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[Construction of a model eye for simulation of Purkinje reflections for determining the radii of curvature and the position of the crystalline lens].

UNLABELLED: Specular reflections at the optical interfaces of the eye, the Purkinje reflections, are used in physiologic optics and ophthalmology for biometric measurements. To date, there is no standard in the measurement of crystalline lens radii of curvature and position. To that end model eyes were designed. MATERIALS AND METHODS: The most important goal was to simulate the Purkinje reflections I, III, and IV, in the human eye as realistically as possible. The casing of the model eye was made of brass; the optical components were made from contact lens material. RESULTS: Several variants of components were manufactured to reproduce the range of variations in human eyes. By combining different components it was possible to vary the radii of curvature of the cornea and of the crystalline lens, axial separations, crystalline lens rotations and decentrations independently and reproducibly. First applications included devices for biometry of the crystalline lens (phacometry), validation of methods for eye alignment measurement, and refractometry. CONCLUSIONS: The properties of the specular reflections of the model eye are very close to the target values in human eyes. One of the advantages of the model eye is the compact design. This model eye is the first measuring standard for phakometry.

Anthropometry↗

Semiflexible amphiphilic polymers: cylindrical-shaped, collagenlike, and toroidal structures.

A coarse-grained model is used to study the conformational properties of semiflexible polymers with amphiphilic monomer units containing both hydrophilic and hydrophobic interaction sites. The hydrophobically driven conformational transitions are studied using molecular dynamics simulations for the chains of varying stiffness, as characterized by intrinsic Kuhn segment lengths that vary over a decade. It is shown that the energy of hydrophobic attraction required for the realization of the coil-to-globule transition increases with increasing chain stiffness. For rather stiff backbone, the coil-to-globule transition corresponds to a first order phase transition. We find that depending on the chain stiffness, a variety of thermodynamically stable anisometric chain morphologies are possible in a solvent selectively poor for hydrophobic sites of amphiphilic monomer units. For flexible chains, the amphiphilic polymer forms a cylindrical globule having blob structure with nearly spherical blobs. With increasing stiffness, the number of blobs composing the globule decreases and the shape of blobs transforms into elongated cylinder. Further increase in stiffness leads to compaction of macromolecules into a collagenlike structure when the chain folds itself several times and different strands wind round each other. In this state, the collagenlike structures coexist with toroidal globules, both conformations having approximately equal energies.

Journal Article↗

Synaptic mechanisms of a tonic EPSP in crustacean visual interneurons: analysis and simulation.

Light-evoked synaptic responses of identified visual interneurons, sustaining fibers (SFs), were quantitatively analyzed, and a neuronal cable model was used to calculate voltage attenuations and predict synaptic responses. The cable model is based on morphological measurements of SFs filled with Lucifer yellow and passive membrane properties assessed by current injection in the proximal portion of the dendritic arbor. The morphological and electrophysiological measurements were made in different preparations on homologues of the same identified interneurons. The excitatory postsynaptic potential (EPSP) elicited with high-intensity light consists of a transient phase (mean amplitude 33.1 mV) and a second phase (the plateau) that decays slowly relative to the membrane time constant (mean amplitude 24.4 mV). The mean extrapolated reversal potentials are -19.1 mV for the transient and -22.3 mV during the plateau. The change in input conductance associated with the plateau phase of the response showed a peak of 121% above the resting input conductance and decayed to approximately 50% above resting conductance over several seconds. Compartmental cable models (18, 19) were used to calculate voltage attenuations and local synaptic conductances within the SF dendritic tree. The dendrites are electrotonically compact, and voltage attenuations average 6% for current flowing distally from the recording site (injected) and 45% for current flowing proximally to the recording site. The steady-state EPSP is associated with a calculated 80% decrease in the net dendritic membrane resistivity. The synaptic response, calculated for an EPSP distributed throughout the dentritic tree (using this conductance change and the measured steady-state reversal potential) was 27.0 mV, compared with an observed mean value of 24.4 mV. The calculated relationship between steady-state EPSP amplitude and dendritic membrane resistivity (Rs) is a sigmoidal function that resembles the intensity/response function of the SF. We can therefore correctly predict the transformation from light intensity to compound EPSP amplitude by calculating the intervening synaptic membrane resistivity and voltage values. These functions are affected in a predictable manner by the passive membrane resistivity (Rm) and the EPSP reversal potentials. Tetrodotoxin (TTX) application abolished all SF spiking but left the EPSP essentially unchanged, suggesting that the neuronal pathway from photoreceptors to SFs is mainly or entirely comprised of nonspiking (i.e., TTX-insensitive) elements.

