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Werner syndrome (WS) is one of a group of human genetic diseases that have recently been linked to deficits in cellular helicase function. We review the spectrum of WS-associated WRN mutations, the organization and potential functions of the WRN protein, and potential mechanistic links between the loss of WRN function and pathogenesis of the WS clinical and cellular phenotypes.
BACKGROUND: Homology modeling is an important technique for making use of the rapidly increasing number of protein sequences in the absence of structural information. The major problems in such modeling, once the alignment has been made, concern the positions of loops and the orientations of sidechains. Although progress has been made in recent years for sidechain prediction, current methods appear to have a limit on the order of 70% in their accuracy. It is important to have an understanding of this limitation, which for energy-based methods could arise from inaccuracies of the potential function. RESULTS: A test of the CHARMM function for sidechain prediction was performed. To eliminate the multiple-residue search problem, the minimum energy positions of individual sidechains in ten proteins were calculated in the presence of all other sidechains in their crystal orientations. This test provides a necessary condition that any energy function useful for sidechain placement must satisfy. For chi1 x chi2 rotations, the accuracies were 77.4% and 89.5%, respectively, and in the presence of crystal waters were 86.5% and 94.9%, respectively. If there was an error, the crystal structure usually corresponded to an alternative local minimum on the calculated energy map. Prediction accuracy correlated with the size of the energy gap between primary and secondary minima. CONCLUSIONS: The results indicate that the errors in current sidechain prediction schemes cannot be attributed to the potential energy function per se. The test used here establishes a necessary condition that any proposed energy-based sidechain prediction method, as well as many statistically based methods, must satisfy.
The full vibrational Hamiltonian for the inversion of NH(3) and H(2)NO has been diagonalized in a basis set that is the direct product of functions of the inversion coordinate and of harmonic vibrational functions independent of this inversion coordinate. The kinetic part of the Hamiltonian matrix is constructed with the use of the closure relation for these vibrational functions. The method is tested with the potential function which is supposed to be harmonic for the vibrations orthogonal to the inversion coordinate: the first computed levels are in good agreement with experimental levels for NH(3). For higher levels, anharmonic terms should be included.
Nearly 20% of yeast genes are required for viability, hindering genetic analysis with knockouts. We created promoter-shutoff strains for over two-thirds of all essential yeast genes and subjected them to morphological analysis, size profiling, drug sensitivity screening, and microarray expression profiling. We then used this compendium of data to ask which phenotypic features characterized different functional classes and used these to infer potential functions for uncharacterized genes. We identified genes involved in ribosome biogenesis (HAS1, URB1, and URB2), protein secretion (SEC39), mitochondrial import (MIM1), and tRNA charging (GSN1). In addition, apparent negative feedback transcriptional regulation of both ribosome biogenesis and the proteasome was observed. We furthermore show that these strains are compatible with automated genetic analysis. This study underscores the importance of analyzing mutant phenotypes and provides a resource to complement the yeast knockout collection.
Hedgehog (Hh) signals regulate invertebrate and vertebrate development, yet the role of the cascade in adipose development was undefined. To analyze a potential function, we turned to Drosophila and mammalian models. Fat-body-specific transgenic activation of Hh signaling inhibits fly fat formation. Conversely, fat-body-specific Hh blockade stimulated fly fat formation. In mammalian models, sufficiency and necessity tests showed that Hh signaling also inhibits mammalian adipogenesis. Hh signals elicit this function early in adipogenesis, upstream of PPARgamma, potentially diverting preadipocytes as well as multipotent mesenchymal prescursors away from adipogenesis and toward osteogenesis. Hh may elicit these effects by inducing the expression of antiadipogenic transcription factors such as Gata2. These data support the notion that Hh signaling plays a conserved role, from invertebrates to vertebrates, in inhibiting fat formation and highlighting the potential of the Hh pathway as a therapeutic target for osteoporosis, lipodystrophy, diabetes, and obesity.
