Crystal structure of mouse RhoA:GTPγS complex in a centered lattice

RhoA, a member of the Rho sub-family of small GTPases, plays a significant signaling role in cell morphogenesis, migration, neuronal development, cell division and adhesion. So far, 4 structures of RhoA:GDP/GTP analogs and 14 structures of RhoA in complex with other proteins have been reported. All RhoA:GDP/GTP analog complexes have been crystallized in primitive lattices and RhoA is monomeric. This is the first time a RhoA:GTP analog complex has been crystallized as a dimer in a centered lattice. The present structure reveals structural differences in the switch-I (residues 28?C42) and switch-II (residues 61?C66) regions, which play important roles in interactions with downstream targets to transduce signals, when compared to the previously reported structures.     

Formation of crystalline arrays of chlorophyll a/b - light-harvesting protein by membrane reconstitution.

The structure of the major protein constituent of photosynthetic membranes in higher plants, the chlorophyll a/b-light harvesting complex (LHC), was studied by x-ray diffraction and electron microscopy. The LHC was purified from Triton X-100 solubilized thylakoid membranes of the pea, and contained 6 mol of chlorophylls a and b per mole of a polypeptide of 27,000 molecular weight. X-ray diffraction showed that in the presence of 10 mM MgCl2, purified LHC forms planar aggregates that stack with a period of 51 A. Within each layer, LHC molecules pack with a center-to-center distance of 85 A but without long-range order. However, when LHC is incorporated into single-walled vesicles of plant lecithin, the addition of NaCl above 10 mM, or MgCl2 above 2 mM, led to the formation of plaques of hexagonal lattices, with a lattice constant of 125 A. The large domain size and high degree of order in the plane of the membrane are evident from the sharp lattice lines observed to 7 A resolution on the equator of the x-ray pattern. Freeze-fracture electron micrographs demonstrated an aligned stacking of the lattices in adjacent membranes, resulting in crystallinity in the third dimension over short distances. Micrographs of negatively stained membranes revealed a hexagonal lattice of the same lattice constant, formed by surface-exposed parts of the LHC molecules which are probably responsible for the ordered stacking of lattices. In both the LHC aggregates and in the reconstituted membrane lattices the diffracted x-ray intensities at 10-A spacing on the equator indicate that the LHC molecule contains paralled alpha-helices or beta-sheets that are oriented perpendicular to the planar arrays.     

Dynamics of mutation and recombination in a replicating population of complementing, defective viral genomes

In a previous study, we documented that serial passage of a biological clone of foot-and-mouth disease virus (FMDV) at high multiplicity of infection (moi) in cell culture resulted in viral populations dominated by defective genomes that included internal in-frame deletions, affecting the L and capsid-coding regions, and were infectious by complementation. In the present study, analyses of the defective genomes present in individual viral plaques, and of consensus nucleotide sequences determined for the entire genomes of sequential samples, have revealed a continuous dynamics of mutation and recombination. At some points of high genetic instability, multiple minority genomes with different internal deletions co-existed in the population. At later passages, a new defective RNA arose and displaced a related, previously dominant RNA. Nucleotide sequences of the different genomic forms found in sequential isolates have revealed an accumulation of mutations at an average rate of 0.12 substitutions per genome per passage. At the regions around the deletion sites, substantial, minor or no nucleotide sequence identity is found, suggesting relaxed sequence requirements for the occurrence of internal deletions. Competition experiments indicate a selective advantage of late phase defective genomes over their precursor forms. The defective genome-based FMDV retained an expansion of host cell tropism, undergone by the standard virus at a previous stage of the same evolutionary lineage. Thus, despite a complex dynamics of mutation and recombination, and phases of high genetic instability, a biologically relevant phenotypic trait was stably maintained after the evolutionary transition towards a primitive genome segmentation. The results extend the concept of a complex spectrum of mutant genomes to a complex spectrum of defective genomes in some evolutionary transitions of RNA viruses.     

