Transmembrane Protein Topology Types

Transmembrane Protein Topology Types

Figure 1.5.2 Membrane proteins containing hydrophobic anchors. A nontransmembrane or monotopic membrane protein is anchored to the membrane via a hydrophobic amino acid sequence. Transmembrane proteins are classified as types I, II, III, and IV (Table 1.5.2). The first transmembrane segment of a multispanning membrane protein can be inserted as in type I, II, or III proteins. This segment functions as a start-transfer peptide. Subsequent transmembrane segments will function as stop-transfer and...

Selection And Preparation Of Dialysis Membrane

Dialysis membranes are available in a number of thicknesses and pore sizes. Thicker membranes are tougher, but restrict solute flow and reach equilibrium more slowly. Pore size is defined by molecular weight cutoff (MWCO) i.e., the size of the smallest particle that cannot penetrate the membrane. The MWCO designation should be used only as a very rough guide if accurate MWCO information is required, it should be determined empirically (see Craig, 1967, for a discussion of parameters affecting...

Analysis of Membrane Proteins in Detergents

The separation of membrane proteins in the presence of detergents (typically a nonionic or zwitterionic detergent) is the same in principle as separation in aqueous solutions. However, in the presence of detergent, the apparent size of the protein will probably increase due to detergent binding to the protein. For this reason, the fractionation range of gel filtration columns specified for water-soluble proteins will not apply to detergent-solubilized proteins (Schagger, 1994). Accurate size...

Info

Basic Protocols 1, 2, and 3 (biuret, Hartree-Lowry, and BCA assays) require one hour for measuring sample, mixing, incubation, and reading the absorbance. Basic Protocol 4 (acid digestion-ninhydrin detection) requires one hour on the first day to measure the sample and seal the tubes, followed by an overnight hydrolysis. On the second day, 1 to 2 hr are required for opening the tubes, neutralization, mixing reagents, heating, and reading the resulting color. Basic Protocol 5 (UV absorption) is...

Background Information

Subcellular fractionation was initially developed with rat liver and, in most cases, involves separation of organelles based on physical properties such as density. However, two major problems have interfered with the widespread use of subcellular fractionation in cell and molecular biology. First, studies of membrane transport and cellular organization have revealed that several subcellular compartments share similar physical properties and hence cofractionate, at least to some extent, in...

Analysis Of Proteins Using Nearuv Spectrophotometry

This procedure identifies proteins using near-UV spectrophotometry. Protein solution is placed in a UV-transparent quartz cuvette, absorption of light is measured as a function of wavelength, and the resulting spectrum is transferred either to a displaying device (e.g., CRT or printer) for inspection or to a computer that can employ a spreadsheet or other program for derivative calculations and or quantitative analyses (see Support Protocol). Acid ethanol cleaning solution (see recipe) 4...

Selective Precipitation By Isoionic Precipitation Dialysis Method

Dialysis Protocol Protein Pictures

One of the older means of rendering proteins salt-free or nearly salt-free (i.e., isoionic) is dialysis (also see unit 4.4 & appendix 3b). However, two problems frequently arise with conventional dialysis (1) when appreciable amounts of protein are present, osmotic effects result in swelling of dialysis bags as salt diffuses outward and (2) often it is quite uncertain where the isoionic point is, even if it is feasible to deionize by dialysis against a buffer. The resin deionization method...

Growth Of Mammalian Cells For Protein Expression

Mammalian cell culture media are complex in comparison to the simple defined media used for propagation of bacteria and yeast. This complexity stems from the need to satisfy the many functions required for normal growth and metabolism of mammalian cells (Bettger and McKeehan, 1986). Nutrients must satisfy the requirements for growth, maintenance of the cell, and expression of products. Additional specific growth factors such as insulin or insulin-like growth factor (IGF) are usually required....

Gel Dialysis Of Protein Samples

This protocol describes a simple method for dialyzing small interfering molecules and salts away from protein samples using an agarose or polyacrylamide gel (see Fig. 3.4.5 Freifelder and Better, 1982). Somewhat dense, well cross-linked gels are used to keep proteins from penetrating the gel while unwanted salts and low-molecular-weight compounds diffuse (are dialyzed away) into the gel. This is a micro to semimicro method, an alternative to conventional dialysis (Craig, 1967), and to the use...

Strategies For Isolation Of Insoluble Proteins

Recombinant proteins expressed in E. coli that are located in the low-speed pellet fraction (see Fig. 6.1.1) following cell lysis are highly aggregated (i.e., inclusion bodies). Inclusion bodies are normally derived from protein aggregation in the cytoplasm, or in the periplasm if a secretion vector was used. As mentioned above, protein can also be located in either the low- or high-speed pellet fractions because of interaction with bacterial nucleic acids. Furthermore, if the protein is known...

Desalting The Sample After Cysteine Modification

Except for the in situ method Basic Protocol 9 , all of the protocols presented leave the protein in the presence of high salt and reaction by-products which are usually not compatible with subsequent analytical techniques. This problem may be remedied by one of the following desalting methods. The methods are presented in increasing order of technological complexity. Protein recovery is a concern because small quantities of protein may be lost in dialysis or gel filtration. Modern...

