Margaret E. Johnson

发表

NERDSS: a non-equilibrium simulator for multibody self-assembly at the cellular scale

Osman N. Yogurtcu, Matthew J Varga, Spencer Loggia, 2019, bioRxiv.

Interface-Resolved Network of Protein-Protein Interactions

Gerhard Hummer, Margaret E. Johnson, G. Hummer, 2013, PLoS Comput. Biol..

Stoichiometric balance of protein copy numbers is measurable and functionally significant in a protein-protein interaction network for yeast endocytosis

Margaret E. Johnson, David O. Holland, 2017, bioRxiv.

Cytosolic proteins can exploit membrane localization to trigger functional assembly

Margaret E. Johnson, Osman N. Yogurtçu, O. Yogurtçu, 2017, bioRxiv.

Understanding the interplay of structure and dynamics in liquids using coarse-grained models and experiment

Margaret E. Johnson, 2009 .

Current status of the AMOEBA polarizable force field.

Margaret E. Johnson, Pengyu Y. Ren, J. Ponder, 2010, The journal of physical chemistry. B.

Free-Propagator Reweighting Integrator for Single-Particle Dynamics in Reaction-Diffusion Models of Heterogeneous Protein-Protein Interaction Systems

Margaret E. Johnson, G. Hummer, 2014, Physical review. X.

An implicit lipid model for efficient reaction-diffusion simulations of protein binding to surfaces of arbitrary topology.

Margaret E. Johnson, A. Sodt, O. Yogurtçu, 2019, The Journal of chemical physics.

An implicit lipid model for efficient reaction-diffusion simulations of protein binding to surfaces of arbitrary topology

Margaret E. Johnson, A. Sodt, O. Yogurtçu, 2019, bioRxiv.

Theory of bi-molecular association dynamics in 2D for accurate model and experimental parameterization of binding rates.

Margaret E. Johnson, O. Yogurtçu, 2015, The Journal of chemical physics.

Assessing thermodynamic-dynamic relationships for waterlike liquids.

Margaret E. Johnson, T. Head-Gordon, T. Head‐Gordon, 2009, The Journal of chemical physics.

Protein-protein binding selectivity and network topology constrain global and local properties of interface binding networks

Margaret E. Johnson, David O. Holland, B. Shapiro, 2017, Scientific Reports.

Representability problems for coarse-grained water potentials.

Margaret E. Johnson, A. Louis, T. Head-Gordon, 2007, The Journal of chemical physics.

Nonspecific binding limits the number of proteins in a cell and shapes their interaction networks

Margaret E. Johnson, G. Hummer, 2010, Proceedings of the National Academy of Sciences.

Hydration water dynamics near biological interfaces.

Margaret E. Johnson, T. Head-Gordon, R. Murarka, 2009, The journal of physical chemistry. B.

Integrating protein copy numbers with interaction networks to quantify stoichiometry in mammalian endocytosis

Margaret E. Johnson, David O. Holland, D. Duan, 2020, bioRxiv.

Cytosolic proteins can exploit membrane localization to trigger functional assembly

Margaret E. Johnson, O. Yogurtçu, 2017, bioRxiv.

Stoichiometric balance of protein copy numbers is measurable and functionally significant in a protein-protein interaction network for yeast endocytosis

Margaret E. Johnson, David O. Holland, 2017, bioRxiv.

Thermodynamics and free energy landscape of BAR-domain dimerization from molecular simulations

Margaret E. Johnson, D. Mohammadyani, M. Varga, 2020, bioRxiv.

Physical Chemistry Chemical Physics This paper is published as part of a PCCP Themed Issue on: Water at interfaces

Margaret E. Johnson, M. Berkowitz, R. Murarka, 2008 .

Representability problems for coarse-grained water potentials.

Margaret E. Johnson, A. Louis, T. Head-Gordon, 2007, The Journal of chemical physics.

Large self-assembled clathrin lattices spontaneously disassemble without sufficient adaptor proteins

Margaret E. Johnson, A. Sodt, Si-Kao Guo, 2022, PLoS Comput. Biol..

Modeling membrane reshaping driven by dynamic protein assemblies.

Margaret E. Johnson, Yiben Fu, 2022, Current opinion in structural biology.

Aqueous peptides as experimental models for hydration water dynamics near protein surfaces.

Margaret E. Johnson, R. Murarka, C. Malardier-Jugroot, 2008, Physical chemistry chemical physics : PCCP.

Protein-protein binding selectivity and network topology constrain global and local properties of interface binding networks

Margaret E. Johnson, David O. Holland, B. Shapiro, 2017, Scientific Reports.

Defects in the HIV immature lattice support essential lattice remodeling within budded virions

Margaret E. Johnson, S. Saffarian, Ipsita Saha, 2022, bioRxiv.

Temporal control by co-factors prevents kinetic trapping in retroviral Gag lattice assembly

Margaret E. Johnson, Yiben Fu, B. Mishra, 2023, bioRxiv.

Speed limits of protein assembly with reversible membrane localization

Margaret E. Johnson, B. Mishra, 2021, bioRxiv.

Modeling the Self-Assembly of Protein Complexes through a Rigid-Body Rotational Reaction-Diffusion Algorithm.

Margaret E. Johnson, 2018, The journal of physical chemistry. B.

Integrating protein copy numbers with interaction networks to quantify stoichiometry in clathrin-mediated endocytosis

Margaret E. Johnson, David O. Holland, Meretta Hanson, 2022, Scientific Reports.

Evolutionary pressure on the topology of protein interface interaction networks.

Gerhard Hummer, Margaret E Johnson, Margaret E. Johnson, 2013, The journal of physical chemistry. B.

Tetrahedral structure or chains for liquid water.

Margaret E. Johnson, T. Head‐Gordon, 2006, Proceedings of the National Academy of Sciences of the United States of America.

Speed limits of protein assembly with reversible membrane localization.

Margaret E. Johnson, B. Mishra, 2021, The Journal of chemical physics.

Effects of co-solvents on peptide hydration water structure and dynamics.

Teresa Head-Gordon, Margaret E Johnson, Margaret E. Johnson, 2010, Physical chemistry chemical physics : PCCP.

Nascent clathrin lattices spontaneously disassemble without sufficient adaptor proteins

Margaret E. Johnson, A. Sodt, Sikao Guo, 2021, bioRxiv.

Structure of the HIV immature lattice allows for essential lattice remodeling within budded virions

Margaret E. Johnson, S. Saffarian, Ipsita Saha, 2023, eLife.

A continuum membrane model predicts curvature sensing by helix insertion

Margaret E. Johnson, Yiben Fu, J. Stachowiak, 2021, bioRxiv.

Structure and water dynamics of aqueous peptide solutions in the presence of co-solvents.

Margaret E. Johnson, A. Soper, C. Malardier-Jugroot, 2010, Physical chemistry chemical physics : PCCP.

Characterization of a dynamic string method for the construction of transition pathways in molecular reactions.

Gerhard Hummer, Margaret E Johnson, Margaret E. Johnson, 2012, The journal of physical chemistry. B.

Optimizing Protein Expression Levels as a Function of Network Topology Minimizes Nonfunctional Complex Formation

Margaret E. Johnson, David O. Holland, 2015 .

Quantifying the roles of space and stochasticity in computer simulations for cell biology and cellular biochemistry

Margaret E. Johnson, R. Murphy, M. Meier-Schellersheim, 2020, Molecular biology of the cell.

Theory of bi-molecular association dynamics in 2D for accurate model and experimental parameterization of binding rates.

Margaret E. Johnson, O. Yogurtçu, 2015, The Journal of chemical physics.