Loosely Packed Research Articles

Mechanochromic luminescence from N,O-Chelated diphenylborinates

A series of N,O-bidentated BPh2 complexes (B1–B3) have been designed and synthesized through the direct reaction of N,O-chelate ligands and diaryl borate solutions. Their crystal structures, photophysical and mechanochromic properties were systematically studied. As verified by both experimental and calculated results, all these compounds possess inherent D-A structures, and adopt highly distorted molecular conformations. Multiple weak intermolecular interactions and relatively loose packing are prevailing in their crystal structures. These favorable structure features promise high solid-state fluorescence efficiency and high color contrast reversible mechanochromic for the three dyes. Moreover, their photophysical and mechanical responsive properties have been found structurally dependent, which are mainly modulated by electronic and steric effects derived from different substitutions in the ligand and the boron atom. As a result, B2 with the most twisted and loosely packed structure shows a most sensitive and pronounced mechanochromic response. Our study thus shows that selection of a N,O-bidentated BPh2 based emitter enables the development of excellent MCL-active materials. The current design strategy will be beneficial for the facile access to various advanced BPh2 based dyes for promising applications in optical force sensors, optoelectronic devices and so on.

Underwater collapse of a loosely packed granular column on an inclined plane: Effects of the Darcy number

As a simple model of submarine landslides, laboratory experiments were performed to determine the effects of Darcy number on the collapse of granular columns in water with loose packing. The Darcy number describes the tendency for pore fluid pressure developed by the contraction process to reduce the friction for loosely packed columns. The experimental results reveal that the collapse depends on the Darcy number, Da, the bed slope, and the initial aspect ratio of the column. Predictive models are provided for the spreading duration, spreading velocity, runout distance, and finial height of the deposit. Comparison of the present results with those of the previous studies reveals that the effects of Da on collapse vary with the packing conditions. Specifically, a positive runout-Da relationship exists in cases of loose packing, while a negative relationship is revealed for dense packing. A simple dynamic analysis is performed to explore observation, which is a consequence of different pore pressures occurring inside columns owing to different packing.

Molecular interactions within the halophilic, thermophilic, and mesophilic prokaryotic ribosomal complexes: clues to environmental adaptation

Using the available crystal structures of 50S ribosomal subunits from three prokaryotic species: Escherichia coli (mesophilic), Thermus thermophilus (thermophilic), and Haloarcula marismortui (halophilic), we have analyzed different structural features of ribosomal RNAs (rRNAs), proteins, and of their interfaces. We have correlated these structural features with the environmental adaptation strategies of the corresponding species. While dense intra-rRNA packing is observed in thermophilic, loose intra-rRNA packing is observed in halophilic (both compared to mesophilic). Interestingly, protein–rRNA interfaces of both the extremophiles are densely packed compared to that of the mesophilic. The intersubunit bridge regions are almost devoid of cavities, probably ensuring the proper formation of each bridge (by not allowing any loosely packed region nearby). During rRNA binding, the ribosomal proteins experience some structural transitions. Here, we have analyzed the intrinsically disordered and ordered regions of the ribosomal proteins, which are subjected to such transitions. The intrinsically disordered and disorder-to-order transition sites of the thermophilic and mesophilic ribosomal proteins are simultaneously (i) highly conserved and (ii) slowly evolving compared to rest of the protein structure. Although high conservation is observed at such sites of halophilic ribosomal proteins, but slow rate of evolution is absent. Such differences between thermophilic, mesophilic, and halophilic can be explained from their environmental adaptation strategy. Interestingly, a universal biophysical principle evident by a linear relationship between the free energy of interface formation, interface area, and structural changes of r-proteins during assembly is always maintained, irrespective of the environmental conditions.

