Biomedical subjects

Dong Xu

Publications and source records attributed to Dong Xu.

At least 91 records · Page 5Linked to original sources

PubMed2003

A computational study of Shewanella oneidensis MR-1: structural prediction and functional inference of hypothetical proteins.

The genomes of many organisms have been sequenced in the last 5 years. Typically about 30% of predicted genes from a newly sequenced genome cannot be given functional assignments using sequence comparison methods. In these situations three-dimensional structural predictions combined with a suite of computational tools can suggest possible functions for these hypothetical proteins. Suggesting functions may allow better interpretation of experimental data (e.g., microarray data and mass spectroscopy data) and help experimentalists design new experiments. In this paper, we focus on three hypothetical proteins of Shewanella oneidensis MR-1 that are potentially related to iron transport/metabolism based on microarray experiments. The threading program PROSPECT was used for protein structural predictions and functional annotation, in conjunction with literature search and other computational tools. Computational tools were used to perform transmembrane domain predictions, coiled coil predictions, signal peptide predictions, sub-cellular localization predictions, motif prediction, and operon structure evaluations. Combined computational results from all tools were used to predict roles for the hypothetical proteins. This method, which uses a suite of computational tools that are freely available to academic users, can be used to annotate hypothetical proteins in general.

ATP-Binding Cassette Transporters↗

PubMed2003

PROSPECT II: protein structure prediction program for genome-scale applications.

A new method for fold recognition is developed and added to the general protein structure prediction package PROSPECT (http://compbio.ornl.gov/PROSPECT/). The new method (PROSPECT II) has four key features. (i) We have developed an efficient way to utilize the evolutionary information for evaluating the threading potentials including singleton and pairwise energies. (ii) We have developed a two-stage threading strategy: (a) threading using dynamic programming without considering the pairwise energy and (b) fold recognition considering all the energy terms, including the pairwise energy calculated from the dynamic programming threading alignments. (iii) We have developed a combined z-score scheme for fold recognition, which takes into consideration the z-scores of each energy term. (iv) Based on the z-scores, we have developed a confidence index, which measures the reliability of a prediction and a possible structure-function relationship based on a statistical analysis of a large data set consisting of threadings of 600 query proteins against the entire FSSP templates. Tests on several benchmark sets indicate that the evolutionary information and other new features of PROSPECT II greatly improve the alignment accuracy. We also demonstrate that the performance of PROSPECT II on fold recognition is significantly better than any other method available at all levels of similarity. Improvement in the sensitivity of the fold recognition, especially at the superfamily and fold levels, makes PROSPECT II a reliable and fully automated protein structure and function prediction program for genome-scale applications.

Algorithms↗

PubMed2003

Phylogenetic relationships between Bacillus species and related genera inferred from comparison of 3' end 16S rDNA and 5' end 16S-23S ITS nucleotide sequences.

The nucleotide sequences of the 3' end of the 16S rDNA and the 16S-23S internal transcribed spacer (ITS) of 40 Bacillaceae species were determined. These included 21 Bacillus, 9 Paenibacillus, 6 Brevibacillus, 2 Geobacillus, 1 Marinibacillus and 1 Virgibacillus species. Comparative sequence analysis of a 220 bp region covering a highly conserved 150 bp sequence located at the 3' end of the 16S rRNA coding region and a conserved 70 bp sequence located at the 5' end of the 16S-23S ITS of the 40 species and six sequences available in GenBank were used to infer the phylogenetic relationships between all 46 taxa. When a maximal distance (D(max), where D refers to the number of nucleotide substitutions per site) of 0.31 was introduced as a threshold to determine groupings, 10 phylogenetically distinct clusters were revealed. Twenty-six Bacillus species were separated in seven groups (I, II, III, IV, V, VI and X), but Bacillus circulans remained ungrouped. All six Brevibacillus species under study were in Group VII. The nine Paenibacillus species fell into two distinct groups (VIII and IX). Species with D(max) values within 0.05 were considered to be very closely related. These were Bacillus psychrophilus and Bacillus psychrosaccharolyticus in Group II; 'Bacillus maroccanus' and Bacillus simplex in Group II; Bacillus amyloliquefaciens, Bacillus atrophaeus, Bacillus mojavensis and Bacillus subtilis in Group VI; Bacillus fusiformis and Bacillus sphaericus in Group VI; Brevibacillus brevis and Brevibacillus formosus in Group VII; Paenibacillus gordonae and Paenibacillus validus in Group VIII; and Bacillus anthracis, Bacillus cereus, Bacillus mycoides and Bacillus thuringiensis in Group X. The phylogenetic classification presented here is, in general, in agreement with current classifications based on phenotypic and molecular data. Our findings suggest, however, that in some cases, further divisions or, conversely, further groupings might be warranted. Should current classifications be re-examined in the light of our results, D(max) values of 0.31 and 0.05, as exemplified here, may prove useful threshold values for the grouping of Bacillaceae into taxa akin to genera and species, respectively. These D(max) thresholds may also reveal, in a different way, bacterial species for which further characterization might be warranted for proper classification and/or reassignment.

