Publications

2023

1. "Elucidation of the folding pathway of a circular permutant of topologically knotted YbeA by tryptophan substitutions."  Puri S., Liu CY, IC, Lai CH, Hsu ST, Lyu PC. Biochemical and Biophysical Research Communications. 2023, Sep. 672:81-88.

2. "PW06 Triggered Fas-FADD to Induce Apoptotic Cell Death In Human Pancreatic Carcinoma MIA PaCa-2 Cells through the Activation of the Caspase-Mediated Pathway." Huang YP, Hsia TC, Yeh CA, Ma YS, Hsu SY, Liu YC, Lyu PC, Lai KC, Peng SF, Lien JC, Hsieh WT. Oxidative Medicine and Cellular Longevity. 2023 Feb. doi.org/10.1155/2023/3479688.

2022

1.  "SeqCP: A sequence-based algorithm for searching circularly permuted proteins." Chen CC, Huang YW, Huang HC, Lo WC, Lyu PC. Comput Struct Biotechnol J. 2022 Nov 14;21:185-201. doi: 10.1016/j.csbj.2022.11.024. eCollection 2023.

2021

1.  "Dissecting the Transcriptomes of Multiple Metronidazole-Resistant and Sensitive Trichomonas vaginalis Strains Identified Distinct Genes and Pathways Associated with Drug Resistance and Cell Death." Huang PJ, Huang CY, Li YX, Liu YC, Chu LJ, Yeh YM, Cheng WH, Chen RM, Lee CC, Chen LC, Lin HC, Chiu SF, Lin WN, Lyu PC, Tang P, Huang KY. Biomedicines 2021 Dec 2; 9(12), 1817. doi: 10.3390/biomedicines9121817.

2. "Structure-Based Functional Analysis of a Hormone Belonging to an Ecdysozoan Peptide Superfamily: Revelation of a Common Molecular Architecture and Residues Possibly for Receptor Interaction." Chen YR, Hsiao NW, Lee YZ, Huang SS, Chang CC, Tsai JR, Lin HC, Toullec JY, Lee CY, Lyu PC. Int J Mol Sci. 2021 Oct 15;22(20):11142. doi: 10.3390/ijms222011142.

3. "LINC01348 suppresses hepatocellular carcinoma metastasis through inhibition of SF3B3-mediated EZH2 pre-mRNA splicing." Lin YH, Wu MH, Liu YC, Lyu PC, Yeh CT, Lin KH. Oncogene. 2021 Jun 17. doi: 10.1038/s41388-021-01905-3. Online ahead of print.

4. "Ergosta-7, 9 (11), 22-trien-3β-ol Interferes with LPS Docking to LBP, CD14, and TLR4/MD-2 Co-Receptors to Attenuate the NF-κB Inflammatory Pathway In vitro and Drosophila." Hsieh WT, Hsu MH, Lin WJ, Xiao YC, Lyu PC, Liu YC, Lin WY, Kuo YH, Chung JG. Int J Mol Sci. 2021 Jun 17;22(12):6511. doi: 10.3390/ijms22126511. 

5. "Imperatorin Interferes with LPS Binding to the TLR4 Co-Receptor and Activates the Nrf2 Antioxidative Pathway in RAW264.7 Murine Macrophage Cells." Huang MH, Lin YH, Lyu PC, Liu YC, Chang YS, Chung JG, Lin WY, Hsieh WT. Antioxidants (Basel). 2021 Feb 27;10(3):362. doi: 10.3390/antiox10030362.

2020

1.  "Cafestol Inhibits High-Glucose-Induced Cardiac Fibrosis in Cardiac Fibroblasts and Type 1-Like Diabetic Rats." Liu JC, Chen PY, Hao WR, Liu YC, Lyu PC, Hong HJ. Evidence-Based Complementary and Alternative Medicine. 2020 Dec 31; vol. 2020, Article ID 4503747, 11 pages, doi: 10.1155/2020/4503747.

2.  "Structural Insights into the Active Site Formation of DUSP22 in N-loop-containing Protein Tyrosine Phosphatases." Lai CH, Chang CC, Chuang HC, Tan TH, Lyu PC. Int J Mol Sci. 2020 Oct 12;21(20):7515. doi: 10.3390/ijms21207515.

3.  "An essential role of acetyl coenzyme A in the catalytic cycle of insect arylalkylamine N-acetyltransferase." Wu CY, Hu IC, Yang YC, Ding WC, Lai CH, Lee YZ, Liu YC, Cheng HC, Lyu PC. Commun Biol. 2020 Aug 14;3(1):441. doi: 10.1038/s42003-020-01177-9.

4.  "Antimicrobial Peptide TP4 Targets Mitochondrial Adenine Nucleotide Translocator 2." Su BC, Liu YC, Ting CH, Lyu PC, Chen JY. Mar Drugs. 2020 Aug 9;18(8):417. doi: 10.3390/md18080417.

2019

1.  "MAP4K3/GLK Promotes Lung Cancer Metastasis by Phosphorylating and Activating IQGAP1." Chuang HC, Chang CC, Teng CF, Hsueh CH, Chiu LL, Hsu PM, Lee MC, Hsu CP, Chen YR, Liu YC, Lyu PC, Tan TH. Cancer Res. 2019 Oct 1;79(19):4978-4993. doi: 10.1158/0008-5472.

2.  "The ligand-mediated affinity of brain-type fatty acid-binding protein for membranes determines the directionality of lipophilic cargo transport." Cheng YY, Huang YF, Lin HH, Chang WW, Lyu PC. Biochim Biophys Acta Mol Cell Biol Lipids. 2019 Dec;1864(12):158506. doi: 10.1016/j.bbalip.2019.08.002.

