Yu-Shan Lin | |
|---|---|
 | |
| Alma mater | |
| Scientific career | |
| Fields | Computational 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 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]
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]
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. [11] [12]
Protein folding
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
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
- 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
- ^ "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&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, © 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) - ^ 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). "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.
- ^ 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.
- ^ 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 α2β1 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 & 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
- Official website
- Yu-Shan Lin publications indexed by Google Scholar
| Authority control databases: Academics |
|---|
Yu-Shan Lin | |
|---|---|
|
| |
| Alma mater | |
| Scientific career | |
| Fields | Computational 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 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]
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]
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. [11] [12]
Protein folding
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
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
- 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
- ^ "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&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, © 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) - ^ 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). "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.
- ^ 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.
- ^ 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 α2β1 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 & 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
- Official website
- Yu-Shan Lin publications indexed by Google Scholar
| Authority control databases: Academics |
|---|