From independent research at Tufts University:
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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.
- 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.
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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).
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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).
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J. Miao, M. Descoteaux, Y.-S. Lin,
“Structure prediction of cyclic peptides by molecular dynamics + machine learning,”
Chem. Sci. 12, 14927‒14936 (2021).
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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.
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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.
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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.
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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).
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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).
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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).
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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.
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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.
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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).
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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.
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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).
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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.
-
D. P. Slough,† S. M. McHugh,† Y.-S. Lin,
“Understanding and designing head-to-tail cyclic peptides,”
Biopolymers 109, e23113 (2018).
†Equal contributions.
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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.
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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.
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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).
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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).
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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).
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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.
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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.
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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).
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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).
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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.
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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.
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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).
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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).
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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.
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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).
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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.
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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.
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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.
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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.
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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).
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B. An, Y.-S. Lin, B. Brodsky,
“Collagen interactions: Drug design and delivery,”
Adv. Drug Deliv. Rev. 97, 69‒84 (2016).
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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!
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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).
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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.
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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:
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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).
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Y.-S. Lin, V. S. Pande,
“Effects of familial mutations on the monomer structure of Aβ42,”
Biophys. J. 103, L47‒L49 (2012).
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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).
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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).
-
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:
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C. J. Tainter, P. A. Pieniazek, Y.-S. Lin, J. L. Skinner,
“Robust three-body water simulation model,”
J. Chem. Phys. 134, 184501 (2011).
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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).
-
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).
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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).
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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).
-
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.
-
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).
-
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.
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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).
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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).
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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:
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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).
-
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).