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Yang, An-Suei 楊安綏

YangAS_6x7研究員兼中心副主任


Email: yangas@gate.sinica.edu.tw
Telephone: 02-27871232
[ CV ]



EDUCATION AND POSITIONS HELD:

  • Ph.D., Department of Chemistry The Johns Hopkins University, 1987
  • Postdoctoral Fellow, Department of Physics University of Virginia, 1987–1988
  • Postdoctoral Fellow, Department of Biochemistry Columbia University, 1988–1991
  • Associate Research Scientist - Research Scientist, Columbia University, 1991–2000
  • Assistant Professor of Pharmacology, Columbia University, 2000–2004
  • Associate Research Fellow, Genomics Research Center, Academia Sinica, 2004 - 2010
  • Research Fellow, Genomics Research Center, Academia Sinica, 2010 - present

HONORS:

  • Fellowship (2000-2002), William J. Matheson foundation at Columbia University.

RESEARCH INTERESTS:

The research direction in this laboratory is to engineer proteins of significant biomedical importance. We develop computational and bioinformatic approaches to design stable protein scaffolds and use phage-based molecular evolution to engineer stability in folding and affinity toward target molecules. The goal is to enhance the insight into molecular basis on protein recognition and to use the engineered proteins in biomedical applications. Specific areas of interest include:computational protein design, recombinant antibody engineering,protein-protein interaction, computational structural biology, structural bioinformatics, phage display of antibody libraries, synthetic antibody fragment library construction.

YangAS_PIC01

Protein engineering with
computationalbiology andphage
based molecular evolution

本實驗室主要的研究方向為蛋白質分子的設計與應用。利用計算生物學與生物資訊技術設計穩定的蛋白質分子,再藉由噬菌體表達技術,篩選具有高度穩定性與專一性功能的蛋白質分子。目的在於加深對蛋白質分子間交互作用的認知及在生物技術上的應用。

SELECTED PUBLICATIONS:

