Papers
From independent research at Tufts University:
The immune-evasive Proline 283 substitution in influenza nucleoprotein increases aggregation propensity without altering the native structure
J. Yoon, Y. M. Zhang, C. Her, R. A. Grant, A. M. Ponomarenko, B. E. Ackermann, T. Hui, Y.-S. Lin, G. T. Debelouchina, M. D. Shoulders, “The immune-evasive Proline 283 substitution in influenza nucleoprotein increases aggregation propensity without altering the native structure,” Sci. Adv. in press (2024).
A boron-dependent antibiotic derived from a calcium-dependent antibiotic
S.-L. Chiou, Y.-J. Chen, C.-T. Lee, M. N. Ho, J. Miao, P.-C. Kuo, C.-C. Hsu, Y.-S. Lin, J. Chu, “A boron-dependent antibiotic derived from a calcium-dependent antibiotic,” Angew. Chem. 63, e202317522 (2024).
Computational prediction of cyclic peptide structural ensembles and application to the design of Keap1 binder
F. Fonseca-Lopez, J. Miao, J. Damjanovic, L. Bischof, M. Braun, Y. Ling, M. Hartmann, Y.-S. Lin,* J. A. Kritzer,* “Computational prediction of cyclic peptide structural ensembles and application to the design of Keap1 binders,” J. Chem. Inf. Model. 63, 6925 (2023).
* Co-corresponding authors
Modeling changes in molecular dynamics time series as Wasserstein barycentric interpolations
J. Damjanovic, Y.-S. Lin,* J. M. Murphy,* “Modeling changes in molecular dynamics time series as Wasserstein barycentric interpolations,”2023 International Conference on Sampling Theory and Applications (SampTA), New Haven, CT, USA, July 10–14, 2023; IEEE Xplore.
* Co-corresponding authors
Genetically-encoded discovery of perfluoroaryl-macrocycles that bind to albumin and exhibit extended circulation in-vivo
J. Y. K. Wong, A. I. Ekanayake, S. Kirberger, R. Qiu, A. I. Ekanayake, P. Kelich, S. Sarkar, J. Li, K. X. Fernandez, E. R. Alvizo-Paez, J. Miao, S. Kalhor-Monfared, J. J. Dwyer, H. Kang, H. Choi, J. M. Nuss, J. C. Vederas, Y.-S. Lin, M. S. Macauley, L. Vukovic, W. Pomerantz, R. Derda, “Genetically-encoded discovery of perfluoroaryl-macrocycles that bind to albumin and exhibit extended circulation in-vivo,” Nat. Commun. 14, 5654 (2023).
Training neural network models using molecular dynamics simulation results to efficiently predict cyclic hexapeptide structural ensembles
T. Hui,† M. L. Descoteaux,† J. Miao,† Y.-S. Lin, “Training neural network models using molecular dynamics simulation results to efficiently predict cyclic hexapeptide structural ensembles,” J. Chem. Theory Comput. 19, 4757–4769 (2023). †Equal contributions.
A backbone-dependent rotamer library with high (φ, ψ) coverage using metadynamics simulations
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.
Binary combinatorial scanning reveals potent poly-alanine-substituted inhibitors of protein–protein interactions
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).
The endoplasmic reticulum proteostasis network profoundly shapes the protein sequence space accessible to HIV envelope
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).
Structure prediction of cyclic peptides by molecular dynamics + machine learning
J. Miao, M. Descoteaux, Y.-S. Lin, “Structure prediction of cyclic peptides by molecular dynamics + machine learning,” Chem. Sci. 12, 14927–14936 (2021).
CATBOSS: Cluster analysis of trajectories based on segment splitting
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.
Elucidating solution structures of cyclic peptides using molecular dynamics simulations
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.
Cyclic peptides: Backbone rigidification and capability of mimicking motifs at protein–protein interfaces
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.
N-Amination converts amyloidogenic tau peptides into soluble antagonists of cellular seeding
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).
Stapled beta-hairpins using 4-mercaptoproline
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).
Genetically-encoded discovery of proteolytically stable bicyclic inhibitors for morphogen NODAL
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).
Visualizing and understanding ordered surface phases during the Ullmann coupling reaction
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.
Beta-branched amino acids stabilize specific conformations of cyclic hexapeptides
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.
Using synthetic peptides and recombinant collagen to understand DDR-collagen interactions
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).
Controlling molecular switching via chemical functionality; ethyl vs. methoxy rotors
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.
The antimalarial chloroquine reduces the burden of persistent atrial fibrillation
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).
