Publications | Johnson Group | Johns Hopkins University

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Jhaveri, A.^#, Loggia, S.^#, Qian, Y., & Johnson, M.E.* Discovering optimal kinetic pathways for self-assembly using automatic differentiation. Accepted, PNAS USA, (2024).
Jiang, A., Gormal, R.S., Wallis, T., Robinson, P.J., Johnson, M.E., Joensuu, M., Meunier, F.A. Dynamin1 long- and short-tail isoforms exploit distinct recruitment and spatial patterns to form endocytic nanoclusters. Accepted, Nature Communications (2024).
Fu, Y., Johnson, D., Beaven, A., Sodt, A., Zeno, W.,& Johnson, M.E.*, Predicting how lipid composition controls protein curvature sensing with a continuum bilayer membrane model. bioRxiv: doi:10.1101/2024.01.15.575755 (2024).
Xie, Q., Lee, S.O., Vissamsetti, N., Guo, S., Johnson, M.E., Fried, S.D. Secretion-Catalyzed Assembly of Protein Biomaterials on a Bacterial Membrane Surface. Angewantde Chemie, e202305178 (2023).
Qian, Y.^#, Evans, D.^#, Mishra, B., Fu, Y., Liu, Z., Guo, S. & Johnson, M.E.* Temporal control by co-factors prevents kinetic trapping in retroviral Gag lattice assembly Biophysical Journal, 122, 1-18. (2023) bioRxiv version
Guo, S., Saha, I., Saffarian, S., & Johnson, M.E.* Structure of the HIV immature lattice allows for essential lattice remodeling within budded virions. eLife 84881 (2023). bioRxiv version
Fu, Y., & Johnson, M.E.* Modeling membrane reshaping driven by dynamic protein assemblies. Curr Opin Struct Biol 78, 102505 (2023).
Guo, S., Sodt, A.J., & Johnson, M.E.* Large self-assembled clathrin lattices spontaneously disassemble without sufficient adaptor proteins. PLoS Comp. Biol. 18, e1009969 (2022).
Duan, D, M. Hanson, D.O. Holland, & M.E. Johnson* Integrating protein copy numbers with interaction networks to quantify stoichiometry in mammalian endocytosis. Sci. Reports, 12, 5413. (2022).
Fu, Y., Zeno, W., Stachowiak, J. & Johnson, M.E.* A continuum membrane model can predict curvature sensing by helix insertion. Soft Matter 17, 10649 (2021).
Mishra, B., & M.E. Johnson* Speed limits of protein assembly with reversible membrane localization. J. Chem. Phys. 154, 194101.(2021)
Jhaveri, A., Maisuria, D., Varga, M., Mohammadyani, D., & M.E. Johnson* Thermodynamics and free energy landscape of BAR-domain dimerization from molecular simulations. J Phys Chem B. 125, 3739-3751. (2021).
Johnson, M.E.*, A. Chen, J. Faeder, P. Henning, I. Moraru, M. Meier-Schellersheim, R. Murphy, T. Prustel, J. Theriot, A. Uhrmacher. Quantifying the roles of space and stochasticity in computer simulations of cell biology and cellular biochemistry. Mol Biol of Cell. 32, 186-210. bioRxiv version (2021).
Varga, M.^#, Fu, Y.^#, Loggia, S., Yogurtcu, O.N., & M.E. Johnson* NERDSS: a nonequilibrium simulator for multibody self-assembly at the cellular scale. Biophysical Journal 118, P3026-P3040 (2020). bioRxiv version.
Fu, Y., Yogurtcu, O.N., Kothari, R., Thorkelsdottir, G., Sodt, A.J., & M.E. Johnson* An implicit lipid model for efficient reaction-diffusion simulations of protein binding to surfaces of arbitrary topology. J Chem Phys 151, 124115. (2019). bioRxiv version.