  • Rajasekaran Mahalingama*, Hung-Pin Peng, An-Suei Yang*, accepted, “Prediction of fatty acid-binding residues on protein surfaces with three-dimensional probability distributions of interacting atoms”, BIOPHYSICAL CHEMISTRY. (SCI)
  • Hung-Pin Peng, Kuo Hao Lee, Jhih-Wei Jian, An-Suei Yang*, accepted, “Origins of specificity and affinity in antibody-protein interactions”, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. (SCI)
  • Rajasekaran Mahalingam*, Hung-Pin Peng, An-Suei Yang*, 2014, “Prediction of FMN-binding residues with three-dimensional probability distributions of interacting atoms on protein surfaces”, JOURNAL OF THEORETICAL BIOLOGY, 343, 154-161. (SCI)
  • Hsu, H.-J., K. H. Lee, J.-W. Jian, H.-J. Chang, C.-M. Yu, Y.-C. Lee, I.-C. Chen, H.-P. Peng, C. Y. Wu, Y.-F. Huang, C.-Y. Shao, K. P. Chiu and A.-S. Yang*, 2014, “Antibody variable domain interface and framework sequence requirements for stability and function by high throughput experiments.”, STRUCTURE, 22(1), 22-34. (SCI)
  • Chang, H.-J., J.-W. Jian, H.-J. Hsu, Y.-C. Lee, H.-S. Chen, J.-J. You, S.-C. Hou, C.-Y. Shao, Y.-J. Chen, K.-P. Chiu, H.-P. Peng, K. H. Lee and A.-S. Yang*, 2014, “Loop sequence features and stability determinants in antibody variable domains by high throughput experiments.”, STRUCTURE, 22(1), 9-21. (SCI)
  • Chang, H.-J. and A.-S. Yang*, 2014, “Design of Phage-Displayed Cystine-Stabilized Mini-Protein Libraries for Proteinaceous Binder Engineering”, Methods in Molecular Biology, 1088, 1-17.
  • Hsu, H.-J. and A.-S. Yang*, 2014, “Substrate Phage Display for Protease Substrate Sequence Characterization: Bovine Factor Xa as a Model System”, Methods in Molecular Biology, 1088, 107-124.
  • Keng-Chang Tsai, Ei-Wen Yang, Jhih-Wei Jian, Po-Chiang Hsu, Hung-Pin Peng, Ching-Tai Chen, Jun-Bo Chen, Jeng-Yih Chang, Wen-Lian Hsu. An-Suei Yang*, 2012, “Prediction of Carbohydrate Binding Sites on Protein Surfaces with 3-Dimensional Probability Density Distributions of Interacting Atoms”, PLoS One, 7(7), e40846. (SCI)
  • Ching-Tai Chen, Hung-Pin Peng, Jhih-Wei Jian, Keng-Chang Tsai, Jeng-Yih Chang, Ei-Wen Yang, Jun-Bo Chen, Wen-Lian Hsu, An-Suei Yang*, 2012, “Protein-Protein Interaction Site Predictions with Three-Dimensional Probability Distributions of Interacting Atoms on Protein Surfaces”, PLoS One, 7(6), e37706. (SCI)
  • Chung-Ming Yu, Hung-Pin Peng, Ing-Chien Chen, Yu-Ching Lee, Jun-Bo Chen, Keng-Chang Tsai, Ching-Tai Chen, Jeng-Yih Chang, Ei-Wen Yang, Po-Chiang Hsu, Jhih-Wei Jian, Hung-Ju Hsu, Hung-Ju Chang, Wen-Lian Hsu, Kai-Fa Huang, Alex Che Ma, An-Suei Yang*, 2012, “Rationalization and Design of the Complementarity Determining Region Sequences in an Antibody-Antigen Recognition Interface”, PLoS One, 7(3), e33340. (SCI)
  • Yu-Ching Lee, Ing-Chien Chen, Chung-Ming Yu, Yi-Jen Huang, Hung-Ju Hsu, and An-Suei Yang*, 2011, “Effects of signal sequence on phage-displayed disulfide-stabilized single chain antibody variable fragment (sc-dsFv) libraries”, BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 411(2), 348-353. (SCI)
  • Ing-Chien Chen, Chung-Ming Yu, Yu-Ching Lee, Yi-Jen Huang, Hung-Ju Hsu, and An-Suei Yang*, 2010, “Signal sequence as a determinant in expressing disulfide-stabilized single chain antibody variable fragments (sc-dsFv) against human VEGF”, MOLECULAR BIOSYSTEMS, 6(7), 1307-1315. (SCI)
  • Yi-Jen Huang, Ing-Chien Chen, Chung-Ming Yu, Yu-Ching Lee, Hung-Ju Hsu, Anna Ching-Ching Tung, Hung-Ju Chang, An-Suei Yang*, 2010, “Engineering Anti-vascular Endothelial Growth Factor Single Chain Disulfide-stabilized Antibody Variable Fragments (sc-dsFv) with Phage-displayed sc-dsFv Libraries”, Journal of Biological Chemistry, 285(11), 7880-7891. (SCI)
  • Hung-Ju Chang, Hung-Ju Hsu, Chi-Fon Chang, Hung-Pin Peng, Yi-Kun Sun, Hui-Ming Yu, Hsi-Chang Shih, Chun-Ying Song, Yi-Ting Lin, Chu-Chun Chen, Chia-Hung Wang, An-Suei Yang*., 2009, “Molecular Evolution of Cystine-Stabilized Miniproteins as Stable Proteinaceous Binders”, STRUCTURE, 17, 620-631. (SCI)
  • Hung-Ju Hsu, Keng-Chang Tsai, Yi-Kun Sun, Hung-Ju Chang, Yi-Jen Huang, Hui-Ming Yu, Chun-Hung Lin, Shi-Shan Mao and An-Suei Yang, 2008, “Factor-XaActive Site Substrate Specificity with Substrate Phage Display and Computational Molecular Modeling”, J. Biol. Chem, 283, 12343-12353. (SCI)
  • Chen CT, Yang EW, Hsu HJ, Sun YK, Hsu WL, Yang AS, 2008, “Protease substrate site predictors derived from machine learning on multilevel substrate phage display data.”, BIOINFORMATICS, 24(23), 2691-7. (SCI)