3.  "CoMutPlotter: a web tool for visual summary of mutations in cancer cohorts." Huang PJ, Lin HH, Lee CC, Chiu LY, Wu SM, Yeh YM, Tang P, Chiu CH, Lyu PC, Tsai PC. BMC Med Genomics. 2019 Jul 11;12(Suppl 5):99. doi:10.1186/s12920-019-0510-y.

4. "Introduction to the Taiwan Biophysical Society. " Lyu PC.  Biophys Rev. 2019 May 22. doi: 10.1007/s12551-019-00530-5.

5. "Untying a Knotted SPOUT RNA Methyltransferase by Circular Permutation Results in a Domain-Swapped Dimer. " Ko KT, Hu IC, Huang KF, Lyu PC, Hsu SD. Structure. 2019 May 14. pii: S0969-2126(19)30126-1. doi:10.1016/j.str.2019.04.004.

6. "TNF-α-induced miR-450a mediates TMEM182 expression to promote oral squamous cell carcinoma motility. " Hsing EW, Shiah SG, Peng HY, Chen YW, Chuu CP, Hsiao JR, Lyu PC, Chang JY. PLoS One. 2019 Mar 20;14(3):e0213463. doi:10.1371/journal.pone.0213463.

7. "Untying a Protein Knot by Circular Permutation. " Chuang YC, Hu IC, Lyu PC, Hsu SD. J Mol Biol. 2019 Feb 15;431(4):857-863. doi:10.1016/j.jmb.2019.01.005.

2018

1. "Nile Tilapia Derived Antimicrobial Peptide TP4 Exerts Antineoplastic Activity Through Microtubule Disruption." Ting CH, Liu YC, Lyu PC, Chen JY. Mar Drugs. 2018 Nov 22;16(12). pii: E462. doi: 10.3390/md16120462.

2017

1. "Cdc7-Dbf4-mediated phosphorylation of HSP90-S164 stabilizes HSP90-HCLK2-MRN complex to enhance ATR/ATM signaling that overcomes replication stress in cancer." Cheng AN, Fan CC, Lo YK, Kuo CL, Wang HC, Lien IH, Lin SY, Chen CH, Jiang SS, Chang IS, Juan HF, Lyu PC, Lee AY. Sci Rep. 2017 Dec 5;7(1):17024.

2016

1. "De novo protein sequencing, humanization and in vitro effects of an antihuman CD34 mouse monoclonal antibody." Fan CY, Huang SY, Chou MY, Lyu PC. Biochem Biophys Rep. 2016 Nov 18;9:51-60.

2. "A clamp-like orientation of basic residues set in a parallelogram is essential for heparin binding." Cheng YY, Cheng CS, Lee TR, Chang WS, Lyu PC. FEBS Lett. 2016 Sep;590(18):3089-97.

3. "Role of the RAD51-SWI5-SFR1 Ensemble in homologous recombination." Su GC, Yeh HY, Lin SW, Chung CI, Huang YS, Liu YC, Lyu PC, Chi P. Nucleic Acids Res. 2016 Jul 27;44(13):6242-51.

4. "Pyrazolylamine Derivatives Reveal the Conformational Switching between Type I and Type II Binding Modes of Anaplastic Lymphoma Kinase (ALK)." Tu CH, Lin WH, Peng YH, Hsu T, Wu JS, Chang CY, Lu CT, Lyu PC, Shih C, Jiaang WT, Wu SY. J Med Chem. 2016 Apr 28;59(8):3906-19.

5. "1H, 15N and 13C resonance assignments of light organ-associated fatty acid-binding protein of Taiwanese fireflies." Tseng KL, Lee YZ, Chen YR, Lyu PC. Biomol NMR Assign. 2016 Apr;10(1):71-4.

2015

1. "Complete Genome Sequence of Xanthomonas campestris pv. campestris Strain 17 from Taiwan." Liu YC, Wang SC, Yu YJ, Fung KM, Yang MT, Tseng YH, Tsai SF, Sun HS, Lyu PC, Chou SH. Genome Announc. 2015 Dec 17;3(6).

2. "Comparative analysis of the folding dynamics and kinetics of an engineered knotted protein and its variants derived from HP0242 of Helicobacter pylori. " Wang LW, Liu YN, Lyu PC, Jackson SE, Hsu ST. J Phys Condens Matter. 2015 Sep 9;27(35):354106.

2014

1. "Biomarker discovery for neuroendocrine cervical cancer." Lin LH, Chang SJ, Hu RY, Lin MW, Lin ST, Huang SH, Lyu PC, Chou HC, Lai ZY, Chuang YJ, Chan HL. Electrophoresis. 2014 Jul;35(14):2039-45.

2. "NMR assignments of a hypothetical pseudo-knotted protein HP0242 from Helicobacter pylori." Chien CT, Wang LW, Liu YN, Hsu BD, Lyu PC, Hsu ST. Biomol NMR Assign. 2014 Oct;8(2):287-9. 

2013

1. "Protein kinase inhibitor design by targeting the Asp-Phe-Gly (DFG) motif: the role of the DFG motif in the design of epidermal growth factor receptor inhibitors." Peng YH, Shiao HY, Tu CH, Liu PM, Hsu JT, Amancha PK, Wu JS, Coumar MS, Chen CH, Wang SY, Lin WH, Sun HY, Chao YS, Lyu PC, Hsieh HP, Wu SY. J Med Chem. 2013 May 23;56(10):3889-903.

2. "Redox-proteomic analysis of doxorubicin resistance-induced altered thiol activity in uterine carcinoma." Lin ST, Lo YW, Chang SJ, Wang WC, Chang MD, Lyu PC, Chen YW, Chou HC, Chan HL. J Pharm Biomed Anal. 2013 May 5;78-79:1-8.

