Asymmetry of the GroEL-GroES complex under physiological conditions as revealed by small-angle x-ray scattering

Despite the well-known functional importance of GroEL-GroES complex formation during the chaperonin cycle, the stoichiometry of the complex has not been clarified. The complex can occur either as an asymmetric 1:1 GroEL-GroES complex or as a symmetric 1:2 GroEL-GroES complex, although it remains uncertain which type is predominant under physiological conditions. To resolve this question, we studied the structure of the GroEL-GroES complex under physiological conditions by small-angle x-ray scattering, which is a powerful technique to directly observe the structure of the protein complex in solution. We evaluated molecular structural parameters, the radius of gyration and the maximum dimension of the complex, from the x-ray scattering patterns under various nucleotide conditions (3 mM ADP, 3 mM ATPγS, and 3 mM ATP in 10 mM MgCl₂ and 100 mM KCl) at three different temperatures (10°C, 25°C, and 37°C). We then compared the experimentally observed scattering patterns with those calculated from the known x-ray crystallographic structures of the GroEL-GroES complex. The results clearly demonstrated that the asymmetric complex must be the major species stably present in solution under physiological conditions. On the other hand, in the presence of ATP (3 mM) and beryllium fluoride (10 mM NaF and 300 μM BeCl₂), we observed the formation of a stable symmetric complex, suggesting the existence of a transiently formed symmetric complex during the chaperonin cycle.     

Two-dimensional crystals of streptavidin on biotinylated lipid layers and their interactions with biotinylated macromolecules.

Streptavidin forms two-dimensional crystals when specifically bound to layers of biotinylated lipids at the air/water interface. The three-dimensional structure of streptavidin determined from the crystals by electron crystallography corresponds well with the structure determined by x-ray crystallography. Comparison of the electron and x-ray crystallographic structures reveals the occurrence of free biotin-binding sites on the surface of the two-dimensional crystals facing the aqueous solution. The free biotin-binding sites could be specifically labeled with biotinylated ferritin. The streptavidin/biotinylated lipid system may provide a general approach for the formation of two-dimensional crystals of biotinylated macromolecules.     

Purification and properties of malate dehydrogenase from the extreme thermophileBacillus caldolyticus

The enzyme malate dehydrogenase (EC 1.1.1.37) from an extreme thermophileB. Caldolyticus was purified to about 91% homogeneity. The molar mass of the enzyme was determined as 73 000 daltons and it is composed of two subunits, each with a molar mass of 37 000. Initial velocity studies with oxaloacetic acid and NADH as substrates at pH 8.1, over a range of temperatures, indicate that the enzyme operates via a sequential type mechanism. Van't Hoff plots of the kinetic parameters displayed sharp changes in slope at characteristic temperatures, whereas the Arrhenius plot exhibited no such breaks over the temperature interval investigated. The enzyme was found to be stable at 41°C and lower temperatures. At 51°C and 59°C an almost immediate 20% reduction in activity was obtained, but no further inactivation occurred during the 60 min of incubation. At 59°C the enzyme lost 50% of its initial activity in about 38 s. High concentration of NADH was observed to greatly stabilize the enzyme at that temperature.It is suggested that the slope changes in the Van't Hoff plots and the stability profies at 51°C and 59°C are representative of a temperature induced conformational change in the enzyme.Proceedings of the Fourth College Park Colloquium on Chemical Evolution:Limits of Life, University of Maryland, College Park, 18–20 October 1978.     

The Molecular Basis of Iron-induced Oligomerization of Frataxin and the Role of the Ferroxidation Reaction in Oligomerization

