How common is the funnel‐like energy landscape in protein‐protein interactions?

The goal of this study is to verify the concept of the funnel-like intermolecular energy landscape in protein-protein interactions by use of a series of computational experiments. Our preliminary analysis revealed the existence of the funnel in many protein-protein interactions. However, because of the uncertainties in the modeling of these interactions and the ambiguity of the analysis procedures, the detection of the funnels requires detailed quantitative approaches to the energy landscape analysis. A number of such approaches are presented in this study. We show that the funnel detection problem is equivalent to a problem of distinguishing between distributions of low-energy intermolecular matches in the funnel and in the low-frequency landscape fluctuations. If the fluctuations are random, the decision about whether the minimum is the funnel is equivalent to determining whether this minimum is significantly different from a would-be random one. A database of 475 nonredundant cocrystallized protein-protein complexes was used to re-dock the proteins by use of smoothed potentials. To detect the funnel, we developed a set of sophisticated models of random matches. The funnel was considered detected if the binding area was more populated by the low-energy docking predictions than by the matches generated in the random models. The number of funnels detected by use of different random models varied significantly. However, the results confirmed that the funnel may be the general feature in protein-protein association.     

The Baermann technique for estimating Protostrongylus infection in bighorn sheep: effect of laboratory procedures

The modified Baermann funnel technique was evaluated to determine the effects of time of baermannization, fecal preparation, type and size of funnel, and type of filter on the number of first stage larvae of Protostrongylus spp. recovered from feces of Rocky Mountain bighorn sheep (Ovis canadensis). More larvae were recovered when fecal pellets were baermannized for 24 hr compared to 8 hr, and when feces were crushed than when left intact. Use of small funnels resulted in the recovery of more larvae per gram of feces than larger funnels, and glass funnels more than plastic ones. There was no difference in recovery of larvae between cheesecloth filters and cellulose filters.     

Structure and function of ciliated peritoneal funnels in the toad kidney (Bufo marinus)

Scanning electron microscopy revealed 600-800 ciliated peritoneal funnels opening onto the ventral surface of each kidney in Bufo marinus. The size and configuration of funnel apertures vary greatly, but individuals course beneath the kidney surface before opening into peritubular blood vessels. Injections of India ink into the peritoneal cavity demonstrate that cilia lining the peritoneal funnels create a current carrying peritoneal fluid into the renal vasculature. Clearance of fluid by the funnels was dependent on pressure in the peritubular vessels, and was increased by arginine vasotocin. Ciliated peritoneal funnels may provide an important route for return of lymphatic fluid from the peritoneal cavity to the vasculature.     

Folding funnels, binding funnels, and protein function.

Folding funnels have been the focus of considerable attention during the last few years. These have mostly been discussed in the general context of the theory of protein folding. Here we extend the utility of the concept of folding funnels, relating them to biological mechanisms and function. In particular, here we describe the shape of the funnels in light of protein synthesis and folding; flexibility, conformational diversity, and binding mechanisms; and the associated binding funnels, illustrating the multiple routes and the range of complexed conformers. Specifically, the walls of the folding funnels, their crevices, and bumps are related to the complexity of protein folding, and hence to sequential vs. nonsequential folding. Whereas the former is more frequently observed in eukaryotic proteins, where the rate of protein synthesis is slower, the latter is more frequent in prokaryotes, with faster translation rates. The bottoms of the funnels reflect the extent of the flexibility of the proteins. Rugged floors imply a range of conformational isomers, which may be close on the energy landscape. Rather than undergoing an induced fit binding mechanism, the conformational ensembles around the rugged bottoms argue that the conformers, which are most complementary to the ligand, will bind to it with the equilibrium shifting in their favor. Furthermore, depending on the extent of the ruggedness, or of the smoothness with only a few minima, we may infer nonspecific, broad range vs. specific binding. In particular, folding and binding are similar processes, with similar underlying principles. Hence, the shape of the folding funnel of the monomer enables making reasonable guesses regarding the shape of the corresponding binding funnel. Proteins having a broad range of binding, such as proteolytic enzymes or relatively nonspecific endonucleases, may be expected to have not only rugged floors in their folding funnels, but their binding funnels will also behave similarly, with a range of complexed conformations. Hence, knowledge of the shape of the folding funnels is biologically very useful. The converse also holds: If kinetic and thermodynamic data are available, hints regarding the role of the protein and its binding selectivity may be obtained. Thus, the utility of the concept of the funnel carries over to the origin of the protein and to its function.     

