PUBLICATIONS

  1. Nernst Equilibrium, Rectification, and Saturation: Insights into Ion Channel Behavior R Carlsen, H Weckel-Dahman, JMJ Swanson (under review, 2024). bioRxiv: https://doi.org/10.1101/2024.08.16.608320

  2. Multiscale Responsive Kinetic Modeling: Quantifying Biomolecular Reaction Flux under Varying Electrochemical Conditions H Weckel-Dahman, R Carlsen, JMJ Swanson, (under review, 2024). bioRxiv: https://doi.org/10.1101/2024.08.01.606205

  3. Selective binding of MLX to triacylglycerol-rich lipid droplets: Mechanisms of cytosolic localization and proteome regulation JR Braun, JMJ Swanson, (under review, 2024). bioRxiv: https://doi.org/10.1101/2024.07.15.603605

  4. One Descriptor to Fold Them All: Harnessing Intuition and Machine Learning to Identify Transferable Lasso Peptide Reaction Coordinates GCM da Hora, MI Oh, JDM Nguyen, JMJ Swanson, Phys. Chem.B (2024) 128(17): 4063-4075.  Cover Story
  5. Lasso Peptides: Exploring the Folding Landscape of Nature’s Smallest Interlocked Motifs GCM da Hora, MI Oh, MC Mifflin, L Digal, AG Roberts, JMJ Swanson, Am. Chem. Soc. (2024) 146 (7): 4444-4454.  Cover Story
  6. Tld1 is a novel regulator of triglyceride lipolysis that demarcates a lipid droplet subpopulation. Speer NO, Braun JR, Reynolds EG, Swanson JMJ, Henne WM. J Cell Biol(2024) 223 (1): e202303026.
  7. tICA-Metadynamics for Identifying Slow Dynamics in Membrane Permeation, MI Oh, GCA da Hora, JMJ Swanson, Chem. Theory Comput. (2023) 19 (23) 8886-8900.
  8. Mycolactone A vs. B: Multiscale Simulations Reveal the Roles of Localization and Association in Isomer-Specific Toxicity, JDM Nguyen, GCA da Hora, JMJ Swanson, Toxins 15(8) 486-1-21 (2023).  Cover Story
  9. Can membrane composition traffic toxins? Mycolactone and preferential membrane interactions, GCM da Hora, JDM Nguyen, JMJ Swanson, Biophys. J. 121 4260-4270 (2022).
  10. Capturing the liquid-crystalline phase transformation: Implications for protein targeting to sterol ester-rich lipid droplets, JR Braun, JMJ Swanson, Membranes 12 949 (2022).
  11. Computational Studies of Lipid Droplets, S. Kim, JMJ Swanson, GA Voth J Phys. Chem. B—Feature Article 126 2145-2154 (2022).
  12. Multiscale Kinetic Analysis of Proteins, JMJ Swanson, Curr. Op. Struct. Biol. 72 169-175 (2021). PMCID: PMC9288830
  13. The CYTOLD and ERTOLD pathways for lipid droplet–protein targeting, MJ Olarte, JMJ Swanson, TC Walther, RV Farese, Trends Biochem. Sci. 47(1) 39-51 (2021).
  14. Toward a Multi-pathway Perspective: pH-Dependent Kinetic Selection of Competing Pathways and the Role of the Internal Glutamate in Cl–/H+ Antiporters, Z Yue, A Bernardi, C Li, AV Mironenko, JMJ Swanson, J. Phys. Chem. B 125, 7975-7984 (2021).
  15. Improving the accuracy and convergence of drug permeation simulations via machine-learned collective variables, F Aydin, AEP Durameric, GCA da Hora, JDM Nguyen, MI Oh, JMJ Swanson, J. Chem. Phys. 155, 045101-01-11  (2021).
  16. Stressed Lipid Droplets: How Neutral Lipids Relieve Surface Tension and Membrane Expansion Drives Protein Association, S Kim, MI Oh, JMJ Swanson, J. Phys. Chem. B 125, 5572-5586 (2021).
  17. CycFlowDec: A Python module for decomposing flow networks using simple cycles, A Bernardi, JMJ Swanson, SoftwareX 14 (2021).
  18. The Surface and Hydration Properties of Lipid Droplets, S Kim, JMJ Swanson, Biophys. J. 119, 1958-1969 (2020).
  19. Determinants of Endoplasmic Reticulum-to-Lipid Droplet Protein Targeting, MJ Olarte, S Kim, ME Sharp, JMJ Swanson, RV Farese, TC Walther, Dev. Cell 54, 471-487 (2020).
