Biomedical subjects

Ming-Jing Hwang

Publications and source records attributed to Ming-Jing Hwang.

15 recordsLinked to original sources

PubMed2006

Role of SUMO-interacting motif in Daxx SUMO modification, subnuclear localization, and repression of sumoylated transcription factors.

Small ubiquitin-like modifier (SUMO) modification has emerged as an important posttranslational control of protein functions. Daxx, a transcriptional corepressor, was reported to repress the transcriptional potential of several transcription factors and target to PML oncogenic domains (PODs) via SUMO-dependent interactions. The mechanism by which Daxx binds to sumoylated factors mediating transcriptional and subnuclear compartmental regulation remains unclear. Here, we define a SUMO-interacting motif (SIM) within Daxx and show it to be crucial for targeting Daxx to PODs and for transrepression of several sumoylated transcription factors, including glucocorticoid receptor (GR). In addition, the capability of Daxx SIM to bind SUMO also controls Daxx sumoylation. We further demonstrate that arsenic trioxide-induced sumoylation of PML correlates with a change of endogenous Daxx partitioning from GR-regulated gene promoter to PODs and a relief of Daxx repression on GR target gene expression. Our results provide mechanistic insights into Daxx in SUMO-dependent transcriptional control and subnuclear compartmentalization.

Adaptor Proteins, Signal Transducing↗

PubMed2006

OPAAS: a web server for optimal, permuted, and other alternative alignments of protein structures.

The large number of experimentally determined protein 3D structures is a rich resource for studying protein function and evolution, and protein structure comparison (PSC) is a key method for such studies. When comparing two protein structures, almost all currently available PSC servers report a single and sequential (i.e. topological) alignment, whereas the existence of good alternative alignments, including those involving permutations (i.e. non-sequential or non-topological alignments), is well known. We have recently developed a novel PSC method that can detect alternative alignments of statistical significance (alignment similarity P-value <10(-5)), including structural permutations at all levels of complexity. OPAAS, the server of this PSC method freely accessible at our website (http://opaas.ibms.sinica.edu.tw), provides an easy-to-read hierarchical layout of output to display detailed information on all of the significant alternative alignments detected. Because these alternative alignments can offer a more complete picture on the structural, evolutionary and functional relationship between two proteins, OPAAS can be used in structural bioinformatics research to gain additional insight that is not readily provided by existing PSC servers.

Internet↗

PubMed2006

Protemot: prediction of protein binding sites with automatically extracted geometrical templates.

UNLABELLED: Geometrical analysis of protein tertiary substructures has been an effective approach employed to predict protein binding sites. This article presents the Protemot web server that carries out prediction of protein binding sites based on the structural templates automatically extracted from the crystal structures of protein-ligand complexes in the PDB (Protein Data Bank). The automatic extraction mechanism is essential for creating and maintaining a comprehensive template library that timely accommodates to the new release of PDB as the number of entries continues to grow rapidly. The design of Protemot is also distinctive by the mechanism employed to expedite the analysis process that matches the tertiary substructures on the contour of the query protein with the templates in the library. This expediting mechanism is essential for providing reasonable response time to the user as the number of entries in the template library continues to grow rapidly due to rapid growth of the number of entries in PDB. This article also reports the experiments conducted to evaluate the prediction power delivered by the Protemot web server. Experimental results show that Protemot can deliver a superior prediction power than a web server based on a manually curated template library with insufficient quantity of entries. AVAILABILITY: http://protemot.csie.ntu.edu.tw/step1.cgi http://bioinfo.mc.ntu.edu.tw/protemot/step1.cgi.

Binding Sites↗

PubMed2006

In silico identification and comparative analysis of differentially expressed genes in human and mouse tissues.

