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J Zeng

Publications and source records attributed to J Zeng.

At least 73 records · Page 4Linked to original sources
PubMed1999

A method for computational combinatorial peptide design of inhibitors of Ras protein.

A computational combinatorial approach is proposed for the design of a peptide inhibitor of Ras protein. The procedure involves three steps. First, a 'Multiple Copy Simultaneous Search' identifies the location of specific functional groups on the Ras surface. This search method allowed us to identify an important binding surface consisting of two beta strands (residues 5-8 and 52-56), in addition to the well known Ras effector loop and switch II region. The two beta strands had not previously been reported to be involved in Ras-Raf interaction. Second, after constructing the peptide inhibitor chain based on the location of N-methylacetamide (NMA) minima, functional groups are selected and connected to the main chain Calpha atom. This step generates a number of possible peptides with different sequences on the Ras surface. Third, potential inhibitors are designed based on a sequence alignment of the peptides generated in the second step. This computational approach reproduces the conserved pattern of hydrophobic, hydrophilic and charged amino acids identified from the Ras effectors. The advantages and limitations of this approach are discussed.

Acetamides↗
PubMed1999

Early training may exacerbate brain damage after focal brain ischemia in the rat.

Early overuse of a lesioned forelimb, induced by immediate immobilization of the intact forelimb after a cortical lesion, has been reported to increase tissue damage and delay functional recovery. To investigate if early training without immobilization of the intact forelimb could increase tissue loss and reduce recovery, the middle cerebral artery was ligated distal to the striatal branches in 25 male spontaneously hypertensive rats. Control rats were housed in standard cages, training rats were transferred to larger cages allowing various activities and received additional special training 1 hour a day starting either 24 hours or 7 days after the ligation. The rats were tested on a rotating pole, in a leg placement test, and in a water maze and they were killed 6 weeks after the ligation. Delayed training resulted in the best overall performance; however, both training groups performed better than standard rats on the rotating pole. The cortical infarct volume was larger in the early training group than in the other two groups (P < .005), possibly related to increased glutamate release and peri-infarct cortical hyperexcitability.

Animals↗
PubMed1999

Protein-protein recognition: an experimental and computational study of the R89K mutation in Raf and its effect on Ras binding.

Binding of the protein Raf to the active form of Ras promotes activation of the MAP kinase signaling pathway, triggering cell growth and differentiation. Raf/Arg89 in the center of the binding interface plays an important role determining Ras-Raf binding affinity. We have investigated experimentally and computationally the Raf-R89K mutation, which abolishes signaling in vivo. The binding to [gamma-35S]GTP-Ras of a fusion protein between the Raf-binding domain (RBD) of Raf and GST was reduced at least 175-fold by the mutation, corresponding to a standard binding free energy decrease of at least 3.0 kcal/mol. To compute this free energy and obtain insights into the microscopic interactions favoring binding, we performed alchemical simulations of the RBD, both complexed to Ras and free in solution, in which residue 89 is gradually mutated from Arg into Lys. The simulations give a standard binding free energy decrease of 2.9+/-1.9 kcal/mol, in agreement with experiment. The use of numerous runs with three different force fields allows insights into the sources of uncertainty in the free energy and its components. The binding decreases partly because of a 7 kcal/mol higher cost to desolvate Lys upon binding, compared to Arg, due to better solvent interactions with the more concentrated Lys charge in the unbound state. This effect is expected to be general, contributing to the lower propensity of Lys to participate in protein-protein interfaces. Large contributions to the free energy change also arise from electrostatic interactions with groups up to 8 A away, namely residues 37-41 in the conserved effector domain of Ras (including 4 kcal/mol from Ser39 which loses a bifurcated hydrogen bond to Arg89), the conserved Lys84 and Lys87 of Raf, and 2-3 specific water molecules. This analysis will provide insights into the large experimental database of Ras-Raf mutations.

Amino Acid Sequence↗
PubMed1999

Prostate biopsy schemes: 3-D visualization-based evaluation.

We have developed a prostate needle biopsy visualization system for the evaluation and optimization of biopsy schemes. Three-dimensional (3-D) prostate surface models have been reconstructed from the digitized whole-mount radical prostetactomy specimens with localized cancers. We have conducted evaluation of five major biopsy schemes with a total of 201 3-D prostate models. These are sextant, 10-pattern, 12-pattern, 14-pattern, and the 5-region schemes. The 10- and 12-pattern biopsy schemes had a 99.0% detection rate, while the rate of traditional sextant biopsy scheme was only 72.6%. The 5-region biopsy scheme had a 90.5% detection rate and the 14-pattern, which includes all the biopsies used in the above schemes, added only one additional positive case (99.5%). Our results suggest that biopsy schemes that use laterally placed biopsies based on the five region anatomical model are superior to the routinely used sextant biopsy scheme. Significant correlation is found between the tumor volume and the positive needle core volume for each of these five schemes. The 10-pattern scheme is the best in cancer detection among these five biopsy schemes.

