The binding interface database (BID): a compilation of amino acid hot spots in protein interfaces

SUMMARY

To make information about protein interactive function easily accessible, we are mining the primary scientific literature for detailed data about protein interfaces. The Binding Interface Database (BID) organizes the vast amount of protein interaction information into tables, graphical contact maps and descriptive functional profiles. Currently data on 170 interacting protein pairs are available with over 1300 mutations described.

AVAILABILITY

The BID database is freely available at http://tsailab.org/BID/ To have your protein of interest entered, contact Tiffany Fischer (tiffbrink@neo.tamu.edu) or Jerry Tsai at the email below

Nongenomic actions of estrogens and xenoestrogens by binding at a plasma membrane receptor unrelated to estrogen receptor alpha and estrogen receptor beta

The molecular mechanism used by environmental chemicals to exert their hormone-like actions is still only partially resolved. Although it generally is accepted that xenoestrogens act at the genomic level by binding to intracellular estrogen receptors, we have shown here that they trigger nongenomic effects in pancreatic beta cells. Both xenoestrogens and the circulating hormone, 17beta-estradiol, bind with high affinity to a common membrane binding site unrelated to the intracellular estrogen receptors ERalpha and ERbeta. This binding site is shared by dopamine, epinephrine, and norepinephrine and has the pharmacological profile of the gammaadrenergic receptor. This study provides an outline of the membrane receptor involved in rapid xenoestrogen actions.

Nutrient toxicity in pancreatic beta-cell dysfunction

Nutrients, such as glucose and fatty acids, have a dual effect on pancreatic beta-cell function. Acute administration of high glucose concentrations to pancreatic beta-cells stimulates insulin secretion. In addition, short term exposure of this cell type to dietary fatty acids potentiates glucose-induced insulin release. On the other hand, long-term exposure to these nutrients causes impaired insulin secretion, characterized by elevated exocytosis at low concentrations of glucose and no response when glucose increases in the extracellular medium. In addition, other phenotypic changes are observed in these conditions. One major step in linking these phenotypic changes to the diabetic pathology has been the recognition of both glucose and fatty acids as key modulators of beta-cell gene expression. This could explain the adaptative response of the cell to sustained nutrient concentration. Once this phase is exhausted, the beta-cell becomes progressively unresponsive to glucose and this alteration is accompanied by the irreversible induction of apoptotic programs. The aim of this review is to present actual data concerning the development of the toxicity to the main nutrients glucose and fatty acids in the pancreatic beta-cell and to find a possible link to the development of type 2 diabetes.

Engineering pancreatic islets

Pancreatic islets are neuroendocrine organs that control blood glucose homeostasis. The precise interplay of a heterogeneous group of cell populations (beta, alpha, delta and PP cells) results in the fine-tuned release of counterbalanced hormones (insulin, glucagon, somatostatin and pancreatic polypeptide respectively). Under the premises of detailed knowledge of the physiological basis underlying this behaviour, two lines of investigation might be inferred: generating computational and operational models to explain and predict this behaviour and engineering islet cells to reconstruct pancreatic endocrine function. Whilst the former is being fuelled by new computational strategies, giving biophysicists the possibility of modelling a system in which new "emergent" properties appear, the latter is benefiting from the useful tools and strategic knowledge achieved by molecular, cell and developmental biologists. This includes using tumour cell lines, engineering islet cell precursors, knowledge of the mechanisms of differentiation, regeneration and growth and, finally, therapeutic cloning of human tissues. Gaining deep physiological understanding of the basis governing these processes is instrumental for engineering new pancreatic islets.

