PUBLICATIONS 2024 21. Limbach, M. N.; Lindberg, E. T.; Olivos, H.; van Tetering, L.; Carlos, S. A.; Martens, J.; Ngo, V. A.; Oomens, J.; Do, T. D. Taming Conformational Heterogeneity on Ion Racetrack to Unveil Principles that Drive Membrane Permeation of Cyclosporines. JACS Au 2024, ASAP PDF. 20. Hirschbeck, S. S.; Lindberg, E. T.; Jang, J. H.; MaKenna, J. R.; Lazar Cantrell, K. L.; Do, T. D. Investigating a novel neurodegenerative disease toxic mechanism involving lipid binding specificity of amyloid oligomers. ACS Chem. Neurosci. 2024, 15, 1523-1532. PDF 19. Nkyaagye, E.; Limbach, M. N.; Do, T. D. Molecular Selectivity in the Binding of Alkali Metals, Alkaline Earth Metals, First-Row Transition Metals, and Lanthanides with Cyclic Depsipeptides. J. Phys. Chem. B 2024, 128, 5, 1209–1219. PDF 2023 18. Limbach, M. N.; Do, T. D. Solvent-Free Nuclear Magnetic Resonance Spectroscopy of Charged Molecules. J. Phys. Chem. A 2023, 127, 9149-9157. PDF Correction PDF 17. Oluwatoba, D. S.; Chakraborty, P.; Bar-Yosef, D.; Limbach, M. N.; Gazit, E.; Do, T. D. The self-assembly of cysteine into nano-fibrils precedes cystine crystal formation: Implications for aggregation inhibition. ACS Appl. Mater. Interfaces 2023, 15, 32177-32187. PDF 16. Long, C. C.; Antevska, A.; Mast, D.; Okyem, S.; Sweedler, J. V.; Do, T. D. Non-Enzymatic Posttranslational Modifications and Peptide Cleavages Observed in Peptide Epimers. J. Am. Soc. Mass Spectrom. Focus: 2023 Emerging Investigators, 2023, 34, 1898-1907. PDF 15. Gray, A. L. H.; Norman, V. N.; Oluwatoba, D. S.; Prosser, R. A. ; Do, T. D. Potential Protective Function of Aβ42 Monomer on Tauopathies. J. Am. Soc. Mass Spectrom. Special Focus Issue on Neurodegenerative Disease Research, 2023, 34, 472-483. PDF 14. Antevska, A.; Long, C. C.; Dupuy, S. D.; Collier, J. J.; Karlstad, M. D.; Do, T. D. Mouse Pancreatic Peptide Hormones Probed at the Sub-Single-Islet Level: The Effects of Acute Corticosterone Treatment. J. Proteome Res. 2023, 22, 235-245. PDF 2022 13. Russell, C. M.; Schaefer, K. G.; Dixson, A.; Gray, A. L. H.; Pyron, R. J.; Alves, D. S.; Moore, N.; Conley, E. A.; Schuck, R. J.; White, T. A.; Do, T. D.; King, G. M.; Barrera, F. N. The Candida albicans virulence factor candidalysin polymerizes in solution to form membrane pores and damage epithelial cells. Elife 2022, 11:e75490. PDF 12. Limbach, M. N.1; Antevska, A.1; Oluwatoba, D. S.; Gray, A. L. H.; Carroll, X. B.; Hoffmann, C. M.; Wang, X.; Voehler, M. W.; Steren, C. A.; Do, T. D. Atomic View of Aqueous Cyclosporine A: Unpacking a Decades-Old Mystery. J. Am. Chem. Soc. 2022, 144, 12602-12607. PDF. CCDC 2149649-2149650 11. Oluwatoba, D. S.; Islam, Md F.; Som, B.; Sindt, A. J.; Smith, M. D.; Shimizu, L. S.; Do, T. D. Evaluating the Effects of Metal Adduction and Charge Isomerism on Ion-Mobility Measurements using m-xylene Macrocycles as Models. J. Am. Soc. Mass Spectrom. 