Single-molecule anisotropy imaging

A novel method, single-molecule anisotropy imaging, has been employed to simultaneously study lateral and rotational diffusion of fluorescence-labeled lipids on supported phospholipid membranes. In a fluid membrane composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, in which the rotational diffusion time is on the order of the excited-state lifetime of the fluorophore rhodamine, a rotational diffusion constant, D(rot) = 7 x 10(7) rad(2)/s, was determined. The lateral diffusion constant, measured by direct analysis of single-molecule trajectories, was D(lat) = 3.5 x 10(-8) cm(2)/s. As predicted from the free-volume model for diffusion, the results exhibit a significantly enhanced mobility on the nanosecond time scale. For membranes of DPPC lipids in the L(beta) gel phase, the slow rotational mobility permitted the direct observation of the rotation of individual molecules characterized by D(rot) = 1.2 rad(2)/s. The latter data were evaluated by a mean square angular displacement analysis. The technique developed here should prove itself profitable for imaging of conformational motions of individual proteins on the time scale of milliseconds to seconds.     

Structural dynamic aspects of protein synthesis on ribosomes

Three types of conformational changes in the translating ribosome are considered: (1) intersubunit movement (ribosome unlocking) during translocation; (2) L7/L12 stalk mobility affected by elongation factors; (3) change of tRNA residue during its transition from the A-site to the P-site. Relevant experimental data are reviewed.     

Protein synthesis by single ribosomes

The ribosome is universally responsible for synthesizing proteins by translating the genetic code transcribed in mRNA into an amino acid sequence. Ribosomes use cellular accessory proteins, soluble transfer RNAs, and metabolic energy to accomplish the initiation, elongation, and termination of peptide synthesis. In translocating processively along the mRNA template during the elongation cycle, ribosomes act as supramolecular motors. Here we demonstrate that ribosomes adsorbed on a surface, as for mechanical or spectroscopic studies, are capable of polypeptide synthesis and that tethered particle analysis of fluorescent beads connected to ribosomes via polyuridylic acid can be used to estimate the rate of polyphenylalanine synthesis by individual ribosomes. This work opens the way for application of biophysical techniques, originally developed for the classical motor proteins, to the understanding of protein biosynthesis.     

Polypeptide synthesis catalyzed by p-hydroxymercuribezoate-modified ribosomes

The stimulation of poly(U)-directed polyphenylalanine synthesis produced by modification ofEscherichia coli ribosomes withp-hydroxymercuribenzoate, at low molar ratios of reagent to ribosomes, is due to an increase in the average chain length of polyphenylalanine synthesized, and not to the activation of inactive ribosomes. At a higher molar ratio ofp-hydroxymercuribenzoate to ribosomes, which produces no overall change in activity, approximately 50% of the active ribosomes present in the untreated preparation have been completely inactivated, and the remaining active ones, like the ribosomes of the stimulated preparation, synthesize polyphenylalanine at an increased rate as compared with the untreated ribosomes.Abbreviations pHMB p-hydroxymercuribenzoate - SucNBr N-bromosuccinimide     

Single-molecule live-cell imaging of clathrin-based endocytosis

Clathrin-coated vesicles carry traffic from the plasma membrane to endosomes. We report here the first real-time visualization of cargo sorting and endocytosis by clathrin-coated pits in living cells. We have visualized the formation of coats by monitoring the incorporation of fluorescently tagged clathrin or its adaptor AP-2 (adaptor protein 2), and have followed clathrin-mediated uptake of transferrin, single LDL (low-density lipoprotein) and single reovirus particles. The intensity of a cargo-loaded clathrin cluster grows steadily during its lifetime, and the time required to complete assembly is proportional to the size of the cargo particle. These results are consistent with a nucleation-growth mechanism and an approximately constant growth rate. There are no preferred nucleation sites. A proportion of the nucleation events appear to be abortive. Cargo incorporation occurs primarily or exclusively in a newly formed coated pit, and loading appears to commit that pit to finish assembly. Our data led to a model in which coated pits initiate randomly, but collapse with high likelihood unless stabilized, presumably by cargo capture.     

A comparative study of protein synthesis in vitro by skeletal muscle ribosomes from livestock

Skeletal muscle was dissected from the forelimbs of animals and stored at -80 degrees C. Protein synthesis activity was determined in cell-free systems. Incorporation of amino acids into protein was expressed per milligramme of ribosomal RNA, per gramme wet weight of skeletal muscle and per milligramme of DNA. Species related differences in activity were observed in skeletal muscle obtained from pig, horse, lamb, sheep, calf and young steer. Intraspecies differences were seen in cattle of different breeds. The protein composition of the muscle tissue showed quantitative differences between the species. Using biopsy specimens, the system could be used to monitor the protein nutrition status of animals and the production of animal proteins.     