3. “Residue-specific annotation of disorder-to-order transition and cathepsin inhibition of a propeptide-like crammer from D. melanogaster. ” Tseng TS, Cheng CS, Hsu ST, Shih MF, He PL, Lyu PC*. PLos One 2013; 8 (1):e54187.

4. “GI-POP: a combinational annotation and genomic island prediction pipeline for ongoing microbial genome projects.” Lee CC, Chen YP, Yao TJ, Ma CY, Lo WC, Lyu PC * , Tang CY*. Gene 2013; 518 (1):114-23.

2012

1. “Crystal structure of circular permuted RoCBM21 (CP90): dimerisation and proximity of binding sites.” Stephen P, Cheng KC, Lyu PC*. PLos One 2012; 7 (11):e50488.

2. “Feature Identification of Compensatory Gene Pairs without Sequence Homology in Yeast.” Peng CH, Lin SH, Peng SC, Lyu PC , Aruta M, Tang CY*. Comp Funct Genomics. 2012; 2012:653174.

3. “Circular permutation prediction reveals a viable backbone disconnection for split proteins: an approach in identifying a new functional split intein.” Lee YT, Su TH, Lo WC, Lyu PC , Sue SC*. PLos One 2012: 7 (8):e43820.

4. “Proteomic analysis of proteins responsible for the development of doxorubicin resistance in human uterine cancer cells.” Lin ST, Chou HC, Chang SJ, Chen YW, Lyu PC , Wang WC, Chang MD, Chan HL *. J Proteomics. 2012 Oct 22; 75 (18):5822-47.

5. “Phylogenomic and domain analysis of iterative polyketide synthases in Aspergillus species.” Lin SH, Yoshimoto M, Lyu PC , Tang CY, Arita M*. Evol Bioinform 2012; 8 :373-87.

6. “Photofrin binds to procaspase-3 and mediates photodynamic treatment-triggered methionine oxidation and inactivation of procaspase-3.” Hsieh YJ, Chien KY, Lin SY, Sabu S, Hsu RM, Chi LM, Lyu PC , Yu JS*. Cell Death Dis. 2012 Jul 12; 3 :e347.

7. “Placenta proteome analysis from Down syndrome pregnancies for biomarker discovery.” Chen CP, Chen YH, Chern SR, Chang SJ, Tsai TL, Li SH, Chou HC, Lo YW, Lyu PC, Chan HL. Mol Biosyst. 2012 Sep; 8 (9):2360-72.

8. “Crystal structure of the dopamine N-acetyltransferase-acetyl-CoA complex provides insights into the catalytic mechanism.” Cheng KC, Liso JN, Lyu PC*. Biochem J. 2012 Sep 15; 446 (3):395-404.

9. “CPred: a web server for predicting viable circular permutations in proteins.” Lo WC, Wang LF, Liu YY, Dai T, Hwang JK, Lyu PC *. Nucleic Acids Res. 2012 Jul; 40 :W232-7.

10.  “Proteome reference map of Drosophila melanogaster head.” Lee TR, Huang SH, Lee CC, Lee HY, Chan HT, Lin KS, Chan HL, Lyu PC*. Proteomics. 2012 Jun; 12 (11):1875-8.

11. "Metabolic classification of microbial genomes using functional probes." Lee CC , Lo WC , Lai SM, Chen YP , Tang CY*, Lyu PC*. BMC Genomics. 2012 Apr 27; 13(1)157.

12. "Proteomic and redox-proteomic analysis of berberine-induced cytotoxicity in breast cancer cells." Chou HC, Lu YC, Cheng CS, Chen YW, Lyu PC, Lin CW, Timms JF, Chan HL. J Proteomics. 2012 Jun 18;75(11):3158-76.

13. "Proteomic analysis of a drosophila IBMPFD model reveals potential pathogenic mechanisms." Chan HT, Lee TR, Huang SH, Lee HY, Sang TK, Chan HL*, Lyu PC*. Mol Biosyst. 2012 Jun; 8(6):1730-41.

14. "A Molten Globule-to-Ordered Structure Transition of Drosophila melanogaster Crammer Is Required for its Ability to Inhibit Cathepsin." Tseng TS, Cheng CS, Chen DJ, Shih MF, Liu YN, Hsu ST*, Lyu PC*. Biochem J. 2012 Mar 15;442(3):563-72.

15. "Circular permutation of the starch-binding domain: inversion of ligand selectivity with increased affinity." Stephen P, Tseng KL, Liu YN, Lyu PC*. Chem Commun (Camb). 2012 Mar 7;48(20):2612-4.

16. "Identification of putative miRNAs from the deep-branching unicellular flagellates." Huang PJ, Lin WC, Chen SC, Lin YH, Sun CH, Lyu PC*, Tang P*. Genomics. 2012 Feb;99(2):101-7.

17. "Construction and analysis of a plant non-specific lipid transfer protein database (nsLTPDB)." Wang NJ, Lee CC, Cheng CS, LoWC, Yang YF, Chen MN, Lyu PC*. BMC Genomics. 2012;13 Suppl 1:S9.

18. "Deciphering the preference and predicting the viability of circular permutations in proteins." LoWC, Dau T, Liu YN, Wang LF, Hwang JK*, Lyu PC*. PLoS One. 2012;7(2):e31791.

2011

1. "Cytoskeleton Network and Cellular Migration Modulated by Nuclear-localized Receptor Tyrosine Kinase ROR1." Tseng HC, Kao HW, Ho MR, Chen YR, Lin TW, Lyu PC, Lin WC. Anticancer Res. 2011 Dec;31(12):4239-49.

2. "Proteomic analysis of gemcitabine-induced drug resistance in pancreatic cancer cells." Chen YW, Liu JY, Lin ST, Li JM, Huang SH, Chen JY, Wu JY, Kuo CC, Wu CL, Lu YC, Chen YH, Fan CY, Huang PC, Law CH, Lyu PC, Chou HC, Chan HL. Mol Biosyst. 2011 Nov;7(11):3065-74.

