Yun Lyna Luo, PhD

Principal Investigator
Associate professor

Yun Lyna Luo, PhD

Principal Investigator
Associate professor
Lyna Luo is an associate professor in the College of Pharmacy at Western University. Her computational research laboratory develops and applies multiscale molecular dynamics and free-energy approaches to understand ion channel gating and ligand binding, and to conduct mechanism-driven and AI-assisted drug design. 

Education

- Postdoctoral Researcher, Argonne National Laboratory, US (2011-2013)
- Postdoctoral Researcher, University of Chicago, US (2008-2011)
- Ph.D., Ecole Normale Supérieure, University of Paris VI, France (2004-2007)
- B.S. and M.S., Zhejiang University, China (1997-2004)

Professional Services

Chair of Biophysical Society (BPS) Membrane Transport Subgroup (2024)
Chair of American Chemical Society (ACS) Division of Computers in Chemistry (COMP) Molecular Mechanics Symposium (since 2022)
Editorial Board Member:  Communications Biology -Nature (since 2022)
Guest Editor: Nature Communications & Communications Biology Joint Collection
Guest Editor: Journal of Computational Chemistry, "Membrane Protein Simulations and Free Energy Approaches" (2020)

Journal Reviewer of

Nature Communications;   Nature Computational Science;   PNAS;  Science Advances;  eLife;  Communication Biology;  Cell Reports; Biophysical Journal;  Journal of the American Chemical Society (JACS);  Journal of Chemical Theory and Computation (JCTC);  Journal of Chemical Information and Modeling (JCIM);  Journal of Physical Chemistry B (JPCB);  Journal of Chemical Physics (JCP),  Journal of Computational Chemistry (JCC);  Journal of Medicinal Chemistry (JMC); Journal of General Physiology (JGP);  PROTEINS: Structure, Function, and Bioinformatics; European Journal of Medicinal Chemistry;  Bioorganic & Medicinal Chemistry Letters; ACS Omega; Trends in Biochemical Sciences; BBA – Biomembrane;  Current Opinion in Structural Biology

 

Research Grants (active)

NIH R01 (MPI: Luo, Lacroix, WesternU)                                                                                  09/2019-08/2028
Pharmacological modulation of piezo1 channels  
NIH R01 (PI: Li, City of Hope, co-I: Luo, WesternU)                                                                09/2023-08/2028
Targeting protein arginine methyltransferase to eradicate acute myeloid leukemia   
NSF 23-548 (PI: Sosnick, UChicago, Luo, WesternU)                                                                07/2024-06/2027
Collaborative research: Sensory membrane protein dynamics studied using ultra-fast simulations
NIH R61-R33 (PI: Chung, Yale U, co-I: Luo WesternU)                                                            11/2023-10/2027
Targeting the sperm-specific calcium channel CatSper for contraception
NIH R01 (PI: Contreras, UC Davis, co-I: Luo, WesternU)                                                         04/2022-03/2027
Gating and regulation of connexin hemichannels
Tower Cancer Research Foundation (PI: Li, City of Hope, co-I: Luo, WesternU)                  01/2023-12/2027
A Novel Approach to Elicit Anti-tumor Immunity Against Acute Myeloid Leukemia
 

Publications

 

Editorials / White Paper

  1. The Need to Implement FAIR Principles in Biomolecular Simulations, Nature Methods 2024, arXiv:2407.16584
  2. Reliability and Reproducibility Checklist for Molecular Dynamics Simulations, Commun Biol 2023, 6,268
  3. Im, W., Banavali, N., Luo, Y*., Celebrating Benoit Roux's 60th Birthday: Quantifying Biology at the Membrane. J Comput Chem 2020, 41, 385-386

Software Update

  1. Hwang W.*, et. al., CHARMM at 45: Enhancements in accessibility, functionality, and speed, J. Phys. Chem. B., 2024, 10.1021/acs.jpcb.4c04100

Viewpoint

  1. Luo, Y.*, Mechanism-Based and Computational-Driven Covalent Drug Design. J. Chem. Inf. Model 2021, 61, 5307-5311

Book Chapters

  1. Delemotte, L* & Luo, Y.*, Molecular Dynamics. Handbook of Ion channels, 2nd Edition, 2023.
  2. Luo, Y.*, Lacroix, J.*, Ion Channels in Biophysics and Physiology: Methods & Challenges to Study Mechanosensitive Ion Channels. Adv Exp Med Biol 2021, 1349, 33-49.
  3. Botello-Smith, W., Luo, Y.*, Concepts, Practices, and Interactive Tutorial for Allosteric Network Analysis of Molecular Dynamics Simulations. Methods Mol Biol 2021, 2302, 311-334.
  4. Luo, Y.*, Lacroix, J., Prabhu, S., Antibody-Drug Conjugates: The 21st Century Magic Bullets for Cancer, Section V Case Studies, Chapter 12: Ado-Trastuzumab Emtansine, Springer, 2015.

