Yu-Shan Lin
Tufts Chemistry


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Yu-Shan Lin
Department of Chemistry
Tufts University
62 Talbot Avenue Pearson 103-X
Medford, MA 02155

Email: yu-shan.lin@tufts.edu

Papers by YSL

    From independent research at Tufts University (13):

  1. L. Peraro, Z. Zou, K. M. Makwana, A. E. Cummings, H. L. Ball, H. Yu, Y.-S. Lin, B. Levine, J. Kritzer, “Density-oriented stapling yields intrinsically cell-penetrant inducers of autophagy,” J. Am. Chem. Soc. accepted.
  2. D. P. Slough, H. Yu, S. M. McHugh, Y.-S. Lin, “Toward accurately modeling N-methylated cyclic peptides,” Phys. Chem. Chem. Phys. 19, 5377 (2017).
  3. S. M. McHugh, H. Yu, D. P. Slough, Y.-S. Lin, “Mapping the sequence—structure relationships of simple cyclic hexapeptides,” Phys. Chem. Chem. Phys. 19, 3315 (2017).
    Equal contributions.
  4. P. Chhum, H. Yu, B. An, B. Doyon, Y.-S. Lin,* B. Brodsky,* “Consequences of glycine mutations in the fibronectin binding sequence of collagen,” J. Biol. Chem. 291, 27073 (2016).
    Equal contributions. *Co-corresponding authors.
  5. S. M. McHugh, J. R. Rogers, S. A. Solomon, H. Yu, Y.-S. Lin, “Computational methods to design cyclic peptides,” Curr. Opin. Chem. Biol. 34, 95 (2016).
    Equal contributions.
  6. M. D. Simon, Y. Maki, A. A. Vinogradov, C. Zhang, H. Yu, Y.-S. Lin, Y. Kajihara, B. L. Pentelute, “D-amino acid scan of two small proteins,” J. Am. Chem. Soc. 138, 12099 (2016).
  7. S. Yigit, H. Yu, B. An, S. Hamaia, R. W. Farndale, D. L. Kaplan, Y.-S. Lin,* B. Brodsky,* “Mapping the effect of Gly mutations in collagen on α2β1 integrin binding,” J. Biol. Chem. 291, 19196 (2016).
    Equal contributions. *Co-corresponding authors.
  8. S. M. McHugh, J. R. Rogers, H. Yu, Y.-S. Lin, “Insights into how cyclic peptides switch conformations,” J. Chem. Theory Comput. 12, 2480 (2016).
    Equal contributions.
  9. B. An, Y.-S. Lin, B. Brodsky, “Collagen interactions: Drug design and delivery,” Adv. Drug Deliv. Rev. 97, 69 (2016).
  10. H. Yu and Y.-S. Lin, “Toward structure prediction of cyclic peptides,” Phys. Chem. Chem. Phys. 17, 4210 (2015). We thank Prof. Wu for kindly providing us with the RSFF1 force field parameters!
  11. J. S. Quartararo, M. R. Eshelman, L. Peraro, H. Yu, J. D. Baleja, Y.-S. Lin, J. A. Kritzer, “A bicyclic peptide scaffold promotes phosphotyrosine mimicry and cellular uptake,” Bioorg. Med. Chem. 22, 6387 (2014).
  12. Y. Zou, A. M. Spokoyny, C. Zhang, M. D. Simon, H. Yu, Y.-S. Lin, B. L. Pentelute, “Convergent diversity-oriented side-chain macrocyclization scan for unprotected polypeptides,” Org. Biomol. Chem. 12, 566 (2014). Cover article.
  13. A. M. Spokoyny, Y. Zou, J. J. Ling, H. Yu, Y.-S. Lin, B. L. Pentelute, “A perfluoroaryl-cysteine SNAr chemistry approach to unprotected peptide stapling,” J. Am. Chem. Soc. 135, 5946 (2013). Featured on the Science & Technology Concentrates in the C&EN.