The role of the mitochondrial protein frataxin in iron storage and detoxification, iron delivery to iron-sulfur cluster biosynthesis, heme biosynthesis, and aconitase repair has been extensively studied during the last decade. However, still no general consensus exists on the details of the mechanism of frataxin function and oligomerization. Here, using small-angle x-ray scattering and x-ray crystallography, we describe the solution structure of the oligomers formed during the iron-dependent assembly of yeast (Yfh1) and Escherichia coli (CyaY) frataxin. At an iron-to-protein ratio of 2, the initially monomeric Yfh1 is converted to a trimeric form in solution. The trimer in turn serves as the assembly unit for higher order oligomers induced at higher iron-to-protein ratios. The x-ray crystallographic structure obtained from iron-soaked crystals demonstrates that iron binds at the trimer-trimer interaction sites, presumably contributing to oligomer stabilization. For the ferroxidation-deficient D79A/D82A variant of Yfh1, iron-dependent oligomerization may still take place, although >50% of the protein is found in the monomeric state at the highest iron-to-protein ratio used. This demonstrates that the ferroxidation reaction controls frataxin assembly and presumably the iron chaperone function of frataxin and its interactions with target proteins. For E. coli CyaY, the assembly unit of higher order oligomers is a tetramer, which could be an effect of the much shorter N-terminal region of this protein. The results show that understanding of the mechanistic features of frataxin function requires detailed knowledge of the interplay between the ferroxidation reaction, iron-induced oligomerization, and the structure of oligomers formed during assembly.     

Biochemical differentiation of plastids and other organelles in rye leaves with a high-temperature-induced deficiency of plastid ribosomes

Summary 1. In developing rye (Secale cereale L.) leaves the formation of plastidic ribosomes was selectively prevented in light as well as in darkness, when the seedlings were grown at an elevated temperature of 32° instead of 22° where normal development ocurred. Plastid ribosome deficient parts of lightgrown leaves were chlorotic at 32°. — 2. At both temperatures the leaves contained under all conditions (light or dark, on H₂O or nutrient solution) equal or very similar amounts of total amino nitrogen. In light, the contents of total protein and dry weight were lower at 32° than at 22°, especially when the plants were grown on nutrient solution. — 3. Mitochondrial marker enzymes had normal or even higher activities in 32°-grown leaves. Respiration rates were similar for segments of leaves grown on water in light either at 32° or at 22° but by 20–30% lower for 32°-grown plants when they had been raised in darkness or on nutrient solution. In contrast to 22°-grown tissue, respiration of 32°-grown leaf segments was rather insensitive to KCN. Comparative inhibitor studies indicated the presence of both the cyanide-sensitive and the cyanide-insensitive pathway of respiration in 32°-grown leaves. — 4. Leaf microbody marker enzymes were present in leaves grown at 32°. From chlorotic parts of 32°-light-grown leaves a typical microbody fraction was isolated on sucrose densitygradients. — 5. Leaves of seedlings grown at 32° contained only very low levels of ribulosediphosphate carboxylase activity and of fraction I protein. Photosynthetic ¹⁴CO₂-fixation of such leaves was only a few per cent of that observed in normal leaves, and no photosynthetic oxygen evolution was observed in chlorotic leaf segments. However, ten other soluble enzymes which are exclusively or partially localized in chloroplasts reached high activities under all conditions at 32° (Table 4). — 6. From chlorotic parts of 32°-light-grown leaves as well as from etiolated 32°-grown leaves a fraction of intact plastids was isolated and purified by sucrose gradient centrifugation which contained several soluble chloroplast enzymes. From the results we conclude that cytoplasmic protein synthesis must contribute a functional chloroplast envelope including the mechanism for the recognition and uptake of chloroplast proteins which are synthesized on cytoplasmic ribosomes.     

The ecology and electrophoretic analysis of the damselfly,Argia vivida hagen,living in a geothermal gradient

The ecology and electrophoretic properties of a damselfly, Argia vivida Hagen, inhabiting a geothermal gradient were studied. Monthly sampling of five sites revealed nymphal colonization along a 15–40°C thermal gradient; greatest densities occurred between 15–27°C. An electrophoretic analysis of proteins suggest that nymphs were adapted to a wide range of temperatures which was evidenced by differential activity of four enzyme systems (glucose-6-phosphate dehydrogenase, lactate dehydrogenase, leucine aminopeptidase, and tetrazolium oxidase). Evidence suggests the nymphs acclimated to different temperatures by altering the structure of important isozymes and expressed certain genetic features characteristic of individuals naturally found at a given temperature.Published with the approval of the Director of the University of Idaho Agriculture Experiment Station as Research Paper No. 78612.     