Biopsy, Needle↗
PubMed1999

99mTc-MIBI single-photon emission-computed tomography in diagnosis of lung cancer and mediastinal metastasis lymph nodes.

AIM: To evaluate the value of technetium-99m-methoxyisobutyl isonitrile (99mTc-MIBI) single-photon emission-computed tomography (SPECT) in diagnosis of lung cancer and in preoperative prediction of mediastinal metastasis lymph nodes. METHODS: After the chest image of 99mTc-MIBI SPECT, fifty patients (40M, 10F; age 56 a +/- 11 a) diagnosed "lung field shadow" underwent the lung focus and mediastinal lymph nodes resection. As the golden standard, pathologic diagnosis was used to evaluate the role of preoperative 99mTc-MIBI SPECT. RESULTS: The sensitivity, specificity, and accuracy of 99mTc-MIBI SPECT were 93%, 50%, and 86%, respectively in lung cancer and 81%, 95%, and 88%, respectively in mediastinal metastasis lymph node. The results were also better than those of chest scan with CT. CONCLUSION: The 99mTc-MIBI SPECT is a useful and noninvasive method for diagnosing lung cancer and predicting mediastinal metastasis lymph nodes, which will guide the surgeon to resect the mediastinal metastasis lymph nodes.

Adult↗
PubMed1999

[Measurement and clinical use of recoil pressure of the respiratory system].

Using the principle that the difference of MIP (maximal inspiratory mouth pressure) between RV (residual volume) and FRC (functional residual capacity) equals Prs (recoil pressure of the respiratory system) at RV, we performed the measurement of Prs at RV in 20 normal subjects, 90 patients with COPD (chronic obstructive pulmonary disease) and 15 patients with ILF (interstitial lung fibrosis). We also performed the correlation analysis of Prs at RV and RV/TLC (total lung capacity) %. The results indicated the Prs values at RV (-2.8 +/- 0.5 kPa) in normal subjects measured in this manner was in accord with the values reported by other authors abroad. The Prs in patients with emphysema decreased and it was highly and negatively correlated with RV/TLC% (r = -0.872), but the Prs in patients with ILF was increased. The results suggest that this method for measurement of Prs is simple, reliable, and clinically useful.

Aged↗
PubMed1999

[Effects of defibrinogenase on photochemically induced middle cerebral artery occlusion in stroke-prone renovascular hypertensive rats].

OBJECTIVE: To investigate the effects of intravenous injection of defibrinogenase on dissoliving dissolve thrombus and salvaging cerebral infarction in stroke-prone renovascular hypertension rats (RHRSP) with middle cerebral artery occlusion(MCAO). METHODS: The MCAO in RHRSP was induced by administration in photosensitive dye, rose bengal, and irradiation of the main MCA with a focus laser beam. The thrombus in MCA and cerebral infarction were examined microscopically in HE stained sections. Infarction size was determined in triphenyltetrazolium chloride stained sections. Defibrinogenase was injected intravenously at 3, 6, 9, 12 hours and 3, 7 days after MCAO, meanwhile the control group received normal saline. All rats were killed at 72 hours and evaluated by pathological methods after treatment. RESULTS: In the treatment group, the thrombi were dissolved totally at 3 hours after MCAO, 75% at 6 hours, 13% at 9 hours. Defibrinogenase failed to dissolve thrombus beyond 12 hours after MCAO, just as control group. In comparison with the control group, defibrinogenase significantly reduced infarction size. There was no evidence of hemorrhage. CONCLUSIONS: Defibrinogenase can reduce infarction size and dissolve thrombus in 6 hours after MCAO without the side effect of hemorrhage.

Ancrod↗
PubMed1999

[Protein tyrosine kinase activation in the repair of rat gastric mucosa after damage].