3. "Comparative analysis of receptor binding by chicken and human interleukin-1beta." Cheng CS, Lu WS, Tu IF, Lyu PC, Yin HS. J Mol Model. 2011 Jun;17(6):1283-94.

4. "Mitochondrial proteomics analysis of tumorigenic and metastatic breast cancer markers."Chen YW, Chou HC, Lyu PC, Yin HS, Huang FL, Chang WS, Fan CY, Tu IF, Lai TC, Lin ST, Lu YC, Wu CL, Huang SH, Chan HL.Funct Integr Genomics. 2011 Jun;11(2):225-39.

5. "Plasma proteomic analysis of the critical limb ischemia markers in diabetic patients with hemodialysis." Hung PH, Chen YW, Cheng KC, Chou HC, Lyu PC, Lu YC, Lee YR, Wu CT, Chan HL. Mol Biosyst. 2011 Jun;7(6):1990-8.

6. "Crystal structure and biophysical characterisation of Helicobacter pylori phosphopantetheine adenylyltransferase." Cheng CS, Chen CH, Luo YC, Chen WT, Chang SY, Lyu PC, Kao MC, Yin HS. Biochem Biophys Res Commun. 2011 May 6;408(2):356-61.

7. "Structural and functional comparison of cytokine interleukin-1 beta from chicken and human." Cheng CS, Chen WT, Lee LH, Chen YW, Chang SY, Lyu PC, Yin HS. Mol Immunol . 2011 Mar; 48(6-7):947-55.

8. "Reconstructing phylogeny from metabolic substrate-product relationships." Chang CW, Lyu PC, Arita M. BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S27.

2010

1. "Characterization of photodynamic therapy responses elicited in A431 cells containing intracellular organelle-localized photofrin." Hsieh YJ, Yu JS*, Lyu PC*. J Cell Biochem. 2010 Nov 1;111(4):821-33.

2. "Detection and alignment of 3D domain swapping proteins using angle-distance image-based secondary structural matching techniques." Chu CH, Lo WC, Wang HW, Hsu YC, Hwang JK, Lyu PC, Pai TW, Tang CY. PLoS One. 2010 Oct 14;5(10):e13361.

3. "Structural basis for the improved potency of peroxisome proliferator-activated receptor (PPAR) agonists." Peng YH, Coumar MS, Leou JS, Wu JS, Shiao HY, Lin CH, Lin WH, Lien TW, Chen X, Hsu JT, Chao YS, Huang CF, Lyu PC, Hsieh HP, Wu SY. Chem Med Chem. 2010 Oct 4;5(10):1707-16.

4. "Human RegIV protein adopts a typical C-type lectin fold but binds mannan with two calcium-independent sites." Ho MR, Lou YC, Wei SY, Luo SC, Lin WC, Lyu PC, Chen C. J Mol Biol. 2010 Oct 1;402(4):682-95.

5. "Anti-atherogenic effect of berberine on LXRalpha-ABCA1-dependent cholesterol efflux in macrophages." Lee TS, Pan CC, Peng CC, Kou YR, Chen CY, Ching LC, Tsai TH, Chen SF, Lyu PC, Shyue SK. J Cell Biochem. 2010 Sep 1;111(1):104-10.

6. "Thermodynamic and Kinetic Studies of a Stable Imperfect DNA Triplex by Spectroscopic and Calorimetric Methods."Wey MT, Lyu PC, Kan LS. J Chin Chem Soc. 2010 Jul;57(3B): 496-504.

7. "Proteomics study of oxidative stress and Src kinase inhibition in H9C2 cardiomyocytes: a cell model of heart ischemia-reperfusion injury and treatment." Chou HC, Chen YW, Lee TR, Wu FS, Chan HT, Lyu PC, Timms JF, Chan HL. Free Radic Biol Med. 2010 Jul 1;49(1):96-108.

8. "DSAP: deep-sequencing small RNA analysis pipeline." Huang PJ, Liu YC, Lee CC, Lin WC, Gan RR, Lyu PC*, Tang P*. Nucleic Acids Res. Jul;38(Web Server issue):W385-91.

9. "Nuclear localization of orphan receptor protein kinase (Ror1) is mediated through the juxtamembrane domain." Tseng HC, Lyu PC, Lin WC. BMC Cell Biol. 2010 Jun 30;11:48.

10. "Design and Synthesis of alpha-Ketoamides as Cathepsin S Inhibitors with Potential Applications against Tumor Invasion and Angiogenesis." Chen JC, Uang BJ, Lyu PC, Chang JY, Liu KJ, Kuo CC, Hsieh HP, Wang HC, Cheng CS, Chang YH, Chang MD, Chang WS, Lin CC. J Med Chem. 2010 Jun 10;53(11):4545-9.

11. "Trypsin-induced proteome alteration during cell subculture in mammalian cells." Huang HL, Hsing HW, Lai TC, Chen YW, Lee TR, Chan HT, Lyu PC, Wu CL, Lu YC, Lin ST, Lin CW, Lai CH, Chang HT, Chou HC, Chan HL. J Biomed Sci.2010 May 11;17:36.

12. "Functional proteomic and structural insights into molecular targets related to the growth inhibitory effect of tanshinone IIA on HeLa cells." Pan TL, Hung YC, Wang PW, Chen ST, Hsu TK, Sintupisut N, Cheng CS, Lyu PC. Proteomics. 2010 Mar;10 (5):914-29.

13. "Identification of MYO18A as a novel interacting partner of the PAK2/betaPIX/GIT1 complex and its potential function in modulating epithelial cell migration." Hsu RM, Tsai MH, Hsieh YJ, Lyu PC, Yu JS. Mol Biol Cell. 2010 Jan;21(2):287-301.

