Yu-Shan Lin Explained

Yu-Shan Lin
Fields:Computational Chemistry
Workplaces:Tufts University
Alma Mater:
Doctoral Advisor:James L. Skinner
Academic Advisors:Vijay S. Pande (postdoctoral)
Website:https://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.[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]

Education

Lin received her BS in chemistry from National Taiwan University in 2004.[8] Lin received her PhD in chemistry in 2009 from University of Wisconsin, Madison, under the guidance of James L. Skinner.[9] She then moved to Stanford, where she was a Bio-X postdoctoral fellow in the lab of Vijay S. Pande.[10] 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.[11]

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.[12] [13]

Protein folding

Lin and her lab are interested in understanding how co- and post-translational modifications and non-natural amino acids impact protein folding.[14] [15] They also work on understanding the effects of amino acid substitutions during evolution on protein stability, folding, and interaction.[16] [17]

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),[18] [19] [20] and Ser phosphorylation.[21] 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

Notes and References

  1. Web site: Faculty Department of Chemistry. 2021-07-13. chem.tufts.edu.
  2. 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. 10.1021/acs.chemrev.0c01087 . 8340081 . 33426882. 0009-2665.
  3. Web site: 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. Jennifer Cochran. Cochran. Jennifer R.. Pentelute. Bradley L.. 2017-10-31. Heterochiral Knottin Protein: Folding and Solution Structure. Biochemistry. 56. 43. 5720–5725. 10.1021/acs.biochem.7b00722. 0006-2960. 5818992. 28952732.
  5. Web site: Biochemists discover mechanism that helps flu viruses evolve. 2021-07-13. MIT News Massachusetts Institute of Technology. en.
  6. 2016-02-01. Collagen interactions: Drug design and delivery. Advanced Drug Delivery Reviews. en. 97. 69–84. 10.1016/j.addr.2015.11.013. 0169-409X. An. Bo. Lin. Yu-Shan. Brodsky. Barbara. 26631222.
  7. 2019-11-01. Using synthetic peptides and recombinant collagen to understand DDR–collagen interactions. Biochimica et Biophysica Acta (BBA) - Molecular Cell Research. en. 1866. 11. 118458. 10.1016/j.bbamcr.2019.03.005. 0167-4889. Chen. Eric A.. Lin. Yu-Shan. 30880148. free.
  8. Web site: Yu-Shan Lin YSL at Tufts. 2021-07-13. ase.tufts.edu.
  9. Web site: Chemistry Tree - James L. Skinner Family Tree. 2021-07-13. academictree.org.
  10. Web site: University. © Stanford. Stanford. California 94305. 2014-03-07. Yu-Shan Lin - Bio-X Postdoctoral Fellow. 2021-07-11. Welcome to Bio-X. en.
  11. Web site: Yu-Shan Lin Faculty Profile . 2024-08-02 . facultyprofiles.tufts.edu.
  12. 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. 10.1021/acs.jpcb.8b01747. 1520-6106. 6071411. 29589926.
  13. 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. Biophysical Journal. English. 116. 3. 433–444. 10.1016/j.bpj.2018.12.015. 0006-3495. 30661666. 6369414. 2019BpJ...116..433C.
  14. 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. 10.1021/acs.jcim.7b00123. 28953376. 1549-9596.
  15. 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. 10.1021/jacs.6b03765. 27494078. 0002-7863.
  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. 2017-09-26. Palese. Peter. Host proteostasis modulates influenza evolution. eLife. 6. e28652. 10.7554/eLife.28652. 28949290. 5614556. 2050-084X . free .
  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. 2018-09-17. Destabilized adaptive influenza variants critical for innate immune system escape are potentiated by host chaperones. PLOS Biology. en. 16. 9. e3000008. 10.1371/journal.pbio.3000008. 1545-7885. 6160216. 30222731 . free .
  18. 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 *. Journal of Biological Chemistry. English. 291. 36. 19196–19207. 10.1074/jbc.M116.726182. 0021-9258. 27432884. 5009287. free .
  19. 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 *. Journal of Biological Chemistry. English. 291. 53. 27073–27086. 10.1074/jbc.M116.753566. 0021-9258. 27799304. 5207138. free .
  20. 2018-09-01. Collagen Gly missense mutations: Effect of residue identity on collagen structure and integrin binding. Journal of Structural Biology. en. 203. 3. 255–262. 10.1016/j.jsb.2018.05.003. 1047-8477. Qiu. Yimin. Mekkat. Arya. Yu. Hongtao. Yigit. Sezin. Hamaia. Samir. Farndale. Richard W.. David L. Kaplan (engineer). Kaplan. David L.. Lin. Yu-Shan. Brodsky. Barbara. 29758270. 6089640.
  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. 2018-12-18. Enzymatic Phosphorylation of Ser in a Type I Collagen Peptide. Biophysical Journal. English. 115. 12. 2327–2335. 10.1016/j.bpj.2018.11.012. 0006-3495. 30527445. 6302033. 2018BpJ...115.2327Q.
  22. Web site: Moderator . 2020-07-27 . Dreyfus Program for Machine Learning in the Chemical Sciences & Engineering Awards . 2023-08-15 . Dreyfus Foundation . en-US.
  23. Web site: OpenEye Outstanding Junior Faculty Award in Computational Chemistry. 2021-07-11. www.acscomp.org. en-US.

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