The structural basis for kainoid selectivity at AMPA receptors revealed by low-mode docking calculations

The kainoids are a class of excitatory and excitotoxic pyrrolidine dicarboxylates that act at ionotropic glutamate receptors. The kainoids bind kainate receptors with high affinity and, while binding affinity is lower at AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptors, they are active in functional assays at this receptor subtype as well. However, kainoids are only partial agonists at AMPA receptors. Currents evoked by kainoids have been described as either slowly desensitizing, partially desensitizing, or non-desensitizing. Recently acquired X-ray crystal structures of the ligand binding domain of the iGluR2, AMPA sensitive receptor suggest that differences in ligand-receptor interactions may influence functional properties of an agonist. In an effort to identify important ligand-receptor interactions of various kainoids, we have conducted a series of low-mode docking searches of AMPA agonists in the iGluR2 binding domain. Kainic acid exhibited alternate low-lying geometries, with loss of hydrogen bonds to domain 2, which may represent a dissociation route not available to other kainoids. The most potent of the kainoids are capable of forming hydrogen bonding interactions that span the two domains of the receptor. In particular, a hydrogen bond between the domoic acid C6' carboxylic acid and Ser652 may prevent a peptide bond rotation that is associated with the desensitized state of the receptor.     

High conservation of the Set1/Rad6 axis of histone 3 lysine 4 methylation in budding and fission yeasts

Histone 3 lysine 4 (H3 Lys(4)) methylation in Saccharomyces cerevisiae is mediated by the Set1 complex (Set1C) and is dependent upon ubiquitinylation of H2B by Rad6. Mutually exclusive methylation of H3 at Lys(4) or Lys(9) is central to chromatin regulation; however, S. cerevisiae lacks Lys(9) methylation. Furthermore, a different H3 Lys(4) methylase, Set 7/9, has been identified in mammals, thereby questioning the relevance of the S. cerevisiae findings for eukaryotes in general. We report that the majority of Lys(4) methylation in Schizosaccharomyces pombe, like in S. cerevisiae, is mediated by Set1C and is Rad6-dependent. S. pombe Set1C mediates H3 Lys(4) methylation in vitro and contains the same eight subunits found in S. cerevisiae, including the homologue of the Drosophila trithorax Group protein, Ash2. Three additional features of S. pombe Set1C each involve PHD fingers. Notably, the Spp1 subunit is dispensable for H3 Lys(4) methylation in budding yeast but required in fission yeast, and Sp_Set1C has a novel proteomic hyperlink to a new complex that includes the homologue of another trithorax Group protein, Lid (little imaginal discs). Thus, we infer that Set1C is highly conserved in eukaryotes but observe that its links to the proteome are not.     

Reversal by dithiothreitol treatment of the block in murine leukemia virus maturation induced by disulfide cross-linking

We previously reported that if murine leukemia virus particles are produced in the presence of the mild oxidizing agent disulfide-substituted benzamide-2, they fail to undergo the normal process of virus maturation. We now show that treatment of these immature particles with a reducing agent (dithiothreitol) induces their maturation in vitro, as evidenced by proteolytic cleavage of Gag, Gag-Pol, and Env proteins and by their morphology. The identification of partial cleavage products in these particles suggests the sequence with which the cleavages occur under these conditions. This may be a useful experimental system for further analysis of retroviral maturation under controlled conditions in vitro.     

Cofactor Tpr2 combines two TPR domains and a J domain to regulate the Hsp70/Hsp90 chaperone system

In the eukaryotic cytosol, Hsp70 and Hsp90 cooperate with various co-chaperone proteins in the folding of a growing set of substrates, including the glucocorticoid receptor (GR). Here, we analyse the function of the co-chaperone Tpr2, which contains two chaperone-binding TPR domains and a DnaJ homologous J domain. In vivo, an increase or decrease in Tpr2 expression reduces GR activation, suggesting that Tpr2 is required at a narrowly defined expression level. As shown in vitro, Tpr2 recognizes both Hsp70 and Hsp90 through its TPR domains, and its J domain stimulates ATP hydrolysis and polypeptide binding by Hsp70. Furthermore, unlike other co-chaperones, Tpr2 induces ATP-independent dissociation of Hsp90 but not of Hsp70 from chaperone-substrate complexes. Excess Tpr2 inhibits the Hsp90-dependent folding of GR in cell lysates. We propose a novel mechanism in which Tpr2 mediates the retrograde transfer of substrates from Hsp90 onto Hsp70. At normal levels substoichiometric to Hsp90 and Hsp70, this activity optimizes the function of the multichaperone machinery.     

