A three dimensional model of the digestion of peptidoglycan by lysozyme

The digestion of single peptidoglycan chains of the recently proposed conformation (Formanek et al., 1974) can be described with the same enzymatic mechanism as proposed by Phillips for a hexasaccharide consisting of alternating N-acetylglucosamine, N-acetylmuramic acid residues (Phillips, 1966). It is shown by model building, that in a peptidoglycan lysozyme complex the peptide chains do not exhibit any sterical hindrance.The digestion of the peptidoglycan sacculus by lysozyme may occur at lattice defects of its paracrystalline structure. A slit of about 30 å lenght and 10–15 å width between peptidoglycan micells may be sufficient for the attachment of lysozyme.     

A three dimensional model of the photosynthetic membranes of Ectothiorhodospira halochloris

The three dimensional organization of the complete photosynthetic apparatus of the extremely halophilic, bacteriochlorophyll b containing Ectothiorhodospira halochloris has been elaborated by several techniques of electron microscopy. Essentially all thylakoidal sacs are disc shaped and connected to the cytoplasmic membrane by small membraneous bridges. In sum, the lumina of all thylakoids (intrathylakoidal space) form one common periplasmic space. Thin sections confirm a paracrystalline arrangement of the photosynthetic complexes in situ. The ontogenic development of the photosynthetic apparatus is discussed based on a structural model derived from serial thin sections.Abbreviations E. Ectothiorhodospira - bchl bacteriochlorophyll - R. Rhodopseudomonas - RC reaction center     

A detailed and validated three dimensional dynamic model of the patellofemoral joint

A detailed 3D anatomical model of the patellofemoral joint was developed to study the tracking, force, contact and stability characteristics of the joint. The quadriceps was considered to include six components represented by 15 force vectors. The patellar tendon was modeled using four bundles of viscoelastic tensile elements. Each of the lateral and medial retinaculum was modeled by a three-bundle nonlinear spring. The femur and patella were considered as rigid bodies with their articular cartilage layers represented by an isotropic viscoelastic material. The geometrical and tracking data needed for model simulation, as well as validation of its results, were obtained from an in vivo experiment, involving MR imaging of a normal knee while performing isometric leg press against a constant 140 N force. The model was formulated within the framework of a rigid body spring model and solved using forth-order Runge-Kutta, for knee flexion angles between zero and 50 degrees. Results indicated a good agreement between the model predictions for patellar tracking and the experimental results with RMS deviations of about 2 mm for translations (less than 0.7 mm for patellar mediolateral shift), and 4 degrees for rotations (less than 3 degrees for patellar tilt). The contact pattern predicted by the model was also consistent with the results of the experiment and the literature. The joint contact force increased linearly with progressive knee flexion from 80 N to 210 N. The medial retinaculum experienced a peak force of 18 N at full extension that decreased with knee flexion and disappeared entirely at 20 degrees flexion. Analysis of the patellar time response to the quadriceps contraction suggested that the muscle activation most affected the patellar shift and tilt. These results are consistent with the recent observations in the literature concerning the significance of retinaculum and quadriceps in the patellar stability.     

A rapid fluorimetric test for lysozyme with purified fluorescamine-labelled peptidoglycan

A sensitive and rapid fluorometric lysozyme assay is described. It is based on the hydrolysis of fluorescamine-labelled peptidoglycan from Micrococcus luteus cell walls. Lysozyme levels as low as 0.1 microgram can be detected.     

A knowledge-based three dimensional model of the Photosystem II reaction center of Chlamydomonas reinhardtii

