Bending stiffness of a crystalline actin bundle

The acrosomal process of the sperm of the horseshoe crab (Limulus polyphemus) is a unique crystalline actin bundle, consisting of multiple actin filaments cross-linked by the actin-bundling protein, scruin. For successful fertilization, the acrosomal bundle must penetrate through a 30 microm thick jelly coat surrounding the egg and thus it must be sufficiently stiff. Here, we present two measurements of the bending stiffness of a single crystalline bundle of actin. Results from these measurements indicate that the actin:scruin composite bundle has an average elastic modulus of 2 GPa, which is similar to that of a single actin filament, and a bending stiffness that is more than two orders of magnitude larger than that of a bundle of uncross-linked actin filaments due to stiffening by the scruin matrix.     

Minimizing false positives in kinase virtual screens

In spite of recent improvements in docking and scoring methods, high false-positive rates remain a common issue in structure-based virtual screening. In this study, the distinctive features of false positives in kinase virtual screens were investigated. A series of retrospective virtual screens on kinase targets was performed on specifically designed test sets, each combining true ligands and experimentally confirmed inactive compounds. A systematic analysis of the docking poses generated for the top-ranking compounds highlighted key aspects differentiating true hits from false positives. The most recurring feature in the poses of false positives was the absence of certain key interactions known to be required for kinase binding. A systematic analysis of 444 crystal structures of ligand-bound kinases showed that at least two hydrogen bonds between the ligand and the backbone protein atoms in the kinase hinge region are present in 90% of the complexes, with very little variability across targets. Closer inspection showed that when the two hydrogen bonds are present, one of three preferred hinge-binding motifs is involved in 96.5% of the cases. Less than 10% of the false positives satisfied these two criteria in the minimized docking poses generated by our standard protocol. Ligand conformational artifacts were also shown to contribute to the occurrence of false positives in a number of cases. Application of this knowledge in the form of docking constraints and post-processing filters provided consistent improvements in virtual screening performance on all systems. The false-positive rates were significantly reduced and the enrichment factors increased by an average of twofold. On the basis of these results, a generalized two-step protocol for virtual screening on kinase targets is suggested.     

Physical factors that affect the number and size of Golgi cisternae

Despite continual membrane reorganization in the Golgi complex, the number of cisternae in a Golgi stack is a stable parameter. The cisternal number is conserved within any given cell line and also after Golgi reassembly, e.g. following brefeldin-A-induced disruption. However, the factors that determine the cisternal number in a single Golgi stack remain to be fully determined. We propose a simple mechanical model of the Golgi stack and present a theoretical analysis of different physical factors that may affect the number of cisternae in a Golgi stack. The model takes into account the Golgi membrane bending elasticity, which is related to the membrane curvature, and the adhesion, which holds the cisternae together. The analysis shows that the equilibrium configuration of the Golgi stack can be regarded as a balance between these two effects - the adhesion, which tends to increase the number of cisternae, is opposed by the membrane resistance to bending, which does not favor highly curved cisternal rims. The adhesion strength that is needed to hold together a typical stack is calculated. In addition, the model is used to analyze changes in the cisternal numbers as a controlled traffic wave enters a Golgi stack and increases the amount of the membrane in that stack.     

Courtship in Drosophila quadrilineata with a unique male behavioral element, abdomen bending

This paper describes courtship of Drosophila quadrilineata of the immigrans group and reports a species-specific element, abdomen bending, that has not been described in Drosophila. The male bends his abdomen right and left as a display to the female. During courtship the male circles around the female, bends his abdomen, and taps her. The male licks the female ovipositor repeatedly, often after the females extrusion. Although the females ovipositor extrusion is thought to indicate rejection of a courting male in many species, the male of D. quadrilineata continues courtship. It is possible that the extrusion is a females mating signal to the courting male. The male of D. quadrilineata mounts the female in a rearward position and the genitalia of both sexes couple after mounting. This mounting position is shared by the species belonging to the immigrans group. We never observed behavior in which it appeared as if the male displayed the black stripes to the female. Males court one another and a courtship chain is frequently formed even in the absence of females. The males abdomen bending and the females extrusion followed by the males licking are discussed.     

The effect of shoot-bending on the amount of diffusible indole-3-acetic acid and its transport in shoots of Japanese pear

The amount of diffusible indole-3-acetic acid (IAA) in shoots ofJapanese pear (Pyrus pyrifolia) decreased when vertical shootswere bent at an angle of 45°. A significant decrease of diffusibleIAA was observed one day after shoot bending (DAB), and the degree ofthis decrease was larger in the apical region of the shoot than in thebasal region. The decrease caused by the shoot bending increased withthe duration of the treatment. The IAA amounts in the bent shoot in theapical, central, and basal segments on 1 DAB were58.2±6.4%, 92.6±7.6%, and79.1±7.1% of the control, while 43.7±4.1%,30.8±2.9%, and 39.4±2.5% on 14 DAB.Radiolabelled IAA transport velocity was also examined, but it was notinfluenced by the shoot angle in the apical region of the shoot.However, the IAA transport velocity in the basal region decreased. Itdropped first on 1 DAB, but it recovered to the control level 3 DAB,then it decreased again on 14 DAB. A large increase in ethyleneproduction was observed in the bent shoot, but it seemed transient anddid not continue for 14 days. These results suggest that the decrease ofdiffusible IAA amounts may be induced not by the decrease of IAAtransport velocity but by the production/supply of IAA in the apicalregion.     

