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Yu-Shan Lin

January 01, 1970

This article is about the chemist. For the visual artist, see Lin Yushan.

Yu-Shan Lin is a computational chemist. She 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]

Yu-Shan Lin
Alma mater
Scientific career
FieldsComputational Chemistry
InstitutionsTufts University
Doctoral advisorJames L. Skinner
Other academic advisorsVijay S. Pande (postdoctoral)
Websitehttps://ase.tufts.edu/chemistry/lin/index.html

Education edit

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]

Research edit

Cyclic peptides edit

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.[11][12]

Protein folding edit

Lin and her lab are interested in understanding how co- and post-translational modifications and non-natural amino acids impact protein folding.[13][14] They also work on understanding the effects of amino acid substitutions during evolution on protein stability, folding, and interaction.[15][16]

Collagen edit

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),[17][18][19] and Ser phosphorylation.[20] 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.[18]

Awards and honors edit

  • Machine Learning in the Chemical Sciences & Engineering Award, Camille and Henry Dreyfus Foundation, 2020[21]
  • 2015: OpenEye Outstanding Junior Faculty Award in Computational Chemistry,[22] American Chemical Society

References edit

  1. ^ "Faculty | Department of Chemistry". chem.tufts.edu. Retrieved July 13, 2021.
  2. ^ a b 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. 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. ^ a b "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. ^ 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.
  12. ^ 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.
  13. ^ 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.
  14. ^ 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.
  15. ^ 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.
  16. ^ 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.
  17. ^ 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.
  18. ^ a b 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.
  19. ^ 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.
  20. ^ 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.
  21. ^ Moderator (July 27, 2020). "Dreyfus Program for Machine Learning in the Chemical Sciences & Engineering Awards". Dreyfus Foundation. Retrieved August 15, 2023.
  22. ^ "OpenEye Outstanding Junior Faculty Award in Computational Chemistry". www.acscomp.org. Retrieved July 11, 2021.

External links edit

January 01, 1970
shan, this, article, about, chemist, visual, artist, yushan, computational, chemist, associate, professor, chemistry, tufts, university, united, states, research, uses, computational, chemistry, understand, design, biomolecules, with, topics, focusing, cyclic,. This article is about the chemist For the visual artist see Lin Yushan Yu Shan Lin is a computational chemist She 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 Yu Shan LinAlma materNational Taiwan University BS University of Wisconsin Madison PhD Scientific careerFieldsComputational ChemistryInstitutionsTufts UniversityDoctoral advisorJames L SkinnerOther academic advisorsVijay S Pande postdoctoral Websitehttps ase tufts edu chemistry lin index html Contents 1 Education 2 Research 2 1 Cyclic peptides 2 2 Protein folding 2 3 Collagen 3 Awards and honors 4 References 5 External linksEducation editLin 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 Research editThis biography of a living person relies too much on references to primary sources Please help by adding secondary or tertiary sources Contentious material about living persons that is unsourced or poorly sourced must be removed immediately especially if potentially libelous or harmful Find sources Yu Shan Lin news newspapers books scholar JSTOR July 2021 Learn how and when to remove this message Cyclic peptides edit 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 11 12 Protein folding edit Lin and her lab are interested in understanding how co and post translational modifications and non natural amino acids impact protein folding 13 14 They also work on understanding the effects of amino acid substitutions during evolution on protein stability folding and interaction 15 16 Collagen edit 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 17 18 19 and Ser phosphorylation 20 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 18 Awards and honors editMachine Learning in the Chemical Sciences amp Engineering Award Camille and Henry Dreyfus Foundation 2020 21 2015 OpenEye Outstanding Junior Faculty Award in Computational Chemistry 22 American Chemical SocietyReferences edit Faculty Department of Chemistry chem tufts edu Retrieved July 13 2021 a b 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 c amp en Cross Linking Technique Could Complement Peptide Stapling April 29 2013 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 Biochemists discover mechanism that helps flu viruses evolve MIT News Massachusetts Institute of Technology Retrieved July 13 2021 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 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 a b Yu Shan Lin YSL at Tufts ase tufts edu Retrieved July 13 2021 Chemistry Tree James L Skinner Family Tree academictree org Retrieved July 13 2021 University c Stanford Stanford California 94305 March 7 2014 Yu Shan Lin Bio X Postdoctoral Fellow Welcome to Bio X Retrieved July 11 2021 a href Template Cite web html title Template Cite web cite web a CS1 maint numeric names authors list link 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 Cummings Ashleigh E Miao Jiayuan Slough Diana P McHugh Sean M Kritzer Joshua A Lin Yu Shan February 5 2019 b 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 Rogers Julia R McHugh Sean M Lin Yu Shan September 27 2017 Predictions for a 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 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 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 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 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 a2b1 Integrin Binding Journal of Biological Chemistry 291 36 19196 19207 doi 10 1074 jbc M116 726182 ISSN 0021 9258 PMC 5009287 PMID 27432884 a b 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 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 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 Moderator July 27 2020 Dreyfus Program for Machine Learning in the Chemical Sciences amp Engineering Awards Dreyfus Foundation Retrieved August 15 2023 OpenEye Outstanding Junior Faculty Award in Computational Chemistry www acscomp org Retrieved July 11 2021 External links editOfficial website Yu Shan Lin publications indexed by Google Scholar Retrieved from https en wikipedia org w index php title Yu Shan Lin amp oldid 1180198977, wikipedia, wiki, book, books, library,

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