Animals↗

Structural stability of soybean lipoxygenase-1 in solution as probed by small angle X-ray scattering.

Soybean lipoxygenase-1 (LOX-1) is used widely as a model for studying the structural and functional properties of the homologous family of lipoxygenases. The crystallographic structure revealed that LOX-1 is organized in a beta-sheet N-terminal domain and a larger, mostly helical, C-terminal domain. Here, we describe the overall structural characterization of native unliganded LOX-1 in solution, using small angle X-ray scattering (SAXS). We show that the scattering pattern of the unliganded enzyme in solution does not display any significant difference compared with that calculated from the crystal structure, and that models of the overall shape of the protein calculated ab initio from the SAXS pattern provide a close envelope to the crystal structure. These data, demonstrating that LOX-1 has a compact structure also in solution, rule out any major motional flexibility of the LOX-1 molecule in aqueous solutions. In addition we show that eicosatetraynoic acid, an irreversible inhibitor of lipoxygenase used to mimic the effect of substrate binding, does not alter the overall conformation of LOX-1 nor its ability to bind to membranes. In contrast, the addition of glycerol (to 5%, v/v) causes an increase in the binding of the enzyme to membranes without altering its catalytic efficiency towards linoleic acid nor its SAXS pattern, suggesting that the global conformation of the enzyme is unaffected. Therefore, the compact structure determined in the crystal appears to be essentially preserved in these various solution conditions. During the preparation of this article, a paper by M. Hammel and co-workers showed instead a sharp difference between crystal and solution conformations of rabbit 15-LOX-1. The possible cause of this difference might be the presence of oligomers in the rabbit lipoxygenase preparations.

5,8,11,14-Eicosatetraynoic Acid↗

Photothermal temperature control of a chemical reaction on a microchip using an infrared diode laser.

We have demonstrated that a miniaturized device with IR laser heating of the solvent, based on a photothermal effect, is capable of fast and localized control of an enzymatic reaction on a microchip under flow conditions. Using noncontact spectroscopic temperature-sensing techniques, we measured temperature dynamics and spatial distribution and compared the measurements with results of numerical simulation analysis. The device was operated at ultrafast heating and cooling rates of 67 and 53 degrees C/s, respectively, which is 30 times faster than conventional systems and 3-6 times faster than electrothermal miniaturized thermocyclers. The IR laser-mediated heater is characterized by a significantly reduced heated volume of only 5 nL, compared to existing chip-based systems with electrothermal heating. Direct heating of a sample with extremely small heat capacity led us to a fast heating rate, and efficient heat removal through heat transfer to the glass substrate resulted in a fast cooling rate. Reproducible temperature levels with dwell times shorter than 0.5 s were achieved. The enzyme reaction on a chip was successfully controlled with 0.6-s time resolution, using periodic photothermal heating by IR laser. The IR diode laser is compact and thus suits well the miniaturized system design. Our work gives the basis for integration in a chip format of a variety of chemical processes that require fast temperature control.

Journal Article↗

K-edge digital subtraction imaging with dichromatic x-ray sources: SNR and dose studies.

The aim of the present work is to analytically evaluate the signal to noise ratio (SNR) and the delivered dose in K-edge digital subtraction imaging (KES) using two types of x-ray sources: a monochromatic x-ray source (available at synchrotron radiation facilities and considered as gold standard) and a quasi-monochromatic compact source. The energy separation DeltaE between the two monochromatic beams is 1 keV and 4 keV for the two sources, respectively. The evaluation has been performed for both radiography and computed tomography. Different geometries have been studied to mimic clinical situations. In mammography, a pathology perfused by a contrast agent has been modelled; in angiography, a vessel superimposed to a ventricle or a stand-alone artery stenosis has been studied. The SNR and the skin dose have been calculated as a function of the detail diameter, the contrast agent (iodine and gadolinium), and its concentration in the tissues. Results show that for DeltaE = 4 keV a slightly higher delivered dose is required to obtain the same SNR with respect to DeltaE < 1 keV. A similar study has been performed for KES-CT. Computer simulations of CT images performed with Snark software are shown to validate the analytical calculations.

