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  Current Research of Ping-Chiang Lyu's Lab:

Biophysics and Bioinformatics

Our laboratory concentrates on the structure, function and design of peptides and proteins. We used several biophysical methods, including nuclear magnetic resonance (nmr), circular dichroism (CD), fluorescence, isothermal titration calorimetry (ITC) as well as molecular simulation to study these biological interesting molecules. We have also switched some of our interests to bioinformatics recently. Some information about our lab can be seen at http://biobug.life.nthu.edu.tw/>http://biobug.life.nthu.edu.tw/ The following are the summary of our research in the recent years:



I. Structure, Folding and Function of Lipid Transfer Proteins (LTPs)
LTPs are well known for their ability to bind with variety of lipid molecules and catalyze the transfer of lipid molecules between membranes in vitro. Besides, some biological functions of the LTPs have been proposed, including biosynthesis of cutin, involvement in defense against pathogens, and managing abiotic stress conditions imparted by temperature and drought situation. LTPs are further subdivided into two different isoforms that differ in their molecular mass, 9kDa (LTP1) and 7kDa (LTP2). We have purified several non-specific lipid transfer proteins (LTPs) from rice (Oryza sativa) seeds and mung bean. The three-dimensional structure of nsLTP2 has been solved for the first time by us. It is found to adopt entirely a new fold containing a triangular hollow box like hydrophobic cavity formed by three prominent helices stabilized. We have also applied molecular modeling and physical methods to study its binding with various ligands. The ultimate goal of this project is to solve LTPs?3D structure and find out their biological function in vivo. The oxidative folding pathway of LTPs have also been studied in our laboratory.



II. Design of glycosaminoglycans (GAGs) binding peptides.
We have de novo designed several lysine rich peptides to mimic the specificity featured in heparin-glycosaminoglycan interaction(s). Circular dichroism experiments revealed that one of the designed peptide (K34 ?SKAQKAQAKQAKQAQKAQKAQAKQAKQW -CONH2) binds to heparin, by an induced-fit mechanism. Heparin induced conformational changes in the peptide backbone has been authenticated using hetero nuclear NMR experiments. The percentage of helix induced by different GAGs was found to be proportional to its binding strength and decreases in the order : heparin > heparin sulfate > dermatan sulfate. We are interesting to designed specific peptides and proteins that can exhibit differential binding ability to various GAGs.



III. Structural Genomics Project of Helicobacter Pylori
The goal of Structural Genomics Project is to discover and analyze the structures as well as functions of all proteins in nature in order to provide a foundation for a fundamental understanding of biology. Eight of research groups in College of Life Sciences have formed a team to target the Structural Genomics Project of Helicobacter Pylori. Our group use nmr as well as bioinformatics methods to solve and analyze the protein structures from H. Pylori.



IV. Bioinformatics approaches to structural biology
  • 1. We have set up several on-line bioinformatics services and mirror sites in our Bioinformatics Center including PDB, SCOP, EMBOSS and ProteinPredict server. Please check (http://bioinfo.life.nthu.edu.tw/) for details.



  • 2. All information needed to create thermo tolerance is encoded in the protein sequences. Due to the advances in the genome sequencing project, the number of sequences deposited in databanks increases exponentially in the last few years. Thus, with a vast number of sequences available, it becomes possible to predict a myriad of protein properties from their amino acid sequences alone. We apply classical statistical method to study the relationship between Tm (melting temperature) values of proteins and their amino sequences. Using the reference thermo indices based on the statistical correlation between the dipeptide constituents and the Tm values of proteins, we are able to obtain prediction accuracy more than 80% for the test data sets. We have also applied this method to the whole genomes of several hyper-thermophilic bacteria, and found that more than 72% of their proteins were of high thermostability (Tm > 65 oC), which is significantly different from those of mesophile genome. We have built a web-based program to predict the range of Tm of any given protein sequences and users can access the web page at http://tm.life.nthu.edu.tw/



  • 3. In collaboration with researchers from National Yang-Ming University and National Chung-Hsing University, we form a structural genomics team to target Xanthomonas campestris genome. Our lab is in charge the bioinformatics part of the project which includes the gene prediction, annotation, target selection and homology modeling. The detail of the project and preliminary results can be seen at http://xcc.life.nthu.edu.tw/.

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