2009

1. "Predicting melting temperature directly from protein sequences." Ku T, Lu P, Chan C, Wang T, Lai S, Lyu PC, Hsiao N. Comput Biol Chem. 2009 Dec;33(6):445-50.

2. "Identification of trypsin-inhibitory site and structure determination of human SPINK2 serine proteinase inhibito." Chen T, Lee TR, Liang WG, Chang WS, Lyu PC*. Proteins. 2009 Oct;77(1):209-19.

3. "Generation of ligand-based pharmacophore model and virtual screening for identification of novel tubulin inhibitors with potent anticancer activity." Chiang YK, Kuo CC, Wu YS, Chen CT, Coumar MS, Wu JS, Hsieh HP, Chang CY, Jseng HY, Wu MH, Leou JS, Song JS, Chang JY, Lyu PC, Chao YS, Wu SY. J Med Chem. 2009 Jul 23;52(14):4221-33.

4. "Alanine substitutions of noncysteine residues in the cysteine-stabilized alphabeta motif."Yang YF, Cheng KC, Tsai PH, Liu CC, Lee TR, Lyu PC*. Protein Sci. 2009 Jul;18(7):1498-506.

5. "iSARST: an integrated SARST web server for rapid protein structural similarity searches." Lo WC, Lee CY, Lee CC, Lyu PC*. Nucleic Acids Res. 2009 Jul 1;37(Web Server issue): W545-51.

6. "Predicting helix-helix interactions from residue contacts in membrane proteins." Lo A, Chiu YY, Rødland EA, Lyu PC, Sung TY, Hsu WL. Bioinformatics. 2009 Apr 15;25(8):996-1003.

7. "CPDB: a database of circular permutation in proteins." Lo WC, Lee CC, Lee CY, Lyu PC*. Nucleic Acids Res. 2009 Jan; 37(Database issue): D328-32.

 2008

1. "The proteins of plant defensin family and their application beyond plant disease control." Yang YF, Lyu PC*. Recent Pat DNA Gene Seq. 2008;2(3):214-8.

2. "Mana-Hox displays anticancer activity against prostate cancer cells through tubulin depolymerization and DNA damage stress." Hsiao CJ, Ho YF, Hsu JT, Chang WL, Chen YC, Shen YC, Lyu PC, Guh JH. Naunyn Schmiedebergs Arch Pharmacol. 2008 Dec;378(6):599-608.

3. "Crystal structure of DFA0005 complexed with alpha-ketoglutarate: a novel member of the ICL/PEPM superfamily from alkali-tolerant Deinococcus ficus." Liao CJ, Chin KH, Lin CH, Tsai PS, Lyu PC, Young CC, Wang AH, Chou SH. Proteins. 2008 Nov 1;73(2):362-71.

4. "Effects of ligand binding on the dynamics of rice nonspecific lipid transfer protein 1: a model from molecular simulations." Lai YT, Cheng CS, Liu YN, Liu YJ, Lyu PC*. Proteins. 2008 Sep;72(4):1189-98.

5. "Enhanced membrane protein topology prediction using a hierarchical classification method and a new scoring function." Lo A, Chiu HS, Sung TY, Lyu PC, Hsu WL. J Proteome Res. 2008 Feb;7(2):487-96.

6. "WRC-213, an l-methionine-conjugated mitoxantrone derivative, displays anticancer activity with reduced cardiotoxicity and drug resistance: identification of topoisomerase II inhibition and apoptotic machinery in prostate cancers." Hsiao CJ, Li TK, Chan YL, Hsin LW, Liao CH, Lee CH, Lyu PC, Guh JH. Biochem Pharmacol. 2008 Feb 15;75(4):847-56.

7. "The possible interaction of CDA14 and protein elongation factor 1alpha." Yang YF, Chou MY, Fan CY, Chen SF, Lyu PC, Liu CC, Tseng TL. Biochim Biophys Acta. 2008 Feb;1784(2):312-8.

8. "Mutagenesis study of rice nonspecific lipid transfer protein 2 reveals residues that contribute to structure and ligand binding." Cheng CS, Chen MN, Lai YT, Chen T, Lin KF, Liu YJ, Lyu PC*. Proteins. 2008 Feb 15;70(3):695-706.

9. "CPSARST: an efficient circular permutation search tool applied to the detection of novel protein structural relationships." Lo WC, Lyu PC*. Genome Biol. 2008 Jan 18;9(1):R11.

2007

1. "Prazosin displays anticancer activity against human prostate cancers: targeting DNA and cell cycle." Lin SC, Chueh SC, Hsiao CJ, Li TK, Chen TH, Liao CH, Lyu PC, Guh JH. Neoplasia. 2007 Oct;9(10):830-9.

2. "Protein structural similarity search by Ramachandran codes." Lo WC, Huang PJ, Chang CH, Lyu PC*. BMC Bioinformatics. 2007 Aug 23;8:307.

3. "A Chaotic Micromixer Modulated by Constructive Vortices Agitation." Yang JT, Huang KJ, Tung KY, Hu IC, Lyu PC. J. Micromechanics and Microengineering 2007 17, 2084-2092.

4. "Structure-based protein engineering for alpha-amylase inhibitory activity of plant defensin." Lin KF, Lee TR, Tsai PH, Hsu MP, Chen CS, Lyu PC*. Proteins. 2007 Aug 1;68(2):530-40.

5. "Solution structure of family 21 carbohydrate-binding module from Rhizopus oryzae glucoamylase." Liu YN, Lai YT, Chou WI, Chang MD, Lyu PC*. Biochem J. 2007 Apr 1;403(1):21-30.

