Publications | Johnson Group | Johns Hopkins University

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Sang, M., Johnson, M.E.* Mechanisms of enhanced or impaired DNA target selectivity driven by protein dimerization. Submitted bioRxiv: doi: 10.1101/2025.02.18.638941 (2025).
Jhaveri, A., Chhibber, S., Kulkarni, N., Johnson, M.E.* Protein dimerization in 2D vs 3D: geometric allostery enhances binding affinity. Submitted, under review bioRxiv: doi: 10.1101/2025.01.16.633485 (2025).
Guo, S., Korolija, N., Milfeld, K., Jhaveri, A., Sang, M., Ying, Y., Johnson, M.E.* Parallelization of particle-based reaction-diffusion simulations using MPI J. Computational Chemistry 46:e70132. bioRxiv preprint (2025).
Soubias, O., S. L. Foley, X. Jian, R. A. Jackson, Y. Zhang, E. M. Rosenberg Jr, J.s Li, F. Heinrich, M. E. Johnson, A. J. Sodt, P. A. Randazzo and R. A. Byrd. The PH domain in the ArfGAP ASAP1 drives catalytic activation through an unprecedented allosteric mechanism, Under Review, Nat Comm bioRxiv preprint (2024).
Feng, X.A., Maryam, Y., Fu, Y., Ness, K.M., Liu, C.,Ahmed, I., Bowman, G.D., Johnson, M.E., Ha, T.J., Wu, C. GAGA Zinc finger transcription factor searches chromatin by 1D-3D facilitated diffusion. Accepted, Nat Struct Mol Biol preprint (2025).
Jhaveri, A.^#, Loggia, S.^#, Qian, Y., & Johnson, M.E.* Discovering optimal kinetic pathways for self-assembly using automatic differentiation. PNAS USA, 121 e2403384121 preprint (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. Nature Communications, 15 4060 preprint (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. Under review preprint (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. preprint (2023).
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 preprint (2023).
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 preprint (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. preprint (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 preprint. (2020).
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. preprint. (2018).
Yogurtcu, O.N., and M.E. Johnson*. Cytosolic proteins can exploit membrane localization to trigger functional assembly. PLoS Comput. Biology 14, e1006031 preprint (2018).
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).