In this Minireview, a comparison of the binding niches of the PS II cofactors from several existing models of the PS II reaction center is provided. In particular, it discusses a three dimensional model of the Photosystem II (PS II) reaction center including D1, D2 and cytochrome b559 proteins from the green alga Chlamydomonas reinhardtii that was specifically generated for this Minireview. This model is the most complete to date and includes accessory chlorophyll_zs, a manganese cluster, two molecules of -carotene and cytochrome b559, all of which are essential components of the PS II reaction center. The modeling of the D1 and D2 proteins was primarily based on homology with the L and M subunits of the anoxygenic purple bacterial photosynthetic reaction centers. The non-homologous loop regions were built using a sequence specific approach by searching for the best-matched protein segments in the Protein Data Bank, and by imposing the matching conformations on the corresponding D1 and D2 regions. Cytochrome b559 which is in close proximity to D1 and D2 was tentatively modeled in / conformation and docked on the Q_B side of the PS II reaction center according to experimental suggestions. An alternate docking on the Q_A side is also shown for comparison. The cofactors in the PS II reaction center were modeled either by adopting the structures from the bacterial counterparts, when available, with modifications based on existing experimental data or by de novo modeling and docking in the most probable positions in the reaction center complex. The specific features of this model are the inclusion of the tetramanganese cluster (with calcium and chloride ions) in a open, C-shaped structure modeled within the D1/D2/cytochrome b559 complex with D1-D170, D1-E189, D1-D342 and D1-A344 as putative ligands; and the modeling of two cis -carotenes and two accessory chlorophyll_zs liganded by D1-H118 and D2-H117. We also analyzed residues in the model which may be involved in the D1 and D2 inter-protein interactions, as well as residues which may be involved in putative bicarbonate and water binding and transport.     

A heterogeneous in vitro three dimensional model of tumour-stroma interactions regulating sprouting angiogenesis

Angiogenesis, the formation of new blood vessels, is an essential process for tumour progression and is an area of significant therapeutic interest. Different in vitro systems and more complex in vivo systems have been described for the study of tumour angiogenesis. However, there are few human 3D in vitro systems described to date which mimic the cellular heterogeneity and complexity of angiogenesis within the tumour microenvironment. In this study we describe the Minitumour model--a 3 dimensional human spheroid-based system consisting of endothelial cells and fibroblasts in co-culture with the breast cancer cell line MDA-MB-231, for the study of tumour angiogenesis in vitro. After implantation in collagen-I gels, Minitumour spheroids form quantifiable endothelial capillary-like structures. The endothelial cell pre-capillary sprouts are supported by the fibroblasts, which act as mural cells, and their growth is increased by the presence of cancer cells. Characterisation of the Minitumour model using small molecule inhibitors and inhibitory antibodies show that endothelial sprout formation is dependent on growth factors and cytokines known to be important for tumour angiogenesis. The model also shows a response to anti-angiogenic agents similar to previously described in vivo data. We demonstrate that independent manipulation of the different cell types is possible, using common molecular techniques, before incorporation into the model. This aspect of Minitumour spheroid analysis makes this model ideal for high content studies of gene function in individual cell types, allowing for the dissection of their roles in cell-cell interactions. Finally, using this technique, we were able to show the requirement of the metalloproteinase MT1-MMP in endothelial cells and fibroblasts, but not cancer cells, for sprouting angiogenesis.     

A view of the three dimensional structure of globular proteins

A view of the three dimensional structure of globular proteins based on continuous networks of hydrogen bonds is proposed. Active sites of enzymes and ion sites are prominent and, within the networks, there are islands of hydrophobic regions giving an overall piebald effect to the appearance of the molecule. This point of view was originally suggested by the results of quantum mechanical computations on the coupling between hydrogen bonds. A formalism for the total energy of a globular protein in water is also suggested.The study of five lines of experimental evidence supports this suggestion. The analysis of the experimental X-ray data for ten globular proteins, using the NETWORK program, revealed the existence of these hydrogen bond networks; X-ray data showed that water molecules tend to occupy fixed positions relative to the protein molecule; a survey has shown that water molecules tend to occupy specific positions relative to the hydrogen bonding side chains; experimental evidence on the bulk properties of lysozyme showed that there exist tightly bound water molecules; graphics studies of the ribonucleaseA molecule demonstrated the networks and the piebald effect. This point of view is pictorially simple and, to illustrate the use of such networks, we discuss the simple ion pairs which occur as substructures within the networks.     

A biophysical model of lysozyme self-association.

The concentration dependence of the self-association of hen egg-white lysozyme was studied spectrophotometrically at pH 6, 25 degrees C, and low ionic strength within a concentration range of 2.5-50 micrograms/ml. Of several possible mathematical models, an ideal or nearly ideal two-stage model representing an equilibrium between monomers and dimers and between dimers and trimers best describes the data. The dimerization and trimerization constants were found to be 2.5 x 10(-2) and 38 x 10(-2). Dialysis experiments confirmed that the mechanism involves three associating species. A "head-to-tail" contact between the associating sites was inferred from dialysis studies of the effect of indole and imidazole derivatives on lysozyme self-association.     