Non-genomic actions of 17beta-oestradiol in mouse pancreatic beta-cells are mediated by a cGMP-dependent protein kinase

1. Intracellular calcium concentration ([Ca2+]i) was measured in mouse whole islets of Langerhans using the calcium-sensitive fluorescent dye Indo-1. 2. Application of physiological concentrations of 17beta-oestradiol in the presence of a stimulatory glucose concentration (8 mM) potentiated the [Ca2+]i signal in 83 % of islets tested. Potentiation was manifested as either an increase in the frequency or duration of [Ca2+]i oscillations. 3. The effects caused by 17beta-oestradiol were mimicked by the cyclic nucleotide analogues 8-bromoguanosine-3',5'-cyclic monophosphate (8-Br-cGMP) and 8-bromoadenosine-3',5'-cyclic monophosphate (8-Br-cAMP). 4. Direct measurements of both cyclic nucleotides demonstrated that nanomolar concentrations of 17beta-oestradiol in the presence of 8 mM glucose increased cGMP levels, yet cAMP levels were unchanged. The increment in cGMP was similar to that induced by 11 mM glucose. 5. Patch-clamp recording in intact cells showed that 8-Br-cGMP reproduced the inhibitory action of 17beta-oestradiol on ATP-sensitive K+ (KATP) channel activity. This was not a membrane-bound effect since it could not be observed in excised patches. 6. The action of 17beta-oestradiol on KATP channel activity was not modified by the specific inhibitor of soluble guanylate cyclase (sGC) LY 83583. This result indicates a likely involvement of a membrane guanylate cyclase (mGC). 7. The rapid decrease in KATP channel activity elicited by 17beta-oestradiol was greatly reduced using Rp-8-pCPT-cGMPS, a specific blocker of cGMP-dependent protein kinase (PKG). Conversely, Rp-cAMPS, which inhibits cAMP-dependent protein kinase (PKA), had little effect. 8. The results presented here indicate that rapid, non-genomic effects of 17beta-oestradiol after interaction with its binding site at the plasma membrane of pancreatic beta-cells is a cGMP-dependent phosphorylation process.

Lysophospholipids trigger calcium signals but not DNA synthesis in cortical astrocytes

Astrocytes generate calcium signals and proliferate in response to a growth factor-like lipid bound to plasma and serum albumin, in a process likely to be important in the formation of glial scars. A number of potential candidates for the physiologically active lipid were investigated. Lysophosphatidic acid, lysophosphatidylcholine, sphingomyelin, and platelet-activating factor all elicited calcium signals of varying magnitudes in cortical astrocytes, although only lysophosphatidic acid elicited calcium signals comparable in amplitude to those induced by the active physiological lipid. None of these lipids, however, caused cell division in astrocytes. There is therefore no invariable relationship between the ability of lipids to induce calcium signals and mitogenic activity. None of the lipids investigated demonstrate the activity of the natural lipid factor in generating both calcium signals and mitotic activity in astrocytes.

Actions of serum and plasma albumin on intracellular Ca2+ in human endothelial cells

1. The effects of serum and plasma albumin on [Ca2+]i in human endothelial cells were examined using single-cell Ca2+ imaging. Two types of endothelial cell were used: human umbilical vein endothelial cells (HUVEC) in primary culture, and the endothelial-derived cell line ECV304. 2. Serum albumin caused a large and transient rise in [Ca2+]i, due to Ca2+ release from an IP3-sensitive internal store, followed by a maintained elevation in [Ca2+]i attributable to Ca2+ influx from the external medium. A half-maximal rise in [Ca2+]i was produced by a concentration of serum albumin of about 1 microgram ml-1. 3. The Ca(2+)-releasing action of serum albumin is abolished by methanol extraction and is therefore attributable to an attached polar lipid. A possible candidate is lysophosphatidic acid, known to be released from platelets during blood coagulation, which produced similar effects to those of serum albumin. 4. In HUVEC, plasma albumin caused a sustained decrease in [Ca2+]i from the mean resting level of 114 nM to 58 nM. No effect of plasma albumin was observed in ECV304 cells. 5. The decrease in [Ca2+]i caused by plasma albumin is due to an uptake into intracellular stores. The store loading substantially potentiates the action of Ca(2+)-releasing agonists such as histamine. 6. The results show that normal plasma albumin, which carries few lipids, lowers [Ca2+]i and potentiates the actions of Ca(2+)-releasing agonists by promoting Ca2+ uptake into intracellular stores. When converted to the serum form, by binding lysophosphatidic acid released during blood coagulation, albumin has a potent effect in elevating [Ca2+]i. Blood coagulation may therefore play a role in regulating vascular tone and capillary permeability.

