Resources | YE LAB AT USF

SELECTED PUBLICATIONS (* Corresponding author)

1. Xudong Wang, Chris Neale, Soo-kyung Kim, William A. Goddard, Libin Ye*. Intermediate-state-trapped Mutants Pinpoint Sequential

Activation process of G protein-coupled Receptor. Nature Communications, 2023, 14(1):1325. More

2. Jesper J. Madsen, Libin Ye, Thomas Frimurer, Ole Olsen. Mechanistic basis of GPCR activation explored by ensemble refinement of

crystallographic structures. Protein Science, 2022, e4456. More

3. Libin Ye*, Xudong Wang, Aidan McFarland, and Jesper J. Madsen. 19F NMR--A promising Tool for Dynamic Conformational Studies of G

Protein-coupled Receptors. Structure, 2022, 30(10):1372-1384. More

4. Xudong Wang, Nabila Busha, Jesper Madsen, Martin Muschol, Libin Ye*. An In-membrane NMR Spectroscopic Approach Probing Native

Ligand-GPCR Interaction. International Journal of Biological Macromolecules. 2022,206:911-916. More

5. Sriram S.K.S. Narayanan, Xudong Wang, Jose Paul, Vladislav Paley, Zijian Weng, Libin Ye*, Ying Zhong*. Disinfection and Electrostatic

Recovery of N95 Respirators by Corona Discharge for Safe Reuse. Environmental Sciences & Technology, 2021: 55(22);15351-15360. More

6. Dennis D. Fernandes, Chris Neale, Gregory-Neal W. Gomes, Yuchong Li, Aimen Malik, Adi Pandey, Alex Orazietti, Xudong Wang, Libin Ye*,

R. Scott Prosser*, and Claudiu C. Gradinaru*. Ligand Modulation of the Conformational Dynamics of the A2A Adenosine Receptor Revealed

bySingle-Molecule Fluorescence. Scientific Reports, 2021, 11(1):5910. More

7. Wenjie Zhao, Xudong Wang, Libin Ye*. Expression and Purification of Yeast-derived GPCR, Ga and Gbg Subunits for Structural and

Dynamic Studies , Bio-protocol, 2021, 11 (4), DOI: 10.21769/BioProtoc.3919. More

8. Xudong Wang, Wenjie, Zhao, Sameer Al-Abdul-Wahid, Yiming Lu, Tao Cheng, Jesper Madsen, Libin Ye*. Tri-fluorinated Keto-Enol

Tautomeric Switch in Probing Domain Rotation of a G Protein-Coupled Receptor. Bioconjugate Chemistry, 2021, 32(1):99-105. More

9. Xudong Wang, Aidan McFarland, Jesper J. Madsen, Eric Aalo, Libin Ye*.The Potential of 19F NMR Application in GPCR Biased Drug

Discovery. Trends in Pharmacological Sciences, 2021,42(1): 19-30. More

10. Guang-Qiang Yin, Sneha Kandapal, Chung-Hao Liu, Heng Wang, Shu-Ting Jiang, Tan Ji, Yu Yan, Sandra Khalife, Libin Ye, Bingqian Xu, Hai-

Bo Yang, Mu-Ping Nieh, Xiaopeng Li*. Metallo-Helicoid with Double Rims: Polymerization Followed by Folding via Intramolecular

Coordination. Angewandte Chemie International Edition, 2020, 59: 2-11. More

Before joining USF

Libin Ye, Chris Neale, Adnan Sljoka, Dmitry Pichugin, Nobuyuki Tsuchimura, Sacha T. Larda, Eps van Ned, Regis Pomes, Angel E. Garcia, Roger Sunahara, Oliver P. Ernst, R. Scott Prosser. Bidirectional allosteric modulation of the A2A adenosine G protein-coupled receptor by physiological cations. Nature Communications, 2018, 9(1):1372. More

Libin Ye, Alexander P. Orazietti, Aditya Pandey, Scott Prosser. High-efficiency expression of yeast-derived G protein-coupled receptor and 19F labeling for dynamical studies. Methods in Molecular Biology (Book chapter), 2018, 1688: 407-421. More

Taehun Kim, Pedram Mehrabi, Zhong Ren, Adnan Sljoka, Christopher Ing, Alexandr Bezginov, Libin Ye, Regis Pomes, R. Scott Prosser, Emil F Pai. The role of dimer asymmetry and subunit dynamics in enzyme catalysis. Science, 2017,355(6322): DOI: 10.1126/science.aag2355. More

Libin Ye, Ned Van Eps, Marco Zimmer, Oliver P. Ernst, R. Scott Prosser. Activation of A2A adenosine G protein-coupled receptor by conformational selection. Nature, 2016, 533: 265–268. More