Algorithms↗

Modelling protein unfolding: hen egg-white lysozyme.

A novel modelling procedure, which rapidly unfolds a protein by enhancing solvent penetration of its core, was used to investigate the unfolding pathway of hen egg-white lysozyme. Early on the unfolding pathway there is a dramatic disruption of the tertiary contacts within the protein, which decouples its domains. Subsequently, the helical domain slowly loses its compactness and the helices fluctuate rapidly. The protein then adopts a 'molten globule-like' structure in which the native beta-sheet is essentially intact. The modelled structures have properties similar to those of lysozyme's experimentally characterized partially folded states and provide insight into its complex (un)folding process. The sequence of unfolding events shows how the unfolding pathway of a multidomain protein may be most similar to its fastest, but not necessarily its dominant, folding pathway.

Animals↗

A multiconductance silicon neuron with biologically matched dynamics.

We have designed, fabricated, and tested an analog integrated-circuit architecture to implement the conductance-based dynamics that model the electrical activity of neurons. The dynamics of this architecture are in accordance with the Hodgkin-Huxley formalism, a widely exploited, biophysically plausible model of the dynamics of living neurons. Furthermore the architecture is modular and compact in size so that we can implement networks of silicon neurons, each of desired complexity, on a single integrated circuit. We present in this paper a six-conductance silicon-neuron implementation, and characterize it in relation to the Hodgkin-Huxley formalism. This silicon neuron incorporates both fast and slow ionic conductances, which are required to model complex oscillatory behaviors (spiking, bursting, subthreshold oscillations).

Action Potentials↗

Consistent dynamics suggests tight regulation of biophysical parameters in a small network of bursting neurons.

The neuronal firing patterns in the pyloric network of crustaceans are remarkably consistent among animals. Although this characteristic of the pyloric network is well-known, the biophysical mechanisms underlying the regulation of the systems output are receiving renewed attention. Computer simulations of the pyloric network recently demonstrated that consistent motor output can be achieved from neurons with disparate biophysical parameters among animals. Here we address this hypothesis by pharmacologically manipulating the pyloric network and analyzing the emerging voltage oscillations and firing patterns. Our results show that the pyloric network of the lobster stomatogastric ganglion maintains consistent and regular firing patterns even when entire populations of specific voltage-gated channels and synaptic receptors are blocked. The variations of temporal parameters used to characterize the burst patterns of the neurons as well as their intraburst spike dynamics do not display statistically significant increase after blocking the transient K-currents (with 4-aminopyridine), the glutamatergic inhibitory synapses (with picrotoxin), or the cholinergic synapses (with atropine) in pyloric networks from different animals. These data suggest that in this very compact circuit, the biophysical parameters are cell-specific and tightly regulated.

4-Aminopyridine↗

Global structure and flexibility of hairpin ribozymes with extended terminal helices.