3' Untranslated Regions↗

PubMed2003

P53-dependent cell-killing by selective repression of thymidine kinase and reduced prodrug activation.

Selective killing of tumor cells is an important goal for cancer therapeutics. The tumor suppressor transcription factor p53 is absent or mutated in more than 50% of human tumors. Thus, determining approaches that use p53 status to regulate therapy may be an important strategy for attaining cancer selectivity. We have shown previously that a designed transcriptional repressor, K2-5F, strongly and selectively reduces the expression of its target gene MDR1. In this study, we exploited p53 status and the strong repressor activity of K2-5F to establish a system for preferential killing of p53-negative cells. In this system, the expression of K2-5F is induced by p53 in normal cells, and the K2-5F repressor then inhibits the expression of herpes simplex virus thymidine kinase (HSV-TK) driven by an MDR1 minipromoter. In p53-deficient cells, little K2-5F is expressed, and thus HSV-TK is expressed, allowing the cells to be killed by ganciclovir (GCV). K2-5F induced by exogenous p53 dramatically reduced the expression of HSV-TK in human embryonic kidney 293 cells, and it subsequently increased cell survival in response to GCV. To further evaluate this approach in a uniform genetic background, we developed Saos-2 cells stably expressing physiological levels of p53 and paired them with wild-type p53-negative Saos-2 cells. Stable expression of moderate levels of p53 in Saos-2 cells was able to induce the expression of K2-5F and reduce HSV-TK expression and resulted in a modest but distinct protection from GCV toxicity. Thus, this system may be suitable for further development as an approach to selective cancer therapy.

Antiviral Agents↗

PubMed2003

Computational assignment of protein backbone NMR peaks by efficient bounding and filtering.

NMR resonance assignment is one of the key steps in solving an NMR protein structure. The assignment process links resonance peaks to individual residues of the target protein sequence, providing the prerequisite for establishing intra- and inter-residue spatial relationships between atoms. The assignment process is tedious and time-consuming, which could take many weeks. Though there exist a number of computer programs to assist the assignment process, many NMR labs are still doing the assignments manually to ensure quality. This paper presents a new computational method based on the combination of a suite of algorithms for automating the assignment process, particularly the process of backbone resonance peak assignment. We formulate the assignment problem as a constrained weighted bipartite matching problem. While the problem, in the most general situation, is NP-hard, we present an efficient solution based on a branch-and-bound algorithm with effective bounding techniques using two recently introduced approximation algorithms. We also devise a greedy filtering algorithm for reducing the search space. Our experimental results on 70 instances of (pseudo) real NMR data derived from 14 proteins demonstrate that the new solution runs much faster than a recently introduced (exhaustive) two-layer algorithm and recovers more correct peak assignments than the two-layer algorithm. Our result demonstrates that integrating different algorithms can achieve a good tradeoff between backbone assignment accuracy and computation time.

Algorithms↗

PubMed2003

CUBIC: identification of regulatory binding sites through data clustering.

Transcription factor binding sites are short fragments in the upstream regions of genes, to which transcription factors bind to regulate the transcription of genes into mRNA. Computational identification of transcription factor binding sites remains an unsolved challenging problem though a great amount of effort has been put into the study of this problem. We have recently developed a novel technique for identification of binding sites from a set of upstream regions of genes, that could possibly be transcriptionally co-regulated and hence might share similar transcription factor binding sites. By utilizing two key features of such binding sites (i.e. their high sequence similarities and their relatively high frequencies compared to other sequence fragments), we have formulated this problem as a cluster identification problem. That is to identify and extract data clusters from a noisy background. While the classical data clustering problem (partitioning a data set into clusters sharing common or similar features) has been extensively studied, there is no general algorithm for solving the problem of identifying data clusters from a noisy background. In this paper, we present a novel algorithm for solving such a problem. We have proved that a cluster identification problem, under our definition, can be rigorously and efficiently solved through searching for substrings with special properties in a linear sequence. We have also developed a method for assessing the statistical significance of each identified cluster, which can be used to rule out accidental data clusters. We have implemented the cluster identification algorithm and the statistical significance analysis method as a computer software CUBIC. Extensive testing on CUBIC has been carried out. We present here a few applications of CUBIC on challenging cases of binding site identification.

