Selected Publications

*Corresponding author

†Contributed equally to this work

  1. Li, Chengxuan; Wei, Tingyi; Cheung, Margaret S; Tsai, M.-Y.* Deciphering the Cofilin Oligomers via Intermolecular Disulfide Bond Formation: A Coarse-grained Molecular Dynamics Approach to Understanding Cofilin’s Regulation on Actin Filaments. J. Phys. Chem. B. Accepted (https://pubs.acs.org/doi/abs/10.1021/acs.jpcb.3c07938)

  2. Lin, T.-Y.; Ma, Y.-W.; Tsai, M.-Y.* Early-stage Oligomerization of Prion-like Polypeptides Reveals the Molecular Mechanism of Amyloid-disrupting Capacity by Proline Residues. J. Phys. Chem. B. 2023, 127 (5), 1074-1088. (https://pubs.acs.org/doi/10.1021/acs.jpcb.2c05463)

  3. Chen, X.; Tsai, M.-Y.*; Wolynes, P. G.* The Role of Charge Density Coupled DNA Bending in Transcription Factor Sequence Binding Specificity: A Generic Mechanism for Indirect Readout. J. Am. Chem. Soc. 2022, 144 (4), 1835–1845. (https://pubs.acs.org/doi/10.1021/jacs.1c11911)

  4. Ma, Y.-W.; Lin, T.-Y.; Tsai, M.-Y.* Fibril Surface-dependent Amyloid Precursors revealed by Coarse-grained Molecular Dynamics Simulation. Front. Mol. Biosci. 2021, 8, 719320.
    (https://doi.org/10.3389/fmolb.2021.719320)

  5. Tsai, M.-Y.*,†;Shen, J.-L.†; Schafer, N. P.; Wolynes, P. G.*, Modeling Protein Aggregation Kinetics: The Method of Second Stochasticization. J. Phys. Chem. B 2021, 125 (4), 1118–1133. (https://pubs.acs.org/doi/10.1021/acs.jpcb.0c10331)

  6. Tsai, M.-Y.; Zheng, W.; Chen, M.; Wolynes, P. G.* Multiple Binding Configurations of Fis Protein Pairs on DNA: Facilitated Dissociation versus Cooperative Dissociation. J. Am. Chem. Soc. 2019, 141 (45), 18113−18126. (https://doi.org/10.1021/jacs.9b08287)

  7. Tsai, M.-Y.; Zhang, B.; Zheng, W.; Wolynes, P. G.* Molecular Mechanism of Facilitated Dissociation of Fis Protein from DNA. J. Am. Chem. Soc. 2016, 138 (41), 13497−13500. (https://pubs.acs.org/doi/abs/10.1021/jacs.6b08416)

  8. Tsai, M.-Y.; Zheng, W.; Balamurugan, D.; Schafer, N. P.; Kim, B. L.; Cheung, M. S.; Wolynes, P. G.* Electrostatics, Structure Prediction, and the Energy Landscapes for Protein Folding and Binding. Protein Sci. 2016, 25 (1), 255–269. (https://doi.org/10.1002/pro.2751)

  9. Tsai, M.-Y.*; Yuan, J.-M.; Teranishi, Y.; Lin, S. H. Thermodynamics of Protein Folding Using a Modified Wako-Saitô-Muñoz-Eaton Model. J. Biol. Phys.2012, 38 (4), 543–571. (https://doi.org/10.1007/s10867-012-9271-y)

Full Publications List

Journal Articles (Sorted by Year)

CCU (2023.2 - Present)

Submitted

  1. Li, Chengxuan; Wei, Tingyi; Cheung, Margaret S; Tsai, M.-Y.* Deciphering the Cofilin Oligomers via Intermolecular Disulfide Bond Formation: A Coarse-grained Molecular Dynamics Approach to Understanding Cofilin’s Regulation on Actin Filaments. J. Phys. Chem. B. Accepted (https://pubs.acs.org/doi/abs/10.1021/acs.jpcb.3c07938)

Manuscripts in preparation

  1. Ma, Yuan-Wei; Wang, Guan-Fang; Tsai, M.-Y.* Exploring Abeta42 Monomer Diffusive Dynamics on Fibril Surfaces through Molecular Simulations. (BioRxiv)

  2. Chou, Yun-Chu; Yung-Ting Lee; Lin, Tong-You; Tsai, M.-Y.* Unraveling the Intricacies of Tryptophan's Fluorescence in Proteins: Exploring Tryptophan Rotamers through Atomistic Simulations.