The spread of infectious diseases in spatially structured populations: an invasory pair approximation

The invasion of new species and the spread of emergent infectious diseases in spatially structured populations has stimulated the study of explicit spatial models such as cellular automata, network models and lattice models. However, the analytic intractability of these models calls for the development of tractable mathematical approximations that can capture the dynamics of discrete, spatially-structured populations. Here we explore moment closure approximations for the invasion of an SIS epidemic on a regular lattice. We use moment closure methods to derive an expression for the basic reproductive number, R(0), in a lattice population. On lattices, R(0) should be bounded above by the number of neighbors per individual. However, we show that conventional pair approximations actually predict unbounded growth in R(0) with increasing transmission rates. To correct this problem, we propose an 'invasory' pair approximation which yields a relatively simple expression for R(0) that remains bounded above, and also predicts R(0) values from lattice model simulations more accurately than conventional pair and triple approximations. The invasory pair approximation is applicable to any spatial model, since it takes into account characteristics of invasions that are common to all spatially structured populations.     

The effects of topology and relative density of lattice liners on traumatic brain injury mitigation

This paper evaluates the effects of topology and relative density of helmet lattice liners on mitigating Traumatic Brain Injury (TBI). Finite Element (FE) models of new lattice liners with prismatic and tetrahedral topologies were developed. A typical frontal head impact in motorcycle accidents was simulated, and linear and rotational accelerations of the head were recorded. A high-fidelity FE model of TBI was loaded with the accelerations to predict the brain response during the accident. The results show that prismatic lattices have better performance in preventing TBI than tetrahedral lattices and EPS that is typically used in helmets. Moreover, varying the cell size through the thickness of the liner improves its performance, but this effect was marginal. The relative density also has a significant effect, with lattices with lower relative densities providing better protection. Across different lattices studied here, the prismatic lattice with a relative density of 6% had the best performance and reduced the peak linear and rotational accelerations, Head Injury Criterion (HIC), brain strain and strain rate by 48%, 37%, 49%, 32% and 65% respectively, compared to the EPS liner. These results can be used to guide the design of lattice helmet liners for better mitigation of TBI.     

Reexamination of the reality or artifacts of the microtrabeculae

The polyethylene glycol (PEG) method revealed that model systems such as erythrocytes and protein solutions, which are supposed to lack structured components, exhibit lattice structures not unlike the microtrabeculae. The compactness of the lattice was dependent on the concentration of proteins. The gelated state of gelatin exhibited lattices more compact than those of the solated state at any given concentration. Comparison of images by PEG and rapid-freezing, deep-etching replica methods showed no basic differences in the ultrastructure of the intestinal epithelial cell. This indicates that the PEG method, including chemical fixation, produces little, if any, disorganization of the cytoskeleton. All of the present findings suggest that cytoplasmic protein, nonstructure-bound or structure-forming, might be present in intact cells which could form microtrabecular structures when specimens are fixed by chemical fixatives without any extractions. Therefore, the microtrabeculae should generally be regarded as a simple marker for the presence of proteinaceous macromolecules. It is also suggested that the microtrabecular lattice, as a whole, might represent a gelated state in a given compartment when another, looser lattice is simultaneously present in the same compartment, i.e., within a single cell.     

Increasing Biomass Production on Limited Land Area Through an Optimal Planting Arrangement

Planting density is a primary consideration in silviculture; however, planting arrangement is often ignored. Most, if not all, forest plantations are arranged in rectangular or square lattices (i.e., grids). Using a simple mathematical model, we investigate the potential influence of planting arrangement on planting density, biomass yield, and rotation period by assuming that efficiently arranging trees is similar to packing congruent circles on a plane. The hexagonal lattice achieves the densest circle packing on a plane; therefore, a hexagonal or triangular lattice arrangement of stems provides the highest planting density for a given spacing. Using packing density to quantify arrangement efficiency, tree crowns in a hexagonal lattice fill approximately 90.7% of available area at initial canopy contact, while tree crowns in a square lattice fill approximately 78.5% of available area at initial canopy contact. The hexagonal lattice permits about a 15% higher density than the square lattice, which allows canopy closure to occur earlier without any change in individual tree growth. Short rotation woody crop (SRWC) systems are excellent candidates under the model’s assumptions of level stand with even-age monoculture. If belowground resources are non-limiting, a hexagonal lattice arrangement shortens rotation period and thus optimizes the biomass yield per land area over time. Higher productivity over time is central to sustainable and efficient use of limited area for bioenergy and biomass products.     