The crystal and solution structures of glyceraldehyde-3-phosphate dehydrogenase reveal different quaternary structures

The presence of an isoform of glyceraldehyde-3-phosphate dehydrogenase (kmGAPDH1p) associated with the cell wall of a flocculent strain of Kluyveromyces marxianus was the first report of a non-cytosolic localization of a glycolytic enzyme, but the mechanism by which the protein is transported to the cell surface is not known. To identify structural features that could account for the multiple localizations of the protein, the three-dimensional structure of kmGAPDH1p was determined by x-ray crystallography and small angle x-ray scattering. The x-ray crystallographic structure of kmGAPDH1p revealed a dimer, although all GAPDH homologs studied thus far have a tetrameric structure with 222 symmetry. Interestingly, the structure of kmGAPDH1p in solution revealed a tetramer with a 70 degrees tilt angle between the dimers. Moreover, the separation between the centers of the dimers composing the kmGAPDH1p tetramer diminished from 34 to 30 A upon NAD(+) binding, this latter value being similar to the observed in the crystallographic models of GAPDH homologs. The less compact structure of apo-kmGAPDH1p could already be the first image of the transition intermediate between the tetramer observed in solution and the dimeric form found in the crystal structure, which we postulate to exist in vivo because of the protein's multiple subcellular localizations in this yeast species.     

X-ray scattering studies of Methylophilus methylotrophus (sp. W3A1) electron-transferring flavoprotein. Evidence for multiple conformational states and an induced fit mechanism for assembly with trimethylamine dehydrogenase

Small angle x-ray solution scattering has been used to generate a low resolution, model-independent molecular envelope structure for electron-transferring flavoprotein (ETF) from Methylophilus methylotrophus (sp. W(3)A(1)). Analysis of both the oxidized and 1-electron-reduced (anionic flavin semiquinone) forms of the protein revealed that the solution structures of the protein are similar in both oxidation states. Comparison of the molecular envelope of ETF from the x-ray scattering data with previously determined structural models of the protein suggests that ETF samples a range of conformations in solution. These conformations correspond to a rotation of domain II with respect to domains I and III about two flexible "hinge" sequences that are unique to M. methylotrophus ETF. The x-ray scattering data are consistent with previous models concerning the interaction of M. methylotrophus ETF with its physiological redox partner, trimethylamine dehydrogenase. Our data reveal that an "induced fit" mechanism accounts for the assembly of the trimethylamine dehydrogenase-ETF electron transfer complex, consistent with spectroscopic and modeling studies of the assembly process.     

Effects of Macromolecular Crowding on the Structure of a Protein Complex: A Small-Angle Scattering Study of Superoxide Dismutase

Macromolecular crowding can alter the structure and function of biological macromolecules. We used small-angle scattering to measure the effects of macromolecular crowding on the size of a protein complex, SOD (superoxide dismutase). Crowding was induced using 400 MW PEG (polyethylene glycol),TEG (triethylene glycol), α-MG (methyl-α-glucoside), and TMAO (trimethylamine n-oxide). Parallel small-angle neutron scattering and small-angle x-ray scattering allowed us to unambiguously attribute apparent changes in radius of gyration to changes in the structure of SOD. For a 40% PEG solution, we find that the volume of SOD was reduced by 9%. Considering the osmotic pressure due to PEG, this deformation corresponds to a highly compressible structure. Small-angle x-ray scattering done in the presence of TEG suggests that for further deformation—beyond a 9% decrease in volume—the resistance to deformation may increase dramatically.     

3 Nsec molecular dynamics simulation of the protein ubiquitin and comparison with X-ray crystal and solution NMR structures.

