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

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          Abstract

          Epsin possesses a conserved epsin N-