Yu-Shan Lin

Yu-Shan Lin
Education
Scientific career
FieldsComputational Chemistry
WorkplacesTufts University
James L. Skinner
Other academic advisors
Vijay S. Pande (postdoctoral)
Websitehttps://ase.tufts.edu/chemistry/lin/index.html

Yu-Shan Lin is a computational chemist. She is a professor and chair of the Department of Chemistry at Tufts University in the United States. Her research lab uses computational chemistry to understand and design biomolecules, with topics focusing on cyclic peptides, protein folding, and collagen.

Education

Lin received her BS in chemistry from National Taiwan University in 2004. Lin received her PhD in chemistry in 2009 from University of Wisconsin, Madison, under the guidance of James L. Skinner. She then moved to Stanford, where she was a Bio-X postdoctoral fellow in the lab of Vijay S. Pande. In 2012, Lin joined the Department of Chemistry at Tufts University and received tenure in 2018. In 2024, Lin was appointed to a full professorship and became chair of the department.

Research

Cyclic peptides

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

Protein folding

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

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), and Ser phosphorylation. 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.

Awards and honors

References

  1. ↑ "Faculty | Department of Chemistry". chem.tufts.edu. Retrieved July 13, 2021.
  2. 1 2 Damjanovic, Jovan; Miao, Jiayuan; Huang, He; Lin, Yu-Shan (February 24, 2021). "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. PMC 8340081. PMID 33426882.
  3. ↑ "c&en: Cross-Linking Technique Could Complement Peptide Stapling, April 29, 2013".
  4. ↑ Mong, Surin K.; Cochran, Frank V.; Yu, Hongtao; Graziano, Zachary; Lin, Yu-Shan; Cochran, Jennifer R.; Pentelute, Bradley L. (October 31, 2017). "Heterochiral Knottin Protein: Folding and Solution Structure". Biochemistry. 56 (43): 5720–5725. doi:10.1021/acs.biochem.7b00722. ISSN 0006-2960. PMC 5818992. PMID 28952732.
  5. ↑ "Biochemists discover mechanism that helps flu viruses evolve". MIT News | Massachusetts Institute of Technology. September 26, 2017. Retrieved July 13, 2021.
  6. ↑ An, Bo; Lin, Yu-Shan; Brodsky, Barbara (February 1, 2016). "Collagen interactions: Drug design and delivery". Advanced Drug Delivery Reviews. 97: 69–84. doi:10.1016/j.addr.2015.11.013. ISSN 0169-409X. PMID 26631222.
  7. ↑ Chen, Eric A.; Lin, Yu-Shan (November 1, 2019). "Using synthetic peptides and recombinant collagen to understand DDR–collagen interactions". Biochimica et Biophysica Acta (BBA) - Molecular Cell Research. 1866 (11): 118458. doi:10.1016/j.bbamcr.2019.03.005. ISSN 0167-4889. PMID 30880148.
  8. 1 2 "Yu-Shan Lin | YSL at Tufts". ase.tufts.edu. Retrieved July 13, 2021.
  9. ↑ "Chemistry Tree - James L. Skinner Family Tree". academictree.org. Retrieved July 13, 2021.
  10. ↑ University, © Stanford; Stanford; California 94305 (March 7, 2014). "Yu-Shan Lin - Bio-X Postdoctoral Fellow". Welcome to Bio-X. Retrieved July 11, 2021.{{cite web}}: CS1 maint: numeric names: authors list (link)
  11. ↑ "Yu-Shan Lin | Faculty Profile". facultyprofiles.tufts.edu. Retrieved August 2, 2024.
  12. ↑ Slough, Diana P.; McHugh, Sean M.; Cummings, Ashleigh E.; Dai, Peng; Pentelute, Bradley L.; Kritzer, Joshua A.; Lin, Yu-Shan (March 28, 2018). "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. PMC 6071411. PMID 29589926.