A novel mathematical model of solid-state digestion

The proposed model of solid-state digestion assumes the development of a distinct zone of depleted waste around each viable seed particle. Biodegradation is envisaged to occur chiefly in thin shells at the interface between depleted and raw waste, at a rate proportional to the interfacial area. These shells are estimated to expand at a constant 5 cm/year. The reaction thus accelerates following a square law until neighbouring shells meet. Deceleration is then rapid as the shells merge. The proposed model agrees with available lysimeter data; first-order decay kinetics do not.     

Effects of fluid structure interaction in a three dimensional model of the spinal subarachnoid space

It is unknown whether spinal cord motion has a significant effect on cerebrospinal fluid (CSF) pressure and therefore the importance of including fluid structure interaction (FSI) in computational fluid dynamics models (CFD) of the spinal subarachnoid space (SAS) is unclear. This study aims to determine the effects of FSI on CSF pressure and spinal cord motion in a normal and in a stenosis model of the SAS. A three-dimensional patient specific model of the SAS and spinal cord were constructed from MR anatomical images and CSF flow rate measurements obtained from a healthy human being. The area of SAS at spinal level T4 was constricted by 20% to represent the stenosis model. FSI simulations in both models were performed by running ANSYS CFX and ANSYS Mechanical in tandem. Results from this study show that the effect of FSI on CSF pressure is only about 1% in both the normal and stenosis models and therefore show that FSI has a negligible effect on CSF pressure.     

Evaluating a three dimensional model of diffuse photosynthetically active radiation in maize canopies

Diffuse photosynthetically active radiation (DPAR) is important during overcast days and for plant parts shaded from the direct beam radiation. Simulation of DPAR interception by individual plant parts of a canopy, separately from direct beam photosynthetically active radiation (PAR), may give important insights into plant ecology. This paper presents a model to simulate the interception of DPAR in plant canopies. A sub-model of a virtual maize canopy was reconstructed. Plant surfaces were represented as small triangular facets positioned according to three-dimensionally (3D) digitized data collected in the field. Then a second sub-model to simulate the 3D DPAR distribution in the canopy was developed by dividing the sky hemisphere into a grid of fine cells that allowed for the anisotropic distribution of DPAR over the sky hemisphere. This model, DSHP (Dividing Sky Hemisphere with Projecting), simulates which DSH (Divided Sky Hemisphere) cells are directly visible from a facet in the virtual canopy, i.e. not obscured by other facets. The DPAR reaching the center of a facet was calculated by summing the amounts of DPAR present in every DSH cell. The distribution of DPAR in a canopy was obtained from the calculated DPARs intercepted by all facets in the canopy. This DSHP model was validated against DPAR measurements made in an actual maize (Zea mays L.) canopy over selected days during the early filling stage. The simulated and measured DPAR at different canopy depths showed a good agreement with a R ² equaling 0.78 (n=120).     

A two dimensional model for saccade generation

A model for the generation of oblique saccades is constructed by extending and modifying the one dimensional local feedback model. It is proposed that the visual system stores target location in inertial coordinates, but that the feedback loop which guides saccades works in retinotopic coordinates. To achieve straight trajectories for centripetal and centrifugal saccades in all meridians, a comparator computes motor error as a vector and uses the vectorial error signal to drive two orthogonally-acting burst generators. The generation of straight saccade trajectories when the extraocular muscles are of unequal strengths requires the introduction of a burst-tonic cell input to motor neurons. The model accounts for the results of two-site stimulation of the superior colliculus and frontal eye fields by allowing simultaneous activation of more than one comparator. The postulated existence of multiple comparators suggests that motor error may be computed topographically.     