Designing well-structured cyclic pentapeptides based on sequence—structure relationships
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.
Understanding and designing head-to-tail cyclic peptides
D. P. Slough,† S. M. McHugh,† Y.-S. Lin, “Understanding and designing head-to-tail cyclic peptides,” Biopolymers 109, e23113 (2018).
†Equal contributions.
Effects of flexibility of the α2 chain of type I collagen on collagenase cleavage
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.
Collagen Gly missense mutations: Effect of residue identity on collagen structure and integrin binding
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.
Enzymatic phosphorylation of Ser in a type I collagen peptide
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).
Destabilized adaptive influenza variants critical for innate immune system escape are potentiated by host chaperones
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).
Enhanced ER proteostasis and temperature differentially impact the mutational tolerance of influenza hemagglutinin
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).
Light-responsive bicyclic peptides
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.
Structural basis for the antiarrhythmic blockade of potassium channel with a small molecule
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.
Predictions for α-helical glycopeptide design from structural bioinformatics analysis
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).
Toward accurately modeling N-methylated cyclic peptides
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).
Mapping the sequence–structure relationships of simple cyclic hexapeptides
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.
Correlated rotational switching in 2D self-assembled molecular rotor arrays
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.
Consequences of depsipeptide substitution on the ClpP activation activity of antibacterial acyldepsipeptides
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).
Heterochiral knottin protein: Folding and solution structure
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).
Host proteostasis modulates influenza evolution
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 in the Boston Globe.
Diversity-oriented stapling yields intrinsically cell-penetrant inducers of autophagy
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).
Computational methods to design cyclic peptides
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.
Insights into how cyclic peptides switch conformations
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.
Consequences of glycine mutations in the fibronectin binding sequence of collagen
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.
Mapping the effect of Gly mutations in collagen on α2β1 integrin binding
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.
D-Amino acid scan of two small proteins
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).
Collagen interactions: Drug design and delivery
B. An, Y.-S. Lin, B. Brodsky, “Collagen interactions: Drug design and delivery,” Adv. Drug Deliv. Rev. 97, 69–84 (2016).
Toward structure prediction of cyclic peptides
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!
A bicyclic peptide scaffold promotes phosphotyrosine mimicry and cellular uptake
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).
Convergent diversity-oriented side-chain macrocyclization scan for unprotected polypeptides
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.
A perfluoroaryl-cysteine SNAr chemistry approach to unprotected peptide stapling
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 in Science & Technology Concentrates in the C&EN.
From postdoctoral research at Stanford University:
A molecular interpretation of 2D IR protein folding experiments with Markov state models
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).
Effects of familial mutations on the monomer structure of Aβ42
Y.-S. Lin, V. S. Pande, “Effects of familial mutations on the monomer structure of Aβ42,” Biophys. J. 103, L47–L49 (2012).
Simple few-state models reveal hidden complexity in protein folding
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).
Are protein force fields getting better? A systematic benchmark on 524 diverse NMR measurements
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).
Investigating how peptide length and a pathogenic mutation modify the structural ensemble of amyloid beta monomer
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:
Robust three-body water simulation model
C. J. Tainter, P. A. Pieniazek, Y.-S. Lin, J. L. Skinner, “Robust three-body water simulation model,” J. Chem. Phys. 134, 184501 (2011).
On the calculation of rotational anisotropy decay, as measured by ultrafast polarization-resolved pump-probe experiments
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).
2D IR lineshapes probe ovispirin peptide conformation and depth in lipid bilayers
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).
Solution structures of rat amylin peptide: Simulation, theory, and experiment
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).
Vibrational spectroscopy and dynamics of water confined inside reverse micelles
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).
Water structure, dynamics, and vibrational spectroscopy in sodium bromide solutions
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.
Gating mechanism of the influenza A M2 channel revealed by 1D and 2D IR spectroscopies
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).
Empirical amide I vibrational frequency map: Applications to isotope-edited membrane peptide bundles
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.
Vibrational line shapes and spectral diffusion in liquid water
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).
Water inertial reorientation: Hydrogen bond strength and the angular potential
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).
Vibrational energy relaxation of the bend fundamental of dilute water in liquid chloroform and d-chloroform
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:
Design and synthesis of intramolecular hydrogen bonding systems. Their application in metal cation sensing based on excited state proton transfer reaction
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).
Competitive intramolecular hydrogen bonding formation and excited-state proton transfer reaction in 1-[(diethylamino)-methyl]-2-hydroxy-3-naphthaldehyde
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).