Apurinic/apyrimidinic (AP) sites are common DNA lesions that arise from spontaneous depurination or by base excision repair (BER) of modified bases. A biotin-containing aldehyde-reactive probe (ARP) [Kubo, K., Ide, H., Wallace, S. S. & Kow, Y. W. (1992) Biochemistry 31, 3703–3708] is used to measure AP sites in living cells. ARP penetrates the plasma membrane of cells and reacts with AP sites in DNA to form a stable ARP–DNA adduct. The DNA is isolated and treated with avidin-horseradish peroxidase (HRP), forming a DNA–HRP complex at each biotin residue, which is rapidly separated from free avidin–HRP by selective precipitation with a DNA precipitating dye (DAPER). The number of AP sites is estimated by HRP activity toward chromogenic substrate in an ELISA assay. The assay integrates the AP sites formed by the different glycosylases of BER during a 1-h incubation and eliminates artifactual depurination or loss of AP sites during DNA isolation. The assay was applied to living cells and nuclei. The number of AP sites after a 1-h incubation in old IMR90 cells was about two to three times higher than that in young cells, and the number in human leukocytes from old donors was about seven times that in young donors. The repair of AP sites was slower in senescent compared with young IMR90 cells. An age-dependent decline is shown in the activity of the glycosylase that removes methylated bases in IMR90 cells and in human leukocytes. The decline in excision of methylated bases from DNA suggests an age-dependent decline in 3-methyladenine DNA glycosylase...
ATP-sensitive potassium channels (KATP channels) regulate cell excitability in response to metabolic changes. KATP channels are formed as a complex of a sulfonylurea receptor (SURx), a member of the ATP-binding cassette protein family, and an inward rectifier K+ channel subunit (Kir6.x). Membrane phospholipids, in particular phosphatidylinositol (PI) 4,5-bisphosphate (PIP2), activate KATP channels and antagonize ATP inhibition of KATP channels when applied to inside-out membrane patches. To examine the physiological relevance of this regulatory mechanism, we manipulated membrane PIP2 levels by expressing either the wild-type or an inactive form of PI-4-phosphate 5-kinase (PIP5K) in COSm6 cells and examined the ATP sensitivity of coexpressed KATP channels. Channels from cells expressing the wild-type PIP5K have a 6-fold lower ATP sensitivity (K1/2, the half maximal inhibitory concentration, ≈ 60 μM) than the sensitivities from control cells (K1/2 ≈ 10 μM). An inactive form of the PIP5K had little effect on the K1/2 of wild-type channels but increased the ATP-sensitivity of a mutant KATP channel that has an intrinsically lower ATP sensitivity (from K1/2 ≈ 450 μM to K1/2 ≈ 100 μM), suggesting a decrease in membrane PIP2 levels as a consequence of a dominant-negative effect of the inactive PIP5K. These results show that PIP5K activity...
The 10th type III module of fibronectin possesses a
β-sandwich structure consisting of seven
β-strands (A–G) that are arranged in two antiparallel
sheets. It mediates cell adhesion to surfaces via its integrin binding
motif, Arg78, Gly79, and Asp80
(RGD), which is placed at the apex of the loop connecting
β-strands F and G. Steered molecular dynamics
simulations in which tension is applied to the protein’s terminal ends
reveal that the β-strand G is the first to break away
from the module on forced unfolding whereas the remaining fold
maintains its structural integrity. The separation of strand G from the
remaining fold results in a gradual shortening of the distance between
the apex of the RGD-containing loop and the module surface, which
potentially reduces the loop’s accessibility to surface-bound
integrins. The shortening is followed by a straightening of the
RGD-loop from a tight β-turn into a linear
conformation, which suggests a further decrease of affinity and
selectivity to integrins. The RGD-loop therefore is located
strategically to undergo strong conformational changes in the early
stretching stages of the module and thus constitutes a mechanosensitive
control of ligand recognition.