Modulation of sulfated glycosaminoglycan and small proteoglycan synthesis by the extracellular matrix

Cell culture in collagen lattice is known to be a more physiological model than monolayer for studying the regulation of extracellular matrix protein deposition. The synthesis of sulfated glycosaminoglycans (GAG) and dermatan sulfate (DS) proteoglycans by 3 cell strains were studied in confluent monolayers grown on plastic surface, in comparison to fully retracted collagen lattices. Cells were labelled with³⁵S-sulfate, followed by GAG and proteoglycan analysis by cellulose acetate and SDS-polyacrylamide gel electrophoresis, respectively. The 3 cell strains contracted the lattice in a similar way. In monolayer cultures, the major part of GAG was secreted into culture medium whereas in lattice cultures of dermal fibroblasts and osteosarcoma MG-63 cells but not fibrosarcoma HT-1080 cells, a higher proportion of GAGs, including dermatan sulfate, was retained within the lattices. Small DS proteoglycans, decorin and biglycan, were detected in fibroblasts and MG-63 cultures. They were preferentially trapped within the collagen gel. In retracted lattices, decorin had a higher M_r than in monolayer. Biglycan was detected in monolayer and lattice cultures of MG-63 cells but in lattice cultures only in the case of fibroblasts. In this last case, an up regulation of biglycan mRNA steady state level and down regulation of decorin mRNA was observed, in comparison to monolayers, indicating that collagen can modulate the phenotypical expression of small proteoglycan genes.Supported by a fellowship from the Centre National de la Recherche Scientifique     

Increased gelsolin expression and retarded collagen lattice contraction with smooth muscle cells from Crohn's diseased intestine

Intestinal smooth muscle cells (SMC) produce the fibrotic tissue, strictures, that characterize Crohn's disease. These SMC change their phenotype from a contractile muscle form to an inflammation-responsive form that migrates and synthesizes a collagen matrix. It is postulated that the inflammatory responsive SMC form associates differently with its surrounding collagen matrix compared to the normal SMC form. SMC derived from Crohn's diseased and uninvolved bowel were sustained in cell culture. Cultured SMC incorporated in collagen lattices have the capacity to reduce the size of that lattice, referred to as lattice contraction. At day 2, Crohn's SMC-populated collagen lattices were reduced to 21% of their initial area, while non-Crohn's SMC collagen lattices were reduced to 8%. Crohn's SMC demonstrate retarded lattice contraction compared to non-Crohn's SMC. When grown in monolayer culture, Crohn's-derived SMC cover 30% more area than non-Crohn's SMC. By Western blot analysis Crohn's SMC express more gelsolin, an actin-binding protein found elevated in cells exhibiting increased cell motility. Was the increased expression of gelsolin related to retarded collagen lattice contraction? Intracellular levels of gelsolin were elevated by the electroporation of plasma gelsolin protein into suspended non-Crohn's SMC. When incorporated in collagen lattices, gelsolin loaded cells showed retarded lattice contraction compared to SMC loaded with albumin. Crohn's SMC show increased expression of gelsolin, which may be associated with a diminished capacity to reorganize collagen fiber bundles. It is suggested that increased concentrations of gelsolin in Crohn's SMC is consistent with enhanced cell migration as a consequence of the inflammatory state of Crohn's diseased intestine.     

Insulin-like growth factor-I (IGF-I) stimulates protein synthesis and collagen gene expression in monolayer and lattice cultures of fibroblasts.

Fibroblasts cultivated in three-dimensional tissue-like matrices are characterized by a slowed metabolism and a decrease of protein synthesis, unless they are submitted to physical tensions. We checked the effects of insulin like growth factor-I (IGF-I), known as a potent stimulator of mitogenesis and protein synthesis for many cell types, in various models of cultures: confluent monolayers, collagen lattices, non-retracting or retracting fibrin lattices. IGF-I (1-100 ng.ml-1) had no effect on cell divisions in lattice cultures. It was able to stimulate collagen lattice retraction when the medium was supplemented with low concentrations of serum. IGF-I at 10 or 100 ng.ml-1 stimulated collagen and non-collagen syntheses in all culture systems, but stimulation of collagen synthesis only began at the highest concentration (100 ng.ml-1) in retracted lattices. Northern blot and dot-blot analyses of mRNAs extracted from monolayer cultures of fibroblasts showed that IGF-I stimulated pro alpha 1(I) collagen synthesis at the pretranslational level. Cycloheximide (7.5 micrograms.ml-1) completely inhibited pro alpha 1(I) collagen gene expression induced by IGF-I. These results show that IGF-I is a potent stimulus for protein synthesis and collagen gene expression in monolayers and tridimensional cultures of fibroblasts, but that it exerts no mitogenic activity in tridimensional lattices. Synergistic associations of IGF-I with other growth factors will have to be found in order to reverse the quiescent status of fibroblasts in lattices.     

