Studies on shell formation. VII. The submicroscopic structure of the shell of the oyster Crassostrea virginica

The submicroscopic structure of the growing surface of the shell of the oyster, Crassostrea virginica, was studied by means of shadowed replicas. The outer edge of the prismatic region consists of a fine grained matrix enclosing crystals, the surfaces of which show a finely pebbled structure. Crystal size varies continously from 0.01 micro to 8 micro. The matrix surface shows no evidence of fibrous structure. The outer portions of the prismatic region exhibit a tile-like arrangement of large crystals separated by granular matrix 0.02 to 0.08 micro in thickness. The exposed crystal surfaces have indentations of varying form which appear as roughly parallel grooves spaced at intervals of approximately 0.3 micro. The final form of this region is believed to result from the random distribution of crystal seeds, which grow without orientation and through coalescence and growth come into contact, producing polygonal areas. The crystal arrangement of the nacreous region is one of overlapping rows of crystals in side to side contact, and with one end of each crystal free, permitting continued increase in length. Crystal angles and plane indices are presented.     

Studies on Shell Formation : VIII. Electron Microscopy of Crystal Growth of the Nacreous Layer of the Oyster Crassostrea virginica

Electron microscope observations have been made by means of the replica method on growth processes of calcite crystals of the nacreous layer of the shell of the oyster, Crassostrea virginica. Layer formation is initiated by the secretion of a conchiolin matrix and the deposition of rounded crystal seeds on or in this material. In some areas crystal seeds are elongate and within a given area show a similar orientation, probably due to slower deposition. The seeds appear to increase in size by dendritic growth, and smaller seeds become incorporated into larger ones which come into contact to form a single layer. With further growth, crystals overlap, forming a step-like arrangement. The direction of growth is frequently different in neighboring regions. Crystal seeds deposited on crystal surfaces are usually elongate and oriented. Well developed crystals have a tabular idiomorphic form and are parallel in their growth. Rounded and irregular crystals were also observed. The crystals show reticular structure with units of the order of 100 A and striations corresponding with the rhombohedral axes of the crystals. The role of the mantle is discussed in relation to the growth patterns of crystals and shell structure.     

STUDIES ON SHELL FORMATION : IX. An Electron Microscope Study of Crystal Layer Formation in the Oyster

Details of crystal growth in the calcitostracum of Crassostrea virginica have been studied with the purpose of analyzing the formation of the overlapping rows of oriented tabular crystals characteristic of this part of the shell. Crystal elongation, orientation, and dendritic growth suggest the presence of strong concentration gradients in a thin layer of solution in which crystallization occurs. Formation of the overlapping rows can be explained by three processes observed in the shell: a two-dimensional tree-like dendritic growth in which one set of crystal branchings creeps over an adjacent set of branchings; three-dimensional dendritic growth; and growth by dislocation of crystal surfaces. Multilayers of crystals may thus be formed at one time. This is favored by infrequent secretion of a covering organic matrix which would inhibit crystal growth. The transitional zone covering the outer part of the calcitostracum and the inner part of the prismatic region is generally characterized by aggregates of small crystals with definite orientation. Growth in this zone appears to take place in a relatively homogeneous state of solution without strong concentration gradients. Thin membranes and bands of organic matrix were commonly observed in the transitional zone bordering the prismatic region. The membrane showed a very fine oriented network pattern.     

Studies on shell formation. VIII. Electron microscopy of crystal growth of the nacreous layer of the oyster Crassostrea virginica

Electron microscope observations have been made by means of the replica method on growth processes of calcite crystals of the nacreous layer of the shell of the oyster, Crassostrea virginica. Layer formation is initiated by the secretion of a conchiolin matrix and the deposition of rounded crystal seeds on or in this material. In some areas crystal seeds are elongate and within a given area show a similar orientation, probably due to slower deposition. The seeds appear to increase in size by dendritic growth, and smaller seeds become incorporated into larger ones which come into contact to form a single layer. With further growth, crystals overlap, forming a step-like arrangement. The direction of growth is frequently different in neighboring regions. Crystal seeds deposited on crystal surfaces are usually elongate and oriented. Well developed crystals have a tabular idiomorphic form and are parallel in their growth. Rounded and irregular crystals were also observed. The crystals show reticular structure with units of the order of 100 A and striations corresponding with the rhombohedral axes of the crystals. The role of the mantle is discussed in relation to the growth patterns of crystals and shell structure.     

