Biomedical subjects

Hao-Teng Chang

Publications and source records attributed to Hao-Teng Chang.

7 recordsLinked to original sources

PubMed2007

Signal peptide of eosinophil cationic protein upregulates transforming growth factor-alpha expression in human cells.

Eosinophil cationic protein (ECP) is a major component of eosinophil granule protein that is used as a clinical bio-marker for asthma and allergic inflammatory diseases. Previously, it has been reported that the signal peptide of human ECP (ECPsp) inhibits the cell growth of Escherichia coli (E. coli) and Pichia pastoris (P. pastoris), but not mammalian A431 cells. The inhibitory effect is due to the lack of human signal peptide peptidase (hSPP), a protease located on the endoplasmic reticulum (ER) membrane, in the lower organisms. In this study, we show that the epidermal growth factor receptor (EGFR) is upregulated by the exogenous ECPsp-eGFP as a result of the increased expression of the transforming growth factor-alpha (TGF-alpha) at both transcriptional and translational levels in A431 and HL-60 clone 15 cell lines. Furthermore, the N-terminus of ECPsp fragment generated by the cleavage of hSPP (ECPspM1-G17) gives rise to over threefold increase of TGF-alpha protein expression, whereas another ECPsp fragment (ECPspL18-A27) and the hSPP-resistant ECPsp (ECPspG17L) do not show similar effect. Our results indicate that the ECPspM1-G17 plays a crucial role in the upregulation of TGF-alpha, suggesting that the ECPsp not only directs the secretion of mature ECP, but also involves in the autocrine system.

Aspartic Acid Endopeptidases↗

PubMed2006

REMUS: a tool for identification of unique peptide segments as epitopes.

We provide a 'R(E)MUS' (reinforced merging techniques for unique peptide segments) web server for identification of the locations and compositions of unique peptide segments from a set of protein family sequences. Different levels of uniqueness are determined according to substitutional relationship in the amino acids, frequency of appearance and biological properties such as priority for serving as candidates for epitopes where antibodies recognize. R(E)MUS also provides interactive visualization of 3D structures for allocation and comparison of the identified unique peptide segments. Accuracy of the algorithm was found to be 70% in terms of mapping a unique peptide segment as an epitope. The R(E)MUS web server is available at http://biotools.cs.ntou.edu.tw/REMUS and the PC version software can be freely downloaded either at http://bioinfo.life.nthu.edu.tw/REMUS or http://spider.cs.ntou.edu.tw/BioTools/REMUS. User guide and working examples for PC version are available at http://spider.cs.ntou.edu.tw/BioTools/REMUS-DOCS.html, and details of the proposed algorithm can be referred to the documents as described previously [H. T. Chang, T. W. Pai, T. C. Fan, B. H. Su, P. C. Wu, C. Y. Tang, C. T. Chang, S. H. Liu and M. D. T. Chang (2006) BMC Bioinformatics, 7, 38 and T. W. Pai, B. H. Su, P. C. Wu, M. D. T. Chang, H. T. Chang, T. C. Fan and S. H. Liu (2006) J. Bioinform. Comput. Biol., 4, 75-92].

Algorithms↗

PubMed2006

A reinforced merging methodology for mapping unique peptide motifs in members of protein families.

BACKGROUND: Members of a protein family often have highly conserved sequences; most of these sequences carry identical biological functions and possess similar three-dimensional (3-D) structures. However, enzymes with high sequence identity may acquire differential functions other than the common catalytic ability. It is probable that each of their variable regions consists of a unique peptide motif (UPM), which selectively interacts with other cellular proteins, rendering additional biological activities. The ability to identify and localize such UPMs is paramount in recognizing the characteristic role of each member of a protein family. RESULTS: We have developed a reinforced merging algorithm (RMA) with which non-gapped UPMs were identified in a variety of query protein sequences including members of human ribonuclease A (RNaseA), epidermal growth factor receptor (EGFR), matrix metalloproteinase (MMP), and Sma-and-Mad related protein families (Smad). The UPMs generally occupy specific positions in the resolved 3-D structures, especially the loop regions on the structural surfaces. These motifs coincide with the recognition sites for antibodies, as the epitopes of four monoclonal antibodies and two polyclonal antibodies were shown to overlap with the UPMs. Most of the UPMs were found to correlate well with the potential antigenic regions predicted by PROTEAN. Furthermore, an accuracy of 70% can be achieved in terms of mapping a UPM to an epitope. CONCLUSION: Our study provides a bioinformatic approach for searching and predicting potential epitopes and interacting motifs that distinguish different members of a protein family.

