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:

  1. J. Y. K. Wong, S. Kirberger, R. Qiu, A. I. Ekanayake, P. Kelich, S. Sarkar, E. R. Alvizo-Paez, J. Miao, S. Kalhor-Monfared, J. J. Dwyer, J. M. Nuss, Y.-S. Lin, M. S. Macauley, L. Vukovic, W. Pomer-antz, R. Derda, “Genetically-encoded discovery of perfluoroaryl-macrocycles that bind to albumin and exhibit extended circulation in-vivo,” in revision.
  2. J. Mortensen,† J. Damjanovic,† J. Miao, T. Hui, Y.-S. Lin, “A backbone-dependent rotamer library with high (φ, ψ) coverage using metadynamics simulations,” Protein Sci. 31, e4491 (2022).
    †Equal contributions.
  3. X. Ye, Y.-C. Lee, Z. Gates, Y. Ling, J. Mortensen, F.-S. Yang, Y.-S. Lin, B. L. Pentelute, “Binary combinatorial scanning reveals potent poly-alanine-substituted inhibitors of protein—protein interactions,” Comm. Chem. 5, 128 (2022).
  4. J. Yoon, E. E. Nekongo, J. E. Patrick, T. Hui, A. M. Phillips, A. I. Ponomarenko, S. J. Hendel, R. M. Sebastian, Y. M. Zhang, V. L. Butty, C. B. Ogbunugafor, Y.-S. Lin, M. D. Shoulders, “The endoplasmic reticulum proteostasis network profoundly shapes the protein sequence space accessible to HIV envelope,” PLOS Biol. 20, e3001569 (2022).
  5. J. Miao, M. Descoteaux, Y.-S. Lin, “Structure prediction of cyclic peptides by molecular dynamics + machine learning,” Chem. Sci. 12, 14927‒14936 (2021).
  6. J. Damjanovic, J. Murphy,* Y.-S. Lin,* “CATBOSS: Cluster analysis of trajectories based on segment splitting,” J. Chem. Inf. Model. 61, 5066‒5081 (2021).
    *Co-corresponding authors.
  7. J. Damjanovic,† J. Miao,† H. Huang,† Y.-S. Lin, “Elucidating solution structures of cyclic peptides using molecular dynamics simulations,” Chem. Rev. 121, 2292‒2324 (2021).
    †Equal contributions.
  8. H. Huang,† J. Damjanovic,† J. Miao, Y.-S. Lin, “Cyclic peptides: Backbone rigidification and capability of mimicking motifs at protein–protein interfaces,” Phys. Chem. Chem. Phys. 23, 607‒616 (2021).
    †Equal contributions.
  9. K. Makwana, M. Sarnowski, J. Miao, Y.-S. Lin, J. Del Valle, “N-amination converts amyloidogenic tau peptides into soluble antagonists of cellular seeding,” ACS Chem. Neurosci. 12, 3928‒3938 (2021).
  10. J. Pace, C. Abakah, A. Moyer, J. Miao, K. Deprey, R. Cerulli, Y.-S. Lin, J. Baleja, D. Baker, J. Kritzer, “Stapled beta-hairpins using 4-mercaptoproline,” J. Am. Chem. Soc. 143, 15039‒15044 (2021).
  11. J. Y.-K. Wong, R. Mukherjee, J. Miao, O. Bilyk, V. Triana, M. Miskolzie, A. Henninot, J. J. Dwyer, S. Kharchenko, A. Iampolska, D. M. Volochnyuk, Y.-S. Lin, L.-M. Postovit, R. Derda, “Genetically-encoded discovery of proteolytically stable bicyclic inhibitors for morphogen NODAL,” Chem. Sci. 12, 9694‒9703 (2021).
  12. T. Balema, J. Miao, N. Wasio, C. Murphy, A. Larson, D. Patel, Y.-S. Lin,* E. C. Sykes,* “Visualizing and understanding ordered surface phases during the Ullmann coupling reaction,” J. Phys. Chem. C. 125, 7675‒7685 (2021).
    *Co-corresponding authors.
  13. A. E. Cummings,† J. Miao,† D. P. Slough, S. M. McHugh, J. A. Kritzer,* Y.-S. Lin,* “Beta-branched amino acids stabilize specific conformations of cyclic hexapeptides,” Biophys. J. 116, 433‒444 (2019).
    †Equal contributions. *Co-corresponding authors.
  14. E. A. Chen and Y.-S. Lin, “Using synthetic peptides and recombinant collagen to understand DDR-collagen interactions,” Biochim. Biophys. Acta Mol. Cell Res. 1866, 118458 (2019).