OBJECTIVE: To investigate the possible role of protein tyrosine kinase (PTK) and its effect on nuclear protein phosphorylation and activating protein 1 (AP-1) activity in the rat gastric epithelial restitution. METHODS: Rat gastric mucosae were damaged with 20 mmol/L Deoxysodium cholate (DOC). Mucosal scrapings from the oxyntic gland area were obtained 3 hours after damage. The cellular membrane and nuclear fractions were dissociated from the extraction of the mucosal scrapings to assay the activity of PTK and AP-1, and the phosphorylation of nuclear protein. Different blockers, including Tyrphostin-51 for PTK and PD098059 for mitogen-activated protein kinase kinase (MAPKK), were used to study the signaling control for a better understanding of the mechanisms of gastric reepithelium. RESULTS: 20 mmol/L DOC caused moderate damage in rat gastric mucosae. PTK activity 3 hours after damage was 1 time that of the primary level, while nuclear protein phosphorylation level was increased about 4 folds. Tyrphostin-51 and PD098059 inhibited such effects by 85.3% and 61.6%, respectively. AP-1 activity was also greatly elevated after gastric mucosal damage and the effect was attenuated by both Tyrpsotin-51 and PD098059. CONCLUSION: PTK activation improves the rat gastric mucosal repair ability in the early phase after damage through the promotion of nuclear protein phospharylation and the increase in AP-1 activity. The effect of PTK is greatly magnified when the signals fly into the cellular nuclea, mainly through MAPK pathway.

Animals↗
PubMed1999

[A comparative study of HRCT and digital subtraction bronchography of bronchiectasis].

OBJECTIVE: To assess the value of HRCT in the diagnosis of bronchiectasis at segmental level. METHODS: 29 cases (522 segments) with bronchiectasis doubted by clinical evaluation were selected and HRCT scan and digital subtraction bronchography (DSB) were performed. RESULTS: HRCT and DSB showed a good identity in the diagnosis of bronchiectasis. Of 92 segments diagnosed as bronchiectasis in HRCT, 84 were agreed with DSB; Of 430 segments diagnosed as no bronchiectasis by HRCT, 425 were agreed with DSB. Sensitivity of HRCT is 94%, specificity is 98%. The main HRCT findings were cylindric and cystic bronchiectasis. CONCLUSIONS: HRCT is superior to bronchography for bronchiectasis. It is the first choice of the image diagnostic modalities for the patients in whom bronchiectasis is suspected.

Adolescent↗
PubMed1999

[The study on the personality factors in patients' satisfaction with their complete dentures].

OBJECTIVE: To find out the relation between personality factors of edentulous patients and the degree of their satisfaction to the complete dentures. METHODS: Under the condition of controlling quality of complete dentures, 165 subjects were investigated by using the patient denture satisfaction questionnaire and the revised Cattell's 16 personality factors questionnaire after wearing the complete dentures for one and three months. RESULTS: The personality factors of edentulous patients such as conscientiousness (G factor), shrewdness (N factor) and so on do affect their denture satisfaction in every aspect of the dentures. CONCLUSION: The oral prosthodontists not only need improving technological quality of prostheses but also need paying attention to patients' psychological characteristics.

Adult↗
PubMed1999

[Flow cytometry for testing chemosensitivity of malignant bone tumors].

OBJECTIVE: To study chemosensitivity and multidrug resistance of malignant bone tumors and to make an individual protocol of chemotherapy with sensitive antitumor agents. METHODS: Apoptosis induced by MTX, ADM, MMC, VP-16, VCR and CTX, and chemosensitivity in 32 fresh specimens of malignant bone tumors were analyzed by flow cytometry (FCM) and quantitative immunofluorescence. The expression of P-glycoprotein (P170) in the specimen and the relation between P170, multidrug resistance, and chemosensitivity were detected. RESULTS: The rate of apoptosis was significantly different in malignant bone tumor cells treated with different drugs: MTX (30.50 +/- 10.22)%, ADM (26.28 +/- 9.35)%, MMC (23.11 +/- 7.38)%, VP-16 (18.17 +/- 6.14)%, VCR (4.44 +/- 2.55)%, and CTX (1.22 +/- 0.59)%. The individual variation of cell apoptosis was prominent in the specimens of same pathological type treated with same agent. There was lower chemosensitivity in the malignant bone tumors with a high expression of P170. CONCLUSIONS: Chemosensitivity testing by flow cytometry is a simple, quick and sensitive assay. Quantitative analysis of expression of P170 could be used to predict multidrug resistance and its chemosensitivity of malignant bone tumors.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed1999

[Characteristics of pulmonary function changes in cough variant asthma and chronic asthmatic bronchitis].

