Cross AI and Structural Biology: designing robust ubiquitin variants to effectively regulate ubiquitin enzymes

時間地點：10:30 am, Jul 03 (Wed), 2024; R1-B1122 Conference Room

研討講者：Kuen-Phon Wu, PhD

June 06, 2024

Abstract

Determining the structures of biomacromolecules like proteins, DNA, RNA, or complex assemblies is often a time-intensive endeavor. This lengthy process hinders our comprehension of the relationship between structure and function in these biomolecules. NMR spectroscopy and X-ray crystallography are traditional methods used for experimental 3D structure determination, with cryoEM emerging as a powerful tool for investigating the dynamics of large molecular weight proteins. Advancements in artificial intelligence (AI) over the past decade have significantly enhanced the speed and accuracy of protein structure prediction. AlphaFold and other deep-learning tools have revolutionized protein engineering and structural determination.

In my presentation, I will provide an overview of how AI has impacted structural biology. These AI-driven approaches not only expedite experimental data processing but also enable the engineering and design of proteins with novel functionalities and drug discovery. The intersection of artificial intelligence and structural biology holds great promise for biomedical applications. I will also introduce a case in which my laboratory employs deep-learning protein design tools to rapidly modify ubiquitin, transforming it from a native substrate to a strong inhibitor. The entire study was robotic and cost-effective compared to other directed evolution approaches such as phage display screening.

The accelerated pace of protein structure determination facilitated by AI not only deepens our understanding of fundamental biological processes but also paves the way for innovative biomedical interventions. By harnessing the power of AI, researchers can more efficiently design therapeutic proteins, unravel disease mechanisms, and advance drug discovery efforts, ultimately contributing to improved healthcare outcomes in the near future.


Kuen-Phon Wu, PhD

Institute of Biological Chemistry

Academia Sinica

Kuen-Phon Wu, PhD

Associate Research Fellow, 

Institute of Biological Chemistry

Academia Sinica, Taipei, Taiwan, 115

Tel: +886-2-27855696 # 5070

Email: kpwu@gate.sinica.edu.tw

Web: https://kpwulab.com 

Academic Positions:

2024.4 – present     Associate Research Fellow,

                                    Institute of Biological Chemistry,

                                    Academia Sinica, Taipei, Taiwan

2019.8 – present     Joint Appointed Assistant Professor,

                                    Institute of Biochemical Sciences,

                                    National Taiwan University, Taipei, Taiwan

2018.11 – 2024.3     Assistant Research Fellow,

                                     Institute of Biological Chemistry,

                                     Academia Sinica, Taipei, Taiwan

2017.8 – 2018.10     MOST-awarded assistant research scholar Institute of Biological Chemistry,

                                     Academia Sinica, Taipei, Taiwan

2012.3 – 2017.7        Post-doctoral fellow Department of Structural Biology,

                                     St. Jude Children’s Research Hospital, Memphis, TN

2010.8 – 2012.2       Post-doctoral fellow Robert Wood Johnson Medical School,

                                     University of Medicine and Dentistry of New Jersey, Piscataway, NJ

Research Interests and expertise:

Post-translational ubiquitination, Biophysics, Drug discovery, Biochemistry, Structural Biology,

Protein folding and misfolding, Protein NMR spectroscopy

Education:

Ph.D., Dept. of Chemistry & Chemical Biology, Rutgers University, Piscataway, NJ (2010 January)

M.Sc., Dept. of Life Sciences, National Tsing Hua University, Hsinchu, Taiwan (2002 June)

B.Sc., Dept. of Life Sciences, National Tsing Hua University, Hsinchu, Taiwan (2000 June)

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Honors, Awards and Scholarships:

● Academia Sinica Career Development Award (2021-2025)

● MOST-awarded assistant research scholar (延攬海外⼈才計畫) (2017-2020)

● Young Investigator Award (May, 2016), the 21st Biophysics conference, Hsinchu, Taiwan

● Graduate Student Excellence Awards (June 2009), Dept. Chemistry and Chemical Biology, Rutgers                 

   University

● Dr. Stanley and Francine Mandeles Graduate Research Award for outstanding research contributions to

    biophysical chemistry (April 2009), Center for Molecular Biophysics & Biophysical Chemistry, Rutgers

    University

● Outstanding student poster award (August 2008), Division of Physical Chemistry, 236th ACS national

    meeting in Philadelphia

● NIH Interdisciplinary Research Workforce fellowship (2007-2008) 

Selected research publications (*:corresponding):

1. What Strengthens Protein-Protein Interactions: Analysis and Applications of Residue Correlation Networks               Hung TI# , Hsieh Y-J# , Lu W-L, Wu K-P*, Chang CA*

