Discrimination between closed and open forms of lipases using electrophoretic techniques

The enhanced catalytic activity of lipases is often associated with structural changes. The three-dimensional (3D) structures showed that the covalently inhibited lipases exist under their open conformations, in contrast to their native closed forms. We studied the inhibition of various lipases--human and dog gastric lipases, human pancreatic lipase, and Humicola lanuginosa lipase--by the octyl-undecyl phosphonate inhibitor, and we measured the subsequent modifications of their respective electrophoretic mobility. Furthermore, the experimental values of the isoelectric points found for the native (closed) and inhibited (open) lipases are in agreement with theoretical calculations based on the electrostatic potential. We concluded that there is a significant difference in the isoelectric points between the closed (native) and open (inhibited) conformations of the four lipases investigated. Thus, analysis of the electrophoretic pattern is proposed as an easy experimental tool to differentiate between a closed and an open form of a given lipase.     

Examination of corneal proteoglycans and glycosaminoglycans by rotary shadowing and electron microscopy

Proteoglycans (PGs) from cornea and their relevant glycosaminoglycan (GAG) chains, dermatan sulphate (DS) and keratin sulphate (KS), were examined by electron microscopy following rotary shadowing, and compared with hyaluronan (HA), chondroitin sulphate (CS), alginate, heparin, heparan sulphate (HS) and methyl cellulose. Corneal DS PG had the tadpole shape previously seen in scleral DS FG, and the images from corneal KS PG could be interpreted similarly, although the GAG (KS) chains were very much fainter than those of DS PG GAG. Isolated GAG (KS, DS, CS, HA, etc.) examined in the same way showed images that decreased very significantly in clarity and contrast, in the sequence HA greater than DS greater than CS greater than KS. The presence of secondary and tertiary structures in the GAGs may be at least partly responsible for these variations. HA appeared to be double stranded, and DS frequently self-aggregated, KS and HS showed tendencies to coil into globular shapes. It is concluded that it is unsafe to assume the absence of GAGs, based on these techniques, and quantitative measurements of length may be subject to error. The results on corneal DS PG confirm and extend the hypothesis that PGs specifically associated with collagen fibrils are tadpole shaped.     

Dermatan sulphate proteoglycans from sclera examined by rotary shadowing and electron microscopy.

Two dermatan sulphate-containing proteoglycans from bovine sclera were examined by rotary shadowing and electron microscopy, and the results were compared with previous biochemical findings. Both the large iduronate-poor proteoglycan (PGI) and the small iduronate-rich proteoglycan (PGII) possessed a globular proteinaceous region. Whereas PGI had a branched extension from the globular region, with five to eight side chains attached to it, PGII had only a single tail, which was of glycosaminoglycuronan. PGII aggregated via globular-region interactions, which were much diminished by reduction and alkylation. PGI aggregated via side chains and globular-region interactions. Although a few PGI aggregates were large, and similar to the hyaluronan-cartilage proteoglycan aggregates [Weidemann, Paulsson, Timpl, Engel & Heinegård (1984) Biochem. J. 224, 331-333], hyaluronan did not cause enhanced aggregation. PGII is very similar in shape to the small cartilage chondroitin sulphate proteoglycan, whereas PGI somewhat resembles the large cartilage chondroitin sulphate proteoglycan, although with many fewer glycosaminoglycan side chains, and probably only one globular region as opposed to two in the cartilage proteoglycan.     

Domain rotations between open, closed and bullet-shaped forms of the thermosome, an archaeal chaperonin

Three conformations of the thermosome, an archaeal group II chaperonin, have been determined by cryo-electron microscopy (EM). We describe an open form of the double-ring oligomer, a closed form and a bullet-shaped form with one ring open and the other closed. Domain movements have been deduced by docking atomic coordinates into the EM maps. The subunit apical domains, bearing the putative substrate binding sites, rotate about 30 degrees upwards and twist in the plane of the ring from the closed to the open conformation. The closed rings have their nucleotide binding pockets closed by the intermediate domains, but in the open rings, the pocket is accessible.     