Deficits in hippocampus-dependent spatial learning that are typical for a subpopulation of aged rats are not associated with loss of neurons or excitatory synapses but accompanied by significant reduction of postsynaptic density (PSD) area in perforated synapses. Here, we examined whether structural alterations in aged learning-impaired rats correlate with altered content of PSD proteins which are critically involved in normal synaptic function. Spatial memory tasks were used to separate male rats into young, aged learning-unimpaired and impaired groups. Semi-quantitative immunohistochemistry revealed significant alterations in the content of the AMPA receptor GluR1 subunit, PSD-95 and synGAP in the hippocampal formation of aged-learning impaired compared to aged-unimpaired and young rats. While synGAP expression was reduced, GluR1 and PSD95 levels were selectively increased in aged-learning-impaired subjects. These findings suggest that age-induced changes of the PSD protein expression levels are more pronounced in learning-impaired rats compared to unimpaired subjects and that the alterations in synaptic protein content may result in reduced synaptic function, potentially underlying the individual differences in mnemonic functions during aging.
The current protein structure database contains unfavorable Asn/Gln amide rotamers in the order of 20%. Here, we derive a set of self-consistent potential functions to identify and correct unfavorable rotamers. Potentials of mean force for all heavy atoms are compiled from a database of high-resolution protein crystal structures. Starting from erroneous data, a refinement-correction cycle quickly converges to a self-consistent set of potentials. The refinement is entirely driven by the deposited structure data and does not involve any assumptions on molecular interactions or any artificial constraints. The refined potentials obtained in this way identify unfavorable rotamers with high confidence. Since the state of Asn/Gln rotamers is largely determined by hydrogen bond interactions, the features of the respective potentials are of interest in terms of molecular interactions, protein structure refinement, and prediction. The Asn/Gln rotamer assignment is available as a public web service intended to support protein structure refinement and modeling.
The potential functional diversity of closely related myosin isoforms found in eukaryotic cells is not yet understood in detail. We have previously provided evidence from functional knockouts of Neuro-2A neuroblastoma cells that myosin IIB is essential for neurite outgrowth. Here we investigate the role of non-muscle myosin IIA in the same cell line. We show that suppression of myosin IIA transcript and protein expression, brought about through exposure to isoform-specific antisense oligonucleotides, caused a rearrangement of the actin cytoskeleton and loss of cell adhesion. This also led to disruption of focal contacts, as evidenced by coincident reduction in paxillin and vinculin immunofluorescence, but did not diminish transcript expression. All effects were fully reversible. Before myosin IIA antisense-induced detachment, neurite outgrowth remained unaffected. By contrast, antisense oligonucleotides directed against myosin IIB transcripts had no effect on adhesion but severely attenuated neurite outgrowth. We infer that the two main isoforms of neuronal conventional myosin, myosins IIA and IIB, have separate but linked functions during neuronal adhesion and neurite outgrowth.
Possible conformations for a cyclic nonapeptide that are consistent with conformation-dependent information obtained from an NMR investigation of the peptide in solution are presented. These several conformations are deduced from the myriad of possible conformations by eliminating from consideration all cyclic species having one or more residues in a conformation that does not correspond to the vicinal coupling constants observed by NMR between the amide and alpha-protons. A Karplus-like relation connecting the dihedral angle [unk]' and the vicinal coupling J(Nalpha) between N-H and C(alpha)-H(alpha) is used to test this correspondence. A further reduction in the number of cyclic conformations under consideration is made possible by rejecting the conformations that have a high intramolecular conformational energy. The intramolecular conformational energy of the cyclic nonapeptide is estimated by summing the independent residue energies. These have been calculated by others with approximate potential functions to account for the intrinsic torsional potentials and the nonbonded steric (6-12 potential) and electrostatic (monopole-monopole) interactions solely dependent upon one or both of the residue rotations, [unk] and Psi, about the N-C(alpha) and C(alpha)-C bonds, respectively.
Phytic acid (PA), a major phosphorus storage compound of most seeds and cereal grains, contributes about 1 to 7% of their dry weight. It may account for more than 70% of the total kernel phosphorus. PA has the strong ability to chelate multivalent metal ions, especially zinc, calcium, and iron. The binding can result in very insoluble salts that are poorly absorbed from the gastrointestinal tract, which results in poor bioavailability (BV) of minerals. Alternatively, the ability of PA to chelate minerals has been reported to have some protective effects, such as decreasing iron-mediated colon cancer risk and lowering serum cholesterol and triglycerides in experimental animals. Data from human studies are still lacking. PA is also considered to be a natural antioxidant and is suggested to have potential functions of reducing lipid peroxidation and as a preservative in foods. Finally, certain inositol phosphates, which may be derived from PA, have been noted to have a function in second messenger transduction systems. The potential nutritional significance of PA is discussed in this review.
