SDS-acrylamide gel electrophoresis and its application to the proteins of poliovirus- and adenovirus-infected human cells

Using T4 Genetics and Laemmli's Development of High Resolution SDS Gel Electrophoresis to Reveal Structural Protein Interactions Controlling Protein Folding and Phage Self-Assembly

One of the most transformative experimental techniques in the rise of modern molecular biology and biochemistry was the development of high resolution Sodium Dodecyl Sulfate (SDS) poly acrylamide gel electrophoresis, which allowed separation of proteins - including structural proteins - in complex mixtures according to their molecular weights. Its development was intimately tied to investigations of the control of virus assembly within phage-infected cells. The method was developed by Ulrich K. Laemmli working in the virus structural group led by Aaron Klug at the famed Medical Research Council Laboratory for Molecular Biology (LMB) at Cambridge, UK. While Laemmli was tackling T4 head assembly, I sat at the next bench working on T4 tail assembly. To date, Laemmli's original paper has been cited almost 300,000 times. His gel procedure and our cooperation allowed us to sort out the sequential protein-protein interactions controlling the viral self-assembly pathways. It is still not fully appreciated that this control involved protein conformational change induced by interaction with an edge of the growing structure. Subsequent efforts of my students and I to understand how temperature sensitive mutations interfered with assembly were important in revealing the intracellular off-pathway aggregation processes competing with productive protein folding. These misfolding processes slowed the initial productivity of the biotechnology industry. The article below describes the scientific origin, context and sociology that supported these advances in protein biochemistry, protein expression, and virus assembly. The cooperation and collaboration that was integral to both the LMB culture and phage genetics fields were key to these endeavors.

The effect of higher order RNA processes on changing patterns of protein domain selection: A developmentally regulated transcriptome of type 1 inositol 1,4,5-trisphosphate receptors

The domain structure of proteins synthesized from a single gene can be remodeled during tissue development by activities at the RNA level of gene expression. The impact of higher order RNA processing on changing patterns of protein domain selection may be explored by systematically profiling single-gene transcriptomes. itpr1 is one of three mammalian genes encoding receptors for the second messenger inositol 1,4,5-trisphosphate (InsP3). Some phenotypic variations of InsP3 receptors have been attributed to hetero-oligomers of subunit isoforms from itpr1, itpr2, and itpr3. However, itpr1 itself is subject to alternative RNA splicing, with 7 sites of transcript variation, 6 within the ORF. We have identified 17 itpr1 subunit species expressed in mammalian brain in ensembles that change with tissue differentiation. Statistical analyses of populations comprising >1,300 full-length clones suggest that subunit variation arises from a variably biased stochastic splicing mechanism. Surprisingly, the protein domains of this highly allosteric receptor appear to be assembled in a partially randomized way, yielding stochastic arrays of subunit species that form tetrameric complexes in single cells. Nevertheless, functional expression studies of selected subunits confirm that splicing regulation is connected to phenotypic variation. The potential for itpr1 subunits to form hetero-tetramers in single cells suggests the expression of a developmentally regulated continuum of molecular forms that could display diverse properties, including incremental sensitivities to agonist activation and varying patterns of Ca2+ mobilization. These studies illuminate the extent to which itpr1 molecular phenotype is induced by higher order RNA processing.

A central anti-DNA idiotype in human and murine systemic lupus erythematosus

The monoclonal anti-DNA autoantibody A52 (IgG2b) was obtained from a (NZB X NZW)F1 (B/W) hybridoma. Two rabbits were immunized with the pure monoclonal antibody and produced anti-idiotypic (Id) antibodies. The purified anti-Id reacted with three different B/W monoclonal anti-DNA antibodies at or close to their DNA binding sites. Moreover, the rabbit antibodies had a profound inhibitory effect on the polyclonal anti-DNA activity in the majority of sera derived from B/W mice and human systemic lupus erythematosus (SLE) patients. The A52 IgG must, therefore, represent a major cross-reactive Id of anti-DNA immunoglobulins. In addition, the rabbit anti-Id antibodies may act as the "internal image" of antigen and should prove useful in modulation of the autoimmune response to DNA in SLE.