Peer-reviewed research articles (corresponding *, key articles in bold)

  1. Lin Y., Lacroix J., Sterling J., Luo Y.,*, Dissecting current rectification through asymmetric nanopores, Biophys. J., bioRxiv 2024.11.14.623680
  2. Wijerathne T., Bhatt A., Jiang W., Luo Y.*, Lacroix J.*, Mammalian PIEZO channels rectify anionic currents, Biophys. J., bioRxiv 2024.08. 23.609388
  3. Kumar D., Harris A.*, Luo Y.*, Molecular permeation through large pore channels: computational approaches and insights, J. Physiology, 2024.
  4. Edmond M., et. al., Luo Y., Barro-Soria R.*, Lipophilic compounds restore function of neurodevelopmental-associated KCNQ3 mutations, Commun. Biol. 2024.
  5. Gaete P., et. al., Luo Y., Contreras J.*, Large-pore connexin hemichannels function like molecule transporters independent of ion conduction, PNAS, 2024, 121 (33) e2403903121
  6. Wen C., Luo, Y.*, Madsen, J.*, Optimizing coarse-grained models for large-scale membrane protein simulations, bioRxiv doi.org/10.1101/2024.05.13.594009, 2024
  7. Li S.*, Wu B., Luo Y., Han W.*, Simulation of functional motion of super large biomolecules with a mixed-resolution model, J. Chem. Theory Comput., 2024
  8. Dong H., et. al., Luo Y., Ling L.*, Targeting PRMT9 mediated arginine methylation suppresses cancer stem cell maintenance and elicits cGAS-mediated anti-cancer immunity, Nature Cancer, 2024
  9. Baudry M., Wang Y., Bi X., Luo Y., et al., Identification and neuroprotective properties of NA-184, a calpain-2 inhibitor, Pharmacology Research & Perspectives, 2024
  10. Jiang W., Wijerathne, T., Zhang H., Lin Y., Jo S., Im W., Lacroix J., Luo Y.*, Structural and thermodynamic framework for PIEZO1 modulation by small molecules, PNAS, 120, e2310933120, 2023
  11. Baudry M., Luo Y., Bi X., Calpain-2 inhibitors as therapy for traumatic brain injury, Neurotherapeutics, 20, 1592-1602, 2023
  12. Jiang W.*, Lacroix J, Luo Y.*, Importance of molecular dynamics equilibrium protocol on protein-lipid interaction near channel pore, Biophysical Reports, 2, 100080, 2022
  13. Lin Y., Luo Y.*, Unifying Single-channel permeability from rare-event sampling and steady-state flux, Frontiers in Molecular Biosciences: Biological Modeling and Simulation, 2022
  14. Jiang W., et. al., Lacroix J.*, Rohacs T.*, Luo Y.*, Crowding-induced opening of the mechanosensitive Piezo1 channel in silico. Commun. Biol. 4, 84, 2021
  15. Jiang, W., Ling, Y., Luo, Y.*, Mechanical properties of anionic asymmetric bilayers from atomistic simulations, J. Chem. Phys., 2021
  16. Jiang, W., Lin, Y., Botello-Smith, W., Contreras, J.*, Harris, A.*, Maragliano, L.*, Luo, Y.*, Free energy and kinetics of cAMP permeation through connexin26 hemichannel via applied voltage and milestoning, Biophys. J., 2021
  17. Sterling J.*, Jiang W., Botello-Smith, W., Luo Y.*, Ion pairing and dielectric decrement in glycosaminoglycan brushes, J. Phys. Chem. B., 2021
  18. Botello-Smith, W, Luo, Y.*, Investigating protein-protein allosteric network using current-flow scheme, J. Comput. Chem, 2020, 41, 552-560
  19. Gaete PS, Lillo MA, López W, Liu Y, Jiang W, Luo Y, Harris AL, Contreras JE., A novel voltage-clamp/dye uptake assay reveals saturable transport of molecules through CALHM1 and connexin channels, J Gen Physiol. 2020, 2;152(11):e202012607.
  20. Anderson S., et. al., Luo Y.*, Botello-Smith W.*, Andresen B.*, In silico prediction of ARB resistance: A first step in creating personalized ARB therapy. PLOS Comput. Biol., 2020.
  21. Xie C., Jiang W., Lacroix J., Luo Y.*, Hao J*, Insight into Molecular Mechanism for Activin A-Induced Bone Morphogenetic Protein Signaling. Int. J. Mol. Sci. 2020, 21, 6498.