ELECTROMECHANICAL COUPLING IN TUBULAR MUSCLE FIBERS : I. The Organization of Tubular Muscle Fibers in the Scorpion Leiurus quinquestriatus

The tubular fibers of the claw-closer muscle of the scorpion have a central core containing nuclei and mitochondria. The myofibrils have the shape of thin lamellae (1 µ) extending radially from the core to the surface membrane (20 µ). The thick myofilaments are organized in a hexagonal array with orbits of 10–13 thin myofilaments. The ratio of thick-to-thin filaments is 1:5. Transverse tubular system (TS) openings are located between lamellated myofibrils. In each sarcomere two TS's are found, one on each side of the H band. The TS is composed of a transverse tubule and tubular pockets (TP). The TP's form diadic contact with the terminal cisternae of the sarcoplasmic reticulum. The TS can be traced from the cell membrane down to the cell core. The surface area of the TS was calculated to be six times that of the outer surface membrane.     

Correlated alternative side chain conformations in the RNA-recognition motif of heterogeneous nuclear ribonucleoprotein A1

The RNA-recognition motif (RRM) is a common and evolutionarily conserved RNA-binding module. Crystallographic and solution structural studies have shown that RRMs adopt a compact α/β structure, in which four antiparallel β-strands form the major RNA-binding surface. Conserved aromatic residues in the RRM are located on the surface of the β-sheet and are important for RNA binding. To further our understanding of the structural basis of RRM-nucleic acid interaction, we carried out a high resolution analysis of UP1, the N-terminal, two-RRM domain of heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1), whose structure was previously solved at 1.75–1.9 Å resolution. The two RRMs of hnRNP A1 are closely related but have distinct functions in regulating alternative pre-mRNA splice site selection. Our present 1.1 Å resolution crystal structure reveals that two conserved solvent-exposed phenylalanines in the first RRM have alternative side chain conformations. These conformations are spatially correlated, as the individual amino acids cannot adopt each of the observed conformations independently. These phenylalanines are critical for nucleic acid binding and the observed alternative side chain conformations may serve as a mechanism for regulating nucleic acid binding by RRM-containing proteins.     

Structure of the Streptococcus pneumoniae Surface Protein and Adhesin PfbA

PfbA (plasmin- and fibronectin-binding protein A) is an extracellular Streptococcus pneumoniae cell-wall attached surface protein that binds to fibronectin, plasmin, and plasminogen. Here we present a structural analysis of the surface exposed domains of PfbA using a combined approach of X-ray crystallography and small-angle X-ray scattering (SAXS). The crystal structure of the PfbA core domain, here called PfbAβ, determined to 2.28 Å resolution revealed an elongated 12-stranded parallel β-helix fold, which structure-based comparisons reveal is most similar to proteins with carbohydrate modifying activity. A notable feature of the PfbAβ is an extensive cleft on one face of the protein with electrochemical and spatial features that are analogous to structurally similar carbohydrate-active enzymes utilizing this feature for substrate accommodation. Though this cleft displays a combination of basic amino acid residues and solvent exposed aromatic amino acids that are distinct features for recognition of carbohydrates, no obvious arrangement of amino acid side chains that would constitute catalytic machinery is evident. The pseudo-atomic SAXS model of a larger fragment of PfbA suggests that it has a relatively well-ordered structure with the N-terminal and core domains of PfbA adopting an extend organization and reveals a novel structural class of surface exposed pneumococcal matrix molecule adhesins.     

The basic keratin 10-binding domain of the virulence-associated pneumococcal serine-rich protein PsrP adopts a novel MSCRAMM fold

Streptococcus pneumoniae is a major human pathogen, and a leading cause of disease and death worldwide. Pneumococcal invasive disease is triggered by initial asymptomatic colonization of the human upper respiratory tract. The pneumococcal serine-rich repeat protein (PsrP) is a lung-specific virulence factor whose functional binding region (BR) binds to keratin-10 (KRT10) and promotes pneumococcal biofilm formation through self-oligomerization. We present the crystal structure of the KRT10-binding domain of PsrP (BR_187–385) determined to 2.0 Å resolution. BR_187–385 adopts a novel variant of the DEv-IgG fold, typical for microbial surface components recognizing adhesive matrix molecules adhesins, despite very low sequence identity. An extended β-sheet on one side of the compressed, two-sided barrel presents a basic groove that possibly binds to the acidic helical rod domain of KRT10. Our study also demonstrates the importance of the other side of the barrel, formed by extensive well-ordered loops and stabilized by short β-strands, for interaction with KRT10.     