2022, 33, 840-850. PDF 10. Gray, A. L. H.; Sawaya, M. R.; Acharyya, D.; Jinchao, L.; Edington, E.; Best, M. D.; Prosser, R. A.; Eisenberg, D. S.; Do, T. D. Atomic View of an Amyloid Dodecamer Exhibiting Selective Cellular Toxic Vulnerability in Acute Brain Slices. Protein Science 2022, 31 (3), 716-727. PDF, PDB ID: 7ROJ, 7ROL 2021 9. Hossain, M. S.; Sindt, A. J.; Goodlett, D. W.; Shields, D.; O'Connor, C. J.; Antevska, A.; Karakalos, S. G.; Smith, M. D.; Garashchuk, S.; Do, T. D.; Gudmundsdottir, A. D.; Shimizu, L. S. Effects of Self-assembly on the Photogeneration of Radical Cations in Halogenated Triphenylamines. J. Phys. Chem. C 2021, 125, 19991-20002. PDF 8. Sade Yazdi, D.; Bar-Yosef, D. L.; Adsi, H.; Kreiser, T.; Sigal, S.; Bera, S.; Zaguri, D.; Shaham-Niv, S.; Oluwatoba, D. S.; Levy, D.; Gartner, M.; Do, T. D.; Frenkel, D.; Gazit, E. Homocysteine fibrillar assemblies display cross-talk with Alzheimer's disease β-amyloid polypeptide. Proc. Natl. Acad. Sci. U.S.A. 2021, 118 (24), e2017575118. PDF 7. Gray, A. L. H.1; Antevska, A.1; Link, B. A.; Bogin, B.; Burke, S.; Dupuy, S.; Collier, J. J.; Levine, Z.; Karlstad, M.; Do, T. D. α-CGRP Disrupts Amylin Fibrillization and Regulates Insulin Secretion: Implications on Diabetes and Migraine. Chem. Sci. 2021, 12, 5853-5864. PDF 6. Gray, A. L. H.; Steren, C. A.; Haynes, I. W.; Bermejo, G. A.; Favretto, F.; Zweckstetter, M.; Do, T. D. Structural Flexibility of Cyclosporine A is Mediated by Amide Cis-Trans Isomerization and the Chameleonic Roles of Calcium. J. Phys. Chem. B 2021, 125, 1378-1391. PDF 2020 5. Gray, A. L. H.; Antevska, A.; Oluwatoba, D. S.; Schonfield, G.; Lazar-Cantrell, K. L.; Do, T. D. Cytotoxicity of α-Helical, Staphylococcus Aureus PSMα3 Investigated by Post Ion-Mobility Dissociation Mass Spectrometry. Anal. Chem. 2020, 92, 11802-11808. PDF 4. Link, B. A.; Ammon, S. J.; Shimizu, L. S.; Do, T. D. Selective Host-Guest Chemistry, Self-Assembly and Conformational Preferences of m-Xylene Macrocycles Probed by Ion-Mobility Spectrometry Mass Spectrometry. Phys. Chem. Chem. Phys. 2020, 20, 9290 - 9300. PDF 2019 3. Haynes, I.; Wu, G.; Haque, Md A.; Li, H.; Do, T. D. Conformational Preference of Macrocycles Investigated by Ion-Mobility Mass Spectrometry and Distance Geometry Modeling. Anal. Chem. 2019, 91, 13439 - 13447. PDF 2. Laos, V.; Do, T. D. ; Bishop, D.; Jin, Y.; Marsh, N.; Quon, B.; Korff, M.; Lazar-Cantrell, K. L.; Buratto, S. K., Bowers, M. T. Characterizing TDP-43(307-319) Oligomeric Assembly to Elucidate Mechanistic and Structural Implications Involved in the Etiology of ALS. ACS Chem. Neurosci. 