Comparison of two different PCR detection methods. Application to the diagnosis of pulmonary tuberculosis

The objectives are to assess the influence of the detection of the amplified DNA fragment on the sensitivity and specificity of the polymerase chain reaction (PCR). One hundred seventy-five sputum samples from 123 patients were processed. Sixty samples were taken from 60 subjects without tuberculosis, and the rest were taken from subjects with tuberculosis confirmed by culture. A fragment of the IS6110 sequence of Mycobacterium tuberculosis, which was detected using two different methods, was amplified. The detection methods used were a digoxigenin-labeled specific probe and chemiluminescent development and reamplification (nested PCR) combined with agarose gel electrophoresis. Sensitivity with probe detection was 75.65% and specificity 100%. Using the nested PCR technique, sensitivity rose to 93.04%, but specificity decreased to 96.6%. PCR is a quick and adequate way to diagnose pulmonary tuberculosis in cases where staining is negative yet there is a clinical suspicion of tuberculosis, even though a standardization process and large scale evaluation are still needed to determine its true usefulness.

[Detection of Mycobacterium tuberculosis in sputum using PCR and chemoluminescent display]

BACKGROUND

Polymerase chain reaction (PCR) using a probe with revealed chemoluminescence applied to the rapid diagnosis of pulmonary tuberculosis was used to detect Mycobacterium tuberculosis in sputum samples.

METHODS

The sputum samples were treated with proteinase K, SDS, NaOH and CTAB. A fragment of the IS6110 sequence of Mycobacterium tuberculosis detected by a probe marked with digoxigenin and revealed chemoluminescence was amplified.

RESULTS

The detection limit of the technique was situated at 10 mycobacteria per sample. Of 120 samples with a positive culture, 88 were positive by chemoluminescence probe (73.3%). The sensitivity decreased to 68.6% (35/51) in samples with negative staining and positive culture.

CONCLUSIONS

The application of molecular biology techniques are a good diagnostic alternative in samples with negative staining and clinical suspicion of tuberculosis. Our system is a cheaper alternative than the commercial systems and is applicable in laboratories unable to use radioactive isotopes.

Plasma albumin induces calcium waves in rat cortical astrocytes

Changes in intracellular calcium were monitored in cultured cortical astrocytes stimulated with albumin. Albumin elicited intracellular calcium mobilisation from intracellular stores, inducing repetitive intracellular calcium oscillations. The oscillations were not blocked by ryanodine, a blocker of the Ca-induced Ca release mechanism, and the release occurred from the same store as is accessed by glutamate and bradykinin, both of which release calcium by an IP3-dependent mechanism. Calcium signals induced by albumin appear therefore to occur via a pure IP3-dependent mechanism. When albumin was applied to confluent monolayers of astrocytes, the oscillations in individual cells were initially unsynchronised, but after several minutes of application, the Ca2 oscillations were observed to synchronise and spread through the astrocyte network as a wave. These intercellular calcium waves were inhibited by the gap junction blocker halothane. Using the fluorescence recovery after photobleaching (FRAP) technique, we demonstrate that the development of propagated waves with prolonged exposure to albumin does not result from an increase in cell coupling. The development of calcium waves on exposure to albumin may be important in the formation of glial scars in the CNS after breakdown of the blood-brain barrier.

Adenosine 5'-triphosphate (ATP) receptors induce intracellular calcium changes in mouse leydig cells