Enzyme Activity and Structural Dynamics Linked to Micelle Formation: A Fluorescence Anisotropy and ESR Study

Activities of the enzymes, protease subtilisin and horse radish peroxidase (HRP) have been increased 50 and 40%, respectively, in the presence of the nonionic surfactant, alkyl polyglucoside, compared with the activities in buffer alone. This enzyme hyperactivity reaches a peak at 3.0 mm of surfactant. Investigation into the structure of surfactant aggregates indicates "giant" micelle superstructures at this range of surfactant concentration of 1.7 μm in diameter--dramatically decreasing to 60 and 70 nm at higher surfactant concentrations, while surface tension measurements indicate two critical micelle concentration inflection points at 0.2 and 5.0 mm, which suggests transitions in micelle structure with respect to concentration. Furthermore, electron spin resonance (ESR) indicates that the micelles in first critical micelle concentration regime are loosely packed relative to the second aggregate phase. We hypothesize that this loose packing results in diminished hydration shell repulsion between the micelles, leading to the large, micrometer-sized aggregates. We further hypothesize that it is the interaction with these loosely packed micelles that affects the flexibility of the HRP and protease enzyme structure. Time-resolved fluorescence anisotropy of subtilisin in Brij-30 indicates increasing flexibility of catalytic active site with surfactant concentration. This is correlated with an increase in enzymatic activity.

E-078 Enhanced flow diversion for ruptured fusiform basilar artery aneurysm: case report

IntroductionRupture of fusiform basilar aneurysm is typically fatal despite best efforts. We report good short-term outcome after endovascular basilar artery recontruction in a patient with fusiform basilar aneurysm who presented...

Dense colloidal fluids form denser amorphous sediments

We relate, by simple analytical centrifugation experiments, the density of colloidal fluids with the nature of their randomly packed solid sediments. We demonstrate that the most dilute fluids of colloidal hard spheres form loosely packed sediments, where the volume fraction of the particles approaches in frictional systems the random loose packing limit, ϕRLP = 0.55. The dense fluids of the same spheres form denser sediments, approaching the so-called random close packing limit, ϕRCP = 0.64. Our experiments, where particle sedimentation in a centrifuge is sufficiently rapid to avoid crystallization, demonstrate that the density of the sediments varies monotonically with the volume fraction of the initial suspension. We reproduce our experimental data by simple computer simulations, where structural reorganizations are prohibited, such that the rate of sedimentation is irrelevant. This suggests that in colloidal systems, where viscous forces dominate, the structure of randomly close-packed and randomly loose-packed sediments is determined by the well-known structure of the initial fluids of simple hard spheres, provided that the crystallization is fully suppressed.

Proteomic Analysis of Aneurysm Healing Mechanism after Coil Embolization: Comparison of Dense Packing with Loose Packing

In clinical practice, durability of occlusion following coil embolization is superior in densely packed, compared with loosely packed, aneurysms. In a rabbit model, we probed, by using proteomics tools, the biologic mechanisms associated with densely packed and completely occluded aneurysms, compared with loosely packed and incompletely occluded aneurysms, to explore the biologic mechanisms of intra-aneurysmal healing following embolization. Elastase-induced, saccular aneurysms were created in 24 rabbits. Aneurysms were allowed to mature, after which aneurysms were either densely (packing attenuation >25%) or loosely (packing attenuation <20%) packed with platinum coils by endovascular means. After 2 weeks (n = 6 for both groups) and 4 weeks (n = 6 for both groups) of implantation, aneurysm samples harboring coils were harvested. Soluble proteins were extracted from the necks and domes of aneurysms, and proteins were studied using proteomics and bioinformatics tools. In dome tissue, 128 proteins at 2 weeks, and 8 proteins at 4 weeks, were differentially expressed in densely packed, compared with loosely packed, aneurysms. In the neck tissue, 2 proteins at 4 weeks were differentially expressed in densely packed aneurysms. Specific pathway analysis revealed that compared with loosely packed aneurysms, densely packed aneurysms were associated with up-regulation of cell-to-cell signaling and cell adhesion at 2 weeks. Conversely, at 4 weeks, densely packed aneurysms showed a decrease in the expression of structural proteins compared with loosely packed aneurysms. These findings may focus efforts on specific targets aimed at improving the long-term healing of intracranial, saccular aneurysms.

