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Z Hu

Publications and source records attributed to Z Hu.

At least 109 records · Page 6Linked to original sources
PubMed2000

Conservation of polar residues as hot spots at protein interfaces.

A number of studies have addressed the question of which are the critical residues at protein-binding sites. These studies examined either a single or a few protein-protein interfaces. The most extensive study to date has been an analysis of alanine-scanning mutagenesis. However, although the total number of mutations was large, the number of protein interfaces was small, with some of the interfaces closely related. Here we show that although overall binding sites are hydrophobic, they are studded with specific, conserved polar residues at specific locations, possibly serving as energy "hot spots." Our results confirm and generalize the alanine-scanning data analysis, despite its limited size. Previously Trp, Arg, and Tyr were shown to constitute energetic hot spots. These were rationalized by their polar interactions and by their surrounding rings of hydrophobic residues. However, there was no compelling reason as to why specifically these residues were conserved. Here we show that other polar residues are similarly conserved. These conserved residues have been detected consistently in all interface families that we have examined. Our results are based on an extensive examination of residues which are in contact across protein interfaces. We utilize all clustered interface families with at least five members and with sequence similarity between the members in the range of 20-90%. There are 11 such clustered interface families, comprising a total of 97 crystal structures. Our three-dimensional superpositioning analysis of the occurrences of matched residues in each of the families identifies conserved residues at spatially similar environments. Additionally, in enzyme inhibitors, we observe that residues are more conserved at the interfaces than at other locations. On the other hand, antibody-protein interfaces have similar surface conservation as compared to their corresponding linear sequence alignment, consistent with the suggestion that evolution has optimized protein interfaces for function.

Amino Acid Sequence↗
PubMed2000

Structural and functional characterization of interaction between hepatitis B virus X protein and the proteasome complex.

Hepatitis B virus (HBV) has a unique fourth open reading frame coding for a 16.5-kDa protein known as hepatitis B virus X protein (HBX). The importance of HBX in the life cycle of HBV has been well established, but the underlying molecular function of HBX remains controversial. We previously identified a proteasome subunit PSMA7 that interacts specifically with HBX in the Saccharomyces cerevisiae two-hybrid system. Here we demonstrate that PSMC1, an ATPase-like subunit of the 19 S proteasome component, also interacts with HBX and PSMA7. Analysis of the interacting domains among PSMA7, PSMC1, and HBX by deletion and site-directed mutagenesis suggested a mutually competitive structural relationship among these polypeptides. The competitive nature of these interactions is further demonstrated using a modified yeast two-hybrid dissociator system. The crucial HBX sequences involved in interaction with PSMA7 and PSMC1 are important for its function as a transcriptional coactivator. HBX, while functioning as a coactivator of AP-1 and acidic activator VP-16 in mammalian cells, had no effect on the transactivation function of their functional orthologs GCN4 and Gal4 in yeast. Overexpression of PSMC1 seemed to suppress the expression of various reporters in mammalian cells; this effect, however, was overcome by coexpression of HBX. In addition, HBX expression inhibited the cellular turnover of c-Jun and ubiquitin-Arg-beta-galactosidase, two well known substrates of the ubiquitin-proteasome pathway. Thus, interaction of HBX with the proteasome complex in metazoan cells may underlie the functional basis of proteasome as a cellular target of HBX.

Adenosine Triphosphatases↗
PubMed2000

Transition-state ensemble in enzyme catalysis: possibility, reality, or necessity?

Proteins are not rigid structures; they are dynamic entities, with numerous conformational isomers (substates). The dynamic nature of protein structures amplifies the structural variation of the transition state for chemical reactions performed by proteins. This suggests that utilizing a transition state ensemble to describe chemical reactions involving proteins may be a useful representation. Here we re-examine the nature of the transition state of protein chemical reactions (enzyme catalysis), considering both recent developments in chemical reaction theory (Marcus theory for SN2 reactions), and protein dynamics effects. The classical theory of chemical reactions relies on the assumption that a reaction must pass through an obligatory transition-state structure. The widely accepted view of enzymatic catalysis holds that there is tight binding of the substrate to the transition-state structure, lowering the activation energy. This picture, may, however, be oversimplified. The real meaning of a transition state is a surface, not a single saddle point on the potential energy surface. In a reaction with a "loose" transition-state structure, the entire transition-state region, rather than a single saddle point, contributes to reaction kinetics. Consequently, here we explore the validity of such a model, namely, the enzymatic modulation of the transition-state surface. We examine its utility in explaining enzyme catalysis. We analyse the possibility that instead of optimizing binding to a well-defined transition-state structure, enzymes are optimized by evolution to bind efficiently with a transition-state ensemble, with a broad range of activated conformations. For enzyme catalysis, the key issue is still transition state (ensemble) stabilization. The source of the catalytic power is the modulation of the transition state. However, our definition of the transition state is the entire transition-state surface rather just than a single well-defined structure. This view of the transition-state ensemble is consistent with the nature of the protein molecule, as embodied and depicted in the protein energy landscape of folding, and binding, funnels.