Protease Cleavage Of Fusion Protein In Solution To Remove Gst Affinity

Uncleaved Thrombin Cleaved Protein

The glutathione-S-transferase GST affinity tag is removed by cleaving with thrombin pGEX-T vectors or factor Xa pGEX-X vectors . Conditions for optimal cleavage of each recombinant fusion protein must be empirically determined. Some of the parameters that can be varied include temperature, enzyme-to-substrate ratio, length of incubation, and buffer conditions. Proteolysis can usually be performed in the glutathione buffer used to elute the fusion protein from the column, either with or without...

Phenylthiocarbamyl Amino Acid Analysis

Phenylthiocarbamyl amino acid analysis PTC-AAA is an established method for picomole-level quantitative analysis based on the reaction of phenylisothiocyanate PITC with amino groups to form phenylthiocarbamyl amino acid derivatives, which are then separated by reversed-phase HPLC and identified and quantified by ultraviolet absor-bance. Since its introduction in the 1980s Koop et al., 1982 Heinrikson and Meredith, 1984 Tarr, 1986 , PTC-AAA has become the most popular precolumn-derivatization...

Graphical Determination Of Specific Productivity Of Cells Producing Heterologous Protein

For definition of specific productivity, see Support Protocol 6. Materials Spreadsheet software with graphical output e.g., Microsoft Excel or Lotus 123 1. Sample cultures at time points 1 and 2, count viable cells, and determine protein concentrations see Support Protocol 6, steps 1 and 2 . 2. Plot the viable cell densities versus time and plot the protein concentrations versus time on x-y formatted charts using spreadsheet software capable of graphical output. 3. Curve-fit the charts with the...

Peptide Sample Preparation by Ether Precipitation

This procedure is suitable for precipitating peptides from organic acids and is used routinely for concentrating synthetic peptides from the trifluoroacetic acid cleavage cocktail following 9-fluorenylmethyloxycarbonyl Fmoc solid-phase peptide synthesis. It can be used to desalt peptides in nonvolatile buffers but is not recommended for removing detergents like SDS. Take appropriate safety precautions when using this technique ether is highly flammable, and a refrigerated centrifuge and fume...

Differential Scanning Calorimetry

Before beginning calorimetry, an instrument baseline is established by a buffer buffer scan. If there are changes in the shape and or relative position of the buffer buffer scan, the cells are probably dirty see Support Protocol 4 for cleaning procedure . Protein solution, dialyzed unit4.4 amp appendix3.b and in dialysis bag see Critical Parameters Equilibration buffer buffer solution used for the last dialysis see Critical Parameters for discussion of buffer selection Spectrophotometer and...

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Figure 6.1.2 Localization of secreted and periplasmic proteins in E. coli. Periplasmic protein produced via a secretion vector can leak into the medium and be recovered by centrifugation supernatant, S1 or filtration. Washing cells with an isotonic solution such as lightly buffered 0.15 M NaCl or 0.25 M sucrose can also release protein S2 . The compartmentalized periplasmic proteins are released by isotonic shock treatment by directly suspending normal cell paste or plasmolyzed cell paste into...

Reagents And Solutions

Use Milli-Q-purified water or equivalent in all recipes and protocol steps. For common stock solutions, see APPENDIX 2E for suppliers, see SUPPLIERS APPENDIX. 100 mM Tris - Cl, pH 7.8 pH as determined at 4 C 100 mM Tris - Cl, pH 7.8 pH as determined at 4 C 10 mM EDTA from 0.5 M stock 0.5 mM phenylmethylsulfonyl fluoride PMSF 5 mM benzamidine - HCl 780 mg liter Prepare immediately before use Purification of PMSF can be added as 2.5 ml liter of 0.2 M PMSF stock solution. 60 mM ethanolamineHCl, pH...

Osmotic Dehydration

Although ultrafiltration is a highly effective procedure for concentrating relatively large volumes, it may be less effective and convenient with small volumes and high protein concentrations. Osmotic dialysis relies on the use of a high concentration of material outside a dialysis tube to draw water and small-molecule solutes from its contents by osmosis, leaving a more concentrated protein solution within the dialysis tubing. Either sucrose or polyethylene glycol PEG Mr 15,000 to 20,000 may...

Diafiltration Or Concentration By Tangentialflow Ultrafiltration

The most rapid method for dialyzing large samples is the use of ultrafiltration membranes fabricated into hollow fibers or spiral-wound layers, or, as in this protocol, in the form of stacked plates. The sample is allowed to flow tangentially over these membranes with recirculation. The semipermeable nature of the membrane then permits water and materials with molecular weights that are substantially below the MWCO value to cross through the membrane surface relatively unimpeded retained...

Hartreelowry Assay For Quantitation Of Total Protein

The original Lowry method for total protein analysis was first described in one of the most cited papers in biochemistry Lowry et al., 1951 . The assay is a colorimetric assay based on cupric ions and Folin-Ciocalteau reagent for phenolic groups. The assay has been reinvestigated many times and sometimes improved. Most of these studies were designed to discern how interfering compounds distort the assay and how detergents solubilize otherwise insoluble proteins. The literature related to this...