TKU (2018.8 - 2023.1)

  1. Lin, T.-Y.; Ma, Y.-W.; Tsai, M.-Y.* Early-stage Oligomerization of Prion-like Polypeptides Reveals the Molecular Mechanism of Amyloid-disrupting Capacity by Proline Residues. J. Phys. Chem. B. 2023, 127 (5), 1074-1088. (https://pubs.acs.org/doi/10.1021/acs.jpcb.2c05463)

  2. Chou, Yun-Chu; Lin, Tong-You; Tsai, M.-Y.* A Rotamer Model to Explain the Temperature Dependence of BSA Protein Fluorescence. J. Chem. Chem. Soc. 2023, 70 (3), 386-393. (https://onlinelibrary.wiley.com/doi/abs/10.1002/jccs.202200528)

  3. Chen, X.; Tsai, M.-Y.*; Wolynes, P. G.* The Role of Charge Density Coupled DNA Bending in Transcription Factor Sequence Binding Specificity: A Generic Mechanism for Indirect Readout. J. Am. Chem. Soc. 2022, 144 (4), 1835–1845. (https://pubs.acs.org/doi/10.1021/jacs.1c11911)

  4. Chen, X.; Lu, W.; Tsai, M.-Y.; Jin, S.; Wolynes, P. G. Exploring the Folding Energy Landscapes of Heme Proteins Using a Hybrid AWSEM-Heme Model. J. Biol. Phys. 2022. (https://doi.org/10.1007/s10867-021-09596-3)

  5. Ma, Y.-W.; Lin, T.-Y.; Tsai, M.-Y.* Fibril Surface-dependent Amyloid Precursors revealed by Coarse-grained Molecular Dynamics Simulation. Front. Mol. Biosci. 2021, 8, 719320. (https://doi.org/10.3389/fmolb.2021.719320)

  6. Tsai, M.-Y.*,†;Shen, J.-L.†; Schafer, N. P.; Wolynes, P. G.*, Modeling Protein Aggregation Kinetics: The Method of Second Stochasticization. J. Phys. Chem. B 2021, 125 (4), 1118–1133. (https://pubs.acs.org/doi/10.1021/acs.jpcb.0c10331)

  7. Jin, S.; Contessoto, V. S.; Chen, M.; Schafer, N. P.; Lu, W.; Chen, X.; Bueno, C.; Hajitaheri, A.; Sirovetz, B. J.; Davtyan, A.; Papoian, G. A.; Tsai, M.-Y.; Wolynes, P. G.* AWSEM-Suite: A Protein Structure Prediction Server Based On Template-guided, Coevolutionary-enhanced Optimized Folding Landscapes. Nucleic Acids Res. 2020, 48 (W1), W25-W30.(https://doi.org/10.1093/nar/gkaa356)

  8. Tsai, M.-Y.; Zheng, W.; Chen, M.; Wolynes, P. G.* Multiple Binding Configurations of Fis Protein Pairs on DNA: Facilitated Dissociation versus Cooperative Dissociation. J. Am. Chem. Soc. 2019, 141 (45), 18113−18126. (https://pubs.acs.org/doi/10.1021/jacs.9b08287)

  9. Tsai, M.-Y.* Role of Physical Nucleation Theory in Understanding Conformational Conversion between Pathogenic and Nonpathogenic Aggregates of Low-Complexity Amyloid Peptides. Res. Chem. Intermed. 2019, 45, 5357-5373. (https://link.springer.com/article/10.1007/s11164-019-03974-2)

Before TKU (before 2018.8)

  1. Lin, X.; Kulkarni, P.; Bocci, F.; Schafer, N. P.; Roy, S.; Tsai, M.-Y.; He, Y.; Chen, Y.; Rajagopalan, K.; Mooney, S. M.; et al. Structural and Dynamical Order of a Disordered Protein: Molecular Insights into Conformational Switching of PAGE4 at the Systems Level. Biomolecules 2019, 9 (2), 77.

  2. Lin, X.; Roy, S.; Jolly, M. K.; Bocci, F.; Schafer, N. P.; Tsai, M.-Y.; Chen, Y.; He, Y.; Grishaev, A.; Weninger, K.; et al. PAGE4 and Conformational Switching: Insights from Molecular Dynamics Simulations and Implications for Prostate Cancer. J. Mol. Biol. 2018, 430 (16), 2422–2438.