Assessing the energy landscape of CAPRI targets by FunHunt

RosettaDock has repeatedly created high-resolution structures of protein complexes in the CAPRI experiment, thanks to the explicit modeling of conformational changes of the monomers at the side chain level. These models can be selected based on their energy. During the search for the lowest-energy model, RosettaDock samples a deep funnel around the native orientation, but additional funnels may appear in the energy landscape, especially in cases where backbone conformational changes occur upon binding. We have previously developed FunHunt, a Support Vector Machine-based classifier that distinguishes the energy funnels around the native orientation from other funnels in the energy landscape. Here we assess the ability of FunHunt to help in model selection in the CAPRI experiment. For all of 12 recent CAPRI targets, FunHunt clearly identifies a near-native funnel in comparison to the funnel around the lowest energy model identified by the RosettaDock global search protocol. FunHunt is also able to choose a near-native orientation among models submitted by predictor groups, demonstrating its general applicability for model selection. This suggests that FunHunt will be a valuable tool in coming CAPRI rounds for the selection of models, and for the definition of regions that need further refinement with restricted backbone flexibility.     

The Orientation Behaviour of Chaffinches, Fringilla coelebs, Caught during Active Migratory Flight, in Relation to the Sun

The few orientation studies that have been carried out with day-migrating birds show that they are able to use solar and magnetic orientation cues for orientation. Previous orientation experiments in Emlen funnels have been carried out either with hand-raised birds or with birds caught during resting periods at stop-over sites. The aim of our study was to test whether birds caught during active flight show a higher concentration of migratory activity in the seasonally appropriate migratory direction in the funnels than birds that had not experienced migration just before the funnel experiments. The topography at the alpine pass Col de Bretolet at the border of Switzerland and France allowed us to capture birds during active migratory flight. These birds were in full migration disposition. Orientation experiments with chaffinches suggested an influence of the sun because chaffinches did not orient in the seasonally expected direction, but probably showed positive phototaxis towards the light of the sun at the opposite side of the funnel. Chaffinches tested under overcast conditions oriented to the north-west which probably was a 'nonsense' orientation and not a reverse migration or compensatory behaviour. We conclude that freshly caught birds are too stressed to show appropriate orientation when tested immediately after catching.     

Accelerated Movement of Nematodes from Soil in Baermann Funnels with Temperature Gradients

Baermann funnels were modified to eliminate or reverse the small temperature gradient (1-2 C/cm) across the soil layer that normally results from water evaporation. Effects of modifications on extraction efficiency were examined at various ambient temperatures and after overnight adaptation of three nematode species at 20 and 30 C. Extraction of Meloidogyne incognita from sandy loam, Tylenchulus semipenetrans from sandy clay loam, and Rotylenchulus reniformis from silt was greatly accelerated simply by covering funnels to prevent evaporation. In most cases, covering increased the nematodes extracted by 10-100 times after 5.5-48 hours. Faster and more efficient extraction of R. reniformis occurred over a wide range of ambient temperature (18-29 C). Effects of ambient temperature and temperature gradient direction on Baermann funnel extraction of R. reniformis were partly inconsistent with the behavior of R. reniformis in agar. Nematodes in agar moved toward cold at some ambient temperatures and toward heat at other temperatures. They always appeared to move toward cold on Baermann funnels. Differences were not attributable to blockage of gas exchange by covers. In agar and in funnels, the patterns of response to ambient temperature were shifted in the direction of the storage temperature.     

