular dichroism spectra of membrane proteins.

The interpretation of the circular dichroism (CD) spectra of proteins to date requires additional secondary structural information of the proteins to be analyzed, such as X-ray or NMR data. Therefore, these methods are inappropriate for a CD database whose secondary structures are unknown, as in the case of the membrane proteins. The convex constraint analysis algorithm (Perczel, A., Hollósi, M., Tusnády, G., & Fasman, G. D., 1991, Protein Eng. 4, 669-679), on the other hand, operates only on a collection of spectral data to extract the common spectral components with their spectral weights. The linear combinations of these derived "pure" CD curves can reconstruct the original data set with great accuracy. For a membrane protein data set, the five-component spectra so obtained from the deconvolution consisted of two different types of alpha helices (the alpha helix in the soluble domain and the alpha T helix, for the transmembrane alpha helix), a beta-pleated sheet, a class C-like spectrum related to beta turns, and a spectrum correlated with the unordered conformation. The deconvoluted CD spectrum for the alpha T helix was characterized by a positive red-shifted band in the range 195-200 nm (+95,000 deg cm2 dmol-1), with the intensity of the negative band at 208 nm being slightly less negative than that of the 222-nm band (-50,000 and -60,000 deg cm2 dmol-1, respectively) in comparison with the regular alpha helix, with a positive band at 190 nm and two negative bands at 208 and 222 nm with magnitudes of +70,000, -30,000, and -30,000 deg cm2 dmol-1, respectively.     

Correlative light-electron microscopy reveals the tubular-saccular ultrastructure of carriers operating between Golgi apparatus and plasma membrane

Transport intermediates (TIs) have a central role in intracellular traffic, and much effort has been directed towards defining their molecular organization. Unfortunately, major uncertainties remain regarding their true structure in living cells. To address this question, we have developed an approach based on the combination of the green fluorescent protein technology and correlative light-electron microscopy, by which it is possible to monitor an individual carrier in vivo and then take a picture of its ultrastructure at any moment of its life-cycle. We have applied this technique to define the structure of TIs operating from the Golgi apparatus to the plasma membrane, whose in vivo dynamics have been characterized recently by light microscopy. We find that these carriers are large (ranging from 0.3-1.7 microm in maximum diameter, nearly half the size of a Golgi cisterna), comprise almost exclusively tubular-saccular structures, and fuse directly with the plasma membrane, sometimes minutes after docking to the fusion site.