To understand with greater clearness the characteristics of pulmonary function changes in patients with cough variant asthma (CVA) and patients with chronic asthmatic bronchitis(CAB), 30 cases of CVA and 25 cases of CAB were examined by pulmonary function test and were compared clinically. The results showed the differences in medical history and some clinical manifestations between the two groups were significant (P < 0.05). The expiratory flow parameters (PEF, MMEF, FEV1) of pulmonary function test in CVA were generally normal; these parameters in CAB group, however, were obviously decreased. The airway challenge test uncovered a 100% positive reaction in CVA patients, but only less than 1/4 of the patients with CAB showed positive reaction. Furthermore, the positive concentration of challenge agents (Mch) required for CVA group was 1/4.7 of the ones for CAB group, and the positive Mch concentrations of the two groups seldom crossed each other. It is concluded that some clinical manifestations of CVA and CAB were significantly different, although many similarities between them do exist; the MEFV curve in pulmonary function test and the airway challenge test can be used to differentiate them well.

Adult↗
PubMed1998

Hydrolysis of GTP on rab11 is required for the direct delivery of transferrin from the pericentriolar recycling compartment to the cell surface but not from sorting endosomes.

Rab11 is a small GTP-binding protein that in cultured mammalian cells has been shown to be concentrated in the pericentriolar endosomal recycling compartment and to play a key role in passage of the recycling transferrin receptor through that compartment [Ullrich, O., Reinsch, S., Urbé, S., Zerial, M. & Parton, R. G. (1996) J. Cell Biol. 135, 913-924]. To obtain insights into the site(s) of action of rab11 within the recycling pathway, we have now compared the effects on recycling at 37 degreesC of overexpression of wild-type rab11 and various mutant forms of this protein in cells that had been loaded with transferrin at either 37 degreesC or 16 degreesC. We show that incubation at 16 degreesC blocks passage of endocytosed transferrin into the recycling compartment and that, whereas the rab11 dominant negative mutant form (S25N) inhibits transferrin recycling after interiorization at either temperature, the wild-type rab11 and constitutively active mutant (Q70L) have no inhibitory effect on the recycling of molecules that were interiorized at 16 degreesC. This differential inhibitory effect shows that two distinct pathways for recycling are followed by the bulk of the transferrin molecules interiorized at the two different temperatures. The incapacity of the constitutively active form of rab11 (Q70L) to inhibit recycling of molecules interiorized at 16 degreesC is consistent with their recycling taking place directly from sorting endosomes, in a process that does not require hydrolysis of GTP on rab11. The fact that the dominant negative (S25N) form of rab11 inhibits recycling of molecules interiorized at both temperatures indicates that activation of rab11 by GTP is required for exit of transferrin from sorting endosomes, regardless of whether this exit is toward the recycling compartment or directly to the plasma membrane.

Animals↗
PubMed1998

Conformation of the Ras-binding domain of Raf studied by molecular dynamics and free energy simulations.

Recognition of Ras by its downstream target Raf is mediated by a Ras-recognition region in the Ras-binding domain (RBD) of Raf. Residues 78-89 in this region occupy two different conformations in the ensemble of NMR solution structures of the RBD: a fully alpha-helical one, and one where 87-90 form a type IV beta-turn. Molecular dynamics simulations of the RBD in solution were performed to explore the stability of these and other possible conformations of both the wild-type RBD and the R89K mutant, which does not bind Ras. The simulations sample a fully helical conformation for residues 78-89 similar to the NMR helical structures, a conformation where 85-89 form a 3(10)-helical turn, and a conformation where 87-90 form a type I beta-turn, whose free energies are all within 0.3 kcal/mol of each other. NOE patterns and H(alpha) chemical shifts from the simulations are in reasonable agreement with experiment. The NMR turn structure is calculated to be 3 kcal/mol higher than the three above conformations. In a simulation with the same implicit solvent model used in the NMR structure generation, the turn conformation relaxes into the fully helical conformation, illustrating possible structural artifacts introduced by the implicit solvent model. With the Raf R89K mutant, simulations sample a fully helical and a turn conformation, the turn being 0.9 kcal/mol more stable. Thus, the mutation affects the population of RBD conformations, and this is expected to affect Ras binding. For example, if the fully helical conformation of residues 78-89 is required for binding, its free energy increase in R89K will increase the binding free energy by about 0.6 kcal/mol.

Algorithms↗
PubMed1998

Ontogeny of basolateral membrane sodium-hydrogen exchange (NHE) activity and mRNA expression of NHE-1 and NHE-4 in rat kidney and jejunum.