Funnels,gas exchange and cliff jumping: natural history of the cliff dwelling ant Malagidris sofina

The Malagasy endemic ant Malagidris sofina (Bolton and Fisher 2014) nests on cliff faces in natural rock alcoves or clay banks. Colonies have single ergatoid queens and reproduce by fission. Each nest has a funnel-shaped entrance that projects horizontally from the cliff face. We examine three hypotheses for the function of the funnels—water exclusion, gas exchange and defense. Entrance funnels are relatively impermeable and divert water from nests, but simple tubes would achieve the same result. Consistent with the gas exchange hypothesis, projected funnel entrances likely increase gas exchange rates over sixfold compared to simple tubes and may increase air flow within the nest. Gas exchange may explain the recurrent evolution of funnel entrances in several ant lineages, especially among cliff dwelling species. We outline M. sofina defense responses to conspecifics and co-occurring ant species, and find no support for a defense role of entrance funnels. Workers display little aggression but respond to several species with an original form of nest defense––cliff jumping—in which workers drop off the cliff face while clinging to invaders and then return to their nest. M. sofina is a restricted range species under threat of extinction by habitat destruction. Its novel lifestyle underscores the urgency of exploration and conservation in a tropical biodiversity hotspot.     

Realistic protein-protein association rates from a simple diffusional model neglecting long-range interactions, free energy barriers, and landscape ruggedness

We develop a simple but rigorous model of protein-protein association kinetics based on diffusional association on free energy landscapes obtained by sampling configurations within and surrounding the native complex binding funnels. Guided by results obtained on exactly solvable model problems, we transform the problem of diffusion in a potential into free diffusion in the presence of an absorbing zone spanning the entrance to the binding funnel. The free diffusion problem is solved using a recently derived analytic expression for the rate of association of asymmetrically oriented molecules. Despite the required high steric specificity and the absence of long-range attractive interactions, the computed rates are typically on the order of 10(4)-10(6) M(-1) sec(-1), several orders of magnitude higher than rates obtained using a purely probabilistic model in which the association rate for free diffusion of uniformly reactive molecules is multiplied by the probability of a correct alignment of the two partners in a random collision. As the association rates of many protein-protein complexes are also in the 10(5)-10(6) M(-1) sec(-1) range, our results suggest that free energy barriers arising from desolvation and/or side-chain freezing during complex formation or increased ruggedness within the binding funnel, which are completely neglected in our simple diffusional model, do not contribute significantly to the dynamics of protein-protein association. The transparent physical interpretation of our approach that computes association rates directly from the size and geometry of protein-protein binding funnels makes it a useful complement to Brownian dynamics simulations.     

Fast-folding protein kinetics,hidden intermediates,and the sequential stabilization model

Do two‐state proteins fold by pathways or funnels? Native‐state hydrogen exchange experiments show discrete nonnative structures in equilibrium with the native state. These could be called hidden intermediates (HI) because their populations are small at equilibrium, and they are not detected in kinetic experiments. HIs have been invoked as disproof of funnel models, because funnel pictures appear to indicate (1) no specific sequences of events in folding; (2) a continuum, rather than a discrete ladder, of structures; and (3) smooth landscapes. In the present study, we solve the exact dynamics of a simple model. We find, instead, that the present microscopic model is indeed consistent with HIs and transition states, but such states occur in parallel, rather than along the single pathway predicted by the sequential stabilization model. At the microscopic level, we observe a huge multiplicity of trajectories. But at the macroscopic level, we observe two pathways of specific sequences of events that are relatively traditional except that they are in parallel, so there is not a single reaction coordinate. Using singular value decomposition, we show an accurate representation of the shapes of the model energy landscapes. They are highly complex funnels.     