Partial amino-acid sequence of the epidermal growth-factor-binding protein

The partial amino acid sequence of the epidermal growth-factor-binding protein was determined. Residues in 108 unique positions, corresponding to 45% of the molecule, were identified. The protein is a serine protease, closely related to the nerve growth factor gamma subunit. It is suggested that the epidermal growth-factor-binding protein, like other serine protease, is synthesized as a single polypeptide chain which undergoes limited endoproteolysis. The isolated material also contained minor amounts of a second serine protease. This protease is closely related to the epidermal growth-factor-binding protein, differing from it in 7 out of the 45 amino acid positions available for comparison. The latter protease may be identical to the previously described protease A.

Antibodies to RNA from autoimmune NZB/NZW mice recognize a similar antigenic determinant and show a large idiotypic diversity

We have identified two RNA-specific hybridoma autoantibodies in fusions of spleen cells from unimmunized NZB/NZW female mice with BALB/c myeloma cells. The two fusion experiments were carried out 2 years apart with different myeloma partners. Specificity analyses showed that the two monoclonal antibodies and the total RNA-binding IgG in NZB/NZW serum recognize a G,C-rich sequence of ribonucleotides. The isolated heavy and light chains of the two antibodies and their papain Fab fragments could be distinguished by NaDodSO4/polyacrylamide gel electrophoresis. Rabbit anti-idiotypic antibodies prepared against the two monoclonal proteins showed unique specificities for the antigen-binding sites of their cognate auto-antibodies. Moreover, the anti-idiotypic antisera had little effect on the RNA-binding capacity of the total IgG from NZB/NZW serum. These results suggest that a wide range of different idiotypes is involved in the autoimmune response to a similar antigenic determinant.

Mechanism of enteroviral inactivation by ozone

The mechanism of enteroviral inactivation by ozone was investigated with poliovirus 1 (Mahoney) as the model virus. Ozone was observed to alter two of the four polypeptide chains present in the viral protein coat of poliovirus 1. However, the alteration of the protein coat did not significantly impair virus adsorption or alter the integrity of the virus particle. Damage to the viral RNA after exposure to ozone was demonstrated by velocity sedimentation analysis. It was concluded that the damage to the viral nucleic acid is the major cause of poliovirus 1 inactivation by ozone.

Structural polypeptides of the enteropathogenic bovine coronavirus strain LY-138

The bovine coronavirus strain LY-138 was purified by differential as well as velocity and isopycnic centrifugation in sucrose or CsCl gradients. The substrate for purification was contents of the small intestine of experimentally inoculated calves. This strain is highly enteropathogenic, but it could not yet be propagated in cultured cells. Intact virions had a density of 1.245 g/cm3 in CsCl and 1.185 g/cm3 in sucrose. A spherical core-like structure with an average diameter of 82 nm remaining after treatment with chloroform had a density of 1.299 g/cm3 in CsCl and 1.201 g/cm3 in sucrose. Seven distinct bands of polypeptides and 4 shoulders were detected after electrophoresis of SDS-solubilized virions in polyacrylamide gels. The approximate molecular weights ranged from 110,000 to 36,000. Four of the bands gave a PAS positive reaction. These 4 glycoproteins and an additional protein with an approximate molecular weight of 70,000 were removed by chloroform treatment. The remaining core-like structure contained the 2 polypeptides VP3 and VP7.

Purification and biophysical properties of human coronavirus 229E

Coronavirus 229E was grown to high titers in diploid fibroblast cells under medium containing twice the normal concentrations of amino acids and vitamins. Growth curves showed maximum virus production at multiplicities of infection of 0.1 and 1; maximum titers of intracellular virus occurred at 22–24 hr and of extracellular virus at 26 hr postadsorption. Tube infectivity titers ranged from 109.0–109.5 TCID50/ml and plaque titers from 1010.2–1010.9 y PFU/ml at the time of peak virus production, when no cytopathology was evident. Virus titer dropped rapidly between 26 and 56 hr, coincident with increasing cytopathology. A single precipitin band was observed in immunodiffusion and immunoelectrophoresis between concentrated virus preparations and antiserum to purified 229E. Neuraminidase and hemagglutinin assays were negative. Virus was purified by two procedures: adsorption to and elution from human “0” erythrocytes and CaHPO4 gel followed by equilibrium sucrose gradient centrifugation, and PEG precipitation followed by equilibrium glycerol/tartrate gradients and rate zonal sucrose or glycerol/tartrate gradients. Final lots of purified virus containing <0.02% of the crude tissue culture proteins had absorption maxima at 256 nm and minima at 241.2 nm and a mean extinction coefficient of E 1cm1% = 54.3 at 256 nm. The fully corrected sedimentation coefficient for the intact virion was S 20,v0 = 381 S. PAGE by different techniques revealed seven polypeptides of mean apparent molecular weights between 16,900 and 196,100. Six contained carbohydrate and one contained lipid. Electropherograms of 3H- and 14C-labeled virus were identical to those of stained gels. Two glycoproteins constituting 25% of the virion protein were identified by bromelin digestion as the spike proteins. The density in sucrose and in potassium tartrate was 1.18 g/ml for the virion and 1.15 g/ml for the “despiked” particle.