Mainly due to computational limitations, past protein molecular dynamics simulations have rarely been extended to 300 psec; we are not aware of any published results beyond 350 psec. The present work compares a 3000 psec simulation of the protein ubiquitin with the available x-ray crystallographic and solution NMR structures. Aside from experimental structure availability, ubiquitin was studied because of its relatively small size (76 amino acids) and lack of disulfide bridges. An implicit solvent model was used except for explicit treatment of waters of crystallization. We found that the simulated average structure retains most of the character of the starting x-ray crystal structure. In two highly surface accessible regions, the simulation was not in agreement with the x-ray structure. In addition, there are six backbone-backbone hydrogen bonds that are in conflict between the solution NMR and x-ray crystallographic structures; two are bonds that the NMR does not locate, and four are ones that the two methods disagree upon the donor. Concerning these six backbone-backbone hydrogen bonds, the present simulation agrees with the solution NMR structure in five out-of-the six cases, in that if a hydrogen bond is present in the x-ray structure and not in the NMR structure, the bond breaks within 700 psec. Of the two hydrogen bonds that are found in the NMR structure and not in the x-ray structure, one forms at 1400 psec and the other forms rarely. The present results suggest that relatively long molecular dynamics simulations, that use protein x-ray crystal coordinates for the starting structure and a computationally efficient solvent representation, may be used to gain an understanding of conformational and dynamic differences between the solid-crystal and dilute-solution states.     

Interactions of hydrophobin proteins in solution studied by small-angle X-ray scattering

Hydrophobins are a group of very surface-active, fungal proteins known to self-assemble on various hydrophobic/hydrophilic interfaces. The self-assembled films coat fungal structures and mediate their attachment to surfaces. Hydrophobins are also soluble in water. Here, the association of hydrophobins HFBI and HFBII from Trichoderma reesei in aqueous solution was studied using small-angle x-ray scattering. Both HFBI and HFBII exist mainly as tetramers in solution in the concentration range 0.5-10 mg/ml. The assemblies of HFBII dissociate more easily than those of HFBI, which can tolerate changes of pH from 3 to 9 and temperatures in the range 5°C-60°C. The self-association of HFBI and HFBII is mainly driven by the hydrophobic effect, and addition of salts along the Hofmeister series promotes the formation of larger assemblies, whereas ethanol breaks the tetramers into monomers. The possibility that the oligomers in solution form the building blocks of the self-assembled film at the air/water interface is discussed.     

Rapid X-ray Photoreduction of Dimetal-Oxygen Cofactors in Ribonucleotide Reductase

Prototypic dinuclear metal cofactors with varying metallation constitute a class of O₂-activating catalysts in numerous enzymes such as ribonucleotide reductase. Reliable structures are required to unravel the reaction mechanisms. However, protein crystallography data may be compromised by x-ray photoreduction (XRP). We studied XPR of Fe(III)Fe(III) and Mn(III)Fe(III) sites in the R2 subunit of Chlamydia trachomatis ribonucleotide reductase using x-ray absorption spectroscopy. Rapid and biphasic x-ray photoreduction kinetics at 20 and 80 K for both cofactor types suggested sequential formation of (III,II) and (II,II) species and similar redox potentials of iron and manganese sites. Comparing with typical x-ray doses in crystallography implies that (II,II) states are reached in <1 s in such studies. First-sphere metal coordination and metal-metal distances differed after chemical reduction at room temperature and after XPR at cryogenic temperatures, as corroborated by model structures from density functional theory calculations. The inter-metal distances in the XPR-induced (II,II) states, however, are similar to R2 crystal structures. Therefore, crystal data of initially oxidized R2-type proteins mostly contain photoreduced (II,II) cofactors, which deviate from the native structures functional in O₂ activation, explaining observed variable metal ligation motifs. This situation may be remedied by novel femtosecond free electron-laser protein crystallography techniques.     

Importance of actin cytoskeleton behaviour during preservation of carrot cell suspensions in liquid nitrogen

Summary Conventional methods for preservation of suspended, highly vacuolated, plant cells in liquid nitrogen (LN) usually involve equilibration in molar concentrations of cryoprotective additives, followed by slow cooling to an intermediate subzero temperature (–40 °C), before quenching in LN. Cryomicroscopy was used to monitor the reversible protoplasmic shrinkage of cryoprotected carrot cells, caused by freeze-induced dehydration. Behaviour of actin filaments was analyzed by fluorescence microscopy after labelling with rhodarnine-conjugated phalloidin, in relation to the type of pretreatment and to survival and regrowth ability after preservation at — 196 °C. Loading with dimethylsulphoxide (Me₂SO, 5%) resulted in high survival rates (70%) and regrowth. After thawing, the actin filament (MF) abundance was reduced, but the structure and distribution of the remaining MFs seemed undisturbed. Higher Me₂SO concentrations caused further reduction of MFs, which appeared fragmented after thawing. MFs were maintained by pretreatment with 0.5 M sorbitol alone but carrot cells did not survive at — 196 °C. The same pretreatment, followed by incubation with cytochalasin D (10 M), which greatly reduced MFs, enabled plasmolyzed carrot cells to survive preservation in liquid nitrogen. Thus, after both Me₂SO and sorbitol plus cytochalasin D pretreatments, partial disruption of actin filaments seemed to accompany (Me₂SO) or promote (sorbitol plus cytochalasin D) freezing tolerance at extremely low temperatures.Abbreviations CD cytochalasin D - FDA fluorescein diacetate - LN liquid nitrogen - MF actin filament - Me₂SO dimethylsulphoxide     

