Mesoscale computational studies of membrane bilayer remodeling by curvature-inducing proteins

N Ramakrishnan, PBS Kumar, R Radhakrishnan - Physics reports, 2014 - Elsevier
Biological membranes constitute boundaries of cells and cell organelles. These membranes
are soft fluid interfaces whose thermodynamic states are dictated by bending moduli …

Systems biology and physical biology of clathrin-mediated endocytosis

V Ramanan, NJ Agrawal, J Liu, S Engles… - Integrative …, 2011 - academic.oup.com
In this review, we describe the application of experimental data and modeling of intracellular
endocytic trafficking mechanisms with a focus on the process of clathrin-mediated …

Minimal mesoscale model for protein-mediated vesiculation in clathrin-dependent endocytosis

NJ Agrawal, J Nukpezah… - PLoS computational …, 2010 - journals.plos.org
In eukaryotic cells, the internalization of extracellular cargo via the endocytic machinery is an
important regulatory process required for many essential cellular functions. The role of …

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

RW Tourdot, N Ramakrishnan, R Radhakrishnan - Physical Review E, 2014 - APS
Curvature-sensing and curvature-remodeling proteins, such as Amphiphysin, Epsin, and
Exo70, are known to reshape cell membranes, and this remodeling event is essential for key …

Multiscale computational models in physical systems biology of intracellular trafficking

RW Tourdot, RP Bradley, N Ramakrishnan… - IET systems …, 2014 - Wiley Online Library
In intracellular trafficking, a definitive understanding of the interplay between protein binding
and membrane morphology remains incomplete. The authors describe a computational …

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

J Liu, R Tourdot, V Ramanan, NJ Agrawal… - Molecular …, 2012 - Taylor & Francis
The membrane-surface migration of curvature-inducing proteins in response to membrane
curvature gradients has been investigated using Monte Carlo simulations of a curvilinear …

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

NJ Agrawal, R Radhakrishnan - Physical Review E—Statistical, Nonlinear, and …, 2009 - APS
We present a computational methodology for incorporating thermal effects and calculating
relative free energies for elastic fluid membranes subject to spatially dependent intrinsic …

A dual-scale model for the caveolin-mediated vesiculation

X Liang, Y Zu, YP Cao, C Yang - Soft Matter, 2013 - pubs.rsc.org
Caveolae-mediated vesiculation refers to the∼ 100 nm cave-like plasma membrane
invaginations, which function as macromolecular transport vesicles that regulate cellular …

Towards biomolecular simulations with explicit inclusion of polarizability: development of a CHARMM polarizable force field based on the classical Drude oscillator …

CM Baker, E Darian, AD MacKerell Jr - 2012 - books.rsc.org
Over the past fifty years, molecular mechanics (MM) has become firmly established as an
important tool in the study of biomolecular systems. It has revolutionized the understanding …

Phenomenology based multiscale models as tools to understand cell membrane and organelle morphologies

R Natesan, R Radhakrishnan - Advances in planar lipid bilayers and …, 2015 - Elsevier
An intriguing question in cell biology is “how do cells regulate their shape?” It is commonly
believed that the observed cellular morphologies are a result of the complex interaction …