Stalk-free membrane fusion of cationic lipids via an interdigitated phase

We have studied the membrane structure of a cationic lipid (N-t-butyl-N′-tetradecyl-3-tetradecylaminopropionamidine, termed diC14-amidine) using X-ray and neutron small-angle scattering as well as dilatometry and ultrasound velocimetry. At high temperatures we found an anomalously thin lamellar fluid phase, which transforms into a loosely packed interdigitated phase below the chain melting transition. Our finding can be understood based on the specific structure of the lipid backbone, which forms a long spacer between the alkyl chains. The loose lipid packing in the gel phase leads to a significant exposure of the hydrophobic lipid core to the aqueous phase. This reduces energy penalties from the removal of water molecules during fusion and explains the untypically increased fusion properties of amidine in the gel phase. Moreover, this fusion in the gel interdigitated state apparently does not require the formation of stalk intermediate structures.

A survey of hemoglobin quaternary structures

We perform an analysis of the quaternary structure and dimer/dimer interface in the crystal structures of 165 human hemoglobin tetramers; 112 are in the T, 17 the R, 14 the Y (or R2) state; 11 are high-affinity T state mutants, and 11 may either be intermediates between the states, or off the allosteric transition pathway. The tertiary structure is fixed within each state, in spite of the different ligands, mutations, and chemical modifications present in individual entries. The geometry of the tetramer assembly is essentially the same in all the R or the Y state entries; it is slightly different in high salt and low salt crystals of T state hemoglobins. The dimer/dimer interface differs in terms of size, chemical composition and polar interactions, between the states. It is loosely packed, like crystal packing contacts or the subunit interface of weakly associated homodimers, and unlike most oligomeric proteins, which have close-packed interfaces. The loose packing is most obvious in the liganded forms, where the tetramer is known to dissociate at low concentration. We identify cavities that contribute to the loose packing of the α1β2 and α2β1 contacts. Two pairs of cavities occur recurrently in both the T and the R state tetramers. They may contribute to the allosteric mechanism by facilitating the subunit movements and the tertiary structure changes that accompany the transition from T to R to Y.

Structure of the M2 Transmembrane Segment of GLIC, a Prokaryotic Cys Loop Receptor Homologue from Gloeobacter violaceus, Probed by Substituted Cysteine Accessibility

GLIC is a homopentameric proton-gated, prokaryotic homologue of the Cys loop receptor family of neurotransmitter-gated ion channels. Recently, crystal structures of GLIC hypothesized to represent an open channel state were published. To explore the channel structure in functional GLIC channels, we tested the ability of p-chloromercuribenzenesulfonate to react with 30 individual cysteine substitution mutants in and flanking the M2 channel-lining segment in the closed state (pH 7.5) and in a submaximally activated state (pH 5.0). Nine mutants did not tolerate cysteine substitution and were not functional. From positions 10' to 27', p-chloromercuribenzenesulfonate significantly modified the currents at pH 7.5 and 5.0 in all mutants except H234C (11'), I235C (12'), V241C (18'), T243C (20'), L245C (22'), and Y250C (27'), which were not functional, except for 12'. Currents for P246C (23') and K247C (24') were only significantly altered at pH 5.0. The reaction rates were all >1000 m(-1) s(-1). The reactive residues were more accessible in the activated than in the resting state. We infer that M2 is tightly associated with the adjacent transmembrane helices at the intracellular end but is more loosely packed from 10' to the extracellular end than the x-ray structures suggest. We infer that the charge selectivity filter is in the cytoplasmic half of the channel. We also show that below pH 5.0, GLIC desensitizes on a time scale of minutes and infer that the crystal structures may represent a desensitized state.

