Analyzing the structural and functional roles of residues from the ‘black’ and ‘gray’ clusters of human S100P protein

Two highly conserved structural motifs observed in members of the EF-hand family of calcium binding proteins. The motifs provide a supporting scaffold for the Ca2+ binding loops and contribute to the hydrophobic core of the EF-hand domain. Each structural motif represents a cluster of three amino acids called cluster I (‘black’ cluster) and cluster II (‘grey’ cluster). Cluster I is more conserved and mostly incorporates aromatic amino acids. In contrast, cluster II is noticeably less conserved and includes a mix of aromatic, hydrophobic, and polar amino acids of different sizes. In the human calcium binding S100 P protein, these ‘black’ and ‘gray’ clusters include residues F15, F71, and F74 and L33, L58, and K30, respectively. To evaluate the effects of these clusters on structure and functionality of human S100 P, we have performed Ala scanning. The resulting mutants were studied by a multiparametric approach that included circular dichroism, scanning calorimetry, dynamic light scattering, chemical crosslinking, and fluorescent probes. Spectrofluorimetric Ca2+-titration of wild type S100 P showed that S100 P dimer has 1–2 strong calcium binding sites (K₁ = 4 × 106 M⁻¹) and two cooperative low affinity (K₂ = 4 × 104 M⁻¹) binding sites. Similarly, the S100 P mutants possess two types of calcium binding sites. This analysis revealed that the alanine substitutions in the clusters I and II caused comparable changes in the S100 P functional properties. However, analysis of heat- or GuHCl-induced unfolding of these proteins showed that the alanine substitutions in the cluster I caused notably more pronounced decrease in the protein stability compared to the changes caused by alanine substitutions in the cluster II. Opposite to literature data, the F15 A substitution did not cause the S100 P dimer dissociation, indicating that F15 is not crucial for dimer stability. Overall, similar to parvalbumins, the S100 P cluster I is more important for protein conformational stability than the cluster II.     

Primary structure of the major β-chain of rat haemoglobins

The amino acid sequence of the major β-chain, ^IIβ, from rat haemoglobins was established with an automated sequencer. Amino acid heterogeneities were found that appear to result from allelic variation at particular residues. We applied several new or unusual techniques in determining the sequence: (1) reaction of the polypeptide with dansylaziridine for detection of cysteine; (2) blockage of the N-terminal residue and the ε-amino group of lysine residues with 1-fluoro-2-nitro-4-trimethylammoniobenzene iodide and subsequent identification of the modified lysine phenylthiohydantoin by absorbance at 420nm; (3) identification of histidine phenylthiohydantoin by its blue fluorescence under long-wave u.v. light; (4) cleavage of the chain into two or three fragments and subsequent sequencing without purification [a detailed statement giving the major phenylthiohydantoins assigned at each step for each sequence run before their alignment in individual sequences has been deposited as Supplementary Publication SUP 50084 (10 pages) at the British Library Lending Division, Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1978) 169, 5]; (5) separation of fragments produced by CNBr cleavage by cation-exchange chromatography; (6) peptide sequencing after attachment of the peptide to cytochrome c. The amino acid sequence was confirmed by amino acid compositions of the complete chain, of CNBr fragments 1 and 3, and of 11 purified tryptic peptides.     

The structure and function of ‘active zone material’ at synapses

The docking of synaptic vesicles on the presynaptic membrane and their priming for fusion with it to mediate synaptic transmission of nerve impulses typically occur at structurally specialized regions on the membrane called active zones. Stable components of active zones include aggregates of macromolecules, ‘active zone material’ (AZM), attached to the presynaptic membrane, and aggregates of Ca²⁺-channels in the membrane, through which Ca²⁺ enters the cytosol to trigger impulse-evoked vesicle fusion with the presynaptic membrane by interacting with Ca²⁺-sensors on the vesicles. This laboratory has used electron tomography to study, at macromolecular spatial resolution, the structure and function of AZM at the simply arranged active zones of axon terminals at frog neuromuscular junctions. The results support the conclusion that AZM directs the docking and priming of synaptic vesicles and essential positioning of Ca²⁺-channels relative to the vesicles'' Ca²⁺-sensors. Here we review the findings and comment on their applicability to understanding mechanisms of docking, priming and Ca²⁺-triggering at other synapses, where the arrangement of active zone components differs.     

‘Conservative’ and ‘variable’ clusters of Alu-family DNA repeats in human chromosomes

The distribution of Alu-family DNA repeats (AFRs) in chromosomes of phytohaemagglutinin-stimulated peripheral blood lymphocytes of four normal donors and non-stimulated bone marrow cells of four patients with acute leukemia (ALL and ANLL) was studied by in situ hybridization using DNA of recombinant phage lambda containing multiple inserts of AFR as a probe. Over some chromosome bands (14cen, 16p13, 16cen) from normal donors and from leukemic patients clusters of silver grains were detected. Over other three bands (3q26, 8p11-p12 and 14q24) the clusters were found only in chromosomes from the four acute leukemia patients, and were absent from chromosomes of healthy donors. The results suggest non-random long-range distribution of AFRs in human chromosomes, and somatic variations in the distribution of the repeats.     