X-ray diffraction analysis of wet isolated bovine rod outer segment disks. A dehydration study

Sequences of X-ray diffraction patterns were obtained from dehydrating, artificially oriented multilayers of isolated, bovine rod outer segment disks. A direct-phase analysis was applied to highly hydrated specimens to determine sequences of low resolution (approx. 30 Å) electron density profiles of the disks as dehydration proceeded. The profiles were found to evolve smoothly as the multilayer lattice simultaneously shrank and became increasingly ordered. The bilayer profiles were largely invariant under dehydration and the evolution of the diffraction consistent with simple decreases in fluid spacings. The specimens were observed to phase separate into characteristic primary and a secondary lattices when the multi-layer became too dehydrated. The small unit cell size of the secondary lattice was suggestive of a lipid phase. Large changes in the diffraction patterns from phase separated specimens were observed upon bleaching of the specimen. The changes were consistent with a reversible disordering of the primary lattice.     

Comparative studies of S-layer proteins from Bacillus stearothermophilus strains expressed during growth in continuous culture under oxygen-limited and non-oxygen-limited conditions.

The specific properties of S-layer proteins from three different Bacillus stearothermophilus strains revealing oblique, square, or hexagonal lattice symmetry were preserved during growth in continuous culture on complex medium only under oxygen-limited conditions in which glucose was used as the sole carbon source. When oxygen limitation was relieved, amino acids became metabolized, cell density increased, and different S-layer proteins from wild-type strains became rapidly replaced by a new common type of S-layer protein with an apparent subunit molecular weight of 97,000 which assembled into an identical oblique (p2) lattice type. During switching from wild-type strains to variants, patches of the S-layer lattices characteristics for wild-type strains, granular regions, and areas with oblique lattice symmetry could be observed on the surface of individual cells from all organisms. The granular regions apparently consisted of mixtures of the S-layer proteins from the wild-type strains and the newly synthesized p2 S-layer proteins from the variants. S-layer proteins from wild-type strains possessed identical N-terminal regions but led to quite different cleavage products upon peptide mapping, indicating that they are encoded by different genes. Chemical analysis including N-terminal sequencing and peptide mapping showed that the oblique S-layer lattices synthesized under increased oxygen supply were composed of identical protein species.     

The Role of Membrane-Mediated Interactions in the Assembly and Architecture of Chemoreceptor Lattices

In vivo fluorescence microscopy and electron cryo-tomography have revealed that chemoreceptors self-assemble into extended honeycomb lattices of chemoreceptor trimers with a well-defined relative orientation of trimers. The signaling response of the observed chemoreceptor lattices is remarkable for its extreme sensitivity, which relies crucially on cooperative interactions among chemoreceptor trimers. In common with other membrane proteins, chemoreceptor trimers are expected to deform the surrounding lipid bilayer, inducing membrane-mediated anisotropic interactions between neighboring trimers. Here we introduce a biophysical model of bilayer-chemoreceptor interactions, which allows us to quantify the role of membrane-mediated interactions in the assembly and architecture of chemoreceptor lattices. We find that, even in the absence of direct protein-protein interactions, membrane-mediated interactions can yield assembly of chemoreceptor lattices at very dilute trimer concentrations. The model correctly predicts the observed honeycomb architecture of chemoreceptor lattices as well as the observed relative orientation of chemoreceptor trimers, suggests a series of “gateway” states for chemoreceptor lattice assembly, and provides a simple mechanism for the localization of large chemoreceptor lattices to the cell poles. Our model of bilayer-chemoreceptor interactions also helps to explain the observed dependence of chemotactic signaling on lipid bilayer properties. Finally, we consider the possibility that membrane-mediated interactions might contribute to cooperativity among neighboring chemoreceptor trimers.     