2019, 10, 4112 - 4123 PDF 1. Neumann, E. K.; Do, T. D. ; Comi, T. J.; Sweedler, J. V. Exploring the Fundamental Structures of Life: Non-targeted, Chemical Analysis of Single Cells and Subcellular Structures. Angew. Chem., Int. Ed. 2019, 31, 9448 - 9465. PDF PRIOR TO UT (07.2010 - 07.2018) 29. Do, T. D.; Checco, J. W.; Tro, M.; Shea, J.-E.; Bowers, M. T. ; Sweedler, J. V. Conformational investigation of the structure–activity relationship of GdFFD and its analogues on an achatin-like neuropeptide receptor of Aplysia californica involved in the feeding circuit . Phys. Chem. Chem. Phys. 2018 , 20, 22047 - 22057. PDF (Co-corresponding author). 28. Do, T. D. ; Ellis, J. F.; Neumann, E. K.; Comi, T. J.; Tillmaand, E.; Lenhart, A.; Rubakhin, S.; Sweedler, J. V. Optically-Guided Single Cell Mass Spectrometry of Rat Dorsal Root Ganglia to Profile Lipids, Peptides and Proteins. ChemPhysChem 2018, 19, 1180 - 1191. PDF 27. Do, T. D. ; Sangwan, S.; de Almeida, N. E. C.; Ilitchev, A. I.; Giammona, M.; Buratto, S. K.; Eisenberg, D.; Bowers, M. T. Distal Amyloid β-Protein Fragments Template Amyloid Assembly. Protein Sci. 2018, 27, 1181-1190. PDF 26. Sangwan, S.; Zhao, A.; Adams, K. L.; Jayson, C. K.; Sawaya, M. R.; Guenther, E. L.; Pan, A. C.; Ngo, J.; Moore, D.; Soriaga, A. B.; Do, T. D.; Goldsmith, L.; Nelson, R.; Bowers, M. T.; Koehler, C. M.; Shaw, D. E.; Novitch, B. G.; Eisenberg, D. S. Atomic Structure of a Toxic, Oligomeric Segment of SOD1 Linked to Amyotrophic Lateral Sclerosis (ALS). Proc. Natl. Acad. Sci. U.S.A. 2017, 114, 8770 - 8775. PDF 25. Comi, T. J.; Neumann, K. E.; Do, T. D.; Sweedler, J. V. microMS: A Python Platform for Image-guided Mass Spectrometry Profiling. J. Am. Soc. Mass Spectrom. 2017, 28, 1919 - 1928. PDF 24. Comi, T. J.; Do, T. D.; Rubakhin, S.; Sweedler, J. V. Categorizing Cells based on their Chemical Profiles: Progress in Single Cell Mass Spectrometry. J. Am. Chem. Soc. 2017, 139, 3920 - 3929. (Perspective) PDF 23. Do, T. D.; Comi, T. J.; Dunham, S. J. B.; Rubakhin, S.; Sweedler, J. V. Single Cell Profiling using Ionic Liquid Enhanced Secondary Ion Mass Spectrometry for Neuronal Cell Type Differentiation. Anal. Chem. 2017, 89, 3078 - 3086. PDF 22. de Almeida, N. E. C.; Do, T. D.; Tro, M.; LaPointe, N. E.; Feinstein, S. C.; Shea, J.-E.; Bowers, M. T. 1,2,3,4,6-penta-O-galloyl-β-D-glucopyranose Binds to the N-terminal Metal Binding Region to Inhibit Amyloid-β protein Oligomer and Fibril Formation. Int. J. Mass Spectrom. 2017, 420, 24 - 34. PDF 21. Kim, B.; Do, T. D.; Hayden, E. Y.; Teplow, D. B.; Bowers, M. T., Shea, J.