Global structure and flexibility of three different hairpin ribozyme constructs have been analyzed by measuring their electric dichroism decay in various buffers at temperatures between 2 and 30 degrees C. The hairpin ribozyme is characterized by two independently folding domains A and B that are connected through a hinge and have to interact to enable catalysis. The analyzed constructs feature extended terminal helices 1 and 4 with 27 and 25 bp, respectively, to increase the sensitivity of the molecular rotational diffusion time constants with respect to the interdomain bending angle. Constructs HP1 and HP2 cannot cleave because of a G+1A change at the 3'-side of the cleavage site; in HP1 the helices 2 and 3 that flank the hinge form a continuous double helical segment; in HP2 and HP3, a six nucleotide bulge confers flexibility to the expected bending site; HP3 is a cleavable form of HP2 with a G+1-base. For comparison, a standard RNA double helix with 72 bp was included in our analysis. The dichroism decay curves of the hairpin constructs after pulses of low electric field strengths can be fitted to single exponentials taus, whereas the curves after pulses of high field strengths require two exponentials. In all cases, time constants increase with RNA concentration, indicating intermolecular interactions. Extrapolation of the tausvalues measured in standard buffer (50 mM Tris (pH 7.5) and 12 mM MgCl2) to zero RNA concentration provide values of 112, 93, and 73 ns for HP1, HP2 and HP3, respectively, at 30 degrees C, indicating increasingly compact structures. The 72 bp RNA reference under corresponding conditions did not show a dependence of its decay time constant on the RNA concentration nor on the field strength; its time constant is 175 ns (standard buffer, 30 degrees C). The observation of two relaxation processes for the hairpin constructs at high field strengths indicates stretching to a more elongated state; the fast process with a time constant of the order of 50 ns is assigned to reversion of stretching, the slow process to overall rotation. The overall rotational time of the stretched state at 20 degrees C is close to that for a completely stretched rigid state; at 30 degrees C the experimental values are around 70 % of that expected for a completely stretched rigid state, indicating flexibility and/or residual bending. Bead models were constructed to simulate dichroism decay curves. The time constants observed for the 72 bp RNA are as expected for a rigid rod with a rise of 2.8 A per base-pair. Based on this rise per base-pair for models of a V and a Y-shape, we estimate average bending angles of 80(+/-20) degrees and 105 (+/-25) degrees, respectively, for the catalytically active hairpin ribozyme HP3. The energy required for stretching is of the order of the thermal energy.

Base Sequence↗

Fiberoptic study on the effects of transluminal angioplasty in experimental occlusive arterial thrombosis.

Percutaneous transluminal coronary angioplasty has been proposed as definitive therapy for coronary recanalization of occluded coronary arteries in patients with acute myocardial infarction (AMI). The effects of transluminal angioplasty (TA) on experimental occlusive canine arterial thrombi that closely simulated the clinical condition was examined by a fiberoptic method. Experimental arterial thrombosis was produced by endothelial denudation and induction of luminal stenosis. Eighteen dogs that showed total occlusion of the iliac artery with thrombi were evaluated. Seven dogs (group A) with 6-hour-old thrombi received 20,000 IU/kg intravenous urokinase (UK) but did not show recanalization. TA was performed with a Gruentzig or Simpson-Robert balloon catheter and its effect was evaluated by a vascular fibroscope. Eight dogs (group B) with 6-hour-old thrombi underwent primary TA. After TA, less than 50% luminal obstruction with residual thrombi was visualized in five dogs (71%) of group A and four dogs (50%) of group B. Residual thrombi showed a doughnut-like or globular type shape and consisted of dense fibrin networks and compact platelet aggregates. All dogs in group B received 20,000 IU/kg intravenous UK after TA, but most of them showed progression of thrombus size despite UK infusion. In conclusion, the results suggest (1) that TA is effective in recanalization of an occluded artery with aged thrombus that is resistant to thrombolytic therapy and (2) that vascular fiberscope is a useful method for evaluation of the effects of TA on occlusive arterial thrombus.

Angioplasty, Balloon↗

Dynamic properties of the N-terminal swapped dimer of ribonuclease A.

Bovine pancreatic ribonuclease (RNase A) forms two 3-dimensional domain-swapped dimers with different quaternary structures. One dimer is characterized by the swapping of the C-terminal region (C-Dimer) and presents a rather loose structure. The other dimer (N-Dimer) exhibits a very compact structure with exchange of the N-terminal helix. Here we report the results of a molecular dynamics/essential dynamics (MD/ED) study carried out on the N-Dimer. This investigation, which represents the first MD/ED analysis on a three-dimensional domain-swapped enzyme, provides information on the dynamic properties of the active site residues as well as on the global motions of the dimer subunits. In particular, the analysis of the flexibility of the active site residues agrees well with recent crystallographic and site-directed mutagenesis studies on monomeric RNase A, thus indicating that domain swapping does not affect the dynamics of the active sites. A slight but significant rearrangement of N-Dimer quaternary structure, favored by the formation of additional hydrogen bonds at subunit interface, has been observed during the MD simulation. The analysis of collective movements reveals that each subunit of the dimer retains the functional breathing motion observed for RNase A. Interestingly, the breathing motion of the two subunits is dynamically coupled, as they open and close in phase. These correlated motions indicate the presence of active site intercommunications in this dimer. On these bases, we propose a speculative mechanism that may explain negative cooperativity in systems preserving structural symmetry during the allosteric transitions.