Roberto Brea, Christian Cole, Brent Lyda, Libin Ye; Scott Prosser, Roger Sunahara, Neal Devaraj. In situ reconstitution of the adenosine A2A receptor in spontaneously formed synthetic liposomes. Journal of the American Chemical Society, 2017, 139(10): 3607-3610. More

Libin Ye, Suvrajit Maji, Piraveen Gopalasingam, Evgeniy Gorbunov, Sergey Tarasov, Oleg Epstein and Judith Klein-Seetharaman. Structure and dynamics of insulin receptor: implication for receptor activation and drug discovery. Drug Discovery Today, 2017, 22(7): 1092-1102. More

Libin Ye, Ned van Eps, Oliver P. Ernst, and Scott Prosser. Utilizing tagged paramagnetic shift reagents to monitor protein dynamics by NMR. BBA-Proteins and Proteomics, 2017, 1865 (11): 1555-1563. More

Scott Prosser, Libin Ye, Aditya Pandey, Alexander Oraietti. Activation processes in ligand-activated G protein-coupled receptors: A case study of the adenosine A2A receptor. Bioessays, 2017, DOI: 10.1002/bies.201700072. More

Libin Ye, Sacha T. Larda, Yi Feng Frank Li, Aashish Manglik, R. Scott Prosser. A comparison of chemistry shift sensitivity of trifluoromethyl tags: optimizing resolution in 19F NMR studies of proteins. Journal of Biomolecular NMR, 2015, 62(1): 97-103. More

Libin Ye*, Xiaolin Zheng, Hongjian Zheng. Effect of sypQ gene on poly-N-acetylglucose-amine biosynthesis in Vibrio parahaemolyticus and its role in infection process. Glycobiology, 2014, 24(4): 351-358. (*corresponding author)

Libin Ye, Xiaoyun Su, George Schmitz, Young Hwan Moon, Roderick I. Mackie, Isaac K. O. Cann. Molecular and biochemical analyses of the GH44 module from CbMan5B/Cel44A, a bifunctional enzyme from the hyperthermophilic bacterium Caldicellulosiruptor bescii. Applied and Environmental Microbiology, 2012：7048-7059.

Libin Ye*, Lu Xu, Jianrong Li. Preparation and anticoagulant activity of a fucosylated polysaccharide sulfate from a sea cucumber Acaudina molpadioidea. Carbohydrate Polymers, 2012, 87(3): 2052-2057. (*corresponding author)

Libin Ye*, Xiaolin Zheng, Jingsong Zhang*, Yingjie Pan. Immuno-regulatory activity and biochemical characterization of a proteoglycan complex, LZ-D-7, from Ganoderma lucidum fruiting bodies. Food Research International, 2011, 44(1): 367-372. (*corresponding author)

Libin Ye, Jingsong Zhang, Shuan Zhou, Sheng Wang, Di Wu, Yinjie Pan. Preparation of a sulfated protein-heteroglycan and inhibiting L1210 cell property. Carbohydrate Polymers, 2009, 77(2): 276-279.

Libin Ye, Jingsong Zhang, Yan Yang, Shuan Zhou, Yanfang Liu, Hui Chen, Yinjie Pan. Structural characterization of a heteropolysaccharide by NMR spectra. Food Chemistry, 2009, 112: 962-966.

Libin Ye, Jingsong Zhang, Kan Zhou, Yan Yang, Shuan Zhou, Wei Jia, Ruixia Hao, Yingjie Pan. Purification, NMR study and immuno-stimulating property of a galactofucan from the fruiting bodies of Ganoderma lucidum.Planta Medica，2008, 74: 1-5.

Libin Ye, Jingsong Zhang, XiJun Ye, Qinjiu Tang, Yanfang Liu, Chunyu Gong, Xiuju Du, Yingjie Pan. Structural elucidation of the polysaccharide moiety of a glycopeptide (GLPCW-II) from Ganoderma lucidum fruiting bodies. Carbohydrate Research, 2008, 343: 746-752.

Libin Ye, Jianrong Li, Jingsong Zhang, Yingjie Pan. NMR characterization for polysaccharide moiety of a glycopeptide. Fitoterapia. 2010, 81: 93-96.

Libin Ye, Jingsong Zhang, Yingjie Pan. Application of NMR techniques in structural analysis of polysaccharide from edible fungi. Acta Edulis Fungi, 2007, 14(4): 68-75.