6. "Design of a Self-Flapping Microfluidid Oscillator and Diagnosis with Fluorescence Methods" Yang JT, Chen CK, Hu IC, Lyu PC. IEEE J. Microelectromechanical Systems. 2007 16, 826-835.

7. "An overlapping crisscross micromixer." Wang L, Yang JT, Lyu PC . Chemical Engineering Science 2007 62, 711-720.

8. "Preliminary X-ray analysis of XC5848, a hypothetical ORFan protein with an Sm-like motif from Xanthomonas campestris." Ruan SK, Chin KH, Shr HL, Lyu PC, Wang AH, Chou SH. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 Jan 1;63(Pt 1):30-3.

2006

1. "Crystallization and preliminary X-ray analysis of XC1015, a histidine triad-like protein from Xanthomonas campestris." Lo WT, Chin KH, Shr HL, Gao FP, Lyu PC, Wang AH, Chou SH. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Dec 1;62(Pt 12):1263-5.

2. "Human pancreatitis-associated protein forms fibrillar aggregates with a native-like conformation." Ho MR, Lou YC, Lin WC, Lyu PC, Huang WN, Chen C. J Biol Chem. 2006 Nov 3;281(44):33566-76.

3. "Cloning, crystallization and preliminary X-ray studies of XC2981 from Xanthomonas campestris, a putative CutA1." Lin CH, Chin KH, Gao FP, Lyu PC, Shr HL, Wang AH, Chou SH. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Nov 1;62(Pt 11):1113-5.

4. "Structural basis for the structure-activity relationships of peroxisome proliferator-activated receptor agonists." Mahindroo N, Peng YH, Lin CH, Tan UK, Prakash E, Lien TW, Lu IL, Lee HJ, Hsu JT, Chen X, Liao CC, Lyu PC, Chao YS, Wu SY, Hsieh HP. J Med Chem. 2006 Oct 19;49(21):6421-4.

5. "Biosynthesis of fluorescent allophycocyanin alpha-subunits by autocatalytic bilin attachment." Hu IC, Lee TR, Lin HF, Chiueh CC, Lyu PC*. Biochemistry. 2006 Jun 13;45(23):7092-9.

6. "Solution Structure of the Plant Defensin VrD1 from Mung bean: A Possible Mechanism for Insecticidal Activity Against Bruchids." Liu YN, Lai YT, Chou WI, Chang MD, Lyu PC*. Biochem J. 2007 Apr 1;403(1):21-30.

7. "Crystal structure of HP0242, a hypothetical protein from Helicobacter pylori with a novel fold." Tsai JY, Chen BT, Cheng HC, Chen HY, Hsaio NW, Lyu PC, Sun YJ. Proteins . 2006 Mar 1;62(4):1138-43.

8. "Japanese encephalitis virus NS2B-NS3 protease binding to phage-displayed human brain proteins with the domain of trypsin inhibitor and basic region leucine zipper." Lin CW, Lin KH, Lyu PC, Chen WJ. Virus Res. 2006 Mar;116(1-2):106-13.

9. "Indol-1-yl acetic acids as peroxisome proliferator-activated receptor agonists: design, synthesis, structural biology, and molecular docking studies." Mahindroo N, Wang CC, Liao CC, Huang CF, Lu IL, Lien TW, Peng YH, Huang WJ, Lin YT, Hsu MC, Lin CH, Tsai CH, Hsu JT, Chen X, Lyu PC, Chao YS, Wu SY, Hsieh HP. J Med Chem. 2006 Feb 9;49(3):1212-6.

2005

1. "Characterization and structural analyses of nsLTP1 from mung bean" Lin KF, Liu YN, Hsu ST, Samuel D, Cheng CS, Bonvin AM, Lyu PC*. Biochemistry. 2005 Apr 19;44(15):5703-12.

2. "Solution structure of a bacterial BolA-like protein XC975 from a plant pathogen Xanthomonas campestris pv. campestris." Chin KH, Lin FY, Hu YC, Sze KH, Lyu PC, Chou SH. J Biomol NMR. 2005 Feb;31(2):167-72.

3. "Anti-phosphopeptide antibody, P-STM as a novel tool for detecting mitotic phosphoproteins: identification of lamins A and C as two major targets." Tsai IC, Hsieh YJ, Lyu PC, Yu JS. J Cell Biochem. 2005 Apr 1;94(5):967-81.

4. "The Cloning, purification, crystallization, and preliminary X-ray crystallographic analysis of XC847, a 3'-5' oligoribonuclease from Xanthomonas campestris."  Wu YY, Chin KH, Chou CC, Lee CC, Shr HL, Lyu PC , Wang AH, Chou SH. Acta. Crystallogr. 2005 F61, 902-5.

5.   "The cloning, expression, crystallization, and preliminary X-ray analysis of a putative multiple antibiotic-resistance repressor protein (MarR) from Xanthomonas campestris."  Tu ZL, Li JN, Chin KH, Chou CC, Lee CC, Shr HL, Lyu PC, Gao FP, Wang AH, Chou SH. Acta. Crystallogr. 2005 F61, 706-8.

6. "Cloning, purification, crystallization, and preliminary X-ray characterization of a conserved hypothetical protein XC6422 from Xanthomonas campestris." Yang CY, Chin KH, Chou CC, Shr HL, Gao FP, Lyu PC, Wang AH, Chou SH. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005 Jul 1;61(Pt 7):703-5.

7.  "In the preparation, crystallization, and preliminary X-ray analysis of XC2382, an ApaG protein of unknown structure from Xanthomonas campestris." Chin KH, Chou CC, Lee CC, Shr HL, Lyu PC, Wang AH, Chou SH. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005 Jul 1;61(Pt 7):700-2.