BACKGROUND: Screening for differentially expressed genes on the genomic scale and comparative analysis of the expression profiles of orthologous genes between species to study gene function and regulation are becoming increasingly feasible. Expressed sequence tags (ESTs) are an excellent source of data for such studies using bioinformatic approaches because of the rich libraries and tremendous amount of data now available in the public domain. However, any large-scale EST-based bioinformatics analysis must deal with the heterogeneous, and often ambiguous, tissue and organ terms used to describe EST libraries. RESULTS: To deal with the issue of tissue source, in this work, we carefully screened and organized more than 8 million human and mouse ESTs into 157 human and 108 mouse tissue/organ categories, to which we applied an established statistic test using different thresholds of the p value to identify genes differentially expressed in different tissues. Further analysis of the tissue distribution and level of expression of human and mouse orthologous genes showed that tissue-specific orthologs tended to have more similar expression patterns than those lacking significant tissue specificity. On the other hand, a number of orthologs were found to have significant disparity in their expression profiles, hinting at novel functions, divergent regulation, or new ortholog relationships. CONCLUSION: Comprehensive statistics on the tissue-specific expression of human and mouse genes were obtained in this very large-scale, EST-based analysis. These statistical results have been organized into a database, freely accessible at our website http://gln.ibms.sinica.edu.tw/product/HMDEG/EST/index.php, for easy searching of human and mouse tissue-specific genes and for investigating gene expression profiles in the context of comparative genomics. Comparative analysis showed that, although highly tissue-specific genes tend to exhibit similar expression profiles in human and mouse, there are significant exceptions, indicating that orthologous genes, while sharing basic genomic properties, could result in distinct phenotypes.

Animals↗

PubMed2004

Alternative alignments from comparison of protein structures.

Comparison of two protein structures often results in not only a global alignment but also a number of distinct local alignments; the latter, referred to as alternative alignments, are however usually ignored in existing protein structure comparison analyses. Here, we used a novel method of protein structure comparison to extensively identify and characterize the alternative alignments obtained for structure pairs of a fold classification database. We showed that all alternative alignments can be classified into one of just a few types, and with which illustrated the potential of using alternative alignments to identify recurring protein substructures, including the internal structural repeats of a protein. Furthermore, we showed that among the alternative alignments obtained, permuted alignments, which included both circular and scrambled permutations, are as prevalent as topological alignments. These results demonstrated that the so far largely unattended alternative alignments of protein structures have implications and applications for research of protein classification and evolution.

Databases, Protein↗

PubMed2004

The UniMarker (UM) method for synteny mapping of large genomes.

MOTIVATION: Synteny mapping, or detecting regions that are orthologous between two genomes, is a key step in studies of comparative genomics. For completely sequenced genomes, this is increasingly accomplished by whole-genome sequence alignment. However, such methods are computationally expensive, especially for large genomes, and require rather complicated post-processing procedures to filter out non-orthologous sequence matches. RESULTS: We have developed a novel method that does not require sequence alignment for synteny mapping of two large genomes, such as the human and mouse. In this method, the occurrence spectra of genome-wide unique 16mer sequences present in both the human and mouse genome are used to directly detect orthologous genomic segments. Being sequence alignment-free, the method is very fast and able to map the two mammalian genomes in one day of computing time on a single Pentium IV personal computer. The resulting human-mouse synteny map was shown to be in excellent agreement with those produced by the Mouse Genome Sequencing Consortium (MGSC) and by the Ensembl team; furthermore, the syntenic relationship of segments found only by our method was supported by BLASTZ sequence alignment.

Algorithms↗

PubMed2004

An important functional role of the N terminus domain of type VI adenylyl cyclase in Galphai-mediated inhibition.

We show herein that removal of the first 86 amino acids (aa) of the N terminus (designated N) of type VI adenylyl cyclase (ACVI) caused the resultant ACVI mutant (ACVI-DeltaA87) to be more greatly inhibited by a Galpha(i)-coupled receptor or activated Galpha(i) protein. Moreover, in vitro binding of the full-length N and C1a domain (designated C1a), which interacts with Galpha(i), was detected. A truncated N terminus (aa 1-86) also interacted with C1a, suggesting that the C1a-interacting region is located within aa 1-86. Mutation analyses further revealed that N might interact with C1a in the region (aa 434-505) where Galpha(i) is bound. Mutations of two residues (Leu-472 and Val-476) located in this N-binding region of C1a suppressed the interaction between recombinant N and C1a and markedly reduced Galpha(i)-mediated inhibition of ACVI-DeltaA87. Further biochemical analyses of the effect of internal mutations of Leu-472/Val-476 on Galpha(i)-mediated inhibition of wild-type ACVI and ACVI-DeltaA87 suggested that N modulates the Galpha(i)-mediated inhibition of ACVI via binding to C1a when the level of Galpha(i) is low (i.e. around the IC(50) value) and that a more complicated interfering mode results when the level of Galpha(i) is high (i.e. approximately 10- to 20-fold of the IC(50) value). Collectively, data presented herein suggest a novel function of the N terminus of ACVI in Galpha(i)-mediated regulation.

Adenylyl Cyclases↗

PubMed2003

Protein structure comparison by probability-based matching of secondary structure elements.