Animals↗

Solution structure of the recombinant penaeidin-3, a shrimp antimicrobial peptide.

Penaeidins are a family of antimicrobial peptides of 47-63 residues isolated from several species of shrimp. These peptides display a proline-rich domain (N-terminal part) and a cysteine-rich domain (C-terminal part) stabilized by three conserved disulfide bonds whose arrangement has not yet been characterized. The recombinant penaeidin-3a of Litopenaeus vannamei (63 residues) and its [T8A]-Pen-3a analogue were produced in Saccharomyces cerevisiae and showed similar antimicrobial activity. The solution structure of the [T8A]-Pen-3a analogue was determined by using two-dimensional 1H NMR and simulated annealing calculations. The proline-rich domain, spanning residues 1-28 was found to be unconstrained. In contrast, the cysteine-rich domain, spanning residues 29-58, displays a well defined structure, which consists of an amphipathic helix (41-50) linked to the upstream and the downstream coils by two disulfide bonds (Cys32-Cys47 and Cys48-Cys55). These two coils are in turn linked together by the third disulfide bond (Cys36-Cys54). Such a disulfide bond packing, which is in agreement with the analysis of trypsin digests by ESI-MS, contributes to the highly hydrophobic core. Side chains of Arg45 and Arg50, which belong to the helix, and side chains of Arg37 and Arg53, which belong to the upstream and the downstream coils, are located in two opposite parts of this globular and compact structure. The environment of these positively charged residues, either by hydrophobic clusters at the surface of the cysteine-rich domain or by sequential hydrophobic residues in the unconstrained proline-rich domain, gives rise to the amphipathic character required for antimicrobial peptides. We hypothesize that the antimicrobial activity of penaeidins can be explained by a cooperative effect between the proline-rich and cysteine-rich features simultaneously present in their sequences.

Amino Acid Sequence↗

Computer modelling of Tetrahymena axonemes at macromolecular resolution. Interpretation of electron micrographs.

A computer-generated model of the structural arrangement of the complete 9+2 ciliary axoneme of Tetrahymena at macromolecular resolution (4 nm) is presented. The model reconciles detailed information about subcomponents from negative-stained, thin-section and freeze-fracture electron micrographs, integrating the images into a consistent three-dimensional picture. This illuminates problems such as the requirement for compaction of dynein to form the arm, difficulties in visualization of the circumferential links, construction of the central sheath, and the comparative periodicities of the inner and outer arms. The model is pragmatic in that it is flexible and easily changed, as new information becomes available. It is also useful in the development of dynamic concepts, such as a spatial description of the dynein cross-bridge cycle, which is illustrated, or relationships between adjacent doublets during sliding and bending.

Animals↗

A new model for the three-dimensional folding of Escherichia coli 16 S ribosomal RNA. III. The topography of the functional centre.

We describe the locations of sites within the 3D model for the 16 S rRNA (described in two accompanying papers) that are implicated in ribosomal function. The relevant experimental data originate from many laboratories and include sites of foot-printing, cross-linking or mutagenesis for various functional ligands. A number of the sites were themselves used as constraints in building the 16 S model. (1) The foot-print sites for A site tRNA are all clustered around the anticodon stem-loop of the tRNA; there is no "allosteric" site. (2) The foot-print sites for P site tRNA that are essential for P site binding are similarly clustered around the P site anticodon stem-loop. The foot-print sites in 16 S rRNA helices 23 and 24 are, however, remote from the P site tRNA. (3) Cross-link sites from specific nucleotides within the anticodon loops of A or P site-bound tRNA are mostly in agreement with the model, whereas those from nucleotides in the elbow region of the tRNA (which also exhibit extensive cross-linking to the 50 S subunit) are more widely spread. Again, cross-links to helix 23 are remote from the tRNAs. (4) The corresponding cross-links from E site tRNA are predominantly in helix 23, and these agree with the model. Electron microscopy data are presented, suggestive of substantial conformational changes in this region of the ribosome. (5) Foot-prints for IF-3 in helices 23 and 24 are at a position with close contact to the 50 S subunit. (6) Foot-prints from IF-1 form a cluster around the anticodon stem-loop of A site tRNA, as do also the sites on 16 S rRNA that have been implicated in termination. (7) Foot-print sites and mutations relating to streptomycin form a compact group on one side of the A site anticodon loop, with the corresponding sites for spectinomycin on the other side. (8) Site-specific cross-links from mRNA (which were instrumental in constructing the 16 S model) fit well both in the upstream and downstream regions of the mRNA, and indicate that the incoming mRNA passes through the well-defined "hole" at the head-body junction of the 30 S subunit.