Comparative analysis of the structure,suberin and wax composition and key gene expression in the epidermis of ‘Dangshansuli’ pear and its russet mutant

Mature fruit of ‘Dangshansuli’ pear has yellow-green skin, while its mutant ‘Xiusu’ has russet fruit skin, which is a genetic variation. To explore the mechanism underlying the russet formation, the fruit spot and epidermal structure were observed, the color, texture, and wax and suberin components were evaluated, and the gene expression levels were confirmed. In the present study, the color, texture and fruit spot of the epidermis differed significantly between ‘Dangshansuli’ and ‘Xiusu’ at 25 days after full bloom (DAFB). The cuticular wax components were alkanes, olefins, alkanoic acids, alcohols and terpenes, and the suberin was composed of fatty acid, α,ω-diacids, ω-hydroxy fatty acids, mainly ferulic acid and primary alcohols in the epidermis of ‘Dangshansuli’ and ‘Xiusu’, which exhibited significant differences at most stages of the development of pear fruits. Moreover, the expression levels of genes involved in wax and suberin were consistent with morphological and biochemical analyses. The results indicated that the suberization of epidermal cells occurred when pear fruit was young and that wax and suberin might contribute to the russet formation on the epidermis of ‘Xiusu’, leading to the significant differences in color, texture, fruit spot, and exocarp structure between ‘Dangshansuli’ and ‘Xiusu’ pears.     

Comprehensive analysis and characterization of the TCR α chain sequences in the common marmoset

The common marmoset (Callithrix jacchus) is useful as a nonhuman primate model of human diseases. Although the marmoset model has great potential for studying autoimmune diseases and immune responses against pathogens, little information is available regarding the genes involved in adaptive immunity. Here, we identified one TCR α constant (TRAC), 46 TRAJ (joining), and 35 TRAV (variable) segments from marmoset cDNA. Marmoset TRAC, TRAJ, and TRAV shared 80%, 68–100%, and 79–98% identity with their human counterparts at the amino acid level, respectively. The amino acid sequences were less conserved in TRAC than in TCRβ chain constant (TRBC). Comparative analysis of TRAV between marmosets and humans showed that the rates of synonymous substitutions per site (d _S ) were not significantly different between the framework regions (FRs) and complementarity determining regions (CDRs), whereas the rates of nonsynonymous substitutions per site (d _N ) were significantly lower in the FRs than in CDRs. Interestingly, the d _N values of the CDRs were greater for TRBV than TRAV. These results suggested that after the divergence of Catarrhini from Platyrrhini, amino acid substitutions were decreased in the FRs by purifying selection and occurred more frequently in CDRβ than in CDRα by positive selection, probably depending on structural and functional constraints. This study provides not only useful information facilitating the investigation of adaptive immunity using the marmoset model but also new insight into the molecular evolution of the TCR heterodimer in primate species.     

Emerging roles for β-arrestin-1 in the control of the pancreatic β-cell function and mass: New therapeutic strategies and consequences for drug screening

Defective insulin secretion is a feature of type 2 diabetes that results from inadequate compensatory increase in β-cell mass, decreased β-cell survival and impaired glucose-dependent insulin release. Pancreatic β-cell proliferation, survival and secretion are thought to be regulated by signalling pathways linked to G-protein coupled receptors (GPCRs), such as the glucagon-like peptide-1 (GLP-1) and the pituitary adenylate cyclase-activating polypeptide (PACAP) receptors. β-arrestin-1 serves as a multifunctional adaptor protein that mediates receptor desensitization, receptor internalization, and links GPCRs to downstream pathways such as tyrosine kinase Src, ERK1/2 or Akt/PKB. Importantly, recent studies found that β-arrestin-1 mediates GLP-1 signalling to insulin secretion, GLP-1 antiapoptotic effect by phosphorylating the proapoptotic protein Bad through ERK1/2 activation, and PACAP potentiation of glucose-induced long-lasting ERK1/2 activation controlling IRS-2 expression. Together, these novel findings reveal an important functional role for β-arrestin-1 in the regulation of insulin secretion and β-cell survival by GPCRs.     

Impact of the ‘tubulin economy’ on the formation and function of the microtubule cytoskeleton

The microtubule cytoskeleton is assembled from a finite pool of α,β-tubulin, the size of which is controlled by an autoregulation mechanism. Cells also tightly regulate the architecture and dynamic behavior of microtubule arrays. Here, we discuss progress in our understanding of how tubulin autoregulation is achieved and highlight work showing that tubulin, in its unassembled state, is relevant for regulating the formation and organization of microtubules. Emerging evidence suggests that tubulin regulates microtubule-associated proteins and kinesin motors that are critical for microtubule nucleation, dynamics, and function. These relationships create feedback loops that connect the tubulin assembly cycle to the organization and dynamics of microtubule networks. We term this concept the ‘tubulin economy’, which emphasizes the idea that tubulin is a resource that can be deployed for the immediate purpose of creating polymers, or alternatively as a signaling molecule that has more far-reaching consequences for the organization of microtubule arrays.     