Projection maps of three members of the KdgM outer membrane protein family

We present the projection structures of the three outer membrane porins KdgM and KdgN from Erwinia chrysanthemi and NanC from Escherichia coli, based on 2D electron crystallography. A wide screening of 2D crystallization conditions yielded tubular crystals of a suitable size and quality to perform high-resolution electron microscopy. Data processing of untilted samples allowed us to separate the information of the two crystalline layers and resulted in projection maps to a resolution of up to 7 Å. All three proteins exhibit a similar putative β-barrel structure and the three crystal forms have the same symmetry. However, there are differences in the packing arrangements of the monomers as well as the densities of the projections. To interpret these projections, secondary structure prediction was performed using β-barrel specific prediction algorithms. The predicted transmembrane β-barrels have a high similarity in the arrangement of the putative β-strands and the loops, but do not match those of OmpG, a related protein porin whose structure was solved.     

Skin Lipids: Localization of Ceramide and Fatty Acid in the Unit Cell of the Long Periodicity Phase

The lipid matrix of the skin’s stratum corneum plays a key role in the barrier function, which protects the body from desiccation. The lipids that make up this matrix consist of ceramides, cholesterol, and free fatty acids, and can form two coexisting crystalline lamellar phases: the long periodicity phase (LPP) and the short periodicity phase (SPP). To fully understand the skin barrier function, information on the molecular arrangement of the lipids in the unit cell of these lamellar phases is very desirable. To determine this arrangement in previous studies, we examined the molecular arrangement of the SPP. In this study, neutron diffraction studies were performed to obtain information on the molecular arrangement of the LPP. The diffraction pattern reveals nine diffraction orders attributed to the LPP with a repeating unit of 129.4 ± 0.5 Å. Using D₂O/H₂O contrast variation, the scattering length density profiles were calculated for protiated samples and samples that included either the perdeuterated acyl chain of the most abundant ceramide or the most abundant perdeuterated fatty acid. Both perdeuterated chains are predominantly located in the central part of the unit cell with substantial interdigitation of the acyl chains in the unit cell center. However, a fraction of the perdeuterated chains is also located near the border of the unit cell with their acyl chains directing toward the center. This arrangement of lipids in the LPP unit cell corresponds with the location of their lipid headgroups at the border and also inside of the unit cell at a well-defined position (±21 Å from the unit cell center), indicative of a three-layer lipid arrangement within the 129.4 ± 0.5 Å repeating unit.     

Structure of the Non-Catalytic Domain of the Protein Disulfide Isomerase-Related Protein (PDIR) Reveals Function in Protein Binding

Protein disulfide isomerases comprise a large family of enzymes responsible for catalyzing the proper oxidation and folding of newly synthesized proteins in the endoplasmic reticulum (ER). Protein disulfide isomerase-related (PDIR) protein (also known as PDIA5) is a specialized member that participates in the folding of α₁-antitrypsin and N-linked glycoproteins. Here, the crystal structure of the non-catalytic domain of PDIR was determined to 1.5 Å resolution. The structure adopts a thioredoxin-like fold stabilized by a structural disulfide bridge with a positively charged binding surface for interactions with the ER chaperones, calreticulin and ERp72. Crystal contacts between molecules potentially mimic the interactions of PDIR with misfolded substrate proteins. The results suggest that the non-catalytic domain of PDIR plays a key role in the recognition of protein partners and substrates.     

Small Angle X-Ray Scattering of the Thylakoid Membranes of Rhodopseudomonas spheroides in Aqueous Suspensions

The diffraction patterns of particles which have the shape of hollow spheres, i.e. vesicles, can be satisfactorily analyzed by means of a new formula of Weick (1974). This formula is used for the small angle X-ray scattering analysis of aqueous suspensions of thylakoids of Rhodopseudomonas spheroides. Some essential results are: (a) The membrane has a rather asymmetric structure with one layer of low electron density at its inner side and two layers of high electron density near the outer surface of the thylakoids. (b) The distance of the electron density maxima of the latter two layers is 45 ± 5 Å. (c) Between the two maxima is a region of an electron density nearly equal to that of water. (d) The sequence of the peaks is - + 0 + with increasing radius. The peaks extend over an interval of 120 ± 10 Å. (e) The thylakoids are strikingly of the same size. Their diameters, if defined by the outmost layer, vary statistically by about 4% and have an average value of approximately 640 Å.     