Libin Ye, Xiaolin Zheng, Jingsong Zhang, Yan Yang, Yucheng Meng, Jianrong Li, Wei Chen, Yingjie Pan. Composition analysis and immunomodulatory capacity of peptidoglycan from Lingzhi or Reishi medicinal mushroom, Ganoderma lucidum (W. Curt.: Fr.) P. Karst. strain 119 (Aphyllophoromycetideae). Internal Journal of Medicinal Mushroom, 2010, 12(2): 157-165.

Christian Theilacker, Zhigniew Kaczyriski, Andrea Kropec, Irina Sava, Libin Ye, Anna Bychowska, Otto Holst, Johannes Huebner. Serodiversity of opsonic antibodies against Enterococcus faecalis-glycans of the cell wall revisited. PLoS One, 2011, 6(3): e17839.

Yan Yang, Libin Ye, Jingsong Zhang, Yanfang Liu, Qinjiu Tang, Wei Jia. Structural analysis of a bioactive polysaccharide, PISP1, from the medicinal mushroom, Phellinus igniarius. Bioscience, Biotechnology, and Biochemistry, 2009, 73(1): 134-139.

Xiuju Du, Jinsgon Zhang, Yan Yang, Libin Ye, Qinjiu Tang, Wei Jia, Yanfang Liu, Shuan Zhou, Ruixiang Hao, Chunyu Gong, Yingjie Pan. Structural elucidation and immuno-stimulating activity of an acidic heteropolysaccharide (TAPA1) from Tremella aurantialba. Carbohydrate Research, 2009, 344(5): 672-678.

Conformational equilibria as a function of mutants.jpg

With the guide of MD (in collaboration with William Goddard from Caltech) and 19F-qNMR, we created a series of conformation-biased mutants, including intermediate-state-trapped construct, allowing us to study the function of the intermediate state in the GPCR signaling efficacy and bias without cross-interferences from the other conformational states, such as the fully activated state. Conformation-biased mutants also allowed us to distinguish the previous overlapped conformers (Libin Ye, et al., Nature ,2016), advancing the 4-state GPCR activation model to 5-state, along with a gatekeeper "cation-pi" microswitch determined that modulates the receptor activation from inactive conformational ensemble to active(-like) ensemble. This structurally conserved microswitch is different from the previously determined ionic lock that mostly regulates the transition between two inactive states.

With the experience of more than a decade working on 19F NMR-GPCR, our lab summarize the progress of 19F NMR applications in GPCR conformational and dynamic studies during the past 20 years. Current challenges and limitations of 19F NMR for macromolecular dynamics also discussed along with experimental strategies that will drive the field forward.

We established an in-membrane NMR approach to study the native ligand-GPCR interactions that will be more genuinely report the interactions between the ligands and receptors, compared to the traditional NMR approaches that usually reconstitute the receptors into the detergent or HDL systems. This advance is important for finding the drug hits. In the meantime, this advance allows us to use NMR to perform a high throughput ligand (>1000 samples) screening on GPCRs with just 250 mL culture, which is impossible to conduct in the reconstituted systems in which 6L culture is only allowed to examine a few samples.

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Conformational dynamics and transitions of biologically active molecules are pivotal for understanding the physiological responses they elicit. In the case of receptor activation, there are major implications elucidating disease mechanisms and drug discovery innovation. Yet, incorporation of these factors into drug screening systems remains challenging in part due to the lack of suitable approaches to include them. Here, we present a novel strategy to probe the GPCR domain rotation by utilizing the 19Fluorine signal variability of a tri-fluorinated keto-enol (TFKE) chemical equilibrium. The method takes advantage of the high sensitivity of the TFKE tautomerism toward micro-environmental changes resulting from receptor conformational transitions upon ligand binding. We validate the method using the adenosine A2AR receptor as a model system with the TFKE was attached to two sites exhibiting opposing motions upon ligand binding, namely V229C6.31 on transmembrane domain VI (TM6) and A289C7.54 on TM7. Our results demonstrate that the TFKE switch is an excellent reporter for the domain rotation and can be used to study the conformational transition and dynamics of relative domain motions. Although further studies are needed in order to establish a quantitative relationship between the rotational angle and the population distribution of different components in a particular system.

Although structure-based virtual drug discovery is revolutionizing the conventional high-throughput cell-based screening system, its limitation is also obvious, together with other critical challenges. In particular, the resolved static snapshots fail to represent a full free-energy landscape due to homogenization in structural determination processing. The loss of conformational heterogeneity and related functional diversity emphasize the necessity of developing an approach that can fill this space. In this regard, NMR holds undeniable potential. However, outstanding questions regarding the NMR application remain. This review summarizes the limitations of current drug discovery and explores the potential of 19F NMR in establishing a conformation-guided drug screening system, advancing the cell- and structure-based discovery strategy for G protein-coupled receptor biased drug screening.