Animals↗
PubMed2000

A new bimetallic assembly magnet [[Ni(tn)2]5[FeIII(CN)6]3]n(ClO4)n.2.5nH2O (tn = trimethylenediamine) with a novel 3-D tunnel structure.

A novel molecular-based magnet of three-dimensional (3-D) cyanide-bridged bimetallic assembly, [[Ni(tn)2]5[FeII(CN)6]3]n(ClO4)n.2.5nH2O where tn = trimethylenediamine, was synthesized and structurally characterized. The compound with an asymmetric unit of C24H52.5Cl0.5Fe1.5N19Ni2.5O3.255 crystallized in the monoclinic system of the space group P2(1)/n with a = 10.173(3) A, b = 16.053(2) A, c = 26.309(3) A, beta = 91.30(2) degrees, and Z = 4. The assembly has a 3-D network structure extended by three different types of FeIII-CN-NiII-NC-FeIII linkages. The iron (FeIII) atoms are located in two different chemical environments, which were confirmed by Mössbauer experimental results. The nickel (NiII) atoms have three different coordination environments. Cryomagnetic properties revealed that 3-D magnetic ordering occurs over the lattice below the Curie temperature around 10 K.

Journal Article↗
PubMed2000

Removal of the tryptophan 139 side chain in Escherichia coli D-3-phosphoglycerate dehydrogenase produces a dimeric enzyme without cooperative effects.

Escherichia coli d-3-phosphoglycerate dehydrogenase (PGDH) is a homotetrameric enzyme whose activity is allosterically regulated by l-serine, the end-product of its metabolic pathway. Previous studies have shown that PGDH displays two modes of cooperative interaction. One is between the l-serine binding sites and the other is between the l-serine binding sites and the active sites. Tryptophan 139 participates in an intersubunit contact near the active site catalytic residues. Site-specific mutagenesis of tryptophan 139 to glycine results in the dissociation of the tetramer to a pair of dimers and in the loss of cooperativity in serine binding and between serine binding and inhibition. The results suggest that the magnitude of inhibition of activity at a particular active site is primarily dependent on serine binding to that subunit but that activity can be modulated in a cooperative manner by interaction with adjacent subunits. The disruption of the nucleotide domain interface in PGDH by mutating Trp-139 suggests the potential for a critical role of this interface in the cooperative allosteric processes in the native tetrameric enzyme.

Allosteric Regulation↗
PubMed2000

Characterization, chromosomal assignment, and tissue expression of a novel human gene belonging to the ARF GAP family.

We have identified and characterized a novel human ADP-ribosylation factor GTPase-activating protein (ARFGAP1) gene that is related to other members of the ARF GAP family. The full-length cDNA for human ARFGAP1 was cloned following the identification of an EST obtained by large-scale cDNA library sequencing through a Blast search of public databases. Structurally, ARFGAP1 encodes a polypeptide of 516 amino acids, which contained a typical GATA-1-type zinc finger motif (CXXCX(16)CXXC) with the four cysteine residues that are highly conserved among other members of the ARF GAP family. The conserved ARF GAP domain may emphasize the biological importance of this gene. The ARFGAP1 gene, which contained 16 exons ranging from 0.5 to 9.3 kb, was mapped to human chromosome 22q13.2-q13.3 using radiation hybridization and in silico analyses. ARFGAP1 is strongly expressed in endocrine glands and testis. Interestingly, the expression of ARFGAP1 in testis is about sixfold higher than that in ovary, indicating a possible role of ARFGAP1 in the physiological function of sperm. Expression of ARFGAP1 in four human fetal tissues and seven cancer cell lines was also detected.

ADP-Ribosylation Factors↗
PubMed2000

Transcriptional activation of the MDR1 gene by UV irradiation. Role of NF-Y and Sp1.