Trinodular structure of fibrinogen. Confirmation by both shadowing and negative stain electron microscopy

Fibrinogen molecules sprayed on mica, dried in vacuo and shadowed with platinum appear as trinodular rods. We describe here the flotation technique of negative staining by which we were able to visualize individual fibrinogen molecules. The fibrinogen molecules in our negatively stained preparations have a trinodular structure identical to that of shadowed molecules. We believe that the 20 nm diameter globules seen in previous negative staining studies are aggregates of these molecules. This is the first study in which both shadowed and negatively stained preparations of fibrinogen support a single, consistent model for the structure of fibrinogen. The molecules in our preparation are 45 nm long (±2.5 nm, our overall estimate of accuracy), the two outer nodules are 6 to 7 nm in diameter and the middle nodule is 4 to 5 nm in diameter.     

Metal ions stabilize a dimeric molten globule state between the open and closed forms of malic enzyme

Malic enzyme is a tetrameric protein with double dimer quaternary structure. In 3-5 M urea, the pigeon cytosolic NADP⁺-dependent malic enzyme unfolded and aggregated into various forms with dimers as the basic unit. Under the same denaturing conditions but in the presence of 4 mM Mn²⁺, the enzyme existed exclusively as a molten globule dimer in solution. Similar to pigeon enzyme (Chang, G. G., T. M. Huang, and T. C. Chang. 1988. Biochem. J. 254:123-130), the human mitochondrial NAD⁺-dependent malic enzyme also underwent a reversible tetramer-dimer-monomer quaternary structural change in an acidic pH environment, which resulted in a molten globule state that is also prone to aggregate. The aggregation of pigeon enzyme was attributable to Trp-572 side chain. Mutation of Trp-572 to Phe, His, Ile, Ser, or Ala abolished the protective effect of the metal ions. The cytosolic malic enzyme was completely digested within 2 h by trypsin. In the presence of Mn²⁺, a specific cutting site in the Lys-352-Gly-Arg-354 region was able to generate a unique polypeptide with M_r of 37 kDa, and this polypeptide was resistant to further digestion. These results indicate that, during the catalytic process of malic enzyme, binding metal ion induces a conformational change within the enzyme from the open form to an intermediate form, which upon binding of L-malate, transforms further into a catalytically competent closed form.     

One channel: open and closed

Structural information about the prokaryotic KirBac3.1 inward rectifier family K(+) channel from Magnetospirillum magnetotacticum is reported. These results from two-dimensional electron cryomicroscopy (EM) shed light on the gating mechanism of members of the Kir channel family.     

A rapid method to visualize human mitochondrial DNA replication through rotary shadowing and transmission electron microscopy

We report a rapid experimental procedure based on high-density in vivo psoralen inter-strand DNA cross-linking coupled to spreading of naked purified DNA, positive staining, low-angle rotary shadowing, and transmission electron microscopy (TEM) that allows quick visualization of the dynamic of heavy strand (HS) and light strand (LS) human mitochondrial DNA replication. Replication maps built on linearized mitochondrial genomes and optimized rotary shadowing conditions enable clear visualization of the progression of the mitochondrial DNA synthesis and visualization of replication intermediates carrying long single-strand DNA stretches. One variant of this technique, called denaturing spreading, allowed the inspection of the fine chromatin structure of the mitochondrial genome and was applied to visualize the in vivo three-strand DNA structure of the human mitochondrial D-loop intermediate with unprecedented clarity.     