Purification and properties of a glycoprotein acid phosphatase from Candida albicans

An acid phosphomonoesterase was purified 87-fold with a 4% recovery from disintegrated cells of Candida albicans by four stages of column chromatography. The purified enzyme was homogeneous by ultracentrifugal, electrophoretic, and immunological analyses. The fully corrected sedimentation coefficient, s(20,w), was calculated to be 5.51s. Molecular weight estimated from ultracentrifugal data was 124.3 x 10(3), from gel chromatography was 115 x 10(3), and from acrylamide gel electrophoretic data was 131 x 10(3). Buoyant density in sucrose was 1.15 g/cm(3). The enzyme was a mannoprotein with a hexose to protein ratio of 7: 1. The Michaelis constant of the enzyme was 3.3 x 10(-4) M for p-nitrophenyl phosphate as substrate, and the pH optimum was 4.5. The enzyme was competitively inhibited by inorganic phosphate (K(i) = 10(-4) M) and by arsenate (K(i) = 0.5 x 10(-4) M). A wide range of inorganic cations and anions did not affect enzyme activity, but Hg(2+), Cd(2+), and Cu(2+) were inhibitory. F(-) was also inhibitory at low concentrations, but the effect was reversed at higher concentrations. Phosphatase activity was completely destroyed by exposure of the enzyme to 70 C for 12 min, but was destroyed only slowly by proteolytic hydrolysis. The purified glycoprotein enzyme gave a line of identity with the "b" antigen of crude C. albicans homogenates in immunodiffusion and immunoelectrophoresis tests with sera from rabbits inoculated with intact C. albicans cells and from humans with proven candidiasis. Preliminary evidence suggests that the mannan and not the protein portion of the enzyme molecule is responsible for this antigenicity.

Protein composition of coronavirus OC 43

A human coronavirus, strain OC 43, was propagated in suckling mouse brain and purified 5000-fold with, a 90% yield. Purity of the virus was confirmed by electrophoretic, ultracentrifugal, and electron microscopic procedures. Immunodiffusion and immunoelectrophoresis tests revealed one precipitin line with normal mouse brain, three with purified virus, and four with crude virus when tested against anti-pure virus or anti-crude virus animal serums. The association of a host cell antigen with the virion was confirmed by standard HI and CF tests. Polyacrylamide gel electrophoresis of solubilized purified virus revealed a minimum of six polypeptides with apparent molecular weights of 191,000 (No. 1), 104,000 (No. 2), 60,000 (No. 3), 47,000 (No. 4), 30,000 (No. 5), and 15,000 daltons (No. 6). A seventh band was occasionally found in the 165,000-dalton region of the gels. Four polypeptides contained carbohydrate and one contained lipid. Polypeptide No. 5 comprised 26% of the total viral protein and glycopolypeptide No. 3 comprised 23%. Three other components accounted for most of the remaining protein: polypeptide No. 4 (16%), glycopolypeptide No. 6 (14%), and glycolipopolypeptide No. 1 (13%). Glycopolypeptide No. 2 was 8% of the total protein. Bromelin digestion of the viral projections (spikes) removed glycopolypeptides No. 2 and No. 6. Association of the remaining polypeptides with structural components of the virion is only tentatively postulated. The buoyant density in potassium tartrate of the bromelin-treated virus was 1.15 g/cm³ and of the intact OC 43 virion was 1.18 g/cm³. By analytical ultracentrifugation the corrected sedimentation coefficient (s⁰_20w) of the OC 43 virion was determined to be 390 ± 16 S, and the apparent molecular weight (MW_a) was calculated to be 112 ± 5 × 10⁶ daltons.