Control by Ca2+ of mitochondrial structure and function in pancreatic β-cells

Mitochondria play a central role in glucose metabolism and the stimulation of insulin secretion from pancreatic β-cells. In this review, we discuss firstly the regulation and roles of mitochondrial Ca²⁺ transport in glucose-regulated insulin secretion, and the molecular machinery involved. Next, we discuss the evidence that mitochondrial dysfunction in β-cells is associated with type 2 diabetes, from a genetic, functional and structural point of view, and then the possibility that these changes may in part be mediated by dysregulation of cytosolic Ca²⁺. Finally, we review the importance of preserved mitochondrial structure and dynamics for mitochondrial gene expression and their possible relevance to the pathogenesis of type 2 diabetes.     

Impacts of methamidophos, copper, and their combinations on bacterial community structure and function in black soil

The potential ecotoxicologial risks of methamidophos, copper, and their combinations on microbial community of black soil ecosystem in the Northeast China were assessed in species richness and structures by using 16S rDNA-PCR-DGGE analysis approach, and functional characteristics at community levels by using BIOLOGGN system analysis method as well as two conventional methods(DHA and SIR). All results of DGGE banding fingerprint pat-terns(amplified by bacterial specific 16S rDNA V3 high variable region universal primer) indicated that the species richness of bacterial community in tested soil was significantly decreased to different extents by using different concentrations of single methamidophos, copper, especially some of their combinations had worse effects than their corresponding single factors. In addition, the structures of soil bacterial community had been disturbed under all stresses applied in this study because of the enrichment of some species and the disappearance of other species from the b     

Fine structure of the ‘Wulst’ region of the domestic fowl in organotypic cultures

Summary Parts of the Wulst region of the chick embryo brain were maintained for 39 days in vitro. Processes of adjacent glial cell form zonulae occludentes and desmosomal junctions in the uppermost stratum of the cultures. Subjacent to this layer, in the neuropil, axodendritic synapses are abundant. 10–20 m below the surface the perikarya of glial cells and neurons are found. The latter form small clusters, plasma membranes of contiguous cells being directly apposed to each other. Axosomatic synapses terminate on the perikarya. Occasionally one terminal synapses on two nerve cells simultaneously. Two types of cilia arise from basal bodies in the cytoplasm of nerve cells. Type I is a slender protrusion of about 0.5 m in diameter, extending into the neuropil. On transverse sections it displays a 9 + 0 pattern of organization of paired micro tubules proximally, and an 8 + 1 configuration more distally. The length of the cilium is approximately 7 m. Type II cilia also originate in the neuronal cytoplasm. The structure of the proximal portion is identical with that of type I cilia. Toward the tip, however, the type II cilium is characterized by a bulbous enlargement which is filled with loosely folded membranes. The fine structural details of this cilium correlate closely to the outer segments of retinal photoreceptor cells during differentiation. The possible role of a light receptor in the Wulst region of birds, controlling biological rhythms, is discussed. Acknowledgements. The authors wish to thank Mrs. H. Frenk for her expert assistance in tissue culture and electron microscopic techniques     

Range structure analysis: unveiling the internal structure of species’ ranges

Assessing risks of local extinction and shifts in species ranges are fundamental tasks in ecology and conservation. Most studies have focused either on the border of species’ range or on complex spatiotemporal dynamics of populations within the spatial distribution of species. The internal properties of species ranges, however, have received less attention due to a general lack of simple tools. We propose a novel approach within a metapopulation framework to study species ranges based on simple mathematical rules. We formulate and test a model of population fluctuations through space to identify key factors that regulate population density. We propose that spatial variability in species abundance reflects the interaction between temporal variability in population dynamics and the spatial variability of population parameters. This approach, that we call range structure analysis, integrates temporal and spatial properties to diagnose how each parameter contributes to species occupancy throughout its geographic range.     

Multiple potential roles of thymosin β4 in the growth and development of hair follicles

The hair follicle (HF) is an important mini-organ of the skin, composed of many types of cells. Dermal papilla cells are important signalling components that guide the proliferation, upward migration and differentiation of HF stem cell progenitor cells to form other types of HF cells. Thymosin β4 (Tβ4), a major actin-sequestering protein, is involved in various cellular responses and has recently been shown to play key roles in HF growth and development. Endogenous Tβ4 can activate the mouse HF cycle transition and affect HF growth and development by promoting the migration and differentiation of HF stem cells and their progeny. In addition, exogenous Tβ4 increases the rate of hair growth in mice and promotes cashmere production by increasing the number of secondary HFs (hair follicles) in cashmere goats. However, the molecular mechanisms through which Tβ4 promotes HF growth and development have rarely been reported. Herein, we review the functions and mechanisms of Tβ4 in HF growth and development and describe the endogenous and exogenous actions of Tβ4 in HFs to provide insights into the roles of Tβ4 in HF growth and development.