Structural study of modified fibrinogen microcrystals by electron microscopy

The same molecular shape of proteolytically modified fibrinogen has been identified in two different crystalline forms: orthorhombic P2₁2₁2 with a = 44.7(± 1.7) nm, b = 11.8(± 1.0) nm, c = 3.8 nm and monoclinic P2₁ with a = 17.7(± 0.6) nm, b = 16.2(± 1.0) nm, c = 4.8 nm and β = 95 °. The shape of the molecule is more detailed than has been reported. It has the commonly accepted elongated form 44.5(± 1.5) nm long with a 2-fold axis perpendicular to the major axis of the molecule. Each end domain shows a distinctive substructure and has an asymmetry similar to that reported by Williams (1981) and Mosesson et al. (1981) from single molecule observations. The ends are flattened, having overall dimensions of approximately 12 nm × 9 nm × 4 nm. The major difference between this model and previous models is the absence of a central nodule. There are, however, two small additional protein-dense regions at 5.0 nm from the centre of the rod connecting the two ends. A rough estimate of the relative heights of the different parts of the molecule was obtained using the two different projections of the molecule obtained from the two different crystalline forms. The molecule appears to be slightly bent at the centre, as predicted by Doolittle (1977).     

Structural polymorphism of oligomeric adiponectin visualized by electron microscopy

Adiponectin, a macromolecular complex similar to the members of the C1q and other collagenous homologues, elicits diverse biological functions, including anti-diabetes, anti-atherosclerosis, anti-inflammation and anti-tumor activities, which have been directly linked to the high molecular weight (HMW) oligomeric structures formed by multiples of adiponectin trimers. Here, we report the 3-D reconstructions of isolated full-length, recombinant murine C39A adiponectin trimer and hexamer of wild-type trimers (the major HMW form) determined by single-particle analysis of electron micrographs. The pleiomorphic ensemble of collagen-like stretches of the trimers leads to a dynamic structure of HMW that partition into two major classes, the fan-shaped (class I) and bouquet-shaped (class II). In both of these, while the N termini cluster into a compact ellipsoid-shaped (∼ 60 Å × 45 Å × 45 Å) volume, the collagenous domains assume a variety of arrangements. The domains are splayed by up to ∼ 90° in class I, can form a close-packed, up to ∼ 100 × 40 Å cylindrical assembly in class II, which can house about half of the 66 putative collagen-like sequence and the rest, tethered to the trimeric globular domains at the C terminus, are highly dynamic. As a result, the globular domains elaborate a variety of arrangements, covering an area of up to ∼ 4.9 × 10⁵ Ų and up to ∼ 320 Å apart, some of which were captured in reconstructions of class II. Our reconstructions suggest that the N-terminal structured domain, agreeing approximately with the expected volume for the octadecameric assembly of the terminal 27 amino acids, is crucial to the formation of the functionally active HMW. On the other hand, conformational flexibility of the trimers at the C terminus can allow the HMW to access and cluster disparate target ligands binding to the globular domains, which may be necessary to activate cellular signaling leading to the remarkable functional diversity of adiponectin.     

Morphological forms and viability of Campylobacter species studied by electron microscopy.

Electron microscopic studies of Campylobacter revealed that different morphological forms predominate at different parts of a colony. At the periphery, cells were almost all spirals, while in the center of the colony cells were mainly coccus shaped. Unusual ring-shaped cells, "donuts", were observed in the raised, peripheral region of the colony. Donut or ring forms have not previously been reported for Campylobacter organisms. Our data indicate that young or actively growing cells are mainly spiral shaped. Older cells undergo a degenerative change to coccoid forms. The donut shape appears to be an intermediate stage between spirals and cocci. Comparisons of plate counts of actively growing and inactive cells confirmed that coccoid cells are probably nonviable.     

Cooperative transition between open and closed conformations in potassium channels

Potassium (K+) ion channels switch between open and closed conformations. The nature of this important transition was revealed by comparing the X-ray crystal structures of the MthK channel from Methanobacterium thermoautotrophicum, obtained in its open conformation, and the KcsA channel from Streptomyces lividans, obtained in its closed conformation. We analyzed the dynamic characteristics and energetics of these homotetrameric structures in order to study the role of the intersubunit cooperativity in this transition. For this, elastic models and in silico alanine-scanning mutagenesis were used, respectively. Reassuringly, the calculations manifested motion from the open (closed) towards the closed (open) conformation. The calculations also revealed a network of dynamically and energetically coupled residues. Interestingly, the network suggests coupling between the selectivity filter and the gate, which are located at the two ends of the channel pore. Coupling between these two regions was not observed in calculations that were conducted with the monomer, which emphasizes the importance of the intersubunit interactions within the tetrameric structure for the cooperative gating behavior of the channel.     