Methyl α-d-glucopyranoside enhances the enzymatic activity of recombinant β-galactosidase inclusion bodies in the araBAD promoter system of Escherichia coli

In this study, we utilized a catabolite repressor to improve the enzymatic activity of recombinant beta-galactosidase inclusion bodies (IBs) produced in Escherichia coli under the araBAD promoter system. Specifically, we employed methyl alpha-D: -glucopyranoside (alpha-MG) to lower the transcription rate of the beta-galactosidase structural gene. In deepwell microtiter plate and lab-scale fermentor culture systems, we demonstrated that the addition of alpha-MG after induction improved the specific beta-galactosidase production, even though beta-galactosidase was still produced as an IB. Particularly, the addition of 0.0025% alpha-MG led to the most significant increase in the specific activity of the beta-galactosidase. Interestingly, the beta-galactosidase IBs obtained in the presence of 0.0025% alpha-MG were more loosely packed, as determined by IB solubilization in guanidine hydrochloride solution. We propose that the reduced gene transcription rate was responsible for the increased specific beta-galactosidase activity and the loose packing that characterized the IBs produced in the presence of alpha-MG. This principle could be applied throughout the enzyme bioprocessing industry in order to enhance the activity of aggregate-prone enzymes within IBs.

Spontaneous Thermal Motion of the GABAA Receptor M2 Channel-lining Segments

The gamma-aminobutyric acid type A (GABA(A)) receptor channel opening involves translational and rotational motions of the five channel-lining, M2 transmembrane segments. The M2 segment's extracellular half is loosely packed and undergoes significant thermal motion. To characterize the extent of the M2 segment's motion, we used disulfide trapping experiments between pairs of engineered cysteines. In alpha1beta1 gamma2S receptors the single gamma subunit is flanked by an alpha and beta subunit. The gamma2 M2-14' position is located in the alpha-gamma subunit interface. Gamma2 13' faces the channel lumen. We expressed either the gamma2 14' or the gamma2 13' cysteine substitution mutants with alpha1 cysteine substitution mutants between 12' and 16' and wild-type beta1. Disulfide bonds formed spontaneously between gamma2 14'C and both alpha1 15'C and alpha1 16'C and also between gamma2 13'C and alpha1 13'C. Oxidation by copper phenanthroline induced disulfide bond formation between gamma2 14'C and alpha1 13'C. Disulfide bond formation rates with gamma2 14'C were similar in the presence and absence of GABA, although the rate with alpha1 13'C was slower than with the other two positions. In a homology model based on the acetylcholine receptor structure, alphaM2 would need to rotate in opposite directions by approximately 80 degrees to bring alpha1 13' and alpha1 15' into close proximity with gamma2 14'. Alternatively, translational motion of alphaM2 would reduce the extent of rotational motion necessary to bring these two alpha subunit residues into close proximity with the gamma2 14' position. These experiments demonstrate that in the closed state the M2 segments undergo continuous spontaneous motion in the region near the extracellular end of the channel gate. Opening the gate may involve similar but concerted motions of the M2 segments.

Crystal structure of human vinculin.

Alterations in the actin cytoskeleton following the formation of cell-matrix and cell-cell junctions are orchestrated by vinculin. Vinculin associates with a large number of cytoskeletal and signaling proteins, and this flexibility is thought to contribute to rapid dissociation and reassociations of adhesion complexes. Intramolecular interactions between vinculin's head (Vh) and tail (Vt) domains limit access of its binding sites for other adhesion proteins. While the crystal structures of the Vh and Vt domains are known, these domains represent less than half of the entire protein and are separated by a large central region of unknown structure and function. Here we report the crystal structure of human full-length vinculin to 2.85 A resolution. In its resting state, vinculin is a loosely packed collection of alpha-helical bundles held together by Vh-Vt interactions. The three new well ordered alpha-helical bundle domains are similar in their structure to either Vh (Vh2 and Vh3) or to Vt (Vt2) and their loose packing provides the necessary flexibility that allows vinculin to interact with its various protein partners at sites of cell adhesion.