Algorithms↗

PubMed2003

Computational analyses of high-throughput protein-protein interaction data.

Protein-protein interactions play important roles in nearly all events that take place in a cell. High-throughput experimental techniques enable the study of protein-protein interactions at the proteome scale through systematic identification of physical interactions among all proteins in an organism. High-throughput protein-protein interaction data, with ever-increasing volume, are becoming the foundation for new biological discoveries. A great challenge to bioinformatics is to manage, analyze, and model these data. In this review, we describe several databases that store, query, and visualize protein-protein interaction data. Comparison between experimental techniques shows that each high-throughput technique such as yeast two-hybrid assay or protein complex identification through mass spectrometry has its limitations in detecting certain types of interactions and they are complementary to each other. In silico methods using protein/DNA sequences, domain and structure information to predict protein-protein interaction can expand the scope of experimental data and increase the confidence of certain protein-protein interaction pairs. Protein-protein interaction data correlate with other types of data, including protein function, subcellular location, and gene expression profile. Highly connected proteins are more likely to be essential based on the analyses of the global architecture of large-scale interaction network in yeast. Use of protein-protein interaction networks, preferably in conjunction with other types of data, allows assignment of cellular functions to novel proteins and derivation of new biological pathways. As demonstrated in our study on the yeast signal transduction pathway for amino acid transport, integration of high-throughput data with traditional biology resources can transform the protein-protein interaction data from noisy information into knowledge of cellular mechanisms.

Animals↗

PubMed2003

Identification of regulatory binding sites using minimum spanning trees.

Recognition of protein-binding sites from the upstream regions of genes is a highly important and unsolved problem. In this paper, we present a new approach for studying this challenging issue. We formulate the binding-site recognition problem as a cluster identification problem, i.e., to identify clusters in a data set that exhibit significantly different features (e.g., density) than the overall background of the data set. We have developed a general framework for solving such a cluster identification problem. The foundation of the framework is a rigorous relationship between data clusters and subtrees of a minimum spanning tree (MST) representation of a data set. We have proposed a formal and general definition of clusters, and have demonstrated that a cluster is always represented as a connected component of the MST, and further it corresponds to a substring of a linear representation of the MST. Hence a cluster identification problem is reduced to a problem of finding substrings with certain features, for which algorithms have been developed. We have applied this MST-based cluster identification algorithm to a number of binding site identification problems. The results are highly encouraging.

Algorithms↗

PubMed2003

[Influence of SEN virus infection on their response to lamivudine in patients with chronic hepatitis B].

OBJECTIVE: To investigate the influence of SEN virus infection on their response to lamivudine in patients with chronic hepatitis B (CHB). METHODS: SEN virus-D and -H DNA were detected in 45 CHB patients who received lamivudine 12 months with nested-PCR, and YMDD motif mutations in HBV DNA were investigated with gene chip. RESULTS: The positive rate of SEN virus DNA was 11.1% (5/45), and there were four out of the five SEN virus DNA positive patients whose HBV DNA was positive, among them, two patients existed YMDD motif mutation. While ten out of the forty SEN virus DNA negative patients appeared HBV DNA positive. The response rate was significant lower in SEN virus-infected patients than that in uninfected patients (chi 2=3.97, P<0.05). CONCLUSION: Coinfection with SEN virus in chronic hepatitis B patients may adversely affect the outcome of treatment with lamivudine

Anti-HIV Agents↗

PubMed2003

[Comparison of the characteristics of suicide attempters treated in general hospitals with and without prior suicide attempts].

OBJECTIVE: We compared the characteristics of persons who had made multiple versus single suicide attempts to determine whether or not these are two independent subgroups and, thus, should be provided with different preventive services. METHODS: We administered a 2 - 3 hour interview that included a structured psychiatric examination to 325 individuals with suicide attempts who were treated at four city and county-level general hospitals. RESULTS: The age, gender, years of education, marital status, work status, and family economic status of the 52 persons who had made more than one suicide attempt were similar to those of the 273 persons who had made a single attempt. But repeaters were less likely than non-repeaters to live in rural villages and to attempt suicide by ingesting agricultural poisons. Moreover, repeaters considered suicide prior to the attempt for a longer time, had a lower quality of life in the prior month, had a stronger suicidal intent, had more chronic life events, had a higher chronic stress score, and were more likely to have mental illness (P's all < 0.05). CONCLUSIONS: Major differences in the characteristics of suicide attempters with and without a prior history of suicide attempts suggest that these are independent subgroups of attempters. These two types of attempted suicide require different preventive approaches.