    From postdoctoral research at Stanford University (5):

  1. C. R. Baiz, Y.-S. Lin, C. S. Peng, K. A. Beauchamp, V. A. Voelz, V. S. Pande, A. Tokmakoff, “A molecular interpretation of 2D IR protein folding experiments with Markov state models,” Biophys. J. 106, 1359 (2014).
  2. Y.-S. Lin, V. S. Pande, “Effects of familial mutations on the monomer structure of Aβ42,” Biophys. J. 103, L47 (2012).
  3. K. A. Beauchamp, R. McGibbon, Y.-S. Lin, V. S. Pande, “Simple few-state models reveal hidden complexity in protein folding,” Proc. Natl. Acad. Sci. U.S.A. 109, 17807 (2012).
  4. K. A. Beauchamp, Y.-S. Lin, R. Das, V. S. Pande, “Are protein force fields getting better? A systematic benchmark on 524 diverse NMR measurements,” J. Chem. Theory Comput. 8, 1409 (2012).
  5. Y.-S. Lin, G. R. Bowman, K. A. Beauchamp, V. S. Pande, “Investigating how peptide length and a pathogenic mutation modify the structural ensemble of amyloid beta monomer,” Biophys. J. 102, 315 (2012).

    From graduate research at UW—Madison (11):

  1. C. J. Tainter, P. A. Pieniazek, Y.-S. Lin, J. L. Skinner, “Robust three-body water simulation model,” J. Chem. Phys. 134, 184501 (2011).
  2. Y.-S. Lin, P. A. Pieniazek, M. Yang, J. L. Skinner, “On the calculation of rotational anisotropy decay, as measured by ultrafast polarization-resolved pump-probe experiments,” J. Chem. Phys. 132, 174505 (2010).
  3. A. M. Woys, Y.-S. Lin, A. S. Reddy, J. J. de Pablo, J. L. Skinner, M. T. Zanni, “2D IR lineshapes probe ovispirin peptide conformation and depth in lipid bilayers,” J. Am. Chem. Soc. 132, 2832 (2010).
  4. A. S. Reddy, L. Wang, Y.-S. Lin, Y. L. Ling, M. T. Zanni, J. L. Skinner, J. J. de Pablo, “Solution structures of rat amylin peptide: Simulation, theory, and experiment,” Biophys. J. 98, 443 (2010).
  5. P. A. Pieniazek, Y.-S. Lin, J. L. Skinner, “Vibrational spectroscopy and dynamics of water confined inside reverse micelles,” J. Phys. Chem. B 113, 15017 (2009).
  6. Y.-S. Lin, B. M. Auer, J. L. Skinner, “Water structure, dynamics, and vibrational spectroscopy in sodium bromide solutions,” J. Chem. Phys. 131, 144511 (2009). Selected as a “Research Highlight" by the editors.
  7. J. Manor, P. Mukherjee, Y.-S. Lin, H. Leonov, J. L. Skinner, M. T. Zanni, I. T. Arkin, “Gating mechanism of the influenza A M2 channel revealed by 1D and 2D IR spectroscopies,” Structure 17, 247 (2009).
  8. Y.-S. Lin, J. M. Shorb, P. Mukherjee, M. T. Zanni, J. L. Skinner, “Empirical amide I vibrational frequency map: Applications to isotope-edited membrane peptide bundles,” J. Phys. Chem. B 113, 592 (2009). Centennial feature article.
  9. J. L. Skinner, B. M. Auer, Y.-S. Lin, “Vibrational line shapes and spectral diffusion in liquid water,” Adv. Chem. Phys. 142, 59, (2009).
  10. D. E. Moilanen, E. E. Fenn, Y.-S. Lin, J. L. Skinner, B. Bagchi, M. D. Fayer, “Water inertial reorientation: Hydrogen bond strength and the angular potential,” Proc. Natl. Acad. Sci. U.S.A. 105, 5295 (2008).
  11. Y.-S. Lin, S. G. Ramesh, J. M. Shorb, E. L. Sibert III, J. L. Skinner, “Vibrational energy relaxation of the bend fundamental of dilute water in liquid chloroform and d-chloroform,” J. Phys. Chem. B 112, 390 (2008).

    From undergraduate research at National Taiwan University (2):

  1. K.-C. Wu, Y.-S. Lin, Y.-S. Yeh, C.-Y. Chen, M. O. Ahmed, P.-T. Chou, Y.-S. Hon, “Design and synthesis of intramolecular hydrogen bonding systems. Their application in metal cation sensing based on excited state proton transfer reaction,” Tetrahedron 60, 11861 (2004).
  2. K.-C. Wu, Y.-M. Cheng, Y.-S. Lin, Y.-S. Yeh, S.-C. Pu, Y.-H. Hu, J.-K. Yu, P.-T. Chou, “Competitive intramolecular hydrogen bonding formation and excited-state proton transfer reaction in 1-[(diethylamino)-methyl]-2-hydroxy-3-naphthaldehyde,” Chem. Phys. Lett. 384, 203 (2004).
§ If you find mistakes or broken links, please email Yu-Shan at yu-shan.lin@tufts.edu Thank you!