Biography:Yu-Shan Lin (chemist)

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Yu-Shan Lin
Yu-shan lin.jpg
Alma mater
  • National Taiwan University (B.S.)
  • University of Wisconsin, Madison (Ph.D.)
Awards
  • OpenEye Outstanding Junior Faculty Award in Computational Chemistry, American Chemical Society
  • Machine Learning in the Chemical Sciences & Engineering Award, Camille and Henry Dreyfus Foundation
Scientific career
FieldsComputational Chemistry
InstitutionsTufts University
Doctoral advisorJames L. Skinner
Other academic advisorsVijay S. Pande (postdoctoral)
Websitehttps://ase.tufts.edu/chemistry/lin/index.html

Yu-Shan Lin is an Associate Professor of Chemistry at Tufts University in the United States.[1] Her research lab uses computational chemistry to understand and design biomolecules, with topics focusing on cyclic peptides,[2][3] protein folding,[4][5] and collagen.[6][7] Lin received the American Chemical Society OpenEye Outstanding Junior Faculty Award in Computational Chemistry in 2015[8] and the Machine Learning in the Chemical Sciences & Engineering Award from the Camille and Henry Dreyfus Foundation in 2020.[9]

Education

Lin received her B.S. in Chemistry from National Taiwan University in 2004.[10] Lin received her Ph.D. in Chemistry in 2009 from University of Wisconsin, Madison, under the guidance of Professor James L. Skinner.[11] She then moved to Stanford, where she was a Bio-X postdoctoral fellow in the lab of Professor Vijay S. Pande.[12] In 2012, Lin joined the Department of Chemistry at Tufts University and received tenure in 2018.[10]

Research

Cyclic peptides

Lin and her lab use computational chemistry to provide information on the solution structures of cyclic peptides.[2] They recently successfully used molecular dynamics simulation with enhanced sampling methods to design well-structured cyclic peptides.[13][14]

Protein folding

Lin and her lab are interested in understanding how co- and post-translational modifications and non-natural amino acids impact protein folding.[15][16] They also work on understanding the effects of amino acid substitutions during evolution on protein stability, folding, and interaction.[17][18]

Collagen

Lin and her lab use molecular dynamics simulations to understand how the structure, stability, and interactions of collagen are perturbed by Gly to Ser substitutions, a very common type of Gly missense mutations in patients with Osteogenesis Imperfecta (OI),[19][20][21] and Ser phosphorylation.[22] Their results suggest a new possible mechanism underlying OI pathology, specifically that mutations may significantly disrupt the triple-helical structure of collagen and render it susceptible to non-collagenase proteolytic enzymes.[20]

Awards and honors

  • 2009–2011: Bio-X Postdoctoral Fellowship,[12] Stanford University
  • 2015: OpenEye Outstanding Junior Faculty Award in Computational Chemistry,[8] American Chemical Society
  • 2020: Machine Learning in the Chemical Sciences & Engineering Award,[9] Camille and Henry Dreyfus Foundation