-E. Aggregation of Chameleon Peptides: Implications of a-Helicity in Fibril Formation. J. Phys. Chem. B 2016 , 120, 5874 - 5883. PDF 20. Feinstein, H. E.; Benbow, S. J.; LaPointe, N. E.; Patel, N.; Ramachandran, S.; Do, T. D.; Gaylord, M. R.; Huskey, N. E.; Dressler N.; Korff M.; Quon, B.; Lazar Cantrell, K.; Bowers, M. T.; Lal, R.; Feinstein, S. C. Oligomerization of the Microtubule Associated Protein Tau is Mediated by its N-terminal Sequences: Implications for Normal and Pathological Tau Action. J. Neurochem. 2016, 137, 939 - 954. PDF (Co-first author) 19. Economou, N. J.; Giammona, M. J.; Do, T. D.; Zheng, X.; Teplow, D. B.; Buratto, S. K.; Bowers, M. T. Amyloid β-protein Assembly: Dodecamers of Aβ42, but not of Aβ40, Seed Fibril Formation. J. Am. Chem. Soc. 2016, 138, 1772 - 1775. PDF 18. Ilitchev, A.; Giammona, M.; Do, T. D.; Shea, J.-E.; Buratto, S. K.; Bowers, M. T. N-Terminus Disulfide Bond of Human Islet Amyloid Polypeptide: Fragment Self-Assembly and Impact on Full Peptide Aggregation. J. Am. Soc. Mass Spectrom. 2016, 27, 1010 - 1018. PDF 17. de Almeida, N. E. C.; Do, T. D.; Tro, M.; LaPointe, N. E.; Feinstein, S. C.; Shea, J.-E.; Bowers, M. T. The Opposite Effects of Cucurbit[7]uril and 1,2,3,4,6-penta-O-galloyl-β-D-glucopyranose on Amyloid Aβ(25-35) Assembly. ACS Chem. Neurosci. 2016, 7, 218 - 226. PDF (Co-first author) 16. Do, T. D.; LaPointe, N. E.; Nelson, R.; Kortee, P.; Feinstein, S. C.; Teplow, D. B.; Eisenberg, D.; Shea, J.-E.; Bowers, M. T. Amyloid β-Protein C-terminal Fragments: Formation of Cylindrins and β-Barrels. J. Am. Chem. Soc. 2016, 138, 549 - 557. PDF 15. Do, T. D.; de Almeida, N. E. C.; LaPointe, N. E.; Chamas, A.; Feinstein, S. C.; Bowers, M. T. Amino Acid Metaclusters: Implications of Growth Trends on Peptide Self-Assembly. Anal. Chem. 2016, 88, 868 - 876. PDF (A. C. is undergraduate mentee) 14. Eschmann, N. A.; Do, T. D.; LaPointe, N. E.; Shea, J.-E.; Feinstein, S. C.; Bowers, M. T.; Han, S. Tau Aggregation Propensity Engrained in its Solution State. J. Phys. Chem. B 2015, 119, 14421 - 14432. PDF (Co-first author) 13. Do, T. D.; Kincannon, W. M.; Bowers, M. T. Phenylalanine Oligomers and Fibrils: The Mechanism of Assembly and the Importance of Tetramers and Counter Ions. J. Am. Chem. Soc. 2015, 137, 10080 -10083. PDF (W. K. is undergraduate mentee) 12. Do, T. D.; Chamas, A.; Zheng, X.; Barnes, A.; Chang, D.; Veldstra, T.; Takhar, H.; Dressler, N.; Trapp, B.; Miller, K.; McMahon, A.; Meredith S. C.; Shea, J.-E.; Lazar Cantrell, K.; Bowers, M. T. Elucidation of the Aggregation Pathways of Helix-Turn-Helix Peptides: Stabilization at the Turn Region is Critical for Fibril Formation. Biochemistry 2015, 54, 4050 - 4062. PDF (A. C. is undergraduate mentee) 11. Ganguly, P.; Do, T. D.; Larini, L.; LaPointe, N. E.; Feinstein, S. C.; Bowers, M. T.; Shea, J.