8. "A putative polyketide synthesis protein XC5357 from Xanthomonas campestris: heterologous expression, crystallization, and preliminary X-ray analysis." Chu CL, Chin KH, Lin FY, Chou CC, Lee CC, Shr HL, Lyu PC, Wang AH, Chou SH. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005 Jul 1;61(Pt 7):697-9.

9. "Cloning, purification, crystallization and preliminary X-ray analysis of XC229, a conserved hypothetical protein from Xanthomonas campestris." Chin KH, Kuo WT, Chou CC, Shr HL, Lyu PC, Wang AH, Chou SH. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005 Jul 1;61(Pt 7):694-6.

10. "Preparation, crystallization, and preliminary X-ray characterization of a conserved hypothetical protein XC1692 from Xanthomonas campestris." Chin KH, Huang ZW, Wei KC, Chou CC, Lee CC, Shr HL, Gao FP, Lyu PC, Wang AH, Chou SH. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005 Jul 1;61(Pt 7):691-3.

2004

1. "Binding Mechanism of Non-specific Lipid Transfer Proteins and their role in Plant Defense." Cheng CS, Samuel D, Liu YJ, Shyu JC, Lai SM, Lin KF, Lyu PC*. Biochemistry. 2004 Nov 2;43(43):13628-36.

2. "Evaluation of Plant non-specific Lipid Transfer Proteins for Potential Application in Drug Delivery." Cheng CS, Chen MN, Liu YJ, Huang LY, Lin KF, Lyu PC *. Enzyme and Microbial Technology 2004, 35, 532-539.

3. "1H, 13C, and 15N resonance assignments and secondary structure of human pancreatitis-associated protein (hPAP)." Ho MR, Lou YC, Lin WC, Lyu PC, Chen C. J Biomol NMR. 2004 Nov;30(3):381-2.

4. "Relationship between local structural entropy and protein thermostabilty." Chan CH, Liang HK, Hsiao NW, Ko MT, Lyu PC, Hwang JK. Proteins. 2004 Dec 1;57(4):684-91.

5. "Distinct Unfolding and Refolding Pathways of Lipid Transfer Proteins LTP-1 and LTP-2." Lin CH, Li L, Lyu PC, Chang JY. Protein J. 2004 Nov;23(8):553-66.

6. " Lipid binding in rice nonspecific lipid transfer protein-1 complexes from Oryza sativa." Cheng HC, Cheng PT, Peng P, Lyu PC, Sun YJ. Protein Sci. 2004 Sep;13(9):2304-15.

7. "Nonsteroidal anti-inflammatory drugs increase expression of inducible COX-2 isoform of cyclooxygenase in spinal cord of rats with adjuvant induced inflammation." Hsueh SF, Lu CY, Chao CS, Tan PH, Huang YW, Hsieh SW, Hsiao HT, Chung NC, Lin SH, Huang PL, Lyu PC, Yang LC. Brain Res Mol Brain Res. 2004 Jun 18;125(1-2):113-9.

8. "3D-QSAR Studies on PU3 Analogues by Comparative Molecular Field Analysis." Liu HC, Lyu PC, Leong MK, Tsai KC, Hsiue GH. Bioorg Med Chem Lett. 2004 Feb 9;14(3):731-4.

2003 ~

1. "Mutagenesis Study on the Zebra Fish SOX9 High-Mobility Group: Comparison of Sequence and Non-Sequence Specific HMG Domains." N. W. Hsiao, D. Samuel, Y. N. Liu, L. C. Chen, T. Y. Yang, G. Jayaraman, P. C. Lyu*. Biochemistry42,11183-93 (2003).

2. "Influence of peptide conformation on oligosaccharide binding characteristics--a study using apamin-based chimeric peptide." C. W. Wu , G. Jayaraman , K. Y. Chien , Y. J. Liu , P. C. Lyu*. Peptides. 24, 1853-1861 (2003).

3. "Computation of the Protein Structure Entrope and its Applications to Protein Folding Processes." C. H. Chan, P. C. Lyu, J. K. Hwang, J. Chin. Chem. Soc. 50, 677-684 (2003).

4. "Relationship Between Protein Structures and Disulfide-Bonding Patterns." C. C. Chuang, C. Y. Chen, J. M. Yang, P. C. Lyu, J. K. Hwang, Proteins: Structure, Function, Bioinformatics.  52, 1-5 (2003).

5. "Fine-grained protein fold assignment by support vector machines using generalized n-peptide coding schemes and jury voting from multiple parameter sets." C. H. Yu, J. Y. Wang, J. M. Yang, P. C. Lyu, C. J. Lin, J. K. Hwang, Proteins: Structure, Function, Bioinformatics. 50, 531-536 (2003).

6. "Solution Structure of Plant non-specific Lipid Transfer Protein-2 Purified from Rice (Oryza Satiya)." D. Samuel, Y. J. Liu, C. S. Cheng, P. C. Lyu*, J. Biol. Chem. 277, 35267-35273 (2002).

7. "Purification and Characterization of a novel 7-kDa non-specific Lipid Transfer Protein from Rice (Oryza sativa)" Y. J. Liu, D. Samuel, C. H. Lin, P. C. Lyu*, Biochem.and Biophys. Res. Commun. 294, 535-40 (2002).

8. "The Prospect and Development of Bioinformatics" P. C. Lyu and J. K. Hwang, Chem. Engineering 48, 97-102 (2001).

9. "Glycosaminoglycan binding studies using de novo designed peptide." G. Jayaraman, C. W. Wu, Y. J. Liu, K. Y. Chien, P. C. Lyu*, FEBS Lett. 482, 154-158 (2000).

10. "A Novel transition metal binding protein: the backward reading sequence of the a-domain of human metallothionein-2. " P. K.-y. Pan, Z. F. Zheng, P. C. Lyu, P. C. Huang,  Euro. J. Bio. 266, 33-39 (1999).