Loose Protein Packing around the Extracellular Half of the GABAA Receptor β1 Subunit M2 Channel-lining Segment

GABA(A) receptors are ligand-gated ion channels formed by the pseudosymmetrical assembly of five homologous subunits around the central channel axis. The five M2 membrane-spanning segments largely line the channel. In the present work we probed the water surface accessibility of the beta(1) subunit M2 segment using the substituted cysteine accessibility method. We assayed the reaction of the negatively charged sulfhydryl-specific reagent, p-chloromercuribenzenesulfonate (pCMBS(-)), by its effect on subsequent currents elicited by EC(50) and saturating GABA concentrations. pCMBS(-), applied with GABA, reacted with 14 of the 19 residues tested. At the M2 cytoplasmic end from 2' to 6' only beta(1)A252C (2') and beta(1)T256C (6') were pCMBS(-)-reactive in the presence of GABA. We infer that the M2 segments are tightly packed in this region. Toward the extracellular half of M2 all residues from beta(1)T262C (12') through beta(1)E270C (20') reacted with pCMBS(-) applied with GABA. We infer that this region is highly mobile and loosely packed against the rest of the protein. Based on differences in pCMBS(-) reaction rates two domains can be distinguished on the putative channel-lining side of M2. A faster reacting domain includes the 2', 9', 12', 13', and 16' residues. The slower reacting face contains the 6', 10', and 14' residues. We hypothesize that these may represent the channel-lining faces in the closed and open states and that gating involves an 80-100 degrees rotation of the M2 segments. These results are consistent with the loose packing of the M2 segments inferred from the structure of the homologous Torpedo nicotinic acetylcholine receptor.

Modification of structural and acidic properties of sol–gel-prepared alumina powders by changing the hydrolysis ratio

The structural and acidic properties of sol–gel prepared alumina powders as catalyst supports were modified by adjusting the hydrolysis ratio, R (i.e. molar ratio of water relative to the alumina precursor, R=[H 2O]/[aluminium-tri-sec-butoxide (ASB)]). Structural properties (e.g. porosity) and acidic properties were measured for alumina powders prepared with various R values, from 3 to 13. For R<9 and R>10, first-order particles were closely packed with ink-bottle-type pore structures, whereas for R=9 or 10, first-order particles were loosely packed with a spatial fractal arrangement that yielded pseudo-cylindrical pore structures. In addition, the alumina powders prepared with R=9 or 10 had larger water pore volume and stronger acidity than those with other R values. These properties unique to the powders prepared with R=9 or 10 were ascribed to relatively short Al–O–Al chain lengths that resulted in loose packing of first-order particles. The results here indicate that alumina powders with favorable properties as catalyst supports (e.g. mean pore diameter) can be tailored by selecting the appropriate R in the sol–gel synthesis process.

Site‐directed spin labeling of a bacterial chemoreceptor reveals a dynamic, loosely packed transmembrane domain

We used site-directed spin labeling and electron paramagnetic resonance spectroscopy to investigate dynamics and helical packing in the four-helix transmembrane domain of the homodimeric bacterial chemoreceptor Trg. We focused on the first transmembrane helix, TM1, particularly on the nine-residue sequence nearest the periplasm, because patterns of disulfide formation between introduced cysteines had identified that segment as the region of closest approach among neighboring transmembrane helices. Along this sequence, mobility and accessibility of the introduced spin label were characteristic of loosely packed or solvent-exposed side chains. This was also the case for eight additional positions around the circumference and along the length of TM1. For the continuous nine-residue sequence near the periplasm, mobility and accessibility varied only modestly as a function of position. We conclude that side chains of TM1 that face the interior of the four-helix domain interact with neighboring helices but dynamic movement results in loose packing. Compared to transmembrane segments of other membrane proteins reconstituted into lipid bilayers and characterized by site-directed spin labeling, TM1 of chemoreceptor Trg is the most dynamic and loosely packed. A dynamic, loosely packed chemoreceptor domain can account for many experimental observations about the transmembrane domains of chemoreceptors.

Micronized ethylcellulose used for designing a directly compressed time-controlled disintegration tablet