    Journal of Molecular Biology (2023) Dec 15;435(24):168337

2. PAICS ubiquitination recruits UBAP2 to trigger liquid-liquid phase separation for purinosome assembly 

    Chou M-C, Wang Y-H, Chen F-Y, Kung C-Y, Wu K-P, Kuo J-C, Chan S-J, Cheng M-L, Chou Y-C, Firestine S,

    Huang J-R, Chen R-H

    Molecular Cell (2023) Nov 16;83(22):4123-4140.e12

3. PTPN23 ubiquitination by WDR4 suppresses EGFR and c-MET degradation to define a lung cancer 

    therapeutic target

    Singh S, Yeat YN, Wang Y-T, Lin S-Y, Kuo I-Y, Wu K-P, Wang W-J, Wang W-C, Su W-C, Wang Y-C, Chen R-

    H

    Cell Death & Disease (2023) Oct 11;14(10):671

4. Structural basis of transcriptional activation by the OmpR/PhoB-family response regulator PmrA

    Lou Y-C*, Huang H-Y, Yeh H-H, Chiang W-H, Chen C*, Wu K-P*

    Nucleic Acids Research (2023) Oct 13;51(18):10049-10058

5. Robust design of effective allosteric activators for Rsp5 E3 ligase using the machine-learning tool   

    ProteinMPNN

    Kao H-W, Lu W-L, Ho M-R, Lin Y-F, Hsieh Y-J, Ko K-P, Hsu S-T D, Wu K-P*

    ACS Synthetic Biology (2023) Aug 18;12(8):2310-2319

6. TRABID inhibition activates cGAS/STING-mediated anti-tumor immunity through mitosis and autophagy

    dysregulation

    Chen Y-H, Chen H-H, Wang W-J, Chen H-Y, Huang W-S, Kao C-H, Lee S-R, Yeat YN, Yan RL, Chang S-J,

    Wu K-P, Chen R-H*

    Nature Communications (2023) May 26;14(1):3050

7. Cryo-EM reveals the structure and dynamics of a 723-residue malate synthase G

    Ho M-R# , Wu Y-M# , Lu Y-C# , Ko T-P, Wu K-P*

    Journal of Structural Biology (2023) Jun;215(2):107958,

8. 2.2 Å Cryo-EM Tetra-Protofilament Structure of the Hamster Prion 108-144 Fibril Reveals an Ordered

    Water Channel in the Center.

    Chen EH# , Kao H-W# , Lee CH# , Huang J Y-C, Wu K-P*, Chen RP*

    J Am Chem Soc. 2022 Jul 20;144(30):13888-13894.

    Highlighted in the 2023 January eNews provided by the NSTC Natural Science Library Service

9. Structural basis for the helical filament formation of Escherichia coli glutamine synthetase.

    Huang P-C, Chen S-K, Chiang W-H, Ho M-R, Wu K-P*

    Protein Sci. 2022 May;31(5):e4304.

10. Tumor suppressor BAP1 nuclear import is governed by transportin-1.

    Yang T-J, Li T-N, Huang R-S, Pan M-Y, Lin S-Y, Lin S, Wu K-P, Wang L-H, Hsu S-T D.

    J Cell Biol. 2022 Jun 6;221(6):e202201094.

11. Identification of disease-linked hyperactivating mutations in UBE3A through large-scale functional variant

    analysis.

    Weston KP, Gao X, Zhao J, Kim KS, Maloney SE, Gotoff J, Parikh S, Leu Y-C, Wu K-P, Shinawi M, Steimel 

    JP, Harrison JS, Yi JJ.

    Nature Communications. 2021 Nov 23;12(1):6809. 

12. Direct Visualization of a 26 kDa Protein by Cryo-Electron Microscopy Aided by a Small Scaffold Protein 

    Chiu Y-H, Ko K-T, Yang T-J, Wu K-P, Ho M-R, Draczkowski P, Hsu S-T D.

    Biochemistry. 2021 Apr 13;60(14):1075-1079

13. VPS34 K29/K48 branched ubiquitination governed by UBE3C and TRABID regulates autophagy, 

    proteostasis and liver metabolism

    Chen Y-H, Huang T-Y, Lin Y-T, Lin S-Y, Li W-H, Hsiao H-J, Yan R-L, Tang H-W, Shen Z-Q, Chen G-C, Wu

    K-P, Tsai T-F, Chen R-H.

    Nature Communications 2021, 12, 1322

14. Insights into Dynamics of Inhibitor and Ubiquitin-Like Protein Binding in SARS-CoV-2 PapainLike

    Protease

    Bosken YK, Cholko T, Lou Y-C, Wu K-P, Chang C-A A.

    Frontiers in Molecular Biosciences, (2020), 7, 174

15. Cryo-EM analysis of a feline coronavirus spike protein reveals a unique structure and camouflaging

    glycans.

    Yang TJ, Chang YC, Ko TP, Draczkowski P, Chien YC, Chang YC, Wu K-P, Khoo KH, Chang HW, Hsu S-T D.