Transient idling of posttermination ribosomes ready to reinitiate protein synthesis

The fate of ribosomes between termination and initiation during protein synthesis is very basic, yet poorly understood. Here we found that translational reinitiation of the alkaline phosphatase gene occurs in Escherichia coli from an internal methionine codon when the authentic translation is prematurely terminated at a nonsense codon that is within seven codons upstream of the reinitiation codon (which we refer to as "reinitiation window"). Changing the reading frame downstream of the stop codon did not abolish the reinitiation, while inactivating the upstream initiation codon abolished the reinitiation. Moreover, depletion of the ribosome recycling factor (RRF), which disassembles posttermination ribosomes in conjunction with elongation factor G, did not influence the observed reinitiation. These findings suggest that posttermination ribosomes can undergo a transient idling state ready to reinitiate protein synthesis even in the absence of the Shine-Dalgarno (SD) sequence within the reinitiation window by evading disengagement from the mRNA.     

The fate of membrane-bound ribosomes following the termination of protein synthesis

Contemporary models for protein translocation in the mammalian endoplasmic reticulum (ER) identify the termination of protein synthesis as the signal for ribosome release from the ER membrane. We have utilized morphometric and biochemical methods to assess directly the fate of membrane-bound ribosomes following the termination of protein synthesis. In these studies, tissue culture cells were treated with cycloheximide to inhibit elongation, with pactamycin to inhibit initiation, or with puromycin to induce premature chain termination, and ribosome-membrane interactions were subsequently analyzed. It was found that following the termination of protein synthesis, the majority of ribosomal particles remained membrane-associated. Analysis of the subunit structure of the membrane-bound ribosomal particles remaining after termination was conducted by negative stain electron microscopy and sucrose gradient sedimentation. By both methods of analysis, the termination of protein synthesis on membrane-bound ribosomes was accompanied by the release of small ribosomal subunits from the ER membrane; the majority of the large subunits remained membrane-bound. On the basis of these results, we propose that large ribosomal subunit release from the ER membrane is regulated independently of protein translocation.     

A soluble fraction requirement in the transfer reaction of protein synthesis by rice embryo ribosomes

The requirements for the transfer of (14)C-phenylalanine from yeast soluble ribonucleic acid to protein in vitro by rice (Oryza sativa L. var. Bluebonnet) ribosomes have been investigated. An absolute requirement for polyuridylic acid, 2-mercaptoethanol, guanosine triphosphate, magnesium, and potassium or ammonium ions and ribosomes has been demonstrated. Ribosomes washed in 0.5% sodium deoxycholate also required the presence of rice supernatant. The optimum concentration of magnesium ion for the reaction was approximately 7 mm, while 60 mm of either ammonium or potassium ion gave maximum transfer of phenylalanine in this heterologous system. The optimum concentration of guanosine triphosphate required varied with the presence or absence of the phosphoenolpyruvate-pyruvate kinase generating system. Without the system, the optimum concentration was 1.5 mm, but in its presence the optimum was approximately 0.1 mm.     

Dextran synthesis by immobilized dextran sucrase

Dextran sucrase has been produced by fermentation of Leuconostoc mesenteroides NRRL B-512, with and without continuous sucrose addition to improve enzyme production. The enzyme preparation has been concentrated from the fermentation broth by ultrafiltration and purified by gel permeation chromatography on Ultrogel. The specific activity of the dextran sucrase was greatly enhanced by calcium chloride addition to the purified enzyme. This enzyme preparation has been immobilized by covalent coupling onto an amino porous silica support (Spherosil) activated with glutaraldehyde. Immobilized dextran sucrase derivatives with an activity up to 830 dextran sucrase units per g. support could thus be obtained. The effect of the support specific area on coupling efficiency and reaction kinetics has been investigated, and the effect of intraparticular diffusion underlined. The molecular weight distribution of the dextran has been determined when varying several parameters.     

Cell-free synthesis of myosin by cardiac myofibrillar ribosomes

Human erythrocyte ghosts were treated with a bifunctional cross-linking reagent, dimethyl adipimidate dihydrochloride. On SDS-polyacrylamide electrophoresis of the cross-linked membrane proteins after solubilization, sialoglycoproteins and the proteins disappeared from the original band positions and appeared in a new band of aggregates.