DNA binding and bending by a chloroplast-encoded HU-like protein overexpressed in Escherichia coli

The Guillardia theta chloroplast hlpA gene encodes a protein resembling bacterial histone-like protein HU. This gene was cloned and overexpressed in Escherichia coli cells, and the resulting protein product, HlpA, was purified and characterized in vitro. In addition to exhibiting a general DNA-binding activity, the chloroplast HlpA protein also strongly facilitated cyclization of a short DNA fragment in the presence of T4 DNA ligase, indicating its ability to mediate very tight DNA curvatures.     

Timing and magnitude of lumbar spine contribution to trunk forward bending and backward return in patients with acute low back pain

Alterations in the lumbo-pelvic coordination denote changes in neuromuscular control of trunk motion as well as load sharing between passive and active tissues in the lower back. Differences in timing and magnitude aspects of lumbo-pelvic coordination between patients with chronic low back pain (LBP) and asymptomatic individuals have been reported; yet, the literature on lumbo-pelvic coordination in patients with acute LBP is scant. A case-control study was conducted to explore the differences in timing and magnitude aspects of lumbo-pelvic coordination between females with (n=19) and without (n=19) acute LBP. Participants in each group completed one experimental session wherein they performed trunk forward bending and backward return at preferred and fast paces. The amount of lumbar contribution to trunk motion (as the magnitude aspect) as well as the mean absolute relative phase (MARP) and deviation phase (DP) between thoracic and pelvic rotations (as the timing aspect) of lumbo-pelvic coordination were calculated. The lumbar contribution to trunk motion in the 2nd and the 3rd quarters of both forward bending and backward return phases was significantly smaller in the patient than the control group. The MARP and the DP were smaller in the patient vs. the control group during entire motion. The reduced lumbar contribution to trunk motion as well as the more in-phase and less variable lumbo-pelvic coordination in patients with acute LBP compared to the asymptomatic controls is likely the result of a neuromuscular adaptation to reduce painful deformation and to protect injured lower back tissues.     

Endoglucanase A from Cellulomonas fimi in which the hinge sequence of human IgA1 is substituted for the linker connecting its two domains is hydrolyzed by IgA proteases from Neisseria gonorrhoeae

The hinge in IgA1 and the linker in endoglucanase A (CenA) are quite similar. The IgA1 hinge is 18 amino acids long and contains only proline, threonine and serine. The linker in CenA is 27 amino acids long and contains only proline, threonine and a single serine. IgA proteases from Neisseria gonorrhoeae cleave Pro-Ser and Pro-Thr bonds within the IgA1 hinge sequence, but they do not attack CenA. When the linker sequence of CenA is replaced with the hinge sequence of IgA1, the hybrid polypeptide is susceptible to the N. gonorrhoeae proteases. It is cleaved within the hinge sequence at the same sites as IgA1.     

Lactose repressor hinge domain independently binds DNA

The short 8–10 amino acid “hinge” sequence in lactose repressor (LacI), present in other LacI/GalR family members, links DNA and inducer‐binding domains. Structural studies of full‐length or truncated LacI‐operator DNA complexes demonstrate insertion of the dimeric helical “hinge” structure at the center of the operator sequence. This association bends the DNA ～40° and aligns flanking semi‐symmetric DNA sites for optimal contact by the N‐terminal helix‐turn‐helix (HtH) sequences within each dimer. In contrast, the hinge region remains unfolded when bound to nonspecific DNA sequences. To determine ability of the hinge helix alone to mediate DNA binding, we examined (i) binding of LacI variants with deletion of residues 1–50 to remove the HtH DNA binding domain or residues 1–58 to remove both HtH and hinge domains and (ii) binding of a synthetic peptide corresponding to the hinge sequence with a Val52Cys substitution that allows reversible dimer formation via a disulfide linkage. Binding affinity for DNA is orders of magnitude lower in the absence of the helix‐turn‐helix domain with its highly positive charge. LacI missing residues 1–50 binds to DNA with ～4‐fold greater affinity for operator than for nonspecific sequences with minimal impact of inducer presence; in contrast, LacI missing residues 1–58 exhibits no detectable affinity for DNA. In oxidized form, the dimeric hinge peptide alone binds to O1 and nonspecific DNA with similarly small difference in affinity; reduction to monomer diminished binding to both O1 and nonspecific targets. These results comport with recent reports regarding LacI hinge interaction with DNA sequences.