Nuclear hormone receptors (NRs) are potential targets for therapeutic approaches to many clinical conditions, including cancer, diabetes, and neurological diseases. The crystal structure of the ligand binding domain of agonist-bound NRs enables the design of compounds with agonist activity. However, with the exception of the human estrogen receptor-α, the lack of antagonist-bound “inactive” receptor structures hinders the rational design of receptor antagonists. In this study, we present a strategy for designing such antagonists. We constructed a model of the inactive conformation of human retinoic acid receptor-α by using information derived from antagonist-bound estrogen receptor-α and applied a computer-based virtual screening algorithm to identify retinoic acid receptor antagonists. Thus, the currently available crystal structures of NRs may be used for the rational design of antagonists, which could lead to the development of novel drugs for a variety of diseases.
Monolayer mixtures of dihydrocholesterol and phospholipids at the
air–water interface are used to model membranes containing cholesterol
and phospholipids. Specific, stoichiometric interactions between
cholesterol and some but not all phospholipids have been proposed to
lead to the formation of condensed complexes. It is reported here that
an externally applied electric field of the appropriate sign can
destabilize these complexes, resulting in their dissociation. This is
demonstrated through the application of an electric field gradient that
leads to phase separations in otherwise homogeneous monolayers. This is
observed only when the monolayer composition is close to the
stoichiometry of the complex. The electric field effect is analyzed
with the same mean field thermodynamic model as that used previously to
account for pairs of upper miscibility critical points in these
mixtures. The concentrations of dihydrocholesterol, phospholipid, and
complex vary strongly and sometimes discontinuously in the monolayer
membrane in the field gradient. The model is an approximation to a
two-dimensional liquid in which molecules freely exchange between free
and complexed form so that the chemical potentials are constant
throughout the membrane. The calculations are illustrated for a complex
of about 15 molecules...
Consistent with the epileptogenic and deleterious effects of the potent neurotoxin kainate, the activation of kainate receptors reduces the synaptic inhibition induced by the amino acid γ-aminobutyric acid (GABA). Extrapolating from these data led to the conclusion that kainate receptors are located presynaptically. However, kainate directly depolarizes the inhibitory interneurons, causing them to fire repeatedly. This effect might indirectly decrease the size of inhibitory postsynaptic currents recorded from pyramidal cells and places in doubt the presynaptic location for kainate receptors. Here we show that both effects, membrane depolarization and the reduction of inhibitory potentials, can be dissociated by several means, particularly by the natural agonist of kainate receptors, glutamate. Indeed, when applied at low concentrations, glutamate inhibited GABA release without affecting the firing rate of GABA interneurons. These results indicate that CA1 interneurons contain two populations of kainate receptors, each with different agonist sensitivity and coupled to distinct signaling pathways.
We describe a procedure for a space-time description of protein structures. The method is capable of determining populations of conformational substates, and amplitudes and directions of internal protein motions. This is achieved by fitting static and dynamic NMR data. The approach is based on the jumping-among-minima concept. First, a wide conformational space compatible with structural NMR data is sampled to find a large set of substates. Subsequently, intrasubstate motions are sampled by using molecular dynamics calculations with force field energy terms. Next, the populations of substates are fitted to NMR relaxation data. By diagonalizing a second moment matrix, directions and amplitudes of motions are identified. The method was applied to the adhesion domain of human CD2. We found that very few substates can account for most of the experimental data. Furthermore, only two types of collective motions have high amplitudes. They represent transitions between a concave (closed) and flat (open) binding face and resemble the change upon counter-receptor (CD58) binding.
We have developed a method for isolation of random peptides that inhibit intracellular processes in bacteria. A library of random peptides expressed as fusions to Escherichia coli thioredoxin (aptamers) were expressed under the tight control of the arabinose-inducible PBAD promoter. A selection was applied to the library to isolate aptamers that interfered with the activity of thymidylate synthase (ThyA) in vivo. Expression of an aptamer isolated by this method resulted in a ThyA− phenotype that was suppressed by simultaneous overexpression of ThyA. Two-hybrid analysis showed that this aptamer is likely to interact with ThyA in vivo. The library also was screened for aptamers that inhibited growth of bacteria expressing them, and five such aptamers were characterized. Four aptamers were bacteriostatic when expressed, whereas one showed a bactericidal effect. Introduction of translational stop codons into various aptamers blocked their activity, suggesting that their biological effects were likely to be due to protein aptamer rather than RNA. Combinatorial aptamers provide a new genetic and biochemical tool for identifying targets for antibacterial drug development.