Folding funnels and conformational transitions via hinge-bending motions

In this article we focus on presenting a broad range of examples illustrating low-energy transitions via hinge-bending motions. The examples are divided according to the type of hinge-bending involved; namely, motions involving fragments of the protein chains, hinge-bending motions involving protein domains, and hinge-bending motions between the covalently unconnected subunits. We further make a distinction between allosterically and nonallosterically regulated proteins. These transitions are discussed within the general framework of folding and binding funnels. We propose that the conformers manifesting such swiveling motions are not the outcome of “induced fit” binding mechanism; instead, molecules exist in an ensemble of conformations that are in equilibrium in solution. These ensembles, which populate the bottoms of the funnels,a priori contain both the “open” and the “closed” conformational isomers. Furthermore, we argue that there are no fundamental differences among the physical principles behind the folding and binding funnels. Hence, there is no basic difference between funnels depicting ensembles of conformers of single molecules with fragment, or domain motions, as compared to subunits in multimeric quaternary structures, also showing such conformational transitions. The difference relates only to the size and complexity of the system. The larger the system, the more complex its corresponding fused funnel(s). In particular, funnels associated with allosterically regulated proteins are expected to be more complicated, because allostery is frequently involved with movements between subunits, and consequently is often observed in multichain and multimolecular complexes. This review centers on the critical role played by flexibility and conformational fluctuations in enzyme activity. Internal motions that extend over different time scales and with different amplitudes are known to be essential for the catalytic cycle. The conformational change observed in enzyme-substrate complexes as compared to the unbound enzyme state, and in particular the hinge-bending motions observed in enzymes with two domains, have a substantial effect on the enzymatic catalytic activity. The examples we review span the lipolytic enzymes that are particularly interesting, owing to their activation at the water-oil interface; an allosterically controlled dehydrogenase (lactate dehydrogenase); a DNA methyltransferase, with a covalently-bound intermediate; large-scale flexible loop motions in a glycolytic enzyme (TIM); domain motion in PGK, an enzyme which is essential in most cells, both for ATP generation in aerobes and for fermentation in anaerobes; adenylate kinase, showing large conformational changes, owing to their need to shield their catalytic centers from water; a calcium-binding protein (calmodulin), involved in a wide range of cellular calcium-dependent signaling; diphtheria toxin, whose large domain motion has been shown to yield “domain swapping” the hexameric glutamate dehydrogenase, which has been studied both in a thermophile and in a mesophile; an allosteric enzyme, showing subunit motion between the R and the T states (aspartate transcarbamoylase), and the historically well-studied lac represoor. Nonallosteric subunit transitions are also addressed with some examples (aspartate receptor andBamHI endonuclease). Hence, using this enzyme-catalysis-centered discussion, we address energy funnel landscapes of large-scale conformational transitions, rather than the faster, quasi-harmonic, thermal fluctuations.     

Eine einfache methode die wirkung eines pflanzenschutzmittels auf die fauna von obstbäumen festzustellen

Summary The comparison of samples of the fruit tree fauna taken before the treatment with an insecticide, two or three days later and the animals died during these three days it is possible to establish the effect of this compound on the whole fauna. For the first an the last sample we used a ?tapping funnel? (Klopftrichter). The died animals were collected in hanged funnels. This method was demonstrated in June 1964 in Praz-Pourri, (Valais, Swizerland) to some members of the C.I.L.B. international working group on integrated control of pests. Two aphicides were proved of wich Isolan was found to be more suitable for the control of aphids in integrated spray programs, as the accessory effect on the aphidivorous capsids was low. By this example there are described all details necessary to carry out and analyze such experiments.      

Filter assay technique and quench-flow experiments: examples of receptor-mediated transmembrane ion-exchange measured with membrane vesicles.

Modifications to a quench-flow apparatus are described which allow a rapid, in-line filter assay with immediate washing, in conditions to give minimum background. A design for an effluent spout is presented, which decelerates the liquid by a large factor, prevents splashes, limits the area of the filter exposed to the sample and allows an immediate wash over a larger area. A design for a filter assay funnel for general use is also presented. These devices feature minimal contact of the funnels with the filter disc. Examples are given in which in-line filtration was used to follow transmembrane ion flux in membrane vesicle preparations. In measurements of transmembrane flux with membrane vesicles and radioisotope the filter assay background can be resolved into three components. These are, (1) the uptake of radioactivity by the filter, (2) the radioactivity inside the vesicles not taking part in the specific measurement and (3) the occlusion of radioactivity in aggregated membrane particles on the filter. These different components depend on the conditions in different ways. Techniques for minimizing the background in filter assays are discussed. The importance of rapid filtration and immediate washing is demonstrated. The examples given illustrate that the function of the acetylcholine receptor from E. electricus is not affected by diisopropylfluorophosphate in the conditions used, and that added GABA is not removed from solution in a brain membrane preparation by the GABA uptake mechanisms in the short times of the experiments.     