Selenium derivatization of nucleic acids for crystallography

The high-resolution structure of the DNA (5′-GTGTACA-C-3′) with the selenium derivatization at the 2′-position of T2 was determined via MAD and SAD phasing. The selenium-derivatized structure (1.28 Å resolution) with the 2′-Se modification in the minor groove is isomorphorous to the native structure (2.0 Å). To directly compare with the conventional bromine derivatization, we incorporated bromine into the 5-postion of T4, determined the bromine-derivatized DNA structure at 1.5 Å resolution, and found that the local backbone torsion angles and solvent hydration patterns were altered in the structure with the Br incorporation in the major groove. Furthermore, while the native and Br-derivatized DNAs needed over a week to form reasonable-size crystals, we observed that the Se-derivatized DNAs grew crystals overnight with high-diffraction quality, suggesting that the Se derivatization facilitated the crystal formation. In addition, the Se-derivatized DNA sequences crystallized under a broader range of buffer conditions, and generally had a faster crystal growth rate. Our experimental results indicate that the selenium derivatization of DNAs may facilitate the determination of nucleic acid X-ray crystal structures in phasing and high-quality crystal growth. In addition, our results suggest that the Se derivatization can be an alternative to the conventional Br derivatization.     

Atomic force microscopy of the morphology of the matrix and mineral components of the otolith of Hyperoglyphe antarctica

The sagittal otolith of Hyperoglyphe antarctica (Centrolophidae: Teleostei) has a prismatic structure in which the anti-sulcal growth axes of each prism consist of a series of nested cones each composed of a mineral layer followed by an organic matrix layer. Broken sections show the mineral layers to be composed of stacks of crystals. Otolith matrix that has been decalcified and air-dried, or critical-pont-dried, retains a periodic structure of repeating high and low matrix density. At high magnifications, both broken whole crystal surfaces and decalcified matrix surfaces have a granular structure. Chloroxbleached whole otoliths also show a granular crystalline structure. At higher magnifications, the air-dried matrix showed a parallel fiber structure with similar dimensions to keratin fibers. © 1995 Wiley-Liss, Inc.     

Settlement of Planulae of the Moon Jellyfish Aurelia aurita onto Hydrophilic Polycarbonate Plates Modified by Atmospheric Plasma Treatment

It has been reported that planula larvae of some jellyfish prefer artificial substrates for settlement. This research focused on the relationship between the settlement of planulae and the wettability of artificial substrate surfaces. We used atmospheric plasmas to change the wettability of the surfaces of polycarbonate (PC) plates because plasma treatment has no chemical side effects. The treatment made the surfaces hydrophilic, as evidenced by the decrease of contact angle from 85° to 35°. X-ray photoelectron spectroscopy revealed that the change of wettability of the PC plates could be attributed to N₂, which was probably ionized in the air above the plates. Scanning electron microscopy revealed no difference in the surface morphology of the plates before and after plasma treatment. Results of bioassays using treated PC plates showed that planulae tended to preferentially settle on hydrophobic surfaces.     

Surface Response of Fluorine Polymer-Incorporated Resin Composites to Cariogenic Biofilm Adherence

Experimental resin composites with incorporated polytetrafluoroethylene (PTFE) particles were developed, which theoretically could improve the surface properties of the materials, including the inhibition of bacterial adherence. To assess the surface properties in relation to biofilm formation and detachment, 23.1% (wt/wt) linear PTFE particles (FL-30) and cross-linked PTFE particles (FC-30) were incorporated into pure resin composites. Pure PTFE plates and pure resin composites without PTFE (F-0) were used as control specimens. Sucrose-dependent Streptococcus mutans biofilms were formed on the specimen blocks inside an oral biofilm reactor for various time periods and analyzed with or without application of driving forces. In addition, water contact angles and surface roughness were measured. The water contact angles of FL-30 (61.2°) and FC-30 (65.8°) were larger than that of F-0 (48.5°). The largest contact angle (107°) was detected on pure PTFE plates. However, the surfaces of FL-30, FC-30, and pure PTFE plates were rougher than that of F-0. Although the surface properties of the materials differed in terms of contact angles and roughness, these factors seemed not to affect biofilm formation on the surfaces within 5 h. Pure PTFE plates harbored almost the same amounts of biofilm as F-0. However, when a very strong driving force was applied, it was clear that there were significantly smaller amounts of biofilms retained on pure PTFE plates, which showed contact angles much higher than those of the other materials. Hydrophobicity of the resin composite was improved by incorporation of PTFE fillers. However, surface resistance against biofilm formation was not improved.     