Membrane-impermeant quaternary derivatives of lidocaine (QX222 and QX314) block cardiac Na+ channels when applied from either side of the membrane, but they block neuronal and skeletal muscle channels poorly from the outside. To find the molecular determinants of the cardiac external QX access path, mutations of adult rat skeletal muscle (μ1) and rat heart (rH1) Na+ channels were studied by two-electrode voltage clamp in Xenopus oocytes. Mutating the μ1 domain I P-loop Y401, which is the critical residue for isoform differences in tetrodotoxin block, to the heart sequence (Y401C) allowed outside QX222 block, but its mutation to brain type (Y401F) showed little block. μ1-Y401C accelerated recovery from block by internal QX222. Block by external QX222 in μ1-Y401C was diminished by chemical modification with methanethiosulfonate ethylammonium (MTSEA) to the outer vestibule or by a double mutant (μ1-Y401C/F1579A), which altered the putative local anesthetic binding site. The reverse mutation in heart rH1-C374Y reduced outside QX314 block and slowed dissociation of internal QX222. Mutation of μ1-C1572 in IVS6 to Thr, the cardiac isoform residue (C1572T), allowed external QX222 block, and accelerated recovery from internal QX222 block...
Array technologies have made it straightforward to monitor simultaneously the expression pattern of thousands of genes. The challenge now is to interpret such massive data sets. The first step is to extract the fundamental patterns of gene expression inherent in the data. This paper describes the application of self-organizing maps, a type of mathematical cluster analysis that is particularly well suited for recognizing and classifying features in complex, multidimensional data. The method has been implemented in a publicly available computer package, genecluster, that performs the analytical calculations and provides easy data visualization. To illustrate the value of such analysis, the approach is applied to hematopoietic differentiation in four well studied models (HL-60, U937, Jurkat, and NB4 cells). Expression patterns of some 6,000 human genes were assayed, and an online database was created. genecluster was used to organize the genes into biologically relevant clusters that suggest novel hypotheses about hematopoietic differentiation—for example, highlighting certain genes and pathways involved in “differentiation therapy” used in the treatment of acute promyelocytic leukemia.
Photopolymerizations are widely used in medicine to create polymer networks for use in applications such as bone restorations and coatings for artificial implants. These photopolymerizations occur by directly exposing materials to light in “open” environments such as the oral cavity or during invasive procedures such as surgery. We hypothesized that light, which penetrates tissue including skin, could cause a photopolymerization indirectly. Liquid materials then could be injected s.c. and solidified by exposing the exterior surface of the skin to light. To test this hypothesis, the penetration of UVA and visible light through skin was studied. Modeling predicted the feasibility of transdermal polymerization with only 2 min of light exposure required to photopolymerize an implant underneath human skin. To establish the validity of these modeling studies, transdermal photopolymerization first was applied to tissue engineering by using “injectable” cartilage as a model system. Polymer/chondrocyte constructs were injected s.c. and transdermally photopolymerized. Implants harvested at 2, 4, and 7 weeks demonstrated collagen and proteoglycan production and histology with tissue structure comparable to native neocartilage. To further examine this phenomenon and test the applicability of transdermal photopolymerization for drug release devices...
We developed an experimental approach with genetically engineered and encapsulated mouse NIH 3T3 fibroblasts to delay the progressive degeneration of photoreceptor cells in dark-eyed Royal College of Surgeons rats. These xenogeneic fibroblasts can survive in 1.5-mm-long microcapsules made of the biocompatible polymer AN69 for at least 90 days under in vitro and in vivo conditions because of their stable transfection with the gene for the 18-kDa form of the human basic fibroblast growth factor (hFGF-2). Furthermore, when transferred surgically into the vitreous cavity of 21-day-old Royal College of Surgeons rats, the microencapsulated hFGF-2-secreting fibroblasts provoked a local delay of photoreceptor cell degeneration, as seen at 45 days and 90 days after transplantation. This effect was limited to 2.08 mm2 (45 days) and 0.95 mm2 (90 days) of the retinal surface. In both untreated eyes and control globes with encapsulated hFGF-2-deficient fibroblasts, the rescued area (of at most 0.08 mm2) was significantly smaller at both time points. Although, in a few ocular globes, surgical trauma induced a reorganization of the retinal cytoarchitecture, neither microcapsule rejection nor hFGF-2-mediated tumor formation were detected in any treated eyes. These findings indicate that encapsulated fibroblasts secreting hFGF-2 or perhaps other agents can be applied as potential therapeutic tools to treat retinal dystrophies.