MOTIVATION: Protein structure comparison (PSC) has been used widely in studies of structural and functional genomics. However, PSC is computationally expensive and as a result almost all of the PSC methods currently in use look only for the optimal alignment and ignore many alternative alignments that are statistically significant and that may provide insight into protein evolution or folding. RESULTS: We have developed a new PSC method with efficiency to detect potentially viable alternative alignments in all-against-all database comparisons. The efficiency of the new PSC method derives from the ability to directly home in on a limited number of viable and ranked alignment solutions based on intuitively derived SSE (secondary structure element)-matching probabilities.

Algorithms↗

PubMed2003

The role of apoptosis signal-regulating kinase 1 in lymphotoxin-beta receptor-mediated cell death.

LIGHT (homologous to lymphotoxins, shows inducible expression, and competes with herpes simplex virus glycoprotein D for herpesvirus entry mediator, a receptor expressed by T lymphocytes) is a member of the tumor necrosis factor superfamily that can interact with lymphotoxin-beta receptor (LTbetaR), herpes virus entry mediator, and decoy receptor (DcR3). In our previous study, we showed that LIGHT is able to induce cell death via the non-death domain containing receptor LTbetaR to activate both caspase-dependent and caspase-independent pathway. In this study, a LIGHT mutein, LIGHT-R228E, was shown to exhibit similar binding specificity as wild type LIGHT to LTbetaR, but lose the ability to interact with herpes virus entry mediator. By using both LIGHT-R228E and agonistic anti-LTbetaR monoclonal antibody, we found that signaling triggered by LTbetaR alone is sufficient to activate both caspase-dependent and caspase-independent pathways. Cross-linking of LTbetaR is able to recruit TRAF3 and TRAF5 to activate ASK1, whereas its activity is inhibited by free radical scavenger carboxyfullerenes. The activation of ASK1 is independent of caspase-3 activation, and kinase-inactive ASK1-KE mutant can inhibit LTbetaR-mediated cell death. This suggests that ASK1 is one of the factors involved in the caspase-independent pathway of LTbetaR-induced cell death.

Amino Acid Chloromethyl Ketones↗

PubMed2002

Protein kinase C inhibits type VI adenylyl cyclase by phosphorylating the regulatory N domain and two catalytic C1 and C2 domains.

We previously showed that phosphorylation of Ser(10) of the N terminus domain of the type VI adenylyl cyclase (ACVI) partly mediated protein kinase C (PKC)-induced inhibition of ACVI. We now report that phosphorylation of the other two cytosolic domains (C1 and C2), which form the catalytic core complex of ACVI, also contributes to PKC-mediated inhibition. In vitro phosphorylation by PKC of the recombinant C1a and C2 domains, and of the synthetic peptides representing potential PKC phosphorylation sites, suggests that Ser(568) and Ser(674) of the C1 domain and Thr(931) of the C2 domain might act as substrates for PKC. We next created several full-length ACVI mutants in which one or more of the four likely PKC phosphorylation sites (Ser(10), Ser(568), Ser(674), and Thr(931)) were mutated to alanine. Simultaneous mutation of at least two of the three likely residues located in the N and C1 domains (Ser(10), Ser(568), and Ser(674)) was required to render ACVI variants completely insensitive to PKC treatment. In contrast, a single mutation of Thr(931) was sufficient to create a functional ACVI mutant that exhibited no detectable PKC-mediated inhibition, demonstrating the essentiality of Thr(931) to PKC-mediated regulation. Based on these results, we propose that the three cytosolic domains of ACVI might form a regulatory complex. Phosphorylation of this regulatory complex at different sites might induce a fine-tuning of the catalytic core complex and subsequently lead to alternation in the catalytic activity of ACVI.

Adenylyl Cyclase Inhibitors↗

PubMed2002

Single nucleotide polymorphism mapping using genome-wide unique sequences.

As more and more genomic DNAs are sequenced to characterize human genetic variations, the demand for a very fast and accurate method to genomically position these DNA sequences is high. We have developed a new mapping method that does not require sequence alignment. In this method, we first identified DNA fragments of 15 bp in length that are unique in the human genome and then used them to position single nucleotide polymorphism (SNP) sequences. By use of four desktop personal computers with AMD K7 (1 GHz) processors, our new method mapped more than 1.6 million SNP sequences in 20 hr and achieved a very good agreement with mapping results from alignment-based methods.

Chromosome Mapping↗

PubMed2002

GEM: a Gaussian Evolutionary Method for predicting protein side-chain conformations.