The MDR1 promoter is subject to control by various internal and external stimuli. We have previously shown that the CCAAT box-binding protein, NF-Y, mediates MDR1 activation by the histone deacetylase inhibitors, trichostatin A and sodium butyrate, through the recruitment of the co-activator, P/CAF. We have now extended our investigation to the activation of MDR1 by genotoxic stress. We show that activation of the MDR1 promoter by UV irradiation is also dependent on the CCAAT box (-82 to -73) as well as on a proximal GC element (-56 to -42). Gel shift and supershift analyses with nuclear extracts prepared from human KB-3-1 cells identified NF-Y as the transcription factor interacting with the CCAAT box, while Sp1 was the predominant factor binding to the GC element. Mutations that abrogated binding of either of these factors reduced or abolished activation by ultraviolet irradiation; moreover, co-expression of a dominant-negative NF-Y protein (NF-YA29) reduced UV-activated transcription. Interestingly, YB-1, a transcription factor that also recognizes the CCAAT motif and had been reported to mediate induction of the MDR1 promoter by ultraviolet light, was incapable of interacting with the double-stranded MDR1 CCAAT box oligonucleotide in nuclear extracts, although it did interact with a single-stranded oligonucleotide. Furthermore, a mutation that abolished activation of MDR1 by UV-irradiation had no effect on YB-1 binding and co-transfection of a YB-1 expression plasmid had a repressive effect on UV-inducible transcription. Taken together, these results indicate a role for both NF-Y and Sp1 in the transcriptional activation of the MDR1 gene by genotoxic stress, and indicate that YB-1, if involved, is not sufficient to mediate this activation.

Base Sequence↗
PubMed2000

Studies on the fluorescence reaction between nucleic acid and the complex of cobalt(II) with 5-(3-fluoro-4-chlorophenylazo)-8-sulfonamidoquinoline and its applications.

Based on the enhancement of the fluorescence intensity of the complex of 5-(3-fluoro-4-chlorophenylazo)-8-sulfonamidoquinoline (FCPBSQ) with Co(2+) by nucleic acid in the presence of Tween 80 and in the weakly basic medium, a fluorescence method for the determination of nucleic acid was proposed. The calibration graphs for the determination of denatured calf thymus DNA (ct DNA), fish sperm DNA (fs DNA), and yeast RNA (yt RNA) were obtained in concentration ranges 0.050-4.0, 0.10-3.0, and 0.050-3.0 microg/ml with limits of detection of 0.010, 0.030, and 0.020 microg/ml, respectively. The method has been satisfactorily used for the determination of DNA in wheat cell extraction and ct DNA, fs DNA, and yt RNA in synthetic samples. Investigations on the binding mode by the Scatchard plots method suggested that both intercalation and electrostatic binding modes existed in this system.

Animals↗
PubMed2000

Genetic engineering of Helicoverpa armigera single-nucleocapsid nucleopolyhedrovirus as an improved pesticide.

The Helicoverpa armigera single-nucleocapsid nucleopolyhedrovirus (HearNPV) has been registered and is commercially produced in China as a biopesticide to control the bollworm in cotton. However, the virus has a relatively slow speed of action. To improve its efficacy, recombinant HearNPVs were generated by deleting the ecdysteroid UDP-glucosyltransferase (egt) gene (HaCXW1 and HaLM2) or by inserting the insect-specific toxin gene AaIT in the egt locus (HaCXW2) of HearNPV using conventional recombination strategies in insect cell culture. The various recombinants remained genetically stable when cultured in HzAM1 insect cells. Bioassay data showed a significant reduction in the time required for all HearNPV recombinants to kill second instar H. armigera larvae. The LT(50) of the egt deletion recombinants HaCXW1 and HaLM2 was about 27% faster than that of wild-type HearNPV. The largest reduction in LT(50) was achieved by inserting the gene for the insect-specific neurotoxin, AaIT, in the egt locus, giving a reduction in LT(50) of 32% compared to wild-type HearNPV. The ability to genetically improve the properties of HearNPV as a biopesticide provides a further opportunity to develop this virus into a commercially viable product to control the bollworm in China.

Animals↗
PubMed2000

Study of immortalization and malignant transformation of human embryonic esophageal epithelial cells induced by HPV18 E6E7.