  3. Zheng, W.; Tsai, M.-Y.; Wolynes, P. G.* Comparing the Aggregation Free Energy Landscapes of Amyloid Beta(1-42) and Amyloid Beta(1-40). J. Am. Chem. Soc. 2017, 139 (46), 16666–16676.

  4. Chen, M.; Tsai, M.-Y.; Zheng, W.; Wolynes, P. G.* The Aggregation Free Energy Landscapes of Polyglutamine Repeats. J. Am. Chem. Soc. 2016, 138 (46), 15197–15203.

  5. Zheng, W.; Tsai, M.-Y.; Chen, M.; Wolynes, P. G.* Exploring the Aggregation Free Energy Landscape of the Amyloid-β Protein (1-40). Proc. Natl. Acad. Sci. U. S. A. 2016, 113 (42), 11835–11840.

  6. Tsai, M.-Y.; Zhang, B.; Zheng, W.; Wolynes, P. G.* Molecular Mechanism of Facilitated Dissociation of Fis Protein from DNA. J. Am. Chem. Soc. 2016, 138 (41), 13497−13500.

  7. Parra, R. G.; Schafer, N. P.; Radusky, L. G.; Tsai, M.-Y.; Guzovsky, A. B.; Wolynes, P. G.; Ferreiro, D. U.* Protein Frustratometer 2: A Tool to Localize Energetic Frustration in Protein Molecules, Now with Electrostatics. Nucleic Acids Res. 2016, 44 (W1), W356–W360.

  8. Shiu, Y.-J.; Hayashi, M.; Shih, O.; Su, C.; Tsai, M.-Y.; Yeh, Y.-Q.; Su, C.-J.; Huang, Y.-S.; Lin, S.-H.; Jeng, U.-S.* Intrinsic Coordination for Revealing Local Structural Changes in Protein Folding-Unfolding. Phys. Chem. Chem. Phys. 2016, 18 (4), 3179–3187.

  9. Tsai, M.-Y.; Zheng, W.; Balamurugan, D.; Schafer, N. P.; Kim, B. L.; Cheung, M. S.; Wolynes, P. G.* Electrostatics, Structure Prediction, and the Energy Landscapes for Protein Folding and Binding. Protein Sci. 2016, 25 (1), 255–269.

  10. Tsai, M.-Y.*; Yuan, J.-M.; Lin, S.-H. Thermodynamic Insight into Protein Aggregation Using a Kinetic Ising Model. J Chin Chem Soc 2015, 62 (1), 21–25.

  11. Tsai, M.-Y.*; Yuan, J.-M.; Yamaki, M.; Lin, C.-K.; Lin, S. H. Molecular Dynamics Insight into the Diverse Thermodynamic Behavior of a Beta-Hairpin Peptide. J Chin Chem Soc 2013, 60 (7), 915–928.

  12. Lin, C.-K.*; Shih, C.-C.; Niu, Y.; Tsai, M.-Y.; Shiu, Y.-J.; Zhu, C.; Hayashi, M.; Lin, S. H. Theoretical Study on Structure and Sum-Frequency Generation (SFG) Spectroscopy of Styrene–Graphene Adsorption System. J. Phys. Chem. C 2013, 117 (4), 1754–1760.

  13. Tsai, M.-Y.*; Yuan, J.-M.; Teranishi, Y.; Lin, S. H. Thermodynamics of Protein Folding Using a Modified Wako-Saitô-Muñoz-Eaton Model. J. Biol. Phys. 2012, 38 (4), 543–571.

  14. Tsai, M. Y.*; Morozov, A. N.; Chu, K. Y.; Lin, S. H. Molecular Dynamics Insight into the Role of Tertiary (foldon) Interactions on Unfolding in Cytochrome c. Chem. Phys. Lett. 2009, 475 (1), 111–115.

  15. Morozov, A. N.*; Shiu, Y. J.; Liang, C. T.; Tsai, M. Y.; Lin, S. H. Nonadditive Interactions in Protein Folding: The Zipper Model of Cytochrome C. J. Biol. Phys. 2007, 33 (4), 255–270.

Book Chapters

  1. Tsai, M.-Y.*; Yuan, J.-M.; Lin, S. H. Chapter 6: Thermodynamics and Kinetics of Protein Folding and Aggregation. In Biophysics and Biochemistry of Protein Aggregation: Experimental and Theoretical Studies on Folding, Misfolding, and Self-Assembly of Amyloidogenic Peptides; Yuan, J.-M., Zhou, H.-X., Eds.; World Scientific, 2017.