  20. Understanding and Tracking the Excess Proton in Ab Initio Simulations; Insights from IR Spectra, C Li, GA Voth, JMJ Swanson, J. Phys. Chem. B 124, 5696-5708 (2020).
  21. Dynamic Protonation Dramatically Affects the Membrane Permeability of Drug-Like Molecules, Z Yue, C Li, GA Voth, JMJ Swanson, J. Am. Chem. Soc. 141 13421-13433 (2019).
  22. Local Conformational Dynamics Regulating Transport Properties of a Cl-/H+ Antiporter, Z Wang, JMJ Swanson, GA Voth,  J. Comput. Chem. 41 (6), 513-519 (2019).
  23. Mycolactone Toxin Membrane Permeation: Atomistic versus Coarse-Grained MARTINI Simulations, F Aydin, R Sun, JMJ Swanson, Biophys. J., 117, 87-98 (2019).
  24. Proton Induced Conformational and Hydration Dynamics in the Influenza A M2 Channel, LC Watkins, R Liang, JMJ Swanson, WR DeGrado, GA Voth, J. Am. Chem. Soc. 141 11667-11676 (2019).
  25. Multiscale Kinetic Modeling Reveals an Ensemble of Cl-/H+ Exchange Pathways in ClC-ec1 Antiporter, HB Mayes, S Lee, GA Voth, JMJ Swanson, J. Am. Chem. Soc., 140, 1793-1804 (2018).
  26. Modulating the Chemical Transport Properties of a Transmembrane Antiporter via Alternative Anion Flux, Z Wang, JMJ Swanson, GA Voth, J. Am. Chem. Soc. 140, 16535-16543 (2018).
  27. Molecular Transport through Membranes: Accurate Permeability Coefficients from Multidimensional Potentials of Mean Force and Local Diffusion Constants, R Sun, Y Han, JMJ Swanson, JS Tan, JP Rose, GA Voth, J. Chem. Phys. 149, 072310-1-11 (2018).
  28. Computational Means of Assessing Proton Pumping in Cytochrome c Oxidase (Complex IV)”, JMJ Swanson, chapter in Mechanisms of Primary Energy Transduction in Biology, edited by Marten Wikström, Chemical Biology series from Royal Society of Chemistry, (2018).  
  29. Membrane Perturbing Properties of Toxin Mycolactone from Mycobacterium Ulcerans, C Lopez, C Unkefer, BI Swanson, JMJ Swanson, S Gnankaran, PLoS Comput. Biol., 14 (2), E1005972-1-22 (2018).
  30. Understanding the Essential Proton Pumping Kinetic Gates and Decoupling Mutations in Cytochrome c Oxidase, R Liang, GA Voth, M Wikström, JMJ Swanson, Proc. Natl. Acad. Sci. USA, 114, 5924-5929 (2017).
  31. Proton Movement and Coupling in the POT Family of Peptide Transporters, J Parker, C Li, A Brinth, Z Wang, L Vogeley, N Solcan, G Ledderboge-Vucnic, JMJ Swanson, M Caffrey, GA Voth, S Newstead, Proc. Natl. Acad. Sci. USA, 114 (50), 13182-13187 (2017).
  32. Acid Activation Mechanism of the Influenza A M2 Proton Channel, R Liang, JMJ Swanson, JJ Madsen, M Hong, WF DeGrado, GA Voth, Proc. Natl. Acad. Sci. USA, 113 (45), E6955–E6964 (2016).
  33. The Origin of Coupled Chloride and Proton Transport in a Cl–/H+ Antiporter, S Lee, HB Mayes, JMJ Swanson, GA Voth, J. Am. Chem. Soc., 138, 14923−14930 (2016).
  34. Coupling Protein Dynamics with Proton Transport in Human Carbonic Anhydrase II, S Taraphder, CM Maupin, JMJ Swanson, GA Voth, J. Phys. Chem. B, 120, 8389−8404 (2016).
  35. Multiscale Simulations Reveal Key Features of the Proton Pumping Mechanism in Cytochrome c Oxidase, R Liang, JMJ Swanson, Y Peng, M Wikström, GA Voth, Proc. Natl. Acad. Sci. USA, 113 (27), 7420-7425 (2016).
  36. Multiscale Simulations Reveal Key Aspects of the Proton Transport Mechanism in the ClC-ec1 Antiporter, S Lee, JMJ Swanson, GA Voth, Biophys. J., 110 (6), 1334-1345 (2016).
  37. Computationally Efficient Multiscale Reactive Molecular Dynamics to Describe Amino Acid Deprotonation in Proteins, S Lee, R Liang, GA Voth, JMJ Swanson, J. Chem. Theory Comput., 12 (2), 879-891 (2016).