In order to study the effect of viruses and tumor promoters on the tumorigenicity of the esophagus, human embryonic esophageal epithelial cells were infected with human papilloma virus HPV18 E6E7-AAV in synergy with 12-O-tetradecanoylphorbol 13-acetate (TPA) to observe their malignant transformation. The cultured esophageal epithelial cells incubated with HPV18 E6E7-AAV were divided into two groups: the SHEEC1 group was exposed to TPA (5 ng/ml) for 4 weeks at the 5th passage of the cells; the SHEE group served as the control and was cultured in the same medium without TPA. The morphological phenotype, the DNA content during the cell cycle and the chromosomes were analyzed. The tumorigenicity was assessed by colony formation after cultivation in soft agar and transplanting the cells into nude mice. HPV18 E6E7 DNA was assayed by fluorescent in situ hybridization (FISH) and the polymerase chain reaction (PCR). The SHEE group, at its 20th passage, grew as a monolayer with the cells showing anchorage dependence and contact inhibition. The chromosome analysis showed diploidy, and soft-agar cultivation and injection into nude mice showed the cells to be non-tumorigenic. They were therefore immortalized cells. In contrast, the SHEEC1 group (TPA group) showed increased DNA synthesis and a proliferative index that was higher (45%) than that of the SHEE group (34%). The number of large colonies of dense multilayer cells (positively transformed foci) in soft agar was high in SHEEC1 group (4.0%) but low in the SHEE group (0.1%). Tumors resulting from transplantation were observed in all six nude mice injected subcutaneously with cells of the SHEEC1 group but no tumor developed in mice receiving cells of the SHEE group. In both groups of cells, HPV18 E6E7 DNA was positively detected by FISH and PCR. The malignant transformation of human embryonic epithelial cells was induced in vitro by HPV18 E6E7 in synergy with TPA. This is a good evidence for the close relationship between HPV and the etiology and pathogenicity of esophageal carcinoma. It is also a reliable model for studying the cellular and molecular mechanisms of carcinogenesis of esophageal carcinoma.

Cell Transformation, Neoplastic↗
PubMed2000

Microdetermination of proteins using m-carboxychlorophosphonazo as detection probe by enhanced resonance light scattering spectroscopy.

Proteins can be determined using a common spectrofluorometer to detect the intensity of resonance light scattering (RLS). Under acidic conditions, the reaction between m-carboxychlorophosphonazo (CPA-mK) and proteins enhances the weak light scattering of CPA-mK drastically. This enhanced intensity is proportional to the concentration of proteins. The linear ranges for human serum albumin are 0.5-35.0 microg/mL, with detection limits of 0.104 microg/mL. The method yields results comparable to those of the calorimetric method using Coomassie Brilliant Blue G-250 (CBB) with relative standard deviations of 0.72-2.10% (n = 10). There is almost no interference by amino acids and most of the metal ions.

Algorithms↗
PubMed2000

Application of a modified simplex method to the multivariable optimization of a new FIA system for the determination of osmium.

A methodology based on the coupling of experimental design and a modified simplex method is proposed for the optimization of a new flow injection-kinetic system for the spectrophotometric determination of Os (IV) with m-acetylchlorophosphonazo, which has for the first time been used as chromogenic reagent in the quantitative analysis of this element. An orthogonal array design is utilized to design the experimental protocol, in which six variables are varied simultaneously, and obtain the initial simplex using 25 experiments. A modified simplex method is applied to continuously optimize the data of the orthogonal array design; the search for optimum conditions of 6 variables using the modified simplex method required only 25 experiments. The efficiency and simplicity of the coupling of the experimental design and the modified simplex method are attractive for the development of new analytical methods. The method has been applied to the determination of Os (IV) in a refined ore as well as in a secondary alloy and provided satisfactory results.

Journal Article↗
PubMed2000

Genomic organization of Helicoverpa armigera single-nucleocapsid nucleopolyhedrovirus.

The genome organization of the Helicoverpa armigera single-nucleocapsid nucleopolyhedrovirus (HearNPV) was investigated and compared to that of other baculoviruses. A detailed physical map was constructed for the restriction enzymes BamHI, BglII, EcoRI, HindIII, KpnI, PstI, SacI and XhoI. The 130.1-kilobase pairs (kb) long viral genome was cloned as restriction fragments into a plasmid library, which covered 97.5% of the viral genome. From this plasmid library about 45 kb of dispersed sequence information was generated. Fifty-three putative open reading frames (ORFs) with homology to ORFs of other baculoviruses were identified and their location on the genome of HearNPV was determined. The arrangement of the ORFs along the HearNPV genome is significantly different from the multiple-nucleocapsid NPVs, AcMNPV, BmNPV and OpMNPV, which have a highly collinear genome, and the granulovirus XcGV. In contrast the genomes of HearNPV and SeMNPV are highly collinear. This close relatedness between an MNPV and an SNPV is supported by the phylogeny of specific genes of these two viruses and suggests that the morphotype (S or M) is only a taxonomic and not a phylogenetic denominator. The data presented here also give further support to the view that the gene distribution along baculovirus genomes can be used as a character to describe baculovirus relatedness independent of gene phylogeny. Five homologous regions (hrs) were located on the genome of HearNPV. This is also the first report of the existence of hrs in SNPVs and this observation suggests that hrs are a common feature of baculovirus genomes.