Structural elements of Pseudomonas aeruginosa based on electron microscopy findings

The study of negatively contrasted preparations was made with the aim of of finding out the possibility of identifying Ps. aeruginosa by the number and location of flagella. 4,800 bacteria were studied by means of an electron microscopy, type JEM-100; of these, 2,443 bacterium had a single polar flagellum, 414 bacteria had 2 and 138 bacteria had 3 polar flagella, while 1,805 cells had no flagella. The presence of bipolar flagella and pili, as well as nonflagellate Ps. aeruginosa cultures, was revealed. The possibility of the existence of noncapsular and capsular forms in one and the same Ps. aeruginosa strain was shown. The use of these data in the systematics of Ps. aeruginosa is anticipated.     

Trapping open and closed forms of FitE—A group III periplasmic binding protein

Periplasmic binding proteins (PBPs) are essential components of bacterial transport systems, necessary for bacterial growth and survival. The two‐domain structures of PBPs are topologically classified into three groups based on the number of crossovers or hinges between the globular domains: group I PBPs have three connections, group II have two, and group III have only one. Although a large number of structures for group I or II PBPs are known, fewer group III PBPs have been structurally characterized. Group I and II PBPs exhibit significant domain motions during transition from the unbound to ligand‐bound form, however, no large conformational changes have been observed to date in group III PBPs. We have solved the crystal structure of a periplasmic binding protein FitE, part of an iron transport system, fit, recently identified in a clinical E. coli isolate. The structure, determined at 1.8 Å resolution, shows that FitE is a group III PBP containing a single α‐helix bridging the two domains. Among the individual FitE molecules present in two crystal forms we observed three different conformations (open, closed, intermediate). Our crystallographic and molecular dynamics results strongly support the notion that group III PBPs also adopt the same Venus flytrap mechanism as do groups I and II PBPs. Unlike other group III PBPs, FitE forms dimers both in solution and in the crystals. The putative siderophore binding pocket is lined with arginine residues, suggesting an anionic nature of the iron‐containing siderophore. Proteins 2009. © 2008 Wiley‐Liss, Inc.     

Structural analysis of EcoRI-DNA complexes as revealed by electron microscopy

Electron microscopy of negatively stained isolated restriction enzyme EcoRI revealed particle projections with triangular or square outlines, indicating that the enzyme, in its tetrameric state, is tetrahedron-like. The two dimers making up the tetramer appear to be arranged in two planes orthogonal to each other. Complexes formed by EcoRI with the plasmids pBR322 or pGW10 were investigated by electron microscopic spreading techniques. In the presence of Mg²⁺, EcoRI was bound to the DNA molecules to form pearl necklace-like aggregates. The number of bound EcoRI particles was much higher as the sum of EcoRI-and 5..AATT..3 sites (with exceptions, the 5..AATT..3 sites may function as one type of EcoRI^* sites) along the DNAs, indicating unspecific binding. In the absence of Mg²⁺, EcoRI was bound to the DNA only at the recognition site for EcoRI and the sites where the tetranucleotide sequence 5..AATT..3 was present. A direct correlation of the local concentrations of the bases A and T within the flanking sequences of the binding sites with the frequency of EcoRI to the DNA was observed. Dimers and tetramers of the enzyme was found to bind to the DNA. Tetramers occasionally exhibited two binding sites for DNA as indicated by the observation of DNA loops originating at the sites of bound tetrameric EcoRI particles.Abbreviations BAC Benzyldimethylalkylammoniumchloride - bp base pairs - Kb kilobases - SDS sodium dodecylsulfate Enzymes (EC 3.1.23.13) Restrictionendonuclease EcoRI - (EC 3.1.23.21) Restrictionendonuclease HindIII - (EC 3.1.23.37) Restrictionendonuclease SalGI Dedicated Professor H. G. Schlegel on occasion of this 60th birthday