  • H. P. Peng and A. S. Yang, 2007, “Modeling protein loops with knowledge-based prediction of sequence-structure alignment”, Bioinformatics, 23(21), 2836-2842. (SCI)
  • Y. M. Shao, W. B. Yang, H. P. Peng, M. F. Hsu, K. C. Tsai, T. H. Kuo, A. H. Wang, P. H. Liang, C. H. Lin, A. S. Yang and C. H. Wong, 2007, “Structure-Based Design and Synthesis of Highly Potent SARS-CoV 3CL Protease Inhibitors”, ChemBioChem, 8, 1654-1657. (SCI)
  • H. Hsu, H. Cheng, H-P. Peng, S-S. Huang, M-Y. Lin and A. S. Yang, 2006, “Assessing Computational Amino Acid beta-turn Propensities with Phage-displayed Combinatorial Library and Directed Evolution”, Structure, 14, 1499-1510. (SCI)
  • R. Kuang, C. S. Leslie and A. S. Yang, 2004, “Protein backbone angle prediction with machine learning approaches”, Bioinformatics, 20, 1612-1621. (SCI)
  • A. S. Yang, L. Y. Wang, 2003, “Local structure prediction with local structure-based sequence profiles”, Bioinformatics, 19, 1267-1274. (SCI)
  • A. S. Yang, L. Y. Wang, 2002, “Local structure-based sequence profile database for local and global protein structure predictions”, Bioinformatics, 18, 1650-1657. (SCI)
  • A. S. Yang, 2002, “Structure-dependent sequence alignment for remotely related proteins”, Bioinformatics, 18, 1658-1665. (SCI)
  • A. S. Yang, B. Honig, 2000, “An integrated approach to the analysis and modeling of protein sequences and structures. I. Protein structural alignment and a quantitative measure for protein structural distance”, J Mol Biol, 301, 665-678. (SCI)
  • A. S. Yang, B. Honig, 2000, “An integrated approach to the analysis and modeling of protein sequences and structures. II. On the relationship between sequence and structural similarity for proteins that are not obviously related in sequence”, J Mol Biol, 301, 679-689. (SCI)
  • A. S. Yang, B. Honig, 2000, “An integrated approach to the analysis and modeling of protein sequences and structures. III. A comparative study of sequence conservation in protein structural families using multiple structural alignments”, J Mol Biol, 201, 691-711. (SCI)
  • A. S. Yang, B. Honig, 1999, “Sequence to structure alignment in comparative modeling using PrISM”, Proteins, Suppl 3, 66-72. (SCI)
  • V. K. Misra, J. L. Hecht, A. S. Yang and B. Honig, 1998, “Electrostatic Contributions to the Binding Free Energy of the cI Repressor to DNA”, Biophys J, 75, 2262-2273. (SCI)
  • A. S. Yang, B. Hitz, B. Honig, 1996, “Free energy determinants of secondary structure formation: III. beta-turns and their role in protein folding”, J Mol Biol, 259, 873-882. (SCI)
  • A. S. Yang, A. S. Brill, 1996, “Thermal access to amplified chemical potential and the determination of equilibrium constants in protein solutions at subfreezing temperatures”, Biophys Chem, 58, 341-354. (SCI)
  • A. S. Yang, B. Honig, 1995, “Free energy determinants of secondary structure formation: I. alpha-Helices”, J Mol Biol, 252, 351-365. (SCI)
  • A. S. Yang, B. Honig, 1995, “Free energy determinants of secondary structure formation: II. Antiparallel beta-sheets”, J Mol Biol, 252, 366-376. (SCI)
  • B. Honig, A. S. Yang, 1995, “The free energy balance in protein folding”, Adv Protein Chem, 46, 27-58.
  • A. S. Yang, B. Honig, 1994, “Structural origins of pH and ionic strength effects on protein stability. Acid denaturation of sperm whale apomyoglobin”, J Mol Biol, 237, 602-614. (SCI)
  • A. S. Yang, M. R. Gunner, R. Sampogna, K. Sharp and B. Honig, 1993, “On the calculation of pKas in proteins”, Proteins, 15, 252-265. (SCI)
  • A. S. Yang, B. Honig, 1993, “On the pH Dependence of Protein Stability”, J Mol Biol, 231, 459-474. (SCI)
  • A. S. Yang, K. A. Sharp and B. Honig, 1992, “Analysis of the heat capacity dependence of protein folding”, J Mol Biol, 227, 889-900. (SCI)
  • A. S. Yang, B. Honig, 1992, “Electrostatic effects on protein stability”, Curr Opin Struct Biol, 2, 40-45.
  • A. S. Yang, A. S. Brill, 1991, “Influence of the freezing process upon fluoride binding to hemeproteins”, Biophys J, 59, 1050-1063. (SCI)
  • A. S. Yang, B. J. Gaffney, 1990, “EPR Detection of Kinetic Responses to Photochemically Generated Protein Cofactors”, J Magn Reson, 90, 580-583. (SCI) (IF: 2.3; SCI ranking: 35.3%,34.9%,53.3%)
  • A. S. Yang, B. J. Gaffney, 1987, “Determination of relative spin concentration in some high-spin ferric proteins using E/D-distribution in electron paramagnetic resonance simulations”, Biophys J, 51, 55-67. (SCI)