  22. Sun J, et. al., Luo Y, Baudry M, Bi X.*, PKA and Ube3a regulate SK2 channel trafficking to promote synaptic plasticity in hippocampus: Implications for Angelman Syndrome, Sci. Rep. 2020, 10, 9824.
  23. Botello-Smith W, Zhang H, Ozkan AD, Jiang W, Pham CN, Lacroix J* and Luo Y*, A molecular Mechanism for the Chemical Activation of the Mechanosensitive Piezo1 Channel, Nat. Commun., DOI: 10.1038/s41467-019-12501-1.
  24. Zhu Y, et. al., Luo Y, Li L.*, Targeting PRMT1-mediated FLT3 methylation disrupts maintenance of MLL-rearranged acute lymphoblastic leukemia, Blood, DOI: 10.1182/blood.2019002457.
  25. Botello-Smith W., Luo,Y.*, Robust determination of protein allosteric signaling pathways, J. Chem. Theory Comput., 2019, 15, 2116-2126.
  26. Capuccino J., et. al., Luo Y.*, Contreras J.*, The connexin26 human mutation N14K disrupts cytosolic intersubunit interactions and promotes channel opening, J. Gen. Physiol., 2019, 151, 382-341.
  27. Zhang H., Jiang W., Chatterjee P., Luo Y.*, Ranking reversible covalent drugs: from free energy perturbation to fragment docking, J. Chem. Inf. Model, 2019, 59, 2093-2102.
  28. He X, et. al., Luo Y, Li L.*, PRMT1-mediated FLT3 arginine methylation promotes maintenance of FLT3-ITD+ acute myeloid leukemia, Blood, 2019, 134, 548-560.
  29. Lacroix J.*, Botello-Smith W., Luo Y., Probing the gating mechanism of the mechanosensitive channel Piezo1 with the small molecule Yoda1, Nat. Commun., 2018, 9, 2029.
  30. Fei Q., et. al., Lambros M.*, Luo Y.*, Molecular mechanism of resveratrol’s lipid membrane protection, Sci. Rep., 2018, 8, 1587.
  31. Abrams C.*, et. al, Luo Y., Alterations at Arg76 of human connexin 46, a residue associated with cataract formation, cause loss of gap junction formation but preserve hemichannel function. Am. J. Physiol. Cell Physiol. 2018, 315, 623-635.
  32. Chatterjee, P.*, Yadav, M., Chauhan, N., Huang, Y., Luo, Y., Cancer cell metabolism featuring Nrf2. Curr. Drug Discov. Technol. 2018, doi: 10.2174/1570163815666180911092443.
  33. Liu M., et. al., Luo Y., Huang Y.*, Effects of bioactive constituents in the Traditional Chinese Medicinal formula Si-Wu-Tang on Nrf2 signaling and neoplastic cellular transformation, Phytomedicine, 2018, 40, 1-9.
  34. Chatterjee P., Botello-Smith W., et. al., Luo Y.*, Can relative binding free energy predict selectivity of reversible covalent inhibitors? J. Am. Chem. Soc. 2017, 139, 17945-17952.
  35. Botello-Smith W., et. al., Hao J.*, Luo Y.*, Polymodal allosteric regulation of type 1 serine/threonine kinase receptors via a conserved electrostatic lock, PLOS Comput. Biol., 2017, 13, e1005711.
  36. Luo Y.*, Rossi A., Harris A., Computational Studies of Molecular Permeation through Connexin26 Channels, Biophys. J., 2016, 110, 584-599. 
  37. Lopez W., Ramachandran J., Alsamarah A., Luo L., Harris A., Contreras J.*, Mechanism of gating by calcium in connexin hemichannels, Proc. Natl. Acad. Sci. U S A, 2016, 113, E7986-E7995.
  38. Luo Y.*, Alsamarah A., Zhang K., Hao J.*, Development of New Therapeutic Agents for Fibrodysplasia Ossificans Progressiva. Curr Mol Med., 2016, 16, 4-11.
  39. Alsamarah A., LaCuran A., Oelschlaeger P., Hao J., Luo Y.*, Uncovering molecular bases underlying bone morphogenetic protein receptor inhibitor selectivity. PLOS ONE, 2015, 10, e0132221.
  40. Sun J., et. al., Luo Y., Baudry M., Bi X.*, UBE3A regulates synaptic plasticity and learning and memory by controlling SK2 channel endocytosis. Cell Rep., 2015, 12, 359-360.