    Proc Natl Acad Sci U S A. (2020),117,1438-1446

16. Insights into links between autophagy and the ubiquitin system from the structure of LC3B bound to the

    LIR motif from the E3 ligase NEDD4

    Qiu Y, Zheng Y, Wu K-P, Schulman BA.

    Protein Science (2017),26 (8), 1674

17. Deubiqutinase activity is required for the proteasomal degradation of misfolded cytosolic proteins upon

    heat-stress.

    Fang NN, Zhu M, Rose A, Wu K-P, Mayor T.

    Nature Communications, (2016), 7, 12907

18. Dual RING E3 Architectures Regulate Multiubiquitination and Ubiquitin Chain Elongation by APC/C.

    Brown NG, VanderLinden R, Watson ER, Weissmann F, Ordureau A, Wu K-P, Zhang W, Yu S, Mercredi PY,

    Harrison JS, Davidson IF, Qiao R, Lu Y, Dube P, Brunner MR, Grace CRR, Miller DJ, Haselbach D, Jarvis

    MA, Yamaguchi M, Yanishevski D, Petzold G, Sidhu SS, Kuhlman B, Kirschner MW, Harper JW, Peters J-

    M, Stark H, Schulman BA.

    Cell, (2016), 165, 1440-1453

19. A cascading activity-based probe sequentially targets E1–E2–E3 ubiquitin enzymes Mulder MPC, Witting

    K, Pruneda JN, Berlin I, Wu K-P, Merkx R, Neefjes J, Schulman BA, Komander D, Oualid FE, Ovaa H.

    Nature Chemical Biology, (2016), 12, 523-530

20. System-wide modulation of HECT E3 ligases with selective ubiquitin variant probes.

    Zhang W*, Wu K-P*, Sartori M, Kamadurai HB, Ordureau A, Jiang C, Mercredi PY, Murchie R, Hu J,

    Persaud A, Mukherjee M, Li N, Doye A, Walker JR, Sheng Y, Hao Z, Li Y, Brown KB, Lemichez E, Chen J,

    Tong Y, Harper JW, Rotin D, Moffat J, Schulman BA, Sidhu SS.

    Molecular Cell. (2016), 62, 121-136. *: Equally contributed authors

21. Unveiling transient protein-protein interactions that modulate inhibition of alpha-synuclein aggregation

    by beta-synuclein, a pre-synaptic protein that co-localizes with alpha-synuclein Janowska M, Wu K-P, Baum

    J. Scientific Reports. (2015), 5, 15164 

22. Fast hydrogen exchange affects 15N relaxation measurement in intrinsically disordered protein.

    Kim S, Wu K-P, Baum J.

    J Biomol NMR. (2013), 55, 249-256

23. Segmental isotope labeling of proteins for NMR structural study using a protein S tag for higher

    expression and solubility.

    Kobayashi H, Swapna GV, Wu K-P, Afinogenova Y, Conover K, Mao B, Montelione GT, Inouye M J.

    Biomol. NMR (2012), 52, 303-313

24. The A53T mutation is key in defining the differences in the aggregation kinetics of human and mouse

    alpha-synuclein.

    Kang L, Wu K-P, Vendruscolo M, Baum J.

    J. Am. Chem. Soc. (2011), 133, 13465-13470

25. Detection of transient interchain interactions in the intrinsically disordered protein alphasynuclein by

    NMR paramagnetic relaxation enhancement.

    Wu K-P and Baum J.

    J. Am. Chem. Soc. (2010), 132, 5546-5547.

26. Structural reorganization of alpha-synuclein at low pH observed by NMR and REMD simulation.

    Wu K-P, Weinstock DS, Narayanan C, Levy RM, Baum J.

    J. Mol. Biol. (2009), 391, 784-796

27. Characterization of conformational ensemble of natively unfolded human and mouse alphasynuclein:

    implication for aggregation.

    Wu K-P, Kim S, Fela DA, Baum J.

    J. Mol. Biol. (2008), 378, 1104-1115

28. Distinguishing among structural ensembles of the GB1 peptide: REMD simulations and NMR

    experiments.

    Weinstock DS, Narayanan C, Felts AK, Andrec M, Levy RM, Wu K-P, Baum J.

    J. Am. Chem. Soc. (2007), 129, 4858-4859

29. Novel solution structure of porcine beta-microseminoprotein.

    Wang I, Lou YC, Wu K-P, Wu SH, Chang WC, Chen C.

    J. Mol. Biol. (2005), 346, 1071-1082

30. Structural basis of a Flavivirus recognized by its neutralizing antibody: Solution structure of the domain

    III of the Japanese Encephalitis virus envelope protein.

    Wu K-P, Wu CW, Tsao YP, Kuo TW, Lou YC, Lin CW, Wu SC, Cheng JW.

    J. Biol. Chem. (2003), 278, 46007-46013