Ethylcellulose (EC) of varying particle sizes has been used as an outer coating layer to design a novel dry-coated tablet with time-controlled drug release. This dry-coated tablet, containing a core tablet of sodium diclofenac and an outer coating layer of EC, was prepared by direct compression. The drug release from dry-coated tablet exhibited an initial lag period that was dependent on the particle size of the EC powder, followed by a stage of rapid drug release. The smaller the EC particle size used the longer the lag time obtained, suggesting the particle size of EC powder could modulate the timing of drug release from such a dry-coated tablet. The period of the lag time for sodium diclofenac released from dry-coated tablets was correlated with the penetration distance of the solvent into dry-coated tablet by an in vitro dye penetration study. The densest packing of EC powders appeared on the upper and lower surfaces of dry-coated tablet after compression, resulting in a tight structure yielding a slower penetration of the solvent. Whereas loose packing of EC powders occurred in the middle of the lateral surface of dry-coated tablet, this loosely packed surface readily allowed solvent penetration and that finally caused the splitting of tablet shell into two halves in the dissolution medium. The results suggest that these dry-coated tablets prepared with different particle sizes of EC powder as an outer coating layer might offer a desirable release profile for drug delivery at the predetermined times and/or sites.

Rain impact soil crust. IV. Packing of sand and silt fractions by raindrops

Comparison of resistance to fast and slow deformation by rain-packed and artificially prepared sand and silt fractions showed that, whereas sands are left in loosely packed states after accrual under rain impact, silts are left more densely packed, i.e. below critical void ratio. This contrast is attributed mainly to the declining importance of hydraulic penetration with pore size. Rain-packed silt is dilatant and cannot deform without expansion which, in turn, requires water entry at a rate compatible with the required deformation. In the short duration of rain-impact events, hydrodynamic time lagging occurs because water can move only slowly through the small silt pores. Consequently, densely packed silt remains essentially rigid. However, drop-outflow sheets are able to entrain silt and distribute it over the surface as densely packed bed-load deposits, thus maintaining its dilatancy. Sand, its larger pores invaded by hydraulic penetration jets which maintain loose packing, cannot behave in this manner. Relative stability of the silt layer on soil surfaces, and its suppression of hydraulic penetration, allow transmission of drop-generated stress waves which cause the immediately underlying soil to become compacted into the main structural element of the rain-impact soil crust.

Effect of transbilayer phospholipid distribution on erythrocyte fusion.

Phospholipid packing has been suggested as a relevant variable in the control of membrane fusion events. To test this possibility in a model system, a comparison was made of the fusability of erythrocytes with a normal asymmetric transbilayer distribution of plasma membrane phospholipids (tightly packed exterior lipids) and erythrocytes with a symmetric transbilayer distribution of phospholipids (more loosely packed exterior lipids), using polyethylene glycol as fusogen. Not only were lipid-symmetric cells more readily fused, but fusions of mixtures of lipid-symmetric and lipid-asymmetric cells indicated that both fusing partners must have a symmetric distribution for fusion to be enhanced. Lipid-symmetric cells may fuse more readily because loose packing of the exterior lipids enhances hydrophobic interactions between cells. Alternatively, enhanced membrane fluidity may facilitate intramembranous particle clustering, previously implicated as a potentiator of fusion. Finally, exposure of phosphatidylserine on the surface of lipid-symmetric erythrocytes may be responsible for their enhanced fusion.

粉体のランダム充てんモデルによる充てん密度と粒度分布との関係

A previous study reported on the relationship between the packing density and the particle size ratio and/or the volume fraction in binary mixture as a part of the investigation for the effect of the particle size distribution on the packing density. In the present study a similar investigation was repeated for the particles which have continuous size distributions, the modified Rosin-Rammler ones. According to the computer simulation using a random packing model the packing density was related to the parameter m (distribution constant) of the modified Rosin-Rammler distribution function. Subsequently the relationship was introduced by using an analytical method based on the binary packing results, and the adequency of the analytical method was also confirmed. The study was further developed onto the packing density of the particle assembly composed of a mixture of two powders with different modified Rosin-Rammler size distributions to investigate the blending effects.The results are summarized as follows:(1) For the powder of modified Rosin-Rammler size distribution the packing density decreases with increase in m.(2) The packing densities of powders with any continuous size distributions can be obtained from the loose binary packing results by an improved analytical method.(3) For the loosely packed bed of two mixed powders with modified Rosin-Rammler size distributions, the packing density was calculated by the above analytical method. The densities change with the parameters, m1 and m2 (distribution constants), De2⁄De1 (ratio of absolute size constants) and X2 (volume fraction). These results give important information on practical use.