CD83 is an immunoglobulin (Ig) superfamily member that is upregulated during the maturation of dendritic cells (DCs). It has been widely used as a marker for mature DCs, but its function is still unknown. To approach its potential functional role, we have expressed the extracellular Ig domain of human CD83 (hCD83ext) as a soluble protein. Using this tool we could show that immature as well as mature DCs bind to CD83. Since CD83 binds a ligand also expressed on immature DCs, which do not express CD83, indicates that binding is not a homophilic interaction. In addition we demonstrate that hCD83ext interferes with DC maturation downmodulating the expression of CD80 and CD83, while no phenotypical effects were observed on T cells. Finally, we show that hCD83ext inhibits DC-dependent allogeneic and peptide-specific T cell proliferation in a concentration dependent manner in vitro. This is the first report regarding functional aspects of CD83 and the binding of CD83 to DCs.
Coupled nonlinear Schrödinger (CNLS) equations with an external elliptic function potential model with high accuracy a quasi-one-dimensional interacting two-component Bose-Einstein condensate (BEC) trapped in a standing wave generated by a few laser beams. The construction of stationary solutions of the two-component CNLS equation with a periodic potential is detailed and their stability properties are studied by direct numerical simulations. Some of these solutions allow reduction to the Manakov system. From a physical point of view the trivial phase solutions can be interpreted as exact Bloch states at the edge of the Brillouin zone. Some of them are stable while others are found to be unstable against weak modulations of long wavelength. By numerical simulations it is shown that the modulationally unstable solutions lead to the formation of localized ground states of the coupled BEC system.
BACKGROUND AND PURPOSE: Genetic influences are important in multifactorial cerebral small-vessel disease (SVD) and may act via endothelial dysfunction. Nitric oxide (NO) synthesized by endothelial nitric oxide synthase (eNOS) is a key mediator of endothelial function. We determined the role of 3 potentially functional eNOS polymorphisms (T-786C, intron 4ab, G894T) located toward the 5' flanking end of the gene as risk factors for SVD and different SVD subtypes: isolated lacunar infarction (n=137) and ischemic leukoaraiosis (n=160). METHODS: Three hundred patients with SVD and 600 community controls were studied. Genotypes were determined through polymerase chain reaction with or without restriction fragment digestion. Nitrate (NO(x)) levels were determined in a subgroup by use of a Griess method. Polymorphisms were tested individually and in combination with haplotype analysis. RESULTS: The intron 4a variant was protective against SVD. This effect was confined to isolated lacunar infarction (odds ratio, 0.55; 95% confidence interval, 0.35 to 0.86; P=0.01). Haplotypes encountered were significantly different in this subtype compared with controls (P=0.001), with the -786C promoter/intron 4a combination particularly underrepresented. NO(x) levels were associated with the T-786C locus (P=0.03) but only in the presence of the intron 4a allele (P=0.07 for interaction). CONCLUSIONS: The intron 4ab insertion/deletion genotype was associated with isolated lacunar infarction. Haplotype and functional studies suggested that the protective effect of the 4a variant could be mediated through changes in eNOS promoter activity and increased NO levels. The specific association with isolated symptomatic lacunar infarction and not ischemic leukoaraiosis may reflect different etiopathogeneses of the 2 subtypes. Lack of NO could predispose to localized microatheroma in proximal arterioles rather than diffuse arteriosclerosis affecting distal perforating vessels.
Most patients who suffer from chronic noninfectious, nonallergic rhinitis (NINAR) cannot be assigned to a syndrome of known etiology. The symptomatology may well resemble that of allergic rhinitis; however, NINAR has lower prevalence of sneezing, conjunctival symptoms, and pruritus and higher prevalence of symptoms compatible with sinus disease. The triggers for the symptoms of NINAR are mainly irritants and changes in atmospheric conditions. Among individuals who develop chronic rhinitis symptoms, the percentage of nonallergic etiology increases steadily with age and is more than 60% beyond the fifth decade of life. Our strategy regarding the pathophysiology of NINAR should be to identify functional abnormalities of nasal mucosa that can potentially result in the alleged nasal symptoms. In this respect, comparison of patients with NINAR to patients with allergic rhinitis and to healthy individuals could shed light into the cause(s) of NINAR. Three potential functional abnormalities are discussed in this article: those associated with the aging process of the nasal mucosa, those resulting in various forms of nasal hyperreactivity, and those reflecting imbalanced neuronal control of end organs of the nose. The most interesting development in the therapy of NINAR is the use of capsaicin. Although placebo-controlled studies are scarce and participants have not been adequately characterized, it is possible that abnormal nociceptor nerve endings play a role in the generation of the symptoms of NINAR. Alternatively, NINAR may represent a condition of increased perceptual acuity to irritants and to environmental changes. This problem may also benefit from defunctionalization of nociceptors.