Experimental and numerical exploration of intrinsic localized modes in an atomic lattice

This review focuses attention on the experimental studies of intrinsic localized modes (ILMs) produced in driven atomic lattices. Production methods involve the application of modulational instability under carefully controlled conditions. One experimental approach is to drive the atomic lattice far from equilibrium to produce ILMs, the second is to apply a driver of only modest strength but nearby in frequency to a plane wave mode so that a slow transformation from large amplitude standing waves to ILMs takes place. Since, in either case, the number of ILMs produced is small, the experimental observation tool appropriate for this task is four-wave mixing. This nonlinear detection technique makes use of the nonlinearity associated with an ILM to enhance its signal over that produced by the more numerous, but linear, spin waves. The final topic deals with numerical simulations of a nonlinear nanoscale atomic lattice where the new feature is running ILMs.     

Contribution of the Plasmin/Matrix Metalloproteinase Cascade to the Retraction of Human Fibroblast Populated Collagen Lattices

To assess the contribution of the plasmin/matrix metalloproteinase cascade in lattices retraction, human gingival fibroblast-populated collagen lattices were supplemented with plasminogen. The rate of lattice retraction was enhanced by addition of plasminogen. This effect was concomitant to plasmin generation, prostromelysin-1 and procollagenase activation. Plasminogen-mediated initiation of that proteolytic cascade was accompanied by conspicuous changes in cell morphology and collagen fibers organization. At day 1 of culture fibroblasts shifted from a rounded (control) to an elongated (in presence of plgn) shape. At the latest stage of retraction, intense vacuolization around fibroblasts was noticed in plgn-supplemented lattices which paralleled the increased collagen degradation. Plgn-enhancing influence on the initial phase of lattice retraction could be totally annihilated by either aprotinin or Batimastat. Those data emphasize the crucial importance of the plasmin–MMP proteolytic cascade in granulation tissue retraction in a healing wound.     

Exciton percolation III. Stochastic and coherent migration in binary and ternary random lattices

We develop a method for calculating energy migration in random heterogeneous aggregates, with potential application to the primary process in photosynthetic units. A Monte Carlo technique is employed to study several types of random walk motion in a random binary lattice. Our computations include 2 and 3 dimensional lattices of different topology and employ correlated steps with a Gaussian distribution of directional memory. The effects of the characteristics of the motion and its parameters are displayed and discussed. The lower threshold for efficient visitation by the walker is given by the critical percolation concentration. However, a higher threshold is found in the case of coherent motion. This new “turning point” appears to play an important role in the process of exciton transport. The exciton percolation formalism is utilized, giving results for ternary random lattices where the third component is very dilute and acts as a sensor. The results are applied to a system representing the ¹1B_2u, naphthalene exciton dynamics in an isotopic and chemically mixed crystal, which by itself is supposed to mimic the exciton transport in the photosynthetic units of green plants. Physically reasonable parameters, trends and limits are discussed. Also, an analytical solution is derived and tested for a physically reasonable limit of semicoherent motion in a perfect lattice. The ramification of this work on bioexciton transfer is discussed, especially concerning the light harvesting units in green plants. It leads to a simple minded model that rationalized the ratio of antenna to active-center molecules. Our most important result is that incoherent exciton transfer, i.e. simple random walk, is the most efficient process for significantly heterogeneous aggregates.     

Fibroblast contraction of collagen lattices in vitro: Inhibition by chronic inflammatory cell mediators