Cytoplasmic calcium ([Ca(2+)](i)) changes evoked by adenosine 5(1)-triphosphate (ATP) were recorded in cultured individual Leydig cells within 10-18 h after cell dispersion. [Ca(2+)](i) was monitored using Fura-2AM loaded cells with a digital ratio imaging system. Five micromolars ATP induced biphasic [Ca(2+)](i) responses in most cells (94%,n=100), characterized by a fast increase from a basal level (126±5 nMSE,n=60 cells) to a peak (5-7 times above basal levels) within seconds, followed by a slow decrease toward a plateau level (2-3 times above basal) within 5 min. The peak phase of the [Ca(2+)](i) response increased with ATP concentrations (1-100 μM ATP) in a dose-dependent manner with an IC(50) of 5.9±1.2 μM, and it desensitized in a reversible manner with repeated application of 5 μM ATP at <5-min intervals. The [Ca(2+)](i) peak response was dependent on Ca(2+) release from an intracellular pool, whereas the plateau phase was dependent on extracellular [Ca(2+)]. ATP did not appear to induce formation of nonspecific membrane pores, since stimulation for 10 min with ATP (10-100 μM) in the presence of extracellular Lucifer yellow (LY) (5 mg/mL) did not result in dye loading of the cells. [Ca(2+)](i) transients were elicited by other adenosine nucleotides with an order of potencies (ATP>Adenosine diphosphate [ADP]>Adenosine> Adenosine monophosphate [AMP]) that was compatible with the expression of P(2) receptors. [Ca(2+)](i) responses were suppressed by the purinergic P(2) receptor antagonist, suramin. These results provide functional evidence for the expression of purinergic P(2) receptors in Leydig cells.

Albumin stimulates uptake of calcium into subcellular stores in rat cortical astrocytes

1. When albumin from either plasma or serum is applied at low concentrations to cortical astrocytes a decrease in the level of [Ca2+]i is observed. At higher concentrations trains of calcium spikes are seen. 2. Removal of the polar lipids which are normally bound to native albumin abolishes the ability to induce spikes, but the decrease in [Ca2+]i is unaffected. The decrease is abolished by the denaturation of albumin and is not reproduced by a number of other proteins, and is therefore a specific action of albumin. We conclude that native albumin has a dual agonist action: the decrease in [Ca2+]i is induced by the albumin protein molecule, while the spikes are induced by a lipid normally bound to it. 3. The decrease is rapid (fastest tau = 12 s) and the rate is dependent on the concentration of albumin. [Ca2+]i falls from 77 nM to around 34 nM in the presence of saturating levels of albumin, and this level appears to be maintained indefinitely. 4. The decrease is due to an uptake of calcium into subcellular stores, as it is not abolished by removal of external Ca2+ or Na+ but is abolished by thapsigargin and cyclopiazonic acid, which are specific inhibitors of the endoplasmic reticulum Ca(2+)-ATPase. 5. When the state of store filling after albumin application is probed with a pulse of glutamate it can be seen that stores fill with the same time course as the decrease in [Ca2+]i. The low level of [Ca2+]i in albumin must therefore be maintained by a suppression of calcium influx rather than by a continued uptake into stores. 6. The calcium uptake potentiates the efficacy of low concentrations of calcium-releasing agonists such as glutamate and bradykinin by almost an order of magnitude. 7. A possible function for the calcium uptake caused by albumin is to potentiate the production of calcium spike trains by promoting refilling of calcium stores in the intervals between spikes. The uptake may play a role in the response of astrocytes to damage in the CNS.

Plasma albumin is a potent trigger of calcium signals and DNA synthesis in astrocytes

Cells in the central nervous system are normally prevented from coming into contact with albumin and other protein components of blood by the existence of a tight blood-brain barrier. Astrocytes and other glial cells proliferate to form glial scars when the blood-brain barrier is breached. In this report we show that albumin is an important blood component responsible for inducing astrocyte proliferation. Albumin also generates maintained trains of calcium spikes in astrocytes. Neither activity depends on blood coagulation, as albumins from both serum and plasma are approximately equally effective. Methanol extraction of albumin abolishes both actions, and recombination of the methanol-extracted factor with extracted albumin restores full activity indistinguishable from that of native albumin. The factor is sensitive to lipase, and the solvent extraction profile is that of a polar lipid.