  15. T. Balema, N. Ulumuddin, C. Murphy, D. Slough, Z. Smith, R. Hannagan, N. Wasio, A. Larson, D. Patel, K. Groden, J.-S. McEwen,* Y.-S. Lin,* E. C. Sykes,* “Controlling molecular switching via chemical functionality; ethyl vs. methoxy rotors,” J. Phys. Chem. C 123 23738‒23746 (2019).
    *Co-corresponding authors.
  16. C. Tobon, L. C. Palacio, B. Chidipi, D. P. Slough, T. Tran, N. Tran, M. Reiser, Y.-S. Lin, B. Herweg, D. Sayad, J. Saiz, S. Noujaim, “The antimalarial chloroquine reduces the burden of persistent atrial fibrillation,” Front. Pharmacol. 10 1392 (2019).
  17. D. P. Slough,† S. M. McHugh,† A. E. Cummings, P. Dai, B. L. Pentelute, J. A. Kritzer, Y.-S. Lin, “Designing well-structured cyclic pentapeptides based on sequence—structure relationships,” J. Phys. Chem. B 122, 3908‒3919 (2018).
    †Equal contributions.
  18. D. P. Slough,† S. M. McHugh,† Y.-S. Lin, “Understanding and designing head-to-tail cyclic peptides,” Biopolymers 109, e23113 (2018).
    †Equal contributions.
  19. A. Mekkat,† E. Poppleton,† B. An, R. Visse, H. Nagase, D. L. Kaplan, B. Brodsky,* Y.-S. Lin,* “Effects of flexibility of the α2 chain of type I collagen on collagenase cleavage,” J. Struct. Biol. 203, 247‒254 (2018).
    †Equal contributions. *Co-corresponding authors.
  20. Y. Qiu, A. Mekkat, H. Yu, S. Yigit, S. Hamaia, R. W. Farndale, D. L. Kaplan, Y.-S. Lin,* B. Brodsky,* “Collagen Gly missense mutations: Effect of residue identity on collagen structure and integrin binding,” J. Struct. Biol. 203, 255‒262 (2018).
    *Co-corresponding authors.
  21. Y. Qiu, E. Poppleton, A. Mekkat, H. Yu, S. Banerjee, S. Wiley, J. Dixon, D. Kaplan, Y.-S. Lin, B. Brodsky, “Enzymatic phosphorylation of Ser in a type I collagen peptide,” Biophys. J. 115, 2327‒2335 (2018).
  22. A. M. Phillips, A. I. Ponomarenko, K. Chen, O. Ashenberg, J. Miao, S. M. McHugh, V. L. Butty, C. A. Whittaker, C. L. Moore, J. D. Bloom, Y.-S. Lin, M. D. Shoulders, “Destabilized adaptive influenza variants critical for innate immune system escape are potentiated by host chaperones,” PLOS Biol. 16, e3000008 (2018).
  23. A. M. Phillips, M. B. Doud, L. O. Gonzalez, V. L. Butty, Y.-S. Lin, J. D. Bloom, M. D. Shoulders, “Enhanced ER proteostasis and temperature differentially impact the mutational tolerance of influenza hemagglutinin,” eLife 7, e38795 (2018).
  24. M. Jafari, H. Yu, J. Wickware, Y.-S. Lin, R. Derda, “Light-responsive bicyclic peptides,” Org. Biomol. Chem. 16, 7588‒7594 (2018). Featured on the Org. Biomol. Chem. Blog.
  25. Y. Takemoto,† D. P. Slough,† G. Meinke, C. Katnik, Z. A. Graziano, C. Bujjibabou, M. Reiser, M. M. Alhadidi, R. Ramirez, O. Salvador-Montañés, S. Ennis, G. Guerrero, M. Haburcak, C. Diehl, J. Cuevas, J. Jalife, A. Bohm, Y.-S. Lin, S. F. Noujaim, “Structural basis for the antiarrhythmic blockade of potassium channel with a small molecule,” FASEB J. 32, 1778‒1793 (2018).
    †Equal contributions.
  26. J. R. Rogers, S. M. McHugh, Y.-S. Lin, “Predictions for α-helical glycopeptide design from structural bioinformatics analysis,” J. Chem. Inf. Model. 57, 2598‒2611 (2017).
  27. D. P. Slough, H. Yu, S. M. McHugh, Y.-S. Lin, “Toward accurately modeling N-methylated cyclic peptides,” Phys. Chem. Chem. Phys. 19, 5377‒5388 (2017).
  28. 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, 3315‒3324 (2017).
    †Equal contributions.
  29. N. Wasio, D. Slough, Z. Smith, C. Ivimey, S. Thomas, III, Y.-S. Lin,* E. C. Sykes,* “Correlated rotational switching in 2D self-assembled molecular rotor arrays,” Nat. Comm. 8, 16057 (2017).
    *Co-corresponding authors.
