Multiscale computational models in physical systems biology of intracellular trafficking

Cell adhesion defines the topology of endocytosis and signaling

(2014) Jean-Philippe Grossier et al.   EMBO JOURNAL

Defining the free-energy landscape of curvature-inducing proteins on membrane bilayers

(2014) Richard W. Tourdot et al.   PHYSICAL REVIEW E

Protein-Mediated Transformation of Lipid Vesicles into Tubular Networks

(2013) Mijo Simunovic et al.   BIOPHYSICAL JOURNAL

Membrane-Mediated Aggregation of Curvature-Inducing Nematogens and Membrane Tubulation

(2013) N. Ramakrishnan et al.   BIOPHYSICAL JOURNAL

Understanding the Role of Amphipathic Helices in N-BAR Domain Driven Membrane Remodeling

(2013) Haosheng Cui et al.   BIOPHYSICAL JOURNAL

Exo70 Generates Membrane Curvature for Morphogenesis and Cell Migration

(2013) Yuting Zhao et al.   DEVELOPMENTAL CELL

Martini Force Field Parameters for Glycolipids

(2013) César A. López et al.   Journal of Chemical Theory and Computation

Coarse-Grained Models for Protein-Cell Membrane Interactions

(2013) Ryan Bradley et al.   Polymers

Coarse-graining of multiprotein assemblies

(2012) Marissa G Saunders et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Molecular view on protein sorting into liquid-ordered membrane domains mediated by gangliosides and lipid anchors

(2012) Djurre H. de Jong et al.   FARADAY DISCUSSIONS

Membrane Binding and Self-Association of the Epsin N-Terminal Homology Domain

(2012) Chun-Liang Lai et al.   JOURNAL OF MOLECULAR BIOLOGY

Single Molecule Kinetics of ENTH Binding to Lipid Membranes

(2012) Sharon Rozovsky et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Curvature Sorting of Peripheral Proteins on Solid-Supported Wavy Membranes

(2012) Wan-Ting Hsieh et al.   LANGMUIR

Mesoscale simulations of curvature-inducing protein partitioning on lipid bilayer membranes in the presence of mean curvature fields

(2012) Jin Liu et al.   MOLECULAR PHYSICS

Mechanism of Membrane Curvature Sensing by Amphipathic Helix Containing Proteins

(2011) Haosheng Cui et al.   BIOPHYSICAL JOURNAL

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Systems biology and physical biology of clathrin-mediated endocytosis

(2011) Vyas Ramanan et al.   Integrative Biology

MDAnalysis: A toolkit for the analysis of molecular dynamics simulations

(2011) Naveen Michaud-Agrawal et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Modeling Anisotropic Elasticity of Fluid Membranes

(2011) N. Ramakrishnan et al.   MACROMOLECULAR THEORY AND SIMULATIONS

Membrane protein sequestering by ionic protein–lipid interactions

(2011) Geert van den Bogaart et al.   NATURE

Actin dynamics counteract membrane tension during clathrin-mediated endocytosis

(2011) Steeve Boulant et al.   NATURE CELL BIOLOGY

A High Precision Survey of the Molecular Dynamics of Mammalian Clathrin-Mediated Endocytosis

(2011) Marcus J. Taylor et al.   PLOS BIOLOGY

Trafficking and signaling in mammalian autophagy

(2010) Sharon A. Tooze et al.   IUBMB LIFE

g_membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation

(2010) Maarten G. Wolf et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Translation of the phosphoinositide code by PI effectors

(2010) Tatiana G Kutateladze   Nature Chemical Biology

Computational model for nanocarrier binding to endothelium validated using in vivo, in vitro, and atomic force microscopy experiments

(2010) J. Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Minimal Mesoscale Model for Protein-Mediated Vesiculation in Clathrin-Dependent Endocytosis

(2010) Neeraj J. Agrawal et al.   PLoS Computational Biology

Membrane-Bending Mechanism of Amphiphysin N-BAR Domains

(2009) Anton Arkhipov et al.   BIOPHYSICAL JOURNAL

New Insights into BAR Domain-Induced Membrane Remodeling

(2009) Gary S. Ayton et al.   BIOPHYSICAL JOURNAL

Chemokine receptor CXCR4 expression in hepatocellular carcinoma patients increases the risk of bone metastases and poor survival

(2009) Zuo-lin Xiang et al.   BMC CANCER

Inhibition of ALK Signaling for Cancer Therapy

(2009) Y. P. Mosse et al.   CLINICAL CANCER RESEARCH

Calculation of free energies in fluid membranes subject to heterogeneous curvature fields

(2009) Neeraj J. Agrawal et al.   PHYSICAL REVIEW E

3D Pressure Field in Lipid Membranes and Membrane-Protein Complexes

(2009) O. H. Samuli Ollila et al.   PHYSICAL REVIEW LETTERS

Simulations of Membrane Tubulation by Lattices of Amphiphysin N-BAR Domains

(2009) Ying Yin et al.   STRUCTURE

The Mechanochemistry of Endocytosis

(2009) Jian Liu et al.   PLOS BIOLOGY

Distinct Dynamics of Endocytic Clathrin-Coated Pits and Coated Plaques

(2009) Saveez Saffarian et al.   PLOS BIOLOGY

Factors Influencing Local Membrane Curvature Induction by N-BAR Domains as Revealed by Molecular Dynamics Simulations

(2008) Philip D. Blood et al.   BIOPHYSICAL JOURNAL

Membrane proteins: molecular dynamics simulations

(2008) E LINDAHL et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

The MARTINI Coarse-Grained Force Field: Extension to Proteins

(2008) Luca Monticelli et al.   Journal of Chemical Theory and Computation

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

Landscape of finite-temperature equilibrium behaviour of curvature-inducing proteins on a bilayer membrane explored using a linearized elastic free energy model

(2008) Neeraj J. Agrawal et al.   MOLECULAR PHYSICS

Membrane recognition by phospholipid-binding domains

(2008) Mark A. Lemmon   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Nucleation of membrane adhesions

(2008) Cheng-Zhong Zhang et al.   PHYSICAL REVIEW E

Membrane lipid segregation in endocytosis

(2008) Sarah A. Nowak et al.   PHYSICAL REVIEW E