[Reticulocytopenia and neutropenia in 3 patients with idiopathic autoimmune hemolytic anemia]

Retyculocytopenia and neutropenia or both abnormalities are very infrequent findings during the evolution of patients with acquired autoimmune hemolytic anemia (AIHA). In this paper we describe the clinical cases of three patients with AIHA in whom six different periods of reticulocytopenia were identified; the first two patients also had neutropenia. At the moment of the diagnosis of the cytopenias, the patients did not have a systemic disease, a viral infection or received immunosuppression able to produce them. In every patient the bone marrow cellularity was increased mostly at the expense of normal and macroerythroblasts, containing significant amounts of the other hematopoietic cells. After the diagnosis of AIHA, the patients received supplementary treatment with folic acid which did not produce a remission. The remissions were related to steroids: the neutrophil counts increased importantly one to ten days after starting the steroid administration, whereas reticulocytes reappeared more slowly from 7 to 30 days post-initiation. In patients with AIHA the occurrence of reticulocytopenia and neutropenia have been related to several causes. The favorable responses to steroids in our cases suggests a relationship of steroid with the immunological changes in AHA. It should be pointed out that it is necessary to prolong the followup as done in our three cases. Although these cytopenias may be independent from the hemolytic anemia, we feel our cases suggest that they could be manifestations of a pathologic state not yet characterized.

[Total parenteral nutrition. A 1-year experience with 96 patients]

In 1987, ninety-six surgical patients, of whom 44 were premature or newborn babies and 52 were infants or older children, received total parenteral nutrition (T.P.N.) at our hospital. A peripheral venous line was utilized on forty patients in the first group and only on 9 in the second group. The excellent results yielded by T.P.N. are self-evident from the low mortality showed by these patients. Thirty-three out of the 44 neonates and premature infants with serious surgical problems survived, being noteworthy the occurrence of just 3 deaths within a series of 13 necrotizing enterocolitis. In the series of 52 infants and older children, composed of 13 digestive patients (with 5 liver transplants), 6 tumoral, 9 neurologic, 4 renal (2 transplantations), 18 cardiac, 1 thoracic and 1 burnt, only 9 patients died. The average duration of T.P.N. was 10 days in the group of premature and newborn infants and 6 days for the nursing infants and older children, save for the 8 patients in whom the treatment had to be prolonged for a few months. We conclude that T.P.N., when applied in time and of short duration should entail no risk at all. In neonate and premature infant a peripheral vein shall be the route of choice. In the nursing infant and older child a central venous line is preferable, if possible the superior vena cava or its major tributary veins.

[Bolande's tumor: significance of its early diagnosis and treatment]

Four patients diagnosed of having a tumor of Bolande and treated at our institution in the past ten years are presented. In two of them, early diagnosis was aided by prenatal echographic techniques; the other two diagnoses were suspected ar three and ten days of age because of an abdominal mass. The four of them underwent a complete study which included: a plain abdominal film, an ultrasound scan and an intravenous urogram; the last three patients were also surveyed by a CT scan of the abdomen. Surgery was undertaken early on all the patients, the time of operation being in every instance within the first month of life. A laparotomy was performed and, once the contralateral kidney had been carefully examined, a nephroureterectomy was implemented, having been able to preserve in all the cases the suprarenal gland in view of the benign nature of the tumor. A histologic study confirmed the diagnosis and revealed the complete delimitation of the tumor by the renal capsule. The authors underscore the importance of this tumor's suspicion in the face of any solid renal mass detected by prenatal echography or in the neonatal period, since early diagnosis and treatment are imperative in order to prevent the ensuing complications in the rare and unfortunate cases that show a malignant tumoral trend.

[The use of clomiphene and menotropins as inducers of multiple follicular growth in a program of in vitro fertilization]

In our IVF & related techniques program, clomiphene 50 mg was used from days 2 to 6 of the cycle in 20 patients and 20 cycles. (17 IVF patients and 3 GIFT patients) menotropins were also used in 2 different schemes: a) 2 ampules in alternated days (12 cases) and b) one ampule daily (8 cases). The patients with the daily scheme required lesser total dose of menotropins and developed higher estradiol levels, although this had none statistic significance, and they also developed a greater number of follicles. There were 16 laparoscopies for ovum capture and 53 oocytes were retrieved (30.2% mature) 10 oocytes were from the GIFT patients. 16 oocytes were fertilized and 8 cleaved. There was only one pregnancy from and IVF patient with the alternated scheme that ended with a first trimester abortion.