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Libin  Ye

Libin Ye

Libin Ye
Assistant Professor

Contact

Office: ISA 6209
Phone: 813/974-6007
Lab: ISA 6014
Email:

Links

Education

  • Ph.D, Nanjing Agricultural University, Nanjing, China (2008)
  • Postdoctoral Fellow, University of Illinois at Urbana-Champaign, Urbana, USA, 2011-2012
  • Postdoctoral Fellow, University of Pittsburgh Medical Center, Pittsburgh, USA, 2012-2013
  • Postdoctoral Fellow, University of Toronto, Toronto, Canada, 2013-2018

Research

Research in the Ye lab mainly focuses on two directions. One is the study of the conformation, dynamics, and signal transduction of G protein-coupled receptors (GPCR) that are associated with neurodegenerative diseases and cancers. The other is to understand the mechanism of pathogenic biofilm biosynthesis in order to develop therapeutic agents against infectious bacteria, especially methicillin- and multidrug-resistant pathogens.

GPCR Conformation and Signaling: How to Design Drugs with Exclusive Therapeutic Effects?

Comprising more than 800 members, GPCR is the largest transmembrane protein family (O'Hayre, Vazquez-Prado et al. 2013; Lv, Liu et al. 2016). They serve as gatekeepers, controlling transduction for a variety of physiological and pathogenic signals, and are involved in almost every aspect of signaling in the human body. It is therefore easy to imagine that any GPCR signaling dysfunction probably leads to a disease such as cancer, cardiac failure, neurological disease, Parkinson’s, obesity, etc. (Rask-Andersen, Masuram et al. 2014). Although only 5% of GPCRs have been subjected to drug discovery, they are already targeted by nearly 40% of FDA-approved medications (Lundstrom 2016). Though structure-based drug discovery has revolutionized conventional cell-based drug discovery, resulting in several GPCR drugs already being advanced into clinical trials, the receptor activation process is dynamic, incorporating a course of continual conformational transitions that is impossible to capture in limited static structural snapshots. Furthermore, due to the intrinsic flexibility and plasticity of GPCRs, elucidation of their  structures often requires particular thermo-stabilization processing to facilitate crystallization, including replacement of intracellular domain III (IL3) with a thermo-stabilized T4 lysozyme or BRIL protein (Rosenbaum, Cherezov et al. 2007; Liu, Chun et al. 2012), thermo-stabilized mutagenesis (Lebon, Warne et al. 2011), nanobody-assisted thermo-stabilization (Manglik, Kobilka et al. 2017) or engineering the G protein (Carpenter and Tate 2017; Carpenter and Tate 2017; Nehme, Carpenter et al. 2017; Wan, Okashah et al. 2018). As a consequence of this processing, both structural heterogeneity and functional diversity of the receptor are diminished. NMR is a superb tool for investigating GPCR conformation, dynamics, and signaling without disrupting receptor integrity. It allows us to gain greater insight into receptor functionality through viewing the complete conformational energy landscape. Using NMR to study conformational transitions as functions of ligands could provide us with a potential avenue for biased drug discovery in line with ligands’ receptor conformational biases.

In our previous study, we were able to delineate the A2A adenosine receptor (A2AR) into four conformational states, including two inactive states and two active states (Ye, Van Eps et al. 2016), with the help of an optimized micro-electrostatically sensitive 19F NMR reporter (Ye, Larda et al. 2015). Conformational transition and allosteric modulation were also investigated at the dissected conformational state level (Ye, Neale et al. 2018). Following this line of research, we would like to further push the frontier of receptor conformational transition research and thereafter apply these approaches to neurodegeneration- and cancer-related GPCRs with the aim of developing specific therapies. The ultimate goal is to develop a strategy for designing biased drugs with exclusive therapeutic effects and fewer side-effects. 

Molecular Mechanism of Biofilm Biosynthesis: How to Battle Infectious Bacteria?

A biofilm is an assemblage of surface-associated microbial cells enclosed by an extracellular polymeric matrix (Visick, Schembri et al. 2016). 80% of microbial infections are known to be mediated through biofilms (Coenye and Bjarnsholt 2016), though which actual component of a biofilm is responsible for a specific pathogenic mechanism remains elusive (Yildiz and Visick 2009). Studies have revealed that biofilm formation depends on specific structural genes including those involved in biosynthesis of extracellular or capsular polysaccharides (Yildiz and Visick 2009). The syp locus includes four genes encoding putative regulators, six genes encoding glycosyltransferases, two encoding export proteins, and six other genes encoding unidentified functional proteins related to biofilm formation and symbiotic colonization (Shibata, Yip et al. 2012). However, the associated proteins have not been sufficiently characterized, leaving the functions of these genes less than fully understood. Previous work has further identified a specific class of polysaccharide, designated polysaccharide intercellular adhesion (PIA) (Vuong, Voyich et al. 2004), to be involved in the adhesion process. Research has indicated PIA could be a type of poly-N-acetylglucosamine (PNAG) (Izano, Sadovskaya et al. 2007), which is produced in accompaniment to biofilm formation in extensively pathogenic bacteria including Staphylococcus aureus, Escherichia coli, Bordetella pertussis, Bordetella parapertussis, Yersinia pestis, Aggregatibacter actinomycetemcomitans, and Staphylococcus epidermidis (Kaplan et al. 2004; Erickson et al. 2008; Hinnebusch and Erickson 2008; Itoh et al. 2008; Choi et al. 2009). Thus, it may be possible to develop a universal therapeutic strategy against this school of bacteria by targeting PNAG (Cerca et al. 2007). Studies have also shown that purified PNAG can elicit protective immunity against coagulase-negative staphylococci, suggesting its potential as a broadly protective vaccine for staphylococci (Maira-Litran et al. 2004). Immunization-induced polyclonal animal antisera and monoclonal antibodies specific to either capsular polysaccharide or PNAG antigens also have excellent in vitro opsonic killing activity in human blood (Skurnik et al. 2010). These results support that polysaccharide components are crucial to pathogenesis.
Building on these findings, the main objective of this research is to address the biosynthesis machinery of polysaccharides related to pathogenic biofilm formation, with an emphasis on biophysically characterizing transmembrane glycosyltransferases involved in polysaccharide synthesis. Ultimately, this work is anticipated to develop strategies to regulate pathogenic biofilm formation, including discovery of glycosyltransferase inhibitors and therapeutic antibodies that target these superficial polysaccharides and related proteins/enzymes as well.

Graduate Students

Wenjie Zhao

Recent Publications

  • 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, DOI: 10.1038/s41467-018-03314-9.
  • 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.
  • 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 
  • 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. (Faculty 1000 recommended)
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.