  30. Y. Li, N. P. Lavey, J. A. Coker, J. E. Knobbe, D. C. Truong, H. Yu, Y.-S. Lin, S. L. Nimmo, A. S. Duerfeldt, “Consequences of depsipeptide substitution on the ClpP activation activity of antibacterial acyldepsipeptides,” ACS Med. Chem. Lett. 8, 1171‒1176 (2017).
  31. S. Mong, F. Cochran, H. Yu, Z. A. Graziano, Y.-S. Lin, J. R. Cochran, B. L. Pentelute, “Heterochiral knottin protein: Folding and solution structure,” Biochemistry 56, 5720‒5725 (2017).
  32. A. M. Phillips, L. O. Gonzalez, E. E. Nekongo, A. I. Ponomarenko, S. M. McHugh, V. Butty, S. S. Levine, Y.-S. Lin, L. A. Mirny, M. D. Shoulders, “Host proteostasis modulates influenza evolution,” eLife 6, e28652 (2017). Featured on MIT News and Boston Globe.
  33. L. Peraro, Z. Zou, K. M. Makwana, A. E. Cummings, H. L. Ball, H. Yu, Y.-S. Lin, B. Levine, J. A. Kritzer, “Diversity-oriented stapling yields intrinsically cell-penetrant inducers of autophagy,” J. Am. Chem. Soc. 139, 7792‒7802 (2017).
  34. 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, 95‒102 (2016).
    †Equal contributions.
  35. S. M. McHugh,† J. R. Rogers,† H. Yu, Y.-S. Lin, “Insights into how cyclic peptides switch conformations,” J. Chem. Theory Comput. 12, 2480‒2488 (2016).
    †Equal contributions.
  36. 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, 27073‒27086 (2016).
    †Equal contributions. *Co-corresponding authors.
  37. 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, 19196‒19207 (2016).
    †Equal contributions. *Co-corresponding authors.
  38. 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, 12099‒12111 (2016).
  39. B. An, Y.-S. Lin, B. Brodsky, “Collagen interactions: Drug design and delivery,” Adv. Drug Deliv. Rev. 97, 69‒84 (2016).
  40. H. Yu and Y.-S. Lin, “Toward structure prediction of cyclic peptides,” Phys. Chem. Chem. Phys. 17, 4210‒4219 (2015). We thank Prof. Wu for kindly providing us with the RSFF1 force field parameters!
  41. 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, 6387‒6391 (2014).
  42. 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, 566‒573 (2014). Cover article.
  43. 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, 5946‒5949 (2013). Featured on the Science & Technology Concentrates in the C&EN.

    From postdoctoral research at Stanford University:

  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, 1359‒1370 (2014).
  2. Y.-S. Lin, V. S. Pande, “Effects of familial mutations on the monomer structure of Aβ42,” Biophys. J. 103, L47‒L49 (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, 17807‒17813 (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, 1409‒1414 (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, 315‒324 (2012).

    From graduate research at UW—Madison:

  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, 2832‒2838 (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, 443‒451 (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, 15017‒15028 (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, 247‒254 (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, 592‒602 (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, 59‒103 (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, 5295‒5300 (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, 390‒398 (2008).

    From undergraduate research at National Taiwan University:

  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, 11861‒11868 (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, 203‒209 (2004).
§ If you find mistakes or broken links, please email Yu-Shan at yu-shan.lin@tufts.edu Thank you!