Work Before WesternU

  1. Jiang W., Phillips J., et. al., Luo Y., Schulten K.*, Roux B.*, Generalized scalable multiple copy algorithms for molecular dynamics simulations in NAMD. Comput. Phys. Commun., 2014, 185 (3), 908-916.
  2. Venable R., Luo Y., Gawrisch K., Roux B., Pastor R.*, Simulations of Anionic Lipid Membranes: Development of Interaction-Specific Ion Parameters and Validation Using NMR Data. J. Phys. Chem. B. 2013 117 (35), 10183-10192.
  3. Lopes P., Huang J., Shim J, Luo Y., Li H., Roux B.*, MacKerell A.*, Polarizable Force field for peptides and protein based the Classical Drude Oscillator. J. Chem. Theory Comput., 2013 9 (12), 5430-5449.
  4. Y. Luo, W. Jiang, H. Yu, A. D. MacKerell, Jr., and B. Roux*, Calibrating the potential function for accurate ion pairing in molecular dynamics simulations of concentration electrolytes solutions. Faraday Discussions, 2013, 160, 135-149.
  5. Jiang J., Luo L. (co-1st), Maragliano L., Roux B.*, Calculation of Free Energy Landscape in Multi-Dimensions with Hamiltonian-Exchange Umbrella Sampling on Petascale Supercomputer. J. Chem. Theory Comput., 2012, 8 (11), 4672-4680.
  6. Luo Y., Harder E., Faibish R., Roux B.*, Computer simulations of water flux and salt permeability of the reverse osmosis FT-30 aromatic polyamide membrane. J. Mem. Sci. 2011, 384 (1-2), 1-9.
  7. Herrou J., Rotskoff G., Luo Y., Roux B., Crosson S.*, The structural basis of a protein partner switch that regulates stress-dependent transcription. Proc. Natl. Acad. Sci. U S A, 2012, 109 (21): E1415-23.
  8. Luo Y., and Roux B.*, Simulation of osmotic pressure in concentrated aqueous salt solutions. J. Phys. Chem. Lett. 2010, 1 (1), 183–189
  9. Luo Y., Egwolf B., Walters D., Roux B.*, Ion selectivity of alpha-hemolysin with beta-cyclodextrin adapter: I. Single ion potential of mean force calculations and diffusion coefficient. J. Phys. Chem. B, 2010, 114 (2), 952–958
  10. Egwolf B., Luo Y., Walters D., Roux B., Ion selectivity of alpha-hemolysin with beta-cyclodextrin adapter:II. Multi ion effects studies with grand canonical monte carlo/brownian dynamics simulations. J. Phys. Chem. B, 2010, 114 (8), 2901–2909
  11. Luo Y., et. al., Fan B.*, Cellular interaction through LewisX cluster: theoretical studies. J. Mol. Model, 2008, 14, 901-910.
  12. Luo Y., et. al., Zhang Y.*, First synthesis of two deoxy Lewisx pentaosyl glycosphingolipids. Glycoconjugate J., 2008, 25, 335-344.
  13. Barbault F., et. al. Fan B.*, Flexible computational docking studies of new aminoglycosides targeting RNA 16S bacterial ribosome site. Eur. J. Med. Chem. 2008, 43, 1648-56.
  14. Luo Y., et. al., Zhang Y.*, Total synthesis of 4d-deoxy Lewisx pentasaccharide. Comptes Rendus Chimie, 2008, 11, 29-37.
  15. Gourmala C, Luo Y., et. al, Fan B.*, Elucidation of the LewisX-LewisX carbohydrate interaction with molecular dynamics simulations. J. Mol. Struct.: THEOCHEM, 2007, 821, 22-29.