The Berg-Purcell Limit Revisited

Biological systems often have to measure extremely low concentrations of chemicals with high precision. When dealing with such small numbers of molecules, the inevitable randomness of physical transport processes and binding reactions will limit the precision with which measurements can be made. An important question is what the lower bound on the noise would be in such measurements. Using the theory of diffusion-influenced reactions, we derive an analytical expression for the precision of concentration estimates that are obtained by monitoring the state of a receptor to which a diffusing ligand can bind. The variance in the estimate consists of two terms, one resulting from the intrinsic binding kinetics and the other from the diffusive arrival of ligand at the receptor. The latter term is identical to the fundamental limit derived by Berg and Purcell (Biophys. J., 1977), but disagrees with a more recent expression by Bialek and Setayeshgar. Comparing the theoretical predictions against results from particle-based simulations confirms the accuracy of the resulting expression and reaffirms the fundamental limit established by Berg and Purcell.     

Shaping a Morphogen Gradient for Positional Precision

Morphogen gradients, which provide positional information to cells in a developing tissue, could in principle adopt any nonuniform profile. To our knowledge, how the profile of a morphogen gradient affects positional precision has not been well studied experimentally. Here, we compare the positional precision provided by the Drosophila morphogenetic protein Bicoid (Bcd) in wild-type (wt) embryos with embryos lacking an interacting cofactor. The Bcd gradient in the latter case exhibits decreased positional precision around mid-embryo compared with its wt counterpart. The domain boundary of Hunchback (Hb), a target activated by Bcd, becomes more variable in mutant embryos. By considering embryo-to-embryo, internal, and measurement fluctuations, we dissect mathematically the relevant sources of fluctuations that contribute to the error in positional information. Using this approach, we show that the defect in Hb boundary positioning in mutant embryos is directly reflective of an altered Bcd gradient profile with increasing flatness toward mid-embryo. Furthermore, we find that noise in the Bcd input signal is dominated by internal fluctuations but, due to time and spatial averaging, the spatial precision of the Hb boundary is primarily affected by embryo-to-embryo variations. Our results demonstrate that the positional information provided by the wt Bcd gradient profile is highly precise and necessary for patterning precision.     

Impact of mate availability, population size, and spatial aggregation of morphs on sexual reproduction in a distylous, aquatic plant

In distylous, self-incompatible plants, clonal propagation, unbalanced floral morph frequencies, and reduced population size can interfere with the functioning of distyly by compromising legitimate intermorph pollinations, resulting in reduced reproductive output. Here, we examined the mating system and the impact of mate availability, population size, and spatial aggregation of morphs on reproductive output in the distylous, clonal, aquatic plant Hottonia palustris. Controlled pollinations under greenhouse conditions detected no spontaneous selfing without the action of a pollen vector (autonomous autogamy) and demonstrated very low fruit and seed development after self-pollination. Intermorph (legitimate) crossings resulted in high reproductive output in both floral morphs (long- and short-styled individuals), whereas intramorph (illegitimate) crossings decreased fruit and seed development by more than 50%, indicating that the species has partial intramorph-incompatibility. In natural populations, small population size and increasing deviation of floral morph frequencies negatively affected reproductive outcome. Individuals of the majority morph type developed significantly fewer fruit and seeds than individuals of the minority morph type. This rapid decline in fecundity was symmetrical, indicating that regardless of which morph was in the majority, the same patterns of negative frequency-dependent mating occurred. Increasing spatial isolation between compatible morphs significantly reduced fruit and seed set in both morphs similarly. This study provides clear indications of frequency- and context-dependent mating in natural populations of a distylous plant species.     

HPLC-photodiode array detection analysis of curcuminoids in Curcuma species indigenous to Indonesia

An optimized HPLC method with photodiode array detection was developed and applied to analyse the curcuminoids curcumin, demethoxycurcumin, and bis-demethoxycurcumin in rhizomes of Curcuma mangga Val &. v. Zijp, C. heyneana Val. & v. Zijp, C. aeruginosa Roxb. and C. soloensis Val. (Zingiberaceae), indigenous to Indonesia. The method was validated with an isocratic system, a short run time of 10 min and a baseline separation. The curcuminoid content was 0.18-0.47% for C. mangga, 0.98-3.21% for C. heyneana, 0.02-0.03% for C. aeruginosa and 0.40% for C. soloensis.