We have developed an evolutionary approach to predicting protein side-chain conformations. This approach, referred to as the Gaussian Evolutionary Method (GEM), combines both discrete and continuous global search mechanisms. The former helps speed up convergence by reducing the size of rotamer space, whereas the latter, integrating decreasing-based Gaussian mutations and self-adaptive Gaussian mutations, continuously adapts dihedrals to optimal conformations. We tested our approach on 38 proteins ranging in size from 46 to 325 residues and showed that the results were comparable to those using other methods. The average accuracies of our predictions were 80% for chi(1), 66% for chi(1 + 2), and 1.36 A for the root mean square deviation of side-chain positions. We found that if our scoring function was perfect, the prediction accuracy was also essentially perfect. However, perfect prediction could not be achieved if only a discrete search mechanism was applied. These results suggest that GEM is robust and can be used to examine the factors limiting the accuracy of protein side-chain prediction methods. Furthermore, it can be used to systematically evaluate and thus improve scoring functions.

Algorithms↗

PubMed2001

Derivation of class II force fields. VIII. Derivation of a general quantum mechanical force field for organic compounds.

A class II valence force field covering a broad range of organic molecules has been derived employing ab initio quantum mechanical "observables." The procedure includes selecting representative molecules and molecular structures, and systematically sampling their energy surfaces as described by energies and energy first and second derivatives with respect to molecular deformations. In this article the procedure for fitting the force field parameters to these energies and energy derivatives is briefly reviewed. The application of the methodology to the derivation of a class II quantum mechanical force field (QMFF) for 32 organic functional groups is then described. A training set of 400 molecules spanning the 32 functional groups was used to parameterize the force field. The molecular families comprising the functional groups and, within each family, the torsional angles used to sample different conformers, are described. The number of stationary points (equilibria and transition states) for these molecules is given for each functional group. This set contains 1324 stationary structures, with 718 minimum energy structures and 606 transition states. The quality of the fit to the quantum data is gauged based on the deviations between the ab initio and force field energies and energy derivatives. The accuracy with which the QMFF reproduces the ab initio molecular bond lengths, bond angles, torsional angles, vibrational frequencies, and conformational energies is then given for each functional group. Consistently good accuracy is found for these computed properties for the various types of molecules. This demonstrates that the methodology is broadly applicable for the derivation of force field parameters across widely differing types of molecular structures. Copyright 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1782-1800, 2001

Journal Article↗

PubMedDate not supplied

Directional shape complementarity at the protein-DNA interface.

Nature utilizes various styles of architecture for DNA-binding proteins to recognize diverse DNA sequences, a process facilitated by a complementary surface between protein and DNA. However, the extent and ways this 'shape complementarity' occurs at the protein-DNA interface have yet to be characterized. Here, by analyzing a set of diverse protein-DNA complexes of known three-dimensional structures, we investigated whether the normal vectors of a protein surface at the interface exhibited any relationship with DNA conformation. Generally, the normal vectors of a DNA-contacting protein surface distinctly preferred certain angles, enabling them to align with certain axes characterizing the conformation of DNA. Thus, a new geometric property of DNA-binding protein is demonstrated, i.e. the "shape complementarity" of protein-DNA recognition clearly bears the property of "directionality".

DNA↗

PubMedDate not supplied

Mutations at KFRDI and VGK domains of enterovirus 71 3C protease affect its RNA binding and proteolytic activities.

The 3C protease (3C(pro)) of enterovirus 71 (EV71) is a good molecular target for drug discovery. Notably, this protease was found to possess RNA-binding activity. The regions responsible for RNA binding were classified as 'KFRDI' (positions 82-86) and 'VGK' (positions 154-156) in 3C(pro) by mutagenesis study. Although the RNA-binding regions are structurally distinct from the catalytic site of EV71 3C(pro), mutations in the RNA-binding regions influenced 3C(pro) proteolytic activity. In contrast, mutations at the catalytic site had almost no influence on RNA binding ability. We identified certain mutations within 3C(pro) which abrogated both the RNA-binding activity of the expressed, recombinant, protease and the ability to rescue virus from an infectious full-length clone of EV71 (pEV71). Interestingly, mutation at position 84 from Arg(R) to Lys(K) was found to retain good RNA binding and proteolytic activity for the recombinant 3C(pro); however, no virus could be rescued when pEV71 with the R84K mutation was introduced into the infectious copy. Together, these results may provide useful information for using 3C(pro) as the molecular target to develop anti-EV71 agents.

3C Viral Proteases↗