Use of a minifluviarium to study responses of young Sarotherodon niloticus (L) to hydrogen-ion concentrations and temperature

The reactions of O+ Sarotherodon niloticus (L) to varying pH and temperature were studied in the laboratory using a minifluviarium. S. niloticus was found to tolerate pH — values as low as 5.0 without any marked effect. At values between 3.0 and 5.0 the fish lost orientation and showed signs of hyperactivity. Below 3.0, they died shortly after removal from the test — yard.Thermal behavior was tested for values ranging between 30° and 43 °C. Young S. niloticus were observed to prefer temperatures between 30° and 36 °C and avoid higher temperatures. Temperatures above 41 °C were lethal. Larger fish (6.0 to 8.0 cm.) showed more tolerance to increasing temperatures, however, when pH was considered, there was no significant difference between the sizes studied (P > 0.05).     

RNA metabolism during puff induction in Drosophila melanogaster

RNA metabolism of the salivary glands of Drosophila melanogaster was studied for possible changes coinciding with the induction of new puffs by heat treatment.—The rate of ³H-uridine incorporation into RNA is identical at 37° C and at 24° C. It declines with time of incubation, possibly indicating the existence of a class of rapidly turning over RNA.—RNA extracted from glands pulselabelled at either 24° or at 37° C displays similar profiles if subjected to gel electrophoresis. Processing of the 38s ribosomal RNA precursor comes to a halt at 37° between 30 and 60 minutes of incubation, i.e., some time after puff induction is completed. At both temperatures newly synthesized pre-ribosomal RNA accumulates with time of incubation more rapidly than heterodisperse RNA, again suggesting that some heterodisperse RNA is of relatively short life span. After short pulses the portion of heterodisperse RNA is larger in glands kept at 37° C than in glands kept at 24° C. With increasing time this difference disappears.—Some of the pulse-labelled, high molecular weight heterodisperse RNA is rapidly degraded, if RNA synthesis is blocked by actinomycin D. If the chase is performed at 24° C, about 30% of the newly synthesized RNA is degraded within about 15 minutes. At 37° C the beginning of degradation appears delayed for about 30 minutes; subsequently the same percentage of RNA is degraded as at 24° C.—The possibility is considered that the local RNA accumulation visualized by the heat-induced puffs may have resulted from a change in RNA degradation rather than from a local stimulation of RNA synthesis.     

Microstructure and aggregation behavior of methylcelluloses prepared in NaOH/urea aqueous solutions

Three water-soluble methylcelluloses (MCs) were prepared through homogeneous reaction in NaOH/urea aqueous solution, using dimethyl sulfate as a methylation reagent. The microstructure of the MC samples was characterized by IR, GC/MS, NMR, while dilute solution properties were measured by SEC–LLS, DLS and viscometer. The total degrees of substitution (DS) of the MC samples were 1.09, 1.42 and 1.56, respectively. However, we found that the relative DS value varies with the position of the hydroxyl group, i.e., C-2 > C-3 ≈ C-6, indicating the difference of reaction activity of different hydroxyl groups. In aqueous solution, MC has a trendency to form aggregates and hard to form actual solution, even at low concentration and low temperature, which was confirmed by the SEC–LLS and DLS result that isolated MC chains and large aggregates coexisted in the dilute aqueous solution. MC aqueous solutions showed two-stage temperature dependence of hydrodynamic radius. In the first stage, i.e., the temperature ranges from 20 to 65 °C, the hydrodynamic radius of MC displayed bimodal distribution, corresponding to the single chains and large aggregates. While in the second stage, i.e., the temperature higher than 70 °C, only large aggregates appeared. The results also proved that the microstructure of MC had a great influence on its physical properties.     

