Yu-Shan Lin

Last updated

Yu-Shan Lin
Yu-shan lin.jpg
Alma mater
Scientific career
FieldsComputational Chemistry
Institutions Tufts University
Doctoral advisor James L. Skinner
Other 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]

Contents

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. [8] 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. [2] 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. [19]

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.
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