Certification of Probability of Sterilization of Liquid by Filtration

Four types of hydrosol filters, two reusable (diatomaceous cylinder and fritted-glass funnel) and two disposable (asbestos pad and membrane filter) were challenged with a heavy bacterial suspension to assess their ability to produce sterile filtrates. Two of the four diatomaceous earth filters, the four fritted-glass funnels, and all of the asbestos pads tested generally gave sterile filtrates. However, only one type of filter, one of the membranes in its manufacturer's own holder, consistently gave sterile filtrates. The two other types of membranes usually gave sterile filtrates if tested in one manufacturer's holder, but all types invariably gave contaminated filtrates when tested in another manufacturer's holder. Contaminated filtrates were generally attributed to a poor reusable filter or to a faulty holder used with a disposable filter. If a high degree of certainty is required for sterile heat-labile filtrate, it is suggested that the liquid be passed through two or more filters in a previously tested and proven system.     

Carbon Dioxide and Temperature Gradielits in Baermann Funnel Extraction of Rotylenchulus reniformis

Vermiform Rotylenchulus reniformis were anesthetized in water by 10-40% CO₂ but were fully motile for 24 hours in water below 5% CO₂. When air containing 2.5% CO₂ was blown onto agar, nematodes accumulated at the point of highest CO₂ concentration. Nematodes also accumulated when chilling (0.2-1 C) of agar by the gas flow at the accumulation point was offset with heat from a fiber optic. In Baermann funnels containing R. reniformis in silt loam and sandy clay loam soils, CO₂ in funnel water increased during 24 hours from 0 to ca. 1%; more CO₂ accumulated below the soil layer than above. Bubbling air with 2.5% CO₂ into water below soil in covered funnels increased the CO₂ gradient and increased nematode extraction, whereas bubbling air without CO₂ below soil purged CO₂ from the water and decreased nematode extraction. Manipulation of CO₂ within funnels usually increased extraction by only 30% and never by more than 3-fold. Controlling temperature gradients consistently increased extraction by 2-30-fold.     

Extraction from soil of apterous Pemphigus populitransversus (Hemiptera: Pemphigidae) feeding on cruciferous vegetable roots

The poplar petiolegall aphid, Pemphigus populitransversus Riley (Hemiptera: Pemphigidae), is a gall-forming aphid attacking leaf petioles of Populus spp., its primary hosts. Its secondary hosts are the roots of cruciferous (Brassicaceae) plants, where it is also commonly known as the "cabbage root aphid." The apterous forms are destructive pests of cruciferous vegetables in many parts of the world. In our experiments, the root-feeding apterous forms were extracted from the soil using a Berlese funnel, which drives the aphids downward by using light and heat. The results show that a majority of apterous aphids (96.9%) were extracted from the soil in 2 h by using a 15-W light bulb in the Berlese funnels, whereas only 18.2% of aphids were extracted using a 25-W light bulb in a similar time period. The 25-W light bulb in the funnel generated too much heat (40-44 degrees C), which dried the soil too fast so that the aphids were unable to crawl downward to the collecting jars or killed the aphids directly. The advantages of using a Berlese funnel equipped with a 15-W light bulb as the light and heat source for sampling and extraction of the root feeding aphids include a uniform handling of each sample, less time spent, extraction of many samples at the same time, and storage of the aphids in containers for later counting in the laboratory. This technique seems to also be useful for extracting other mobile, small soil-dwelling arthropods.     