Mammalian nervous system function involves billions of neurons which are interconnected in a multitude of neural circuits. Here we describe a genetic approach to chart neural circuits. By using an olfactory-specific promoter, we selectively expressed barley lectin in sensory neurons in the olfactory epithelium and vomeronasal organ of transgenic mice. The lectin was transported through the axons of those neurons to the olfactory bulb, transferred to the bulb neurons with which they synapse, and transported through the axons of bulb neurons to the olfactory cortex. The lectin also was retrogradely transported from the bulb to neuromodulatory brain areas. No evidence could be obtained for adverse effects of the lectin on odorant receptor gene expression, sensory axon targeting in the bulb, or the generation or transmission of signals by olfactory sensory neurons. Transneuronal transfer was detected prenatally in the odor-sensing pathway, but only postnatally in the pheromone-sensing pathway, suggesting that odors, but not pheromones, may be sensed in utero. Our studies demonstrate that a plant lectin can serve as a transneuronal tracer when its expression is genetically targeted to a subset of neurons. This technology can potentially be applied to a variety of vertebrate and invertebrate neural systems and may be particularly valuable for mapping connections formed by small subsets of neurons and for studying the development of connectivity as it occurs in utero.
To test the utility of gene therapeutic approaches for the treatment of pain, a recombinant herpes simplex virus, type 1, has been engineered to contain the cDNA for an opioid peptide precursor, human preproenkephalin, under control of the human cytomegalovirus promoter. This virus and a similar recombinant containing the Escherichia coli lacZ gene were applied to the abraded skin of the dorsal hindpaw of mice. After infection, the presence of β-galactosidase in neuronal cell bodies of the relevant spinal ganglia (lacZ-containing virus) and of human proenkephalin (preproenkephalin-encoding virus) in the central terminals of these neurons indicated appropriate gene delivery and expression. Baseline foot withdrawal responses to noxious radiant heat mediated by Aδ and C fibers were similar in animals infected with proenkephalin-encoding and β-galactosidase-encoding viruses. Sensitization of the foot withdrawal response after application of capsaicin (C fibers) or dimethyl sulfoxide (Aδ fibers) observed in control animals was reduced or eliminated in animals infected with the proenkephalin-encoding virus for at least 7 weeks postinfection. Hence, preproenkephalin cDNA delivery selectively blocked hyperalgesia without disrupting baseline sensory neurotransmission. This blockade of sensitization was reversed by administration of the opioid antagonist naloxone...
Potassium uptake by higher plants is the result of high- or low-affinity transport accomplished by different sets of transporters. Although K+ channels were thought to mediate low-affinity uptake only, the molecular mechanism of the high-affinity, proton-dependent K+ uptake system is still scant. Taking advantage of the high-current resolution of the patch-clamp technique when applied to the small Arabidopsis thaliana guard cells densely packed with voltage-dependent K+ channels, we could directly record channels working in the concentration range of high-affinity K+ uptake systems. Here we show that the K+ channel KAT1 expressed in Arabidopsis guard cells and yeast is capable of mediating potassium uptake from media containing as little as 10 μM of external K+. Upon reduction of the external K+ content to the micromolar level the voltage dependence of the channel remained unaffected, indicating that this channel type represents a voltage sensor rather than a K+-sensing valve. This behavior results in K+ release through K+ uptake channels whenever the Nernst potential is negative to the activation threshold of the channel. In contrast to the H+-coupled K+ symport shown to account for high-affinity K+ uptake in roots, pH-dependent K+ uptake into guard cells is a result of a shift in the voltage dependence of the K+ channel. We conclude that plant K+ channels activated by acid pH may play an essential role in K+ uptake even from dilute solutions.