  38. Hydrated Excess Protons Can Create Their Own Water Wires, Y Peng, JMJ Swanson, S Kang, R Zhou, GA Voth, J. Phys. Chem. B, 119 (29), 9212–9218 (2015).
  39. Multiscale Reactive Molecular Dynamics for Absolute pKa Predictions and Amino Acid Deprotonation, G Nelson, Y Peng, DW Silverstein, JMJ Swanson, J. Chem. Theory Comp., 10 (7), 2729-2737 (2014).
  40. Multiscale Simulation Reveals a Multifaceted Mechanism of Proton Permeation through the Influenza A M2 Channel, R Liang, H Li, JMJ Swanson, GA Voth, Proc. Natl. Acad. Sci. USA 111 (26), 9396-9401 (2014).
  41. Benchmark Study of the SCC-DFTB Approach for a Biomolecular Proton Channel, R Liang, JMJ Swanson, GA Voth, J. Chem. Theory Comp., 10 (1), 451-462 (2014).
  42. Using Force-Matching to Reveal Essential Differences between Density Functionals in Ab Initio Molecular Dynamics Simulations, S Izvekov, JMJ Swanson, J. Chem. Phys., 134, 194109-1-14 (2011).
  43. Intricate Role of Water in Proton Transport through Cytochrome c Oxidase, HJ Lee,*, E Svahn*, JMJ Swanson*, H Lepp, GA Voth, P Brzezinski, GB Gennis, JACS, 132 (45), 16225-16239 (2010) (*co-authors contributed equally to this work).
  44. The Role of Charge Transfer in the Structure and Dynamics of the Hydrated Proton, JMJ Swanson, Simons, J, J. Phys. Chem. B, 113 (15), 5149-5161 (2009).
  45. Coarse-Graining in Interaction Space, S Izvekov,*, JMJ Swanson*, GA Voth, J. Phys. Chem. B, 112 (15), 4711-4724 (2008) (*both co-authors contributed equally to this work).
  46. Proton Solvation and Transport in Aqueous and Biomolecular Systems: Insights from Computer Simulations, JMJ Swanson, CM Maupin, H Chen, MK Petersen, J Xu, Y Wu, GA Voth, J. Phys. Chem. B – Feature Article and Cover, 111, 17 (2007).
  47. Optimizing the Poisson-Boltzmann Dielectric Boundary with Explicit Solvent Forces and Energies: Lessons Learned with Atom-Centered Dielectric Functions, JMJ Swanson, JA Wagoner, NA Baker, JA McCammon, J. Chem. Theory Comput., 3, 170-183 (2007).
  48. Coupling Nonpolar and Polar Solvation Free Energies in Implicit Solvent Models, J Dzubiella, JMJ Swanson, JA McCammon, J. Chem. Phys., 124, 084905 (2006).
  49. Coupling Hydrophobicity, Dispersion, and Electrostatics in Continuum Solvent Models, J Dzubiella, JMJ Swanson, JA McCammon, Phys. Rev. Lett., 96, 087802 (2006).
  50. The Entropic Cost of Protein-Protein Association: A Case Study on Acetylcholinesterase Binding to Fasciculin-2, DDL Minh, JM Bui, CE Chang, T Jain, JMJ Swanson, JA McCammon, Biophys. J., 89, L25-L27 (2005).
  51. Limitations of Atom-Centered Dielectric Functions in Implicit Solvent Models, JMJ Swanson, J Mongan, and JA McCammon, J. Phys. Chem. B, 109, 31, 14769-14772 (2005).
  52. Optimized Radii for Poisson-Boltzmann Calculations with the AMBER Force Field, JMJ Swanson, SA Adcock, and JA McCammon, J. Chem. Theory Comput. 3, 484-493 (2005).
  53. Revisiting Free Energy Calculations: A Theoretical Connection to MM/PBSA and Direct Calculation of the Association Free Energy, JMJ Swanson, RH Henchman, and JA McCammon, Biophys. J., 86, 67-74 (2004).
  54. Computer Simulation of Water in Cytochrome C Oxidase, X Zheng, D Medvedev, J Swanson, A Stuchebrukhov, Biochim. Biophys. Acta, 1557, 99-107 (2003).
DEPARTMENT OF CHEMISTRY   |   HENRY EYRING CENTER FOR THEORETICAL CHEMISTRY   |   BIOPHYSICS AT THE U
BIOLOGICAL CHEMISTRY PROGRAM   |   CENTER FOR CELL AND GENOME SCIENCE