M.E. Johnson* Modeling the Self-Assembly of Protein Complexes through a Rigid-Body Rotational Reaction-Diffusion Algorithm. J Phys Chem B. 122, 11771-11783 (2018).
Holland, D.O., & M.E. Johnson* Stoichiometric Balance of protein copy numbers is measurable and functionally significant in a protein-protein interaction network for yeast endocytosis. PLoS Comput. Biology 14, e1006022. (2018). bioRxiv preprint: https://doi.org/10.1101/205674.
Yogurtcu, O.N., and M.E. Johnson*. Cytosolic proteins can exploit membrane localization to trigger functional assembly. PLoS Comput. Biology 14, e1006031 (2018) bioRxiv preprint: https://doi.org/10.1101/164152.
Holland, D.O., Shapiro, B.H., Xue, P., & M.E. Johnson* Protein-protein binding selectivity and network topology constrain global and local properties of interface binding networks. Sci. Reports. 7, 5631 (2017).
Yogurtcu, O.N., and M.E. Johnson*. Theory of bi-molecular association dynamics in 2D for accurate model and experimental parameterization of binding rates. J. Chem. Phys. 143, 084117 (2015).
Johnson, M.E.*, and G. Hummer. Free propagator reweighting integrator for single-particle dynamics in reaction-diffusion models of heterogeneous protein-protein interactions systems. Phys. Rev. X 4, 031037 (2014).
Johnson, M.E.*, and G. Hummer. Interface-resolved network of protein-protein interactions.PLoS Comput. Biol. 9, e1003065 (2013).
Johnson, M.E., and G. Hummer. Evolutionary Pressure on the Topology of Protein Interface Interaction Networks. J. Phys. Chem. B. 117, 13098-13106 (2013).
Johnson, M.E., and G. Hummer. Characterization of a dynamic string method for the construction of transition pathways in molecular reactions. J. Phys. Chem. B. 116, 8573-83 (2012).
Johnson, M.E., and G. Hummer. Nonspecific binding limits the number of proteins in a cell and shapes their interaction topology. PNAS USA. 106, 138-142 (2011).
Ponder, J.W., C.J. Wu, P.Y. Ren, V.S. Pande, J.D. Chodera, M.J. Schneiders, I. Haque, D.L. Mobley, D.S. Lambrecht, R.A. DiStasio, M. Head-Gordon, G.N.I. Clark, M.E. Johnson, T. Head-Gordon. Current Status of the AMOEBA polarizable force field. J. Phys. Chem. B. 114, 2549-2564 (2010).
Johnson, M.E.*, C. Malardier Jugroot, and T. Head-Gordon. Effects of cosolvents on peptide hydration water structure and dynamics. Phys. Chem. Chem. Phys. 12, 393-405 (2010).
Malardier-Jugroot, C., D.T. Bowron, A.K. Soper, M.E. Johnson, and T. Head-Gordon. 2010. Structure and water dynamics of aqueous peptide solutions in the presence of co-solvents. Phys. Chem. Chem. Phys. 12, 382-392 (2010).
Johnson, M.E., and T. Head-Gordon. Assessing thermodynamic-dynamic relationships for waterlike liquids. J. Chem. Phys. 130, 214510 (2009).
Johnson, M.E., C. Malardier-Jugroot, R.K. Murarka, and T. Head-Gordon. Hydration water dynamics near biological interfaces. J. Phys. Chem. B. 113, 4080-4092 (2009).
Malardier-Jugroot, C., M.E. Johnson, R.K. Murarka, and T. Head-Gordon. Aqueous peptides as experimental models for hydration water dynamics near protein surfaces. Phys. Chem. Chem. Phys. 10, 4903-4908 (2008).
Johnson, M.E., T. Head-Gordon, and A.A. Louis. Representability problems for coarse grained water potentials. J. Chem. Phys. 126, 144500 (2007).
Head-Gordon, T., and M.E. Johnson. Tetrahedral structure of chains for liquid water. PNAS USA 103, 7973-7977 (2006).