Comparison of trap designs for use with aggregation pheromone and synthetic co-attractant in a user-friendly attract and kill system to control Carpophilus spp. (Coleoptera: Nitidulidae)

Abstract  Three field experiments were conducted in stone fruit orchards in the Goulburn Valley, northern Victoria, Australia to identify a user-friendly trap for use in attract and kill stations for control of Carpophilus spp. (Coleoptera: Nitidulidae). A funnel trap design was compared with two types of delta trap in one experiment and two types of Lucitrap in another experiment. All traps were baited with synthetic co-attractant and synthetic pheromone. The funnel trap was the most effective type of trap tested. The funnel traps caught significantly more beetles than either the delta traps with bio-attractant or delta traps wrapped with insecticide impregnated banana wrap. No difference was observed between catches in either delta trap design. Lucitraps without covers caught significantly more beetles than Lucitraps with covers but funnel traps caught significantly more beetles than either type of Lucitrap. Beetle numbers caught in the funnel traps were three to five times higher than in Lucitrap. The use of funnel traps in attract and kill stations to protect stone fruit crops by suppressing the Carpophilus spp. population gave superior control to 'grower normal practice of spraying insecticides' both in terms of Carpophilus spp. numbers and in terms of reduction in percentage of fruit damaged.     

Cunning simplicity of protein folding landscapes

Funnel-like landscapes are widely used to visualize protein folding. It might seem that any funnel-like energy landscape helps to avoid the 'Levinthal paradox', i.e. to avoid sampling the impossibly large number of conformations for a folding protein. This cunning suggestion, reinforced by beautiful drawings of the energy funnels, stimulated some simple models of protein folding; one of them [D.J. Bicout and A. Szabo (2000) Protein Sci., 9, 452-465] is especially straightforward and instructive. A thorough analysis of this strict funnel model (which does not consider a nucleation of phase separation in the course of folding) shows that it cannot provide a simultaneous explanation for both major features observed for protein folding: (i) folding within non-astronomical time, and (ii) co-existence of the native and the unfolded states during the folding process. On the contrary, the nucleation mechanism of protein folding can account for both these major features simultaneously.     

Immunohistochemical Study of Leucine-Enkephalin and Delta Opioid Receptor in Mantles and Feet of the Octopus Octopus ocellatus Gray

The study was supposed to determine whether leucine-enkephalin (leu-Enk) or delta opioid receptor was presented in mantles and feet of the Octopus Octopus ocellatus. The results showed that they were found in the mantles, wrists, interbrachial membrane, and funnels of the Octopus Octopus ocellatus. The immunoreactivities of leu-Enk and delta opioid receptor were observed in the epithelial cells of dorsal mantle, wrist and interbrachial membrane. Strong one was presented in both the connective tissue which was close to the epithelium of dorsal mantle, wrist and interbrachial membrane and a small amount of connective tissue cells and nerve fibers, while less positive in other parts. A little of immunoreactive material was also observed in the ventral mantle and funnel, for example, weak one was in the epithelial tissue, the adjacent cells and nerve fibers. The different densities of leu-Enk and delta opioid receptor in mantles and feet of the Octopus O. ocellatus may be related to the different functions.     

Structure and function of the Nautilus statocyst.

The two equilibrium receptor organs (statocysts) of Nautilus are avoid sacks, half-filled with numerous small, free-moving statoconia and half with endolymph. The inner surface of each statocyst is lined with 130,000-150,000 primary sensory hair cells. The hair cells are of two morphological types. Type A hair cells carry 10-15 kinocilia arranged in a single ciliary row; they are present in the ventral half of the statocyst. Type B hair cells carry 8-10 irregularly arranged kinocilia; they are present in the dorsal half of the statocyst. Both type of hair cells are morphologically polarized. To test whether these features allow the Nautilus statocyst to sense angular accelerations, behavioural experiments were performed to measure statocyst-dependent funnel movements during sinusoidal oscillations of restrained Nautilus around a vertical body axis. Such dynamic rotatory stimulation caused horizontal phase-locked movements of the funnel. The funnel movements were either in the same direction (compensatory funnel response), or in the opposite direction (funnel follow response) to that of the applied rotation. Compensatory funnel movements were also seen during optokinetic stimulation (with a black and white stripe pattern) and during stimulations in which optokinetic and statocyst stimulations were combined. These morphological and behavioural findings show that the statocysts of Nautilus, in addition to their function as gravity receptor organs, are able to detect rotatory movements (angular accelerations) without the specialized receptor systems (crista/cupula systems) that are found in the statocysts of coleoid cephalopods. The findings further indicate that both statocyst and visual inputs control compensatory funnel movements.