Hydration and Hydrodynamic Interactions of Lysozyme: Effects of Chaotropic versus Kosmotropic Ions

Using static and dynamic light scattering we have investigated the effects of either strongly chaotropic, nearly neutral or strongly kosmotropic salt ions on the hydration shell and the mutual hydrodynamic interactions of the protein lysozyme under conditions supportive of protein crystallization. After accounting for the effects of protein interaction and for changes in solution viscosity on protein diffusivity, protein hydrodynamic radii were determined with ±0.25 Å resolution. No changes to the extent of lysozyme hydration were discernible for all salt-types, at any salt concentration and for temperatures between 15-40°C. Combining static with dynamic light scattering, we also investigated salt-induced changes to the hydrodynamic protein interactions. With increased salt concentration, hydrodynamic interactions changed from attractive to repulsive, i.e., in exact opposition to salt-induced changes in direct protein interactions. This anti-correlation was independent of solution temperature or salt identity. Although salt-specific effects on direct protein interactions were prominent, neither protein hydration nor solvent-mediated hydrodynamic interactions displayed any obvious salt-specific effects. We infer that the protein hydration shell is more resistant than bulk water to changes in its local structure by either chaotropic or kosmotropic ions.     

Dotted chromosomes produced in sodium phosphate solution supersaturated with NaHCO3

Dotted chromosomes were consistently produced in both BrdU and non-BrdU substituted Chinese hamster cells after treatment with 1.0 M Na-phosphate solution, adjusted to pH 9.0 with a supersaturating amount of NaHCO₃, and at a temperature of 80–95° C. — A series of changes in chromosome morphology was produced as the temperature of the solution was progressively increased. In BrdU-treated cells, G-banding and differentially stained sister chromatids were sequentially produced prior to the appearance of dots. In non-BrdU treated cells, only G-banding was produced before dot formation. In general, the patterns of dots correspond to the G-banding patterns. — Chromatids, with uni- or bifilarly BrdU substituted DNA or with normal DNA, required differential temperatures for the production of dots. Since the temperature required for dot formation was always slightly higher than that required for producing differentially stained chromatids, this phenomenon can be used as an important indicator for determining the optimal temperature required for revealing differentially stained chromatids.     

Factors affecting oviposition and fecundity in the grain miteAcarus siro L. (Acarina:Acaridae), especially temperature and relative humidity

Oviposition and fecundity in the grain miteAcarus siro were studied at 5–30°C and 62.5–90% RH. At and above 20°C, 80% RH, mating and oviposition occurred soon after emergence, but at lower temperatures and humidities egg laying was progressively delayed from one to several days. Females needed to mate repeatedly in order to achieve maximum egg production, optimum conditions for which were 15°C, 90% RH, where total output per female averaged 435 with a maximum of 858. Oviposition rates were highest at higher temperatures, the mean daily rate at 20 and 25°C, 90% RH, rising to maximum levels of 28/29 eggs per female per day on day six.Oviposition followed clearly defined patterns, favourable conditions producing rapid increases in the mean daily oviposition rate to high peak levels reached at an early stage in the oviposition period. Less favourable conditions resulted in reduced outputs and lower, more uniform rates of egg laying. The mean oviposition period, varying with humidity, fell from 72–122 days at 5°C to 9–13 days at 30°C and the mean incubation period from 42–70 days at 5°C to 3–4 days at 30°C. Egg viability increased with increasing humidity but was little affected by temperature and unaffected by age of the female at time of oviposition.Males tended to live longer than females at most conditions; longevity—depending on humidity—averaging 13–15 days at 30°C and 129–175 days at 5°C. Adult life for females averaged 12–19 days at 30°C and 88–169 days at 5°C. An index of suitability, calculated from egg number, viability and duration of the egg stage and oviposition period, indicated that the most favourable conditions for oviposition and hatching were 20–25°C and 80–90% RH.