11. "Calcium binding mode of g-carboxyglutamic acids in Conantokins. " C. H. Lin, F. C. H. Chan, J. K. Hwang, P. C. Lyu*,Protein Engineering 12, 589-595 (1999).

12. "Membrane packing geometry of diphytanoylphosphatidylcholine is highly sensitive to hydration: Phospholipid polymorphism induced by molecular rearrangement in the headgroup region. " C. H. Hsieh, S. C. Sue, P. C. Lyu and W.-g. Wu, Biophysical J. 73, 870-877 (1997).

13. "Role of modified glutamic acids in the helical structure of conantokin T. " C. H. Lin, C. S. Chen, K. S. Hsu, D. S. King and P. C. Lyu, FEBS Lett. 407, 243-248 (1997).

14. "Conantokin-T selectively antagonizes N-Methyl-D-Aspartate evoked responses in rat hippocampal slice." C. C. Huang, P. C. Lyu, C. H. Lin and K. S. Hsu, Toxicon 35, 355-363(1997).

15. "CD spectroscopy and the helix-coil transition in peptides and polypeptides." N. R. Kallenbach, P. C. Lyu and H. X. Zhou, In: Circular Dichroism and the Conformational Analysis of Biomolecules. ed. G. D. Fasman, Plenum Press, New York, 1996. pp.201-259.

16. "Stability and folding of the SH3 domain of Bruton's Tyrosine Kinase." Y. J. Chen, S. H. Lin, S. R. Tzeng, H. V. Patel, P. C. Lyu and J. W. Cheng, Proteins: Struc. Funct. Genet. 26, 465-471 (1996).

17. "Inhibition of calcium channels in rat hippocampal CA1 neurons by conantokin-T." K. S. Hsu, C. C. Huang and  P. C. Lyu, Neuroscience Lett. 220, 113-116 (1996).

18. "Solution conformation of a peptide corresponding to residues 151-172 of HIV-1 integrase using NMR and CD spectroscopy." J. W. Cheng, C. C. Cheng, P. C. Lyu, S. T. Chen and T. H. Lin, Int. J. Peptide Protein Res. 47, 117-122 (1996).

19. "Structure of a C-Terminal a-Helix Cap in a Synthetic Peptide." H. X. Zhou, P. C. Lyu, D. E. Wemmer and N. R. Kallenbach, J. Am. Chem. Soc. 116, 1139-1140 (1994).

20. "Alpha Helix Capping in Synthetic Model Peptides by Reciprocal Side Chain-Main Chain Interactions: Evidence for an N Terminal "Capping Box". " H. X. Zhou, P. C. Lyu, D. E. Wemmer and N. R. Kallenbach. Proteins: Struct. Funct. Genet.18,1-7 (1994).

21. "Capping interactions in Isolated a Helices: Position Dependent Substitution Effects and Structure of a Serine Capped Peptide Helix."  P. C. Lyu, D. E. Wemmer, H. X. Zhou, R. J. Pinker and N. R. Kallenbach. Biochemistry 32, 421-425 (1993).

22. "The Energetic Contribution of Solvent Exposed Ion Pairs to Alpha Helix Structure." P. C. Lyu, P. J. Gans and N. R. Kallenbach, J. Mol. Biol. 223, 343-350 (1992).

23. "The Helix-Coil Transition in Heterogeneous Peptides with Side Chain Interaction." P. J. Gans, P. C. Lyu, Woody, R. W. and N. R. Kallenbach, Biopolymers 31, 1605-1614 (1991).

24. "Alpha Helix Stabilization by Natural and Unnatural Amino Acids with Alkyl Side Chains." P. C. Lyu, J. C. Sherman, A. Chen and N. R. Kallenbach. Proc. Natl. Acad. Sci. U.S.A. 88, 5317-5320 (1991).

25. "Local Effect of Glycine Substitution in a Model Helical Peptide." P. C. Lyu, P. Wang, M. I. Liff and N. R. Kallenbach, J. Am. Chem. Soc. 113, 3568-3572 (1991).

26. "Analysis of Asymmetry in the Distribution of Helical Residues in Peptides by 1H NMR." M. I. Liff, P. C. Lyu and N. R. Kallenbach, J. Am. Chem. Soc. 113, 1014-1019 (1991).

27. "Side Chain Contribution to the Stability of Alpha Helical Structure in Peptides." P. C. Lyu, M. I. Liff, L. A. Marky and N. R. Kallenbach, Science 250, 669-673 (1990).

28. "Characterization of Block Oligomeric Peptides by 2D 1H NMR." M. I. Liff, P. C. Lyu and N. R. Kallenbach, Polymer Preprints 139-140 (1990).

29. "Evaluation of Side-chain Contributions to a-Helix Stability." P. C. Lyu, L. A. Marky and N. R. Kallenbach, Peptides, Proceedings of the Eleventh American peptide Symposium. J. E. Rivier and G. R. Marshall Eds. ESCOM. 632-634 (1990).

30. "The Role of Ion Pairs in a-Helix Stability: Two New Designed Helical Peptides." P. C. Lyu, L. A. Marky and N. R. Kallenbach, J. Am. Chem. Soc. 111, 2733-2734 (1989).

31. "Crystal Structure of 1,2-Diphenyl-3-nitrocyclopropene and ab Initio Calculations of 3-Nitrocyclopropene." C. J. Cheer, D. Bernstein, A. Greenberg and P. C. Lyu, J. Am. Chem. Soc. 110, 226-230 (1988).

32. "Substituent Effects on the Geometries of Prismanes." A. Greenberg, H. E. Chen, P. C. Lyu and J. F. Liebman, J. Mol. Struct. (Theochem) 163, 89-99 (1988).

Last update:  2012/05/09 PCL