Base Sequence↗

The existence of multiple tetrameric conformers of chicken liver pyruvate carboxylase and their roles in dilution inactivation.

The time-dependent loss of enzymic activity and tetrameric structure of chicken liver pyruvate carboxylase (EC 6.4.1.1) after dilution below 2 units/ml was apparently monophasic and first-order. When examined over a range of initial enzyme concentrations, both activity and tetrameric structure decayed to equilibrium levels which were dependent on the initial concentration. The observed rate constants for the loss of enzymic activity (i) showed no apparent dependence on the initial enzyme concentration, and (ii) were of similar magnitude to the corresponding rate constants of dissociation. Computer simulations of the most likely kinetic model suggest that the predominant form of the dissociated enzyme is the monomer. Dilution of pyruvate carboxylase in the presence of the allosteric activator acetyl-CoA largely prevented the subsequent dissociation of the tetrameric molecule. In addition, acetyl-CoA was able to cause a degree of activation and reassociation when added after dilution inactivation had been allowed to occur. Electron-microscopic observation showed the treatment with avidin before dilution markedly decreased the degree of dissociation of the enzyme tetramer. This structure-stabilizing effect of avidin was dependent on preincubation of the concentrated enzyme solution with acetyl-CoA. We propose that, over a range of protein concentrations, the tetrameric enzyme exists in two forms that are in equilibrium, and that acetyl-CoA alters the equilibrium to favour the more compact form.

Acetyl Coenzyme A↗

Effect of proline and glycine residues on dynamics and barriers of loop formation in polypeptide chains.

Glycine and proline residues are frequently found in turn and loop structures of proteins and are believed to play an important role during chain compaction early in folding. We investigated their effect on the dynamics of intrachain loop formation in various unstructured polypeptide chains. Loop formation is significantly slower around trans prolyl peptide bonds and faster around glycine residues compared to any other amino acid. However, short loops are formed fastest around cis prolyl bonds with a time constant of 6 ns for end-to-end contact formation in a four-residue loop. Formation of short loops encounters activation energies in the range of 15 to 30 kJ/mol. The altered dynamics around glycine and trans prolyl bonds can be mainly ascribed to their effects on the activation energy. The fast dynamics around cis prolyl bonds, in contrast, originate in a higher Arrhenius pre-exponential factor, which compensates for an increased activation energy for loop formation compared to trans isomers. All-atom simulations of proline-containing peptides indicate that the conformational space for cis prolyl isomers is largely restricted compared to trans isomers. This leads to decreased average end-to-end distances and to a smaller loss in conformational entropy upon loop formation in cis isomers. The results further show that glycine and proline residues only influence formation of short loops containing between 2 and 10 residues, which is the typical loop size in native proteins. Formation of larger loops is not affected by the presence of a single glycine or proline residue.

Computer Simulation↗

The conformation of amine- and amide-terminated poly(propylene imine) dendrimers as investigated by molecular simulation methods.

The parameters that influence the conformation of poly(propylene imine) dendrimers were investigated by molecular simulations using molecular mechanics and simulated annealing methods. Dendrimers with two types of peripheral units able to communicate via hydrogen bonding-amine and amide moieties-were considered in order to study the role that secondary interactions among the end groups have in the spatial organization of the dendritic branches. Radial atomic density profiles and radial atomic probability distributions were used to extract global properties, such as the degree of packing of the branches, the distribution of the monomers throughout the molecular volume, and the extent and characteristics of the surface region. Information was also obtained about the nature, location, and extent of formation of the hydrogen bonds, as well as their evolution with dendrimer generation and their assembly into networks. The analyses were supported by a detailed investigation of the first two generations, with an emphasis on the relationship between hydrogen bonding and the compactness and stability of the molecules; this allowed us to account for the generational evolution of hydrogen bonding that is experimentally observed in several poly(propylene imine) dendrimers.

Journal Article↗