Cell biology is in transition from reductionism, to a more integrated science which is now preoccupied by molecular interactions acting in modules. Large-scale quantitative analysis of gene expression, including cDNA microarrays and proteomic analysis, is now applied to heart failure and atherosclerosis. The technology is still at the beginning and is limited by variations in the array platforms and gene products as well as sensitivity or specificity of the selected probes. These limitations are progressively going to be reduced, but still they do exist. Biological systems are scale free networks made from genes, proteins or traits that interact one another and form networks and functional modules. Networks emerge through the addition of new nodes which are preferentially attached to more connected nodes to form hubs, according to the "rich-gets-richer" mechanism, and there are large networks which include central genes (nexus). Both hubs and nexus are attractive candidate for targeting new therapy. An important study from King JY et al. (Physiol Genomics 2005; 23: 103-18) exemplifies this concept by showing the first realistic pathways to understand atherosclerosis. The 4 steps of the design are based on histological grading and microarrays analysis and include an association network constructed from PubMed and the construction of sub-networks in which genes whose expression was differentially regulated were indicated. Connectivity analysis networks revealed new important modular pathways. In heart failure, no attempts have been made to organize the data into functional modulus. Since the causes of heart failure are well documented, the problem is to identify functional modules responsible for myocardial dysfunction. Several potential functional modules can be identified so far. Indeed, cardiac remodeling results from two types of changes in gene expression, namelly the reexpression of the foetal programme which has a mechanical origin and several well documented interfering determinants that modified the basic remodelling, including senescence, obesity, diabetes, ischemia, and the neurohormonal reaction.
Skeletal muscle hypertrophy in young male rats was found to be accompanied by adaptive changes in neuromuscular spindles. The changes consisted in connective capsule thickening, increased diameter of NMS and intrafusal muscle fibers, expanded afferent and efferent nerve terminals, increased microcirculatory bed capacity. The quantitative and qualitative shifts observed in NMS structure are morphologically equivalent to the rise in their functional potential, which forms the basis for the functional changes in conditions of increasing skeletal muscle hypertrophy.
Regulation of HLA class II transcription is complex, with both locus-specific and allele-specific polymorphisms associated with consensus regulatory region promoter elements. In order to evaluate the potential function of allele-specific elements, HLA-DQB1 transcripts and in vivo footprinting of the DQB1 promoter were studied in human cell lines inducible for HLA class II expression. In the heterozygous melanoma cell line Me9229/18, differential expression was observed for two DQB1 alleles. This variation was reflected in both steady-state and inducible transcripts, although methylation patterns of the promoter elements were similar for both alleles. This in vivo allelic difference expression, which correlates with previous studies of in vitro reporter gene transcription, indicates the potential for functionally important differences in tissue-specific and inducible expression attributable to promoter region polymorphism in HLA genes.
The application of photosynthetic bacteria (PB) in water remediation has demonstrated exceptional advantages in terms of high efficiency and low-carbon benefits. However, the limited understanding of PB across natural aquatic environments has constrained the rational development of this strategy. Here, we analyzed 3198 genomic sequencing samples from seven types of natural aquatic ecosystems to investigate the distribution and functions of 42 PB genera commonly used in water remediation. The results showed that the average abundance of the targeted PB reached 9.83 %, with the highest value of 14.93 % observed in River, while Lake harbored the greatest PB genus diversity. PB genera exhibited high sensitivity to salinity, with Rhodoferax dominating freshwater habitats, whereas Rhodovulum was predominant in marine environments. Notably, co-occurrence network analysis revealed that PB were closely associated with microbial community stability and optimized interspecific interactions. Aquatic microbial communities with high PB abundance were characterized by efficient division-of-labor modules, accompanied by enhanced PB-associated functional potential for carbon fixation, denitrification, and sulfur oxidation. In summary, this study systematically elucidates the regional biogeographical patterns and ecological roles of PB in natural aquatic environments, providing a comprehensive scientific basis and theoretical guidance for the development and practical application of PB-based water remediation technologies.