Fibroblast-populated collagen lattices (FPCL), prepared in petri dishes with serum-containing culture medium and incubated at 37°C, undergo progressive and symmetric contraction (reduction in size) over a period of days. The in vitro contraction process requires viable cells with intact cytoskeletal elements, is associated with cell elongation, and is believed to represent a fibroblast function which also occurs in vivo during wound healing and tissue fibrosis. We report that soluble mediators elaborated by chronic inflammatory cells cultured in vitro, when added to FPCL, inhibit lattice contraction. Granulomas, isolated from the liver of Schistosoma mansoni-infected mice, secrete a factor(s) with an estimated molecular weight between 13,700 and 43,000 daltons (gel filtration: Sephadex G-200) and pl = 6 (preparative isoelectrofocusing in granular gel) which inhibits lattice contraction but is not toxic to fibroblasts. Supernatants (cell-free conditioned culture medium) of cultured macrophages isolated from these granulomas also contain this activity. The contraction inhibitory activity present in granuloma culture supernatants is abrogated by the addition of indomethacin to the lattices, while the addition of prostaglandin E₂ (PGE₂) alone to lattices inhibits contraction. Furthermore, culture supernatants interfere with fibroblast elongation in lattices. We propose that the ability of fibroblasts to contract collagen lattices in vitro and a fibrotic mass in vivo may be regulated by soluble products of chronic inflammatory cells, including macrophages. This process may be mediated by fibroblast-derived prostaglandins which alter cytoskeletal functions and has implications for understanding regulation of tissue fibrogenesis in a variety of diseases.     

Mapping the interactions of the single-stranded DNA binding protein of bacteriophage T4 (gp32) with DNA lattices at single nucleotide resolution: polynucleotide binding and cooperativity

We here use our site-specific base analog mapping approach to study the interactions and binding equilibria of cooperatively-bound clusters of the single-stranded DNA binding protein (gp32) of the T4 DNA replication complex with longer ssDNA (and dsDNA) lattices. We show that in cooperatively bound clusters the binding free energy appears to be equi-partitioned between the gp32 monomers of the cluster, so that all bind to the ssDNA lattice with comparable affinity, but also that the outer domains of the gp32 monomers at the ends of the cluster can fluctuate on and off the lattice and that the clusters of gp32 monomers can slide along the ssDNA. We also show that at very low binding densities gp32 monomers bind to the ssDNA lattice at random, but that cooperatively bound gp32 clusters bind preferentially at the 5′-end of the ssDNA lattice. We use these results and the gp32 monomer-binding results of the companion paper to propose a detailed model for how gp32 might bind to and interact with ssDNA lattices in its various binding modes, and also consider how these clusters might interact with other components of the T4 DNA replication complex.     

The innermost chorionic layer of Drosophila. II. Three-dimensional structure determination of the 90 degrees crystal form by electron microscopy

The innermost chorionic layer (ICL) within egg shells of Drosophila is composed of a family of related, thin three-dimensional crystals that form a continuous sheath encapsulating the egg shell lumen. Junctions formed by interdigitating lattices play a central role in the construction of this macroscopic assembly. The three-dimensional structure of a two-dimensional crystal isolated from the ICL, with a primitive lattice angle delta of 90 degrees, has been determined from a complete tilt series of a negatively contrasted specimen at a resolution of 25 A. Inspection of the three-dimensional transform after data merging revealed that the space group is c222 and this symmetry was employed to generate a three-dimensional structure. The basic structural unit of the ICL is an octamer, described formally as a tetramer of dimers with point group symmetry 222. There are two classes of dimer in the octamer designated alpha and beta. The chorin octamer is composed of two classes of bent dimers, which make intramolecular contacts at the top and bottom of the molecule. The alpha-dimers are curved outwards away from the crystallographic 2-fold axis, while the beta-dimers are curved towards the molecular center. In addition, lattice contacts are formed primarily by beta-chorin dimers at both the top and bottom surfaces of the unit cell. The molecular weight of a chorin octamer determined from the analysis is about 6 X 10(5). The conformation of the chorin octamer determined here suggests that permutations of a basic molecular mechanism may be adequate to explain both the observed lattice polymorphisms of the ICL and the formation of interplate junctions necessary for the assembly of the macroscopic sheath.     

Results of primary culture of malignant melanoma explants by the so-called compact covering lattices method

Results from primary cultures of malignant melanomas explants can be amplified. The original method is based upon collagen lattices use. The collagen is retracted by human fibroblasts obtained from human angiomas. The cultured tumor fragments are covered by the lattices, which are now adhering to the flask. Six primitive malignant melanomas and three cutaneous metastases were cultured according to the classical method and the new method described here. Compact covering lattices allow a regular melanocytic redifferentiation either in primitive malignant melanomas or in cutaneous metastases. The results point out: the microenvironment's role in tumour growth; the different behaviour of primitive tumours and metastases.