References

  1. ↑ "Faculty | Department of Chemistry". http://chem.tufts.edu/people/faculty. 
  2. ↑ 2.0 2.1 Damjanovic, Jovan; Miao, Jiayuan; Huang, He; Lin, Yu-Shan (2021-02-24). "Elucidating Solution Structures of Cyclic Peptides Using Molecular Dynamics Simulations". Chemical Reviews 121 (4): 2292–2324. doi:10.1021/acs.chemrev.0c01087. ISSN 0009-2665. https://doi.org/10.1021/acs.chemrev.0c01087. 
  3. ↑ "c&en: Cross-Linking Technique Could Complement Peptide Stapling, April 29, 2013". https://cen.acs.org/articles/91/i17/Cross-Linking-Technique-Complement-Peptide.html. 
  4. ↑ Mong, Surin K.; Cochran, Frank V.; Yu, Hongtao; Graziano, Zachary; Lin, Yu-Shan; Cochran, Jennifer R.; Pentelute, Bradley L. (2017-10-31). "Heterochiral Knottin Protein: Folding and Solution Structure". Biochemistry 56 (43): 5720–5725. doi:10.1021/acs.biochem.7b00722. ISSN 0006-2960. PMID 28952732. PMC 5818992. https://doi.org/10.1021/acs.biochem.7b00722. 
  5. ↑ "Biochemists discover mechanism that helps flu viruses evolve" (in en). https://news.mit.edu/2017/biochemists-discover-mechanism-helps-flu-viruses-evolve-0926. 
  6. ↑ "Collagen interactions: Drug design and delivery" (in en). Advanced Drug Delivery Reviews 97: 69–84. 2016-02-01. doi:10.1016/j.addr.2015.11.013. ISSN 0169-409X. https://www.sciencedirect.com/science/article/abs/pii/S0169409X1500277X. 
  7. ↑ "Using synthetic peptides and recombinant collagen to understand DDR–collagen interactions" (in en). Biochimica et Biophysica Acta (BBA) - Molecular Cell Research 1866 (11): 118458. 2019-11-01. doi:10.1016/j.bbamcr.2019.03.005. ISSN 0167-4889. https://www.sciencedirect.com/science/article/pii/S016748891930028X. 
  8. ↑ 8.0 8.1 "OpenEye Outstanding Junior Faculty Award in Computational Chemistry" (in en-US). https://www.acscomp.org/awards/the-comp-acs-outstanding-junior-faculty-award. 
  9. ↑ 9.0 9.1 "Dreyfus Program for Machine Learning in the Chemical Sciences & Engineering Awards" (in en-US). 2020-07-27. https://www.dreyfus.org/dreyfus-program-for-machine-learning-in-the-chemical-sciences-engineering-2/. 
  10. ↑ 10.0 10.1 "Yu-Shan Lin | YSL at Tufts". https://ase.tufts.edu/chemistry/lin/pplYSL.html. 
  11. ↑ "Chemistry Tree - James L. Skinner Family Tree". https://academictree.org/chemistry/tree.php?pid=63222. 
  12. ↑ 12.0 12.1 University, © Stanford; Stanford; California 94305 (2014-03-07). "Yu-Shan Lin - Bio-X Postdoctoral Fellow" (in en). https://biox.stanford.edu/people/yu-shan-lin. 
  13. ↑ Slough, Diana P.; McHugh, Sean M.; Cummings, Ashleigh E.; Dai, Peng; Pentelute, Bradley L.; Kritzer, Joshua A.; Lin, Yu-Shan (2018-03-28). "Designing Well-Structured Cyclic Pentapeptides Based on Sequence–Structure Relationships". The Journal of Physical Chemistry B 122 (14): 3908–3919. doi:10.1021/acs.jpcb.8b01747. ISSN 1520-6106. PMID 29589926. PMC 6071411. https://pubs.acs.org/doi/full/10.1021/acs.jpcb.8b01747. 
  14. ↑ Cummings, Ashleigh E.; Miao, Jiayuan; Slough, Diana P.; McHugh, Sean M.; Kritzer, Joshua A.; Lin, Yu-Shan (2019-02-05). "β-Branched Amino Acids Stabilize Specific Conformations of Cyclic Hexapeptides" (in English). Biophysical Journal 116 (3): 433–444. doi:10.1016/j.bpj.2018.12.015. ISSN 0006-3495. PMID 30661666. https://www.cell.com/biophysj/abstract/S0006-3495(18)34529-6. 
  15. ↑ Rogers, Julia R.; McHugh, Sean M.; Lin, Yu-Shan (2017-09-27). "Predictions for α-Helical Glycopeptide Design from Structural Bioinformatics Analysis". Journal of Chemical Information and Modeling 57 (10): 2598–2611. doi:10.1021/acs.jcim.7b00123. ISSN 1549-9596. https://pubs.acs.org/doi/full/10.1021/acs.jcim.7b00123. 
  16. ↑ Simon, Mark D.; Maki, Yuta; Vinogradov, Alexander A.; Zhang, Chi; Yu, Hongtao; Lin, Yu-Shan; Kajihara, Yasuhiro; Pentelute, Bradley L. (2016-09-21). "d-Amino Acid Scan of Two Small Proteins". Journal of the American Chemical Society 138 (37): 12099–12111. doi:10.1021/jacs.6b03765. ISSN 0002-7863. https://doi.org/10.1021/jacs.6b03765. 
  17. ↑ Phillips, Angela M; Gonzalez, Luna O; Nekongo, Emmanuel E; Ponomarenko, Anna I; McHugh, Sean M; Butty, Vincent L; Levine, Stuart S; Lin, Yu-Shan et al. (2017-09-26). Palese, Peter. ed. "Host proteostasis modulates influenza evolution". eLife 6: e28652. doi:10.7554/eLife.28652. ISSN 2050-084X. https://doi.org/10.7554/eLife.28652. 
  18. ↑ Phillips, Angela M.; Ponomarenko, Anna I.; Chen, Kenny; Ashenberg, Orr; Miao, Jiayuan; McHugh, Sean M.; Butty, Vincent L.; Whittaker, Charles A. et al. (2018-09-17). "Destabilized adaptive influenza variants critical for innate immune system escape are potentiated by host chaperones" (in en). PLOS Biology 16 (9): e3000008. doi:10.1371/journal.pbio.3000008. ISSN 1545-7885. PMID 30222731. PMC 6160216. https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000008. 
  19. ↑ Yigit, Sezin; Yu, Hongtao; An, Bo; Hamaia, Samir; Farndale, Richard W.; Kaplan, David L.; Lin, Yu-Shan; Brodsky, Barbara (2016-09-02). "Mapping the Effect of Gly Mutations in Collagen on α2β1 Integrin Binding *" (in English). Journal of Biological Chemistry 291 (36): 19196–19207. doi:10.1074/jbc.M116.726182. ISSN 0021-9258. PMID 27432884. https://www.jbc.org/article/S0021-9258(20)31043-7/abstract. 
  20. ↑ 20.0 20.1 Chhum, Panharith; Yu, Hongtao; An, Bo; Doyon, Brian R.; Lin, Yu-Shan; Brodsky, Barbara (2016-12-01). "Consequences of Glycine Mutations in the Fibronectin-binding Sequence of Collagen *" (in English). Journal of Biological Chemistry 291 (53): 27073–27086. doi:10.1074/jbc.M116.753566. ISSN 0021-9258. PMID 27799304. https://www.jbc.org/article/S0021-9258(20)34381-7/abstract. 
  21. ↑ "Collagen Gly missense mutations: Effect of residue identity on collagen structure and integrin binding" (in en). Journal of Structural Biology 203 (3): 255–262. 2018-09-01. doi:10.1016/j.jsb.2018.05.003. ISSN 1047-8477. https://www.sciencedirect.com/science/article/abs/pii/S1047847718301187. 
  22. ↑ Qiu, Yimin; Poppleton, Erik; Mekkat, Arya; Yu, Hongtao; Banerjee, Sourav; Wiley, Sandra E.; Dixon, Jack E.; Kaplan, David L. et al. (2018-12-18). "Enzymatic Phosphorylation of Ser in a Type I Collagen Peptide" (in English). Biophysical Journal 115 (12): 2327–2335. doi:10.1016/j.bpj.2018.11.012. ISSN 0006-3495. PMID 30527445. https://www.cell.com/biophysj/abstract/S0006-3495(18)31258-X. 

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