Adult↗

PubMed2003

Automated protein NMR resonance assignments.

NMR resonance peak assignment is one of the key steps in solving an NMR protein structure. The assignment process links resonance peaks to individual residues of the target protein sequence, providing the prerequisite for establishing intra- and inter-residue spatial relationships between atoms. The assignment process is tedious and time-consuming, which could take many weeks. Though there exist a number of computer programs to assist the assignment process, many NMR labs are still doing the assignments manually to ensure quality. This paper presents (1) a new scoring system for mapping spin systems to residues, (2) an automated adjacency information extraction procedure from NMR spectra, and (3) a very fast assignment algorithm based on our previous proposed greedy filtering method and a maximum matching algorithm to automate the assignment process. The computational tests on 70 instances of (pseudo) experimental NMR data of 14 proteins demonstrate that the new score scheme has much better discerning power with the aid of adjacency information between spin systems simulated across various NMR spectra. Typically, with automated extraction of adjacency information, our method achieves nearly complete assignments for most of the proteins. The experiment shows very promising perspective that the fast automated assignment algorithm together with the new score scheme and automated adjacency extraction may be ready for practical use.

Algorithms↗

PubMed2002

Studies of the mechanism of phenol hydroxylase: effect of mutation of proline 364 to serine.

An active site residue in phenol hydroxylase (PHHY), Pro364, was mutated to serine to investigate its role in enzymatic catalysis. In the presence of phenol, the reaction between the reduced flavin of P364S and oxygen is very fast, but only 13% of the flavin is utilized to hydroxylate the substrate, compared to nearly 100% for the wild-type enzyme. The oxidative half-reaction of PHHY using m-cresol as a substrate is similarly affected by the mutation. Pro364 was suggested to be important in stabilizing the transition state of the oxygen transfer step by forming a hydrogen bond between its carbonyl oxygen and the C4a-hydroperoxyflavin [Ridder, L., Mullholland, A. J., Rietjens, I. M. C. M., and Vervoort, J. (2000) J. Am. Chem. Soc. 122, 8728-8738]. The P364S mutation may weaken this interaction by increasing the flexibility of the peptide chain; hence, the transition state would be destabilized to result in a decreased level of hydroxylation of phenol. However, when the oxidative half-reaction was studied using resorcinol as a substrate, the P364S mutant form was not significantly different from the wild-type enzyme. The rate constants for all the reaction steps as well as the hydroxylation efficiency (coupling between NADPH oxidation and resorcinol consumption) are comparable to those of the wild-type enzyme. It is suggested that the function of Pro364 in catalysis, stabilization of the transition state, is not as important in the reaction with resorcinol, possibly because the position of hydroxylation is different with resorcinol than with phenol and m-cresol.

Amino Acid Substitution↗

PubMed2002

Residues in the first extracellular loop of a G protein-coupled receptor play a role in signal transduction.

The Saccharomyces cerevisiae pheromone, alpha-factor (WHWLQLKPGQPMY), and Ste2p, its G protein-coupled receptor, were used as a model system to study ligand-receptor interaction. Cys-scanning mutagenesis on each residue of EL1, the first extracellular loop of Ste2p, was used to generate a library of 36 mutants with a single Cys residue substitution. Mutation of most residues of EL1 had only negligible effects on ligand affinity and biological activity of the mutant receptors. However, five mutants were identified that were either partially (L102C and T114C) or severely (N105C, S108C, and Y111C) compromised in signaling but retained binding affinities similar to those of wild-type receptor. Three-dimensional modeling, secondary structure predictions, and subsequent circular dichroism studies on a synthetic peptide with amino acid sequence corresponding to EL1 suggested the presence of a helix corresponding to EL1 residues 106 to 114 followed by two short beta-strands (residues 126 to 135). The distinctive periodicity of the five residues with a signal-deficient phenotype combined with biophysical studies suggested a functional involvement in receptor activation of a face on a 3(10) helix in this region of EL1. These studies indicate that EL1 plays an important role in the conformational switch that activates the Ste2p receptor to initiate the mating pheromone signal transduction pathway.

Amino Acid Sequence↗

PubMed2002

A role for mitochondria as potential regulators of cellular life span.