Structure of the Intermediate Filament-Binding Region of Desmoplakin

Desmoplakin (DP) is a cytoskeletal linker protein that connects the desmosomal cadherin/plakoglobin/plakophilin complex to intermediate filaments (IFs). The C-terminal region of DP (DPCT) mediates IF binding, and contains three plakin repeat domains (PRDs), termed PRD-A, PRD-B and PRD-C. Previous crystal structures of PRDs B and C revealed that each is formed by 4.5 copies of a plakin repeat (PR) and has a conserved positively charged groove on its surface. Although PRDs A and B are linked by just four amino acids, B and C are separated by a 154 residue flexible linker, which has hindered crystallographic analysis of the full DPCT. Here we present the crystal structure of a DPCT fragment spanning PRDs A and B, and elucidate the overall architecture of DPCT by small angle X-ray scattering (SAXS) analysis. The structure of PRD-A is similar to that of PRD-B, and the two domains are arranged in a quasi-linear arrangement, and separated by a 4 amino acid linker. Analysis of the B-C linker region using secondary structure prediction and the crystal structure of a homologous linker from the cytolinker periplakin suggests that the N-terminal ~100 amino acids of the linker form two PR-like motifs. SAXS analysis of DPCT indicates an elongated but non-linear shape with R_g = 51.5 Å and D_max = 178 Å. These data provide the first structural insights into an IF binding protein containing multiple PRDs and provide a foundation for studying the molecular basis of DP-IF interactions.     

Quantification of the Contact Area at the Head-Stem Taper Interface of Modular Hip Prostheses

Corrosion of modular taper junctions of hip implants may be associated with clinical failure. Taper design parameters, as well as the intraoperatively applied assembly forces, have been proposed to affect corrosion. Fretting corrosion is related to relative interface shear motion and fluid ingress, which may vary with contact force and area. It was hypothesised in this study that assembly forces modify the extent and distribution of the surface contact area at the taper interface between a cobalt chrome head and titanium stem taper with a standard threaded surface profile. Local abrasion of a thin gold coating applied to the stem taper prior to assembly was used to determine the contact area after disassembly. Profilometry was then used to assess permanent deformation of the stem taper surface profile. With increasing assembly force (500 N, 2000 N, 4000 N and 8000 N) the number of stem taper surface profile ridges in contact with the head taper was found to increase (9.2±9.3%, 65.4±10.8%, 92.8±6.0% and 100%) and the overall taper area in contact was also found to increase (0.6±0.7%, 5.5±1.0%, 9.9±1.1% and 16.1±0.9%). Contact was inconsistently distributed over the length of the taper. An increase in plastic radial deformation of the surface ridges (-0.05±0.14 μm, 0.1±0.14 μm, 0.21±0.22 μm and 0.96±0.25 μm) was also observed with increasing assembly force. The limited contact of the taper surface ridges at lower assembly forces may influence corrosion rates, suggesting that the magnitude of the assembly force may affect clinical outcome. The method presented provides a simple and practical assessment of the contact area at the taper interface.     

Feasibility of the Assessment of Cholesterol Crystals in Human Macrophages Using Micro Optical Coherence Tomography

The presence of cholesterol crystals is a hallmark of atherosclerosis, but until recently, such crystals have been considered to be passive components of necrotic plaque cores. Recent studies have demonstrated that phagocytosis of cholesterol crystals by macrophages may actively precipitate plaque progression via an inflammatory pathway, emphasizing the need for methods to study the interaction between macrophages and crystalline cholesterol. In this study, we demonstrate the feasibility of detecting cholesterol in macrophages in situ using Micro-Optical Coherence Tomography (µOCT), an imaging modality we have recently developed with 1-µm resolution. Macrophages containing cholesterol crystals frequently demonstrated highly scattering constituents in their cytoplasm on µOCT imaging, and µOCT was able to evaluate cholesterol crystals in cultured macrophage cells. Our results suggest that µOCT may be useful for the detection and characterization of inflammatory activity associated with cholesterol crystals in the coronary artery.     

Three-dimensional electron diffraction of plant light-harvesting complex

Electron diffraction patterns of two-dimensional crystals of light-harvesting chlorophyll a/b-protein complex (LHC-II) from photosynthetic membranes of pea chloroplasts, tilted at different angles up to 60°, were collected to 3.2 Å resolution at -125°C. The reflection intensities were merged into a three-dimensional data set. The Friedel R-factor and the merging R-factor were 21.8 and 27.6%, respectively. Specimen flatness and crystal size were critical for recording electron diffraction patterns from crystals at high tilts. The principal sources of experimental error were attributed to limitations of the number of unit cells contributing to an electron diffraction pattern, and to the critical electron dose. The distribution of strong diffraction spots indicated that the three-dimensional structure of LHC-II is less regular than that of other known membrane proteins and is not dominated by a particular feature of secondary structure.