  13. ↑ Cummings, Ashleigh E.; Miao, Jiayuan; Slough, Diana P.; McHugh, Sean M.; Kritzer, Joshua A.; Lin, Yu-Shan (February 5, 2019). "β-Branched Amino Acids Stabilize Specific Conformations of Cyclic Hexapeptides". Biophysical Journal. 116 (3): 433–444. Bibcode:2019BpJ...116..433C. doi:10.1016/j.bpj.2018.12.015. ISSN 0006-3495. PMC 6369414. PMID 30661666.
  14. ↑ Rogers, Julia R.; McHugh, Sean M.; Lin, Yu-Shan (September 27, 2017). "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. PMID 28953376.
  15. ↑ Simon, Mark D.; Maki, Yuta; Vinogradov, Alexander A.; Zhang, Chi; Yu, Hongtao; Lin, Yu-Shan; Kajihara, Yasuhiro; Pentelute, Bradley L. (September 21, 2016). "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. PMID 27494078.
  16. ↑ Phillips, Angela M; Gonzalez, Luna O; Nekongo, Emmanuel E; Ponomarenko, Anna I; McHugh, Sean M; Butty, Vincent L; Levine, Stuart S; Lin, Yu-Shan; Mirny, Leonid A; Shoulders, Matthew D (September 26, 2017). Palese, Peter (ed.). "Host proteostasis modulates influenza evolution". eLife. 6 e28652. doi:10.7554/eLife.28652. ISSN 2050-084X. PMC 5614556. PMID 28949290.
  17. ↑ Phillips, Angela M.; Ponomarenko, Anna I.; Chen, Kenny; Ashenberg, Orr; Miao, Jiayuan; McHugh, Sean M.; Butty, Vincent L.; Whittaker, Charles A.; Moore, Christopher L.; Bloom, Jesse D.; Lin, Yu-Shan (September 17, 2018). "Destabilized adaptive influenza variants critical for innate immune system escape are potentiated by host chaperones". PLOS Biology. 16 (9) e3000008. doi:10.1371/journal.pbio.3000008. ISSN 1545-7885. PMC 6160216. PMID 30222731.
  18. ↑ Yigit, Sezin; Yu, Hongtao; An, Bo; Hamaia, Samir; Farndale, Richard W.; Kaplan, David L.; Lin, Yu-Shan; Brodsky, Barbara (September 2, 2016). "Mapping the Effect of Gly Mutations in Collagen on α2β1 Integrin Binding *". Journal of Biological Chemistry. 291 (36): 19196–19207. doi:10.1074/jbc.M116.726182. ISSN 0021-9258. PMC 5009287. PMID 27432884.
  19. 1 2 Chhum, Panharith; Yu, Hongtao; An, Bo; Doyon, Brian R.; Lin, Yu-Shan; Brodsky, Barbara (December 1, 2016). "Consequences of Glycine Mutations in the Fibronectin-binding Sequence of Collagen *". Journal of Biological Chemistry. 291 (53): 27073–27086. doi:10.1074/jbc.M116.753566. ISSN 0021-9258. PMC 5207138. PMID 27799304.
  20. ↑ Qiu, Yimin; Mekkat, Arya; Yu, Hongtao; Yigit, Sezin; Hamaia, Samir; Farndale, Richard W.; Kaplan, David L.; Lin, Yu-Shan; Brodsky, Barbara (September 1, 2018). "Collagen Gly missense mutations: Effect of residue identity on collagen structure and integrin binding". Journal of Structural Biology. 203 (3): 255–262. doi:10.1016/j.jsb.2018.05.003. ISSN 1047-8477. PMC 6089640. PMID 29758270.
  21. ↑ Qiu, Yimin; Poppleton, Erik; Mekkat, Arya; Yu, Hongtao; Banerjee, Sourav; Wiley, Sandra E.; Dixon, Jack E.; Kaplan, David L.; Lin, Yu-Shan; Brodsky, Barbara (December 18, 2018). "Enzymatic Phosphorylation of Ser in a Type I Collagen Peptide". Biophysical Journal. 115 (12): 2327–2335. Bibcode:2018BpJ...115.2327Q. doi:10.1016/j.bpj.2018.11.012. ISSN 0006-3495. PMC 6302033. PMID 30527445.
  22. ↑ Moderator (July 27, 2020). "Dreyfus Program for Machine Learning in the Chemical Sciences & Engineering Awards". Dreyfus Foundation. Retrieved August 15, 2023.
  23. ↑ "OpenEye Outstanding Junior Faculty Award in Computational Chemistry". www.acscomp.org. Retrieved July 11, 2021.