Animals↗
PubMed2000

Use of artificial neural networks to predict the gas chromatographic retention index data of alkylbenzenes on carbowax-20M

Quantitative structure-activity relationships (QSARs) quantify the connection between the structure and properties of molecules and allow the prediction of properties from structural parameters. Models of relationships between structure and retention index of alkylbenzenes were constructed by means of a multilayer neural network using extended delta-bar-delta (EDBD) algorithms. The 165 group data belong to 129 alkylbenzenes at different temperatures on carbowax-20M. We proposed a new method to describe the structure of the alkylbenzene with a simple set of six numeric code depending on its molecular formula. A set of six numbers and the temperature were used as input parameters to predict the retention indices. The performance of different order of structural coding was investigated. The networks' architecture and the learning times were optimized. The optimum ANNs could give excellent prediction results. In addition, the multiple linear regression (MLR) and nonlinear multivariate regression were applied. We have shown in our studies that, based on the structural numeric codes, ANNs give more accurate predictions of retention index data of alkykbenzenes than regression analysis.

Journal Article↗
PubMed2000

Multiple-input microcantilever sensors

A surface-micromachined micro-electro-mechanical-system (MEMS) process has been used to demonstrate multiple-input chemical sensing using selectively coated cantilever arrays. Cantilever motion due to absorption-induced stress was readout using a custom-designed, eight-channel integrated circuit. Combined hydrogen and mercury vapor detection was achieved with a palm-sized, self-powered module with spread-spectrum telemetry reporting.

Journal Article↗
PubMed2000

The synthesis and application of 1-(o-nitrophenyl)-3-(2-thiazolyl)triazene for the determination of palladium(II) by the resonance enhanced Rayleigh light-scattering technique.

The resonance Rayleigh light-scattering (RRLS) signal of a new triazene reagent; 1-(o-nitrophenyl)-3-(2-thiazolyl)triazene (o-NPTT), was firstly synthesized and characterized in this paper at 500-600 nm wavelength range and can be enhanced remarkably by Pd2+. According to this phenomenon, a new method was developed for the determination of Pd2+ by the RRLS technique in the presence of Tween-80. The calibration graph showed good linearity over a concentration range of 5.0-700 microg l(-1) with a detection limit of 1.0 microg l(-1). There are almost no foreign ions interfered in the determination at a more than fivefold concentration of Pd2+. The method is relatively sensitive, of good selectivity and has been successfully used for the determination of trace palladium in the slag of fertilizer factories and catalyst samples.

Palladium↗
PubMed2000

Application of a biomagnetic measurement system (BMS) to the evaluation of gastrointestinal transit of intestinal pressure-controlled colon delivery capsules (PCDCs) in human subjects.

PURPOSE: For determination of the transit time through various parts of the gastrointestinal (GI) tract, we developed a method that provides the location of disintegration and drug release. This method involves GI magnetomarkergraphy (GIMG) using a 129-channel Shimadzu vector biomagnetic measurement system (BMS). METHODS: To magnetically label the pressure-controlled colon delivery capsule (PCDC) containing 75.0 +/- 0.5 mg of caffeine as a tracer drug, small capsule caps containing 90 mg of ferric oxide powdered magnetite (Fe2O3) were attached to PCDCs. After orally administration to fasted human volunteers, saliva samples were collected hourly and salivary caffeine concentration was measured. At the same time, locations of the magnetic PCDC were detected by BMS just after the PCDCs were magnetized with the coils of a magnetic resonance imaging (MRI) system. The magnetic field distributions were analyzed and the estimated positions were shown on the MRI picture of the same subject's abdominal structure. RESULTS: We magnetized PCDC with permanent magnets or an electromagnet before ingestion and the estimated locations of PCDC in the GI tract exhibited high estimation error. In order to increase the precision of estimated localization of PCDCs, PCDCs were magnetized within the coils of the MRI. As a result, these PCDCs had strong magnetic dipoles that were parallel to the sensor unit of BMS in every measurement, and therefore the spatial resolution of the PCDC's two-dimensional positions in the organs of the GI tract was within a range of several millimeters. CONCLUSIONS: GIMG is a powerful tool for the study of colon delivery efficiencies of PCDCs. The main advantage of GIMG is the capability to obtain even more detailed knowledge of the behavior and fate of solid pharmaceutical formulations during GI passage.

Abdomen↗