-E. Tau Assembly: The Dominant Role of PHF6 (VQIVYK) in Microtubule Binding Region Repeat R3. J. Phys. Chem. B 2015, 119, 4582 - 4593. PDF 10. Do, T. D.; Bowers, M. T. Diphenylalanine Self Assembly: Novel Ion Mobility Methods Show the Essential Role of Water. Anal. Chem. 2015, 87, 4245 - 4252. PDF 9. Do, T. D.; Economou, N. J.; Chamas, A.; Buratto, S. K.; Shea, J.-E.; Bowers, M. T. Interactions between Amyloid-β and Tau Fragments Promote Aberrant Aggregates: Implications for Amyloid Toxicity. J. Phys. Chem. B 2014, 118, 11200 - 11230. PDF (A. C. is undergraduate mentee) 8. Do, T. D.; LaPointe, N. E.; Sangwan, S.; Teplow, D. B.; Feinstein, S. C.; Sawaya, M. R.; Eisenberg, D. S.; Bowers, M. T. Factors that Drive Peptide Assembly from Native to Amyloid Assembly: Experimental and Theoretical Analysis of [Leu-5]-Enkephalin Mutants. J. Phys. Chem. B 2014, 118, 7247 - 7256. PDF 7. Rowley, J. G.; Do, T. D.; Cleary, D. A.; Parkinson, B. A. Combinatorial Discovery Through a Distributed Outreach Program: Investigation of the Photoelectrolysis Activity of p-type Fe, Cr, Al Oxide. ACS Appl. Mater. Interfaces 2014, 6, 9046 - 9052. PDF 6. Bleiholder, C.; Do, T. D.; Wu, C.; Economou, N. J.; Bernstein, S. S.; Buratto, S. K.; Shea, J.-E.; Bowers, M. T. Ion Mobility Spectrometry Reveals the Mechanism of Amyloid Formation of Aβ(25-35) and its Modulation by Inhibitors at the Molecular Level: Epigallocatechin gallate and scyllo-inositol. J. Am. Chem. Soc. 2013, 135, 16926 - 16937. PDF (Co-first author) 5. Do, T. D.; LaPointe, N. E.; Economou, N. J.; Buratto, S. K.; Feinstein, S. C.; Shea, J.-E.; Bowers, M. T. Effects of pH and Charge State on Peptide Assembly: the YVIFL Model System. J. Phys. Chem. B 2013, 117, 10759 - 10768. PDF 4. Do, T. D.; Economou, N. J.; LaPointe, N. E.; Kincannon, W.; Buratto, S. K.; Feinstein, S. C.; Teplow, D. B.; Bowers, M. T. Factors That Drive Peptide Assembly and Fibril Formation: Experimental and Theoretical Analysis of Sup35 NNQQNY Mutants. J. Phys. Chem. B 2013, 117, 8436 - 8446. PDF (W. K. is undergraduate mentee) 3. Larini, L.; Gessel, M. M.; LaPointe, N. E.; Do, T. D.; Bowers, M. T.; Feinstein, S. C.; Shea, J.-E. Initiation of Assembly of Tau(273-284) and its ΔK280 Mutant: An Experimental and Computational Study. Phys. Chem. Chem. Phys. 2013, 15, 8916 - 8928. PDF (Co-first author) 2. Bleiholder, C.; Contreras, S.; Do, T. D.; Bowers, M. T. A Novel Projection Approximation Algorithm for the Fast and Accurate Computation of Molecular Collision Cross Sections (II). Model parameterization and definition of empirical shape factors for proteins. Int. J. Mass Spectrom. 2013, 345-347, 89 - 96. PDF 1. Warren, G. L.; Do, T. D.; Kelley, B. P; Nicholls, A; Warren, S. D. Essential Considerations for Using Protein-Ligand Structures in Drug Discovery. Drug Discov. Today 2012, 17, 1270 - 1281. PDF