Na+/H+ exchange (NHE) activity varies with ontogenic state in rat intestinal basolateral membrane vesicles (BLMV). The current investigation sought to determine if these observations are due to differential expression of BLM NHE isoforms, NHE-1 and NHE-4. In rat kidney, BLMV sodium uptake levels were similar in 2, 3 and 6 week rats (13.28+/-0.68, 14.03+/-0.84, and 11.71+/-0.66 nmol Na+/mg protein/30 s, respectively), and lower in adults (5.53+/-0.24) (n=4; p<0.001 between 2 week rats and adults, and between 3 week rats and adults; p<0.01 between 6 week rats and adults). In rat jejunum, BLMV uptake was highest in adults (13.07+/-0.86 nmol Na+/mg protein/30 s), and decreased in 6, 3, and 2 week rats (4.48+/-0.75, 2.94+/-0.68, and 1.59+/-0.58, respectively) (n=4; p<0.001 between all groups and adults). Control immunoblot experiments with NHE-3 antiserum showed that BLMV preps were not contaminated with significant amounts of this brush-border membrane specific protein. Northern blots with isoform-specific probes showed highest renal NHE-1 hybridization intensities in 2 and 3 week rats (11.00+/-0.25 and 12.07+/-0.16 phosphorimage units, respectively), and lower intensities in 6 week and adult animals (4.30+/-0.95, and 4.40+/-1.40, respectively) (n=4; p<0.01 between 2 week animals and 6 week and adult animals, and between 3 week animals and 6 week and adult animals). NHE-1 probes in the intestine showed no hybridization intensity differences between groups: 2 week-7.09+/-1.10, 3 week-5.39+/-0.56, 6 week-8. 24+/-1.57, and adult-8.99+/-2.20 (n=3). NHE-4 specific probes in the kidney showed hybridization intensity levels of 9.22+/-0.35 in 2 week animals, 12.12+/-1.26 in 3 week animals, 5.63+/-0.81 in 6 week animals, and 3.52+/-0.57 in adults (n=4; p<0.05 between 2 week and adults; p<0.01 between 3 week and 6 week animals, and between 3 week and adults). No NHE-4 message was detected in rat jejunum by Northern blot analysis or by reverse transcriptase-PCR. These results suggest that ontogenic NHE activity at the jejunal BLM is not related to differential expression of NHE-1, while NHE activity at the renal BLM may in part be related to differential ontogenic expression of NHE-1 and NHE-4.

Animals↗
PubMed1998

Specific interaction of conformational polypeptides derived from HIV gp120 with human T lymphocyte CD4 receptor.

Specifically cross-linked peptides (peptomers) have been prepared from the repeating sequences of the C4 domains of glycoproteins 120 present in different isolates of human immunodeficiency virus (HIV). In order to investigate if the HIV C4 peptomers could function as gp120 protein, we have used a novel protein-binding assay to examine if and which components of the peptomers could interact with CD4 receptor in vitro. Here, we demonstrate that all the polymeric components of the HIV-1 C4 peptomer could bind to recombinant soluble CD4 protein. A similar result was also obtained with HIV-2 C4 peptomer except that the binding occured only in those of constituents having molecular weights higher than that of trimer. Remarkably, the CD4-binding was demonstrated to be specific to the HIV C4 peptomers as it did not occur with control peptomers such as Poly V3 MN and Poly NINA whose peptide sequences bore no homology to those of the HIV C4 peptomers. Furthermore, consistent with previous findings, no interaction of HIV-1 C4 monomeric peptide (419-436) with CD4 was detected under the same conditions. Since it is known that the HIV C4 peptomers have much higher contents of alpha-helical conformation than those of their monomeric peptides, we conclude that the secondary structure is a pivotal determinant for the successful CD4-binding by the peptomers. Our finding reveals a more defined molecular nature of the gp120-CD4 interaction and may be important for designing HIV vaccines and therapeutics which target the first step in the virus infection.

Amino Acid Sequence↗
PubMed1998

Acute effect of ethanol on lens cation homeostasis.

This study examined the effect of ethanol on the calcium homeostasis of the bovine lens. After acute exposure of the whole lens to physiologically related ethanol concentration, the calcium content of the lens cortex increased from 0.345 +/- 0.075 to 0.476 +/- 0.047 micromol/g (p < 0.05). In contrast, other cation levels such as sodium, potassium, and magnesium did not change. In the study of the lens calcium transport, ethanol caused an increase in the calcium permeability of the lens lipid membrane by about 12% at 30 mM ethanol. Ethanol did not alter the calcium pump activity at ethanol concentration up to 400 mM. Above 600 mM ethanol, the calcium pump was almost completely inhibited. It has been suggested that moderate to heavy alcohol consumption is a risk factor for cataracts. This study indicates that acute ethanol exposure can cause a loss in the lens calcium homeostasis, which maybe one of the cellular mechanisms to contribute to the cataract development in the alcoholic individual.

Animals↗