Algorithms↗

PubMed2006

Unique peptide identification of RNase A superfamily sequences based on reinforced merging algorithms.

Human ribonuclease A (RNaseA) superfamily consists of eight RNases with high similarity in which RNase2 and RNase3 share 76.7% identity. The evolutionary variation of RNases results in differential structures and functions of the enzymes. To distinguish the characteristics of each RNase, we developed reinforced merging algorithms (RMA) to rapidly identify the unique peptide motifs for each member of the highly conserved human RNaseA superfamily. Many motifs in RNase3 identified by RMA correlated well with the antigenic regions predicted by DNAStar. Two unique peptide motifs were experimentally confirmed to contain epitopes for monoclonal antibodies (mAbs) specifically against RNase3. Further analysis of homologous RNases in different species revealed that the unique peptide motifs were located at the correspondent positions, and one of these motifs indeed matched the epitope for a specific anti-bovine pancreatic RNaseA (bpRNaseA) antibody. Our method provides a useful tool for identification of unique peptide motifs for further experimental design. The RMA system is available and free for academic use at http://bioinfo.life.nthu.edu.tw/rma/ and http://spider.cs.ntou.edu.tw/bioinformatics/RMA.html.

Algorithms↗

PubMed2004

Membrane-bound carboxypeptidase E facilitates the entry of eosinophil cationic protein into neuroendocrine cells.

ECP (eosinophil cationic protein) is a major component of eosinophil granule proteins, and is used as a clinical biomarker for asthma and allergic inflammatory disease. ECP has been implicated in damage to the cell membrane of many tissue types, but the mechanism is not well known. In the present study, mECP-eGFP-6H, a recombinant fusion protein containing mature ECP (mECP), enhanced green fluorescence protein (eGFP) and a His(6) tag (6H), has been expressed, purified and added to GH3 neuroendocrine cells to study the internalization ability of ECP. We found that mECP-eGFP-6H entered into GH3 neuroendocrine cells and inhibited the growth of the cells with an IC(50) of 0.8 microM. By yeast two-hybrid screening and immunoprecipitation, we have identified a specific protein-protein interaction between mECP and CPE (carboxypeptidase E), a well characterized metalloprotease. Further in vivo yeast two-hybrid screening has also revealed that residues 318-387 located in a region of unknown function in mature CPE are indispensable for association with mECP. In addition, the uptake of mECP-eGFP-6H is suppressed by dominant-negative expression of the recycling defect mutant pre-pro-HA-CPE(S471A,E472A) in GH3 cells, suggesting that the entry of mECP-eGFP-6H is associated with the recycling of CPE in GH3 cells. Taken together, we have demonstrated that CPE possesses a novel function to facilitate the entry of ECP to neuroendocrine cells, and such an endocytotic process allows the cytotoxic ECP to inhibit growth of the target cells.

Amino Acid Sequence↗

PubMed2003

Constrained multiple sequence alignment tool development and its application to RNase family alignment.

In this paper, we design a heuristic algorithm of computing a constrained multiple sequence alignment (CMSA for short) for guaranteeing that the generated alignment satisfies the user-specified constraints that some particular residues should be aligned together. If the number of residues needed to be aligned together is a constant alpha, then the time-complexity of our CMSA algorithm for aligning K sequences is O(alphaKn(4)), where n is the maximum of the lengths of sequences. In addition, we have built up such a CMSA software system and made several experiments on the RNase sequences, which mainly function in catalyzing the degradation of RNA molecules. The resulting alignments illustrate the practicability of our method.

Algorithms↗

PubMed2002

Constrained multiple sequence alignment tool development and its application to RNase family alignment.

In this paper, we design an algorithm of computing a constrained multiple sequence alignment (CMSA for short) for guaranteeing that the generated alignment satisfies the user-specified constraints that some particular residues should be aligned together. If the number of residues needed to be aligned together is a constant alpha, then the time-complexity of our CMSA algorithm for aligning K sequences is O (alphaKn4), where n is the maximum of the lengths of sequences. In addition, we have build up such a CMSA software system and made several experiments on the RNase sequences, which mainly function in catalyzing the degradation of RNA molecules. The resulting alignments illustrate the practicability of our method.

Algorithms↗