We demonstrate that by simply raising extracellular pyruvate levels, and hence increasing metabolic supply, human diploid fibroblasts undergo a concentration-dependent induction of cellular senescence. Fibroblasts treated with pyruvate undergo a rapid growth arrest accompanied by elevated levels of the cell-cycle regulatory molecules p53, p21, and p16. These cells also exhibit a rise in mitochondrial oxidant production and a fall in intracellular glutathione levels. Exposure of pyruvate treated cells to the antioxidant and glutathione precursor N-acetylcysteine restores cell growth and reverses the increase in senescence-associated beta-galactosidase activity. Similarly, we demonstrate that by increasing mitochondrial number via retroviral-mediated expression of the mitochondrial biogenesis regulator PGC-1 there is also a reduction in cell growth and the more rapid induction of senescence. These results suggest that mitochondria appear to play a central role in regulating cellular life span.

Acetylcysteine↗

PubMed2002

Molecular cloning and pharmacological characterization of bovine calcitonin receptor-like receptor from bovine aortic endothelial cells.

A complementary DNA encoding calcitonin receptor-like receptor (CRLR) was isolated from a bovine aortic endothelial cell library. The bovine CRLR has 462 amino acids and 92% homology with the human CRLR. In a reverse transcriptase-polymerase chain reaction assay, bovine CRLR was found to be widely distributed, including in the heart and lungs. Stable transfection of bovine CRLR in human embryonic kidney cells (HEK-293) resulted in specific high-affinity [125I] rat adrenomedulin (rADM)-binding (dissociation constant=145+/-15 pM). ADM-stimulated adenylyl cyclase activity with an EC50 value of 5.0+/-1.2 nM. The human ADM receptor antagonist hADM(22-52) inhibited [125I]rADM-binding and ADM-stimulated adenylyl cyclase activity. Interactions between bovine CRLR and individual receptor activity modifying proteins (RAMPs) were also investigated. Transient co-transfection of bovine CRLR cDNA with human receptor activity modifying protein 1 (hRAMP1) cDNA in HEK-293 cells resulted in the expression of a CRLR that displayed high-affinity binding to calcitonin gene-related peptide. Co-transfection of bovine CRLR with human RAMP2 or RAMP3 cDNAs in HEK-293 cells displayed high-affinity ADM receptors. These observations suggest that in the absence of exogenous RAMPs heterologous expression of bovine CRLR results in an ADM receptor phenotype.

Adrenomedullin↗

PubMed2002

Polymeric bis(N,N-dimethylacetamide)tetrakis(thiocyanato)cadmium(II)mercury(II).

The title complex, [[CdHg(SCN)(4)(C(4)H(9)NO)(2)](2)](n), contains two crystallographically independent Cd(II) centres and two Hg(II) centres. Each Cd(II) atom is bound to four N atoms belonging to SCN groups and to two O atoms from N,N-dimethylacetamide (DMA) ligands in an octahedral geometry. Each Hg(II) centre is tetrahedrally coordinated by four SCN S atoms.

Journal Article↗

PubMed2002

catena-Poly[[bis(thiocyanato-kappa N)cadmium(II)]-di-mu-thiourea-kappa(4)S:S].

The Cd(II) ion in the title complex, [Cd(SCN)(2)[SC(NH(2))(2)](2)](infinity), is situated at a centre of symmetry, and is bound to two N atoms belonging to thiocyanate groups and to four S atoms of bridging thiourea ligands. The structure consists of infinite chains of slightly distorted edge-shared Cd-centred octahedra. The bridging S atoms of two thiourea ligands comprise the common edge. Some thermal properties are described.

Journal Article↗

PubMed2002

Regulation of cellular oncosis by uncoupling protein 2.

Cell death can proceed through at least two distinct pathways. Apoptosis is an energy-dependent process characterized morphologically by cell shrinkage, whereas oncosis is a form of cell death induced by energy depletion and initially characterized by cell swelling. We demonstrate in HeLa cells but not in normal diploid fibroblasts that modest increases in the expression level of uncoupling protein 2 (UCP-2) leads to a rapid and dramatic fall in mitochondrial membrane potential and to a reduction of mitochondrial NADH and intracellular ATP. In HeLa cells, increased UCP-2 expression leads to a form of cell death that is not inhibited by the anti-apoptotic gene product Bcl-2 and that morphologically resembles cellular oncosis. We further describe the creation of a dominant interfering mutant of UCP-2 whose expression increases resting mitochondrial membrane potential and selectively increases the resistance to cell death following oncotic but not apoptotic stimuli. These results suggest that distinct genetic programs may regulate the cellular response to either apoptotic or oncotic stimuli.

Apoptosis↗