Chromatin structure of the chicken lysozyme gene domain as determined by chromatin fractionation and micrococcal nuclease digestion

The chromatin structure encompassing the lysozyme gene domain in hen oviduct nuclei was studied by measuring the partitioning of coding and flanking sequences during chromatin fractionation and by analyzing the nucleosome repeat in response to micrococcal nuclease digestion. Following micrococcal nuclease digestion, nuclei were sedimented to obtain a chromatin fraction released during digestion (S1) and then lysed in tris(hydroxymethyl)aminomethane-(ethylenedinitrilo)tetraacetic acid-[ethylenebis(oxyethylenenitrilo)]tetraacetic acid and centrifuged again to yield a second solubilized chromatin fraction (S2) and a pelleted fraction (P2). By dot-blot hybridization with 14 specific probes, it is found that the fractionation procedure defines three classes of sequences within the lysozyme gene domain. The coding sequences, which partition with fraction P2, are flanked by class I flanking sequences, which partition with fractions S1 and P2 and which extend over 11 kilobases (kb) on the 5'side and probably over about 4 kb on the 3' side. The partitioning of class II flanking sequences, which are located distal of class I flanking sequences, is different from that of class I flanking sequences. Coding sequences lack a canonical nucleosome repeat, class I flanking sequences possess a disturbed nucleosome repeat, and class II flanking sequences generate an extended nucleosomal ladder. Coding and class I flanking sequences are more readily digested by micrococcal nuclease than class II flanking sequences and the inactive beta A-globin gene. In hen liver, where the lysozyme gene is inactive, coding and class I flanking sequences fractionate into fractions S2 and P2.(ABSTRACT TRUNCATED AT 250 WORDS)     

The action of lysozyme on peptidoglycan with N-unsubstituted glucosamine residues. Isolation of glycan fragments and their susceptibility to lysozyme.

1. A peptidoglycan preparation N-acetylated at about 30% of glucosamine residues was obtained by the treatment of the lysozyme-resistant cell wall paptidoglycan of Bacillus cereus with acetic anhydride at pH 7. Fractionation of dialyzable material resulting from lysozyme digestion of the glycan component of this peptidoglycan preparation yielded five oligosaccharides designated as S1 to S5 besides the disaccharide GlcNAc-MurAc. 2. Oligosaccharide S3, which accounted for about 30% of the disaccharide units recovered as disaccharides and oligosaccharides, was identified as GlcN-MurAc-GlcNAc-MurAc. Oligosaccharide S1, accounting for about 20% of the disaccharide units recovered, was characterized as GlcN-MurAc-GlcN-MurAc-GlcNAc-MurAc, while oligosaccharide S2, present in a smaller amount, as GlcNAc-MurAc-GlcN-MurAc-glcNAc-MurAc. Oligosaccharides S4, and S5, present in small amounts, were identified as GlcNAc-MurAc-GlcNAc-MurAc and MurAc-GlcNAc-MurAc, respectively. 3. Oligosaccharides S1, S3 and S5 proved to be completely insusceptible to lysozyme, whereas S2 was digsted by lysozyme to produce GlcNAc-MurAc and S3. S1 was found to act as a more potent inhibitor than S3 in lysozyme-catalyzed digestion of polysaccharides. 4. The results obtained show that the lysozyme-catalyzed hydrolysis of peptidoglycan oligosaccharides had an obligatory requirement for the N-acetyl group on the glucosamine residue located in subsite C in the enzyme-substrate complex.     

A three dimensional finite element study on dental implant design

Implant diameter and length are the most effective parameters affecting stress distribution in surrounding bones. In order to extract simplified design equations to better understand implants behavior, 25 different implant designs with gradual increase in diameter and length were analyzed in 3D using Finite Element Method. Four types of loadings were applied on each design: tension of 50 N, compression of 100 N, bending of 20 N, and torque of 2 Nm to derive design curves.Analysis of results showed that increasing implant diameter and length generate better stress distribution on spongy and cortical bones. Approximate design equations and curves were obtained as a result of this study.     

A kinetic model for anaerobic digestion of biological sludge

The principal objective of this study was the development and evaluation of a comprehensive kinetic model capable of predicting digester performance when fed biological sludge, preliminary conversion mechanisms such as cell death, lysis, and hydrolysis responsible for rendering viable biological sludge organisms to available substrate were studied in depth. The results of this study indicate that hydrolysis of the dead, particulate biomass-primarily consisting of protein-is the slowest step, and therefore kinetically controls the overall process of anaerobic digestion of biological sludge. A kinetic model was developed which could accurately describe digester performance and predict effluent quality.