The North Atlantic northern right whale (Eubalaena glacialis) is considered the most endangered large whale species. Its population has recovered only slowly since the cessation of commercial whaling and numbers about 300 individuals. We applied mark-recapture statistics to a catalog of photographically identified individuals to obtain the first statistically rigorous estimates of survival probability for this population. Crude survival decreased from about 0.99 per year in 1980 to about 0.94 in 1994. We combined this survival trend with a reported decrease in reproductive rate into a branching process model to compute population growth rate and extinction probability. Population growth rate declined from about 1.053 in 1980 to about 0.976 in 1994. Under current conditions the population is doomed to extinction; an upper bound on the expected time to extinction is 191 years. The most effective way to improve the prospects of the population is to reduce mortality. The right whale is at risk from entanglement in fishing gear and from collisions with ships. Reducing this human-caused mortality is essential to the viability of this population.
An experimental difficulty in unraveling circuits in the mammalian nervous system is the identification of postsynaptic targets of a given neuron. Besides ultrastructural reconstructions, simultaneous recordings from pairs of cells in brain slices have been used to identify connected neurons. We describe in this paper a technique using calcium imaging that allows rapid identification of potential postsynaptic targets. This method consists of stimulating one neuron (“trigger”) while imaging a population of cells to detect which other neurons (“followers”) are activated by the trigger. By using bulk-loading of calcium indicators in slices of mouse visual cortex, we demonstrate that neurons that display somatic calcium transients time-locked to the spikes of a trigger neuron can be monosynaptically connected to it. This technique could be applied to reconstruct and assay circuits in the central nervous system.
An a priori model-independent method for the
determination of accurate spectra of photocycle intermediates is
developed. The method, singular value decomposition with self-modeling
(SVD-SM), is tested on simulated difference spectra designed to mimic
the photocycle of the Asp-96 → Asn mutant of
bacteriorhodopsin. Stoichiometric constraints,
valid until the onset of the recovery of bleached
bacteriorhodopsin at the end of the photocycle,
guide the self-modeling procedure. The difference spectra of the
intermediates are determined in eigenvector space by confining the
search for their coordinates to a stoichiometric plane. In the absence
of random noise, SVD-SM recovers the intermediate spectra and their
time evolution nearly exactly. The recovery of input spectra and
kinetics is excellent although somewhat less exact when realistic
random noise is included in the input spectra. The difference between
recovered and input kinetics is now visually discernible, but the same
reaction scheme with nearly identical rate constants to those assumed
in the simulation fits the output kinetics well. SVD-SM relegates the
selection of a photocycle model to the late stage of the analysis. It
thus avoids derivation of erroneous model-specific spectra that result
from global model-fitting approaches that assume a model at the outset.
Singular value decomposition with self-modeling is applied to resolve the intermediate spectra and kinetics of the Asp96 → Asn mutant bacteriorhodopsin. The search for the difference spectra of the intermediates is performed in eigenvector space on the stoichiometric plane. The analysis of data at pH values ranging from 4 to 8 and temperatures between 5 and 25°C reveals significant, early partial recovery of the initial state after photoexcitation. The derived spectra are not biased by assumed photocycles. The intermediate spectra derived in the initial step differ from spectra determined in prior analyses, which results in intermediate concentrations with improved stoichiometric properties. Increasingly more accurate photocycles follow with increasing assumed complexity, of which parallel models are favored, consistent with recent, independent experimental evidence.
Cytoplasmic aminoacyl-tRNA synthetases of higher eukaryotes acquired extra peptides in the course of their evolution. It has been thought that these appendices are related to the occurrence of the multiprotein complex consisting of at least eight different tRNA synthetase polypeptides. This complex is believed to be a signature feature of metazoans. In this study, we used multiple sequence alignments to infer the locations of the peptide appendices from human cytoplasmic tRNA synthetases found in the multisynthetase complex. The selected peptide appendices ranged from 22 aa of aspartyl-tRNA synthetase to 267 aa of methionyl-tRNA synthetase. We then made genetic constructions to investigate interactions between all 64 combinations of these peptides that were individually fused to nonsynthetase test proteins. The analyses identified 11 (10 heterologous and 1 homologous) interactions. The six peptide-dependent interactions paralleled what had been detected by crosslinking methods applied to the isolated multisynthetase complex. Thus, small peptide appendices seem to link together different synthetases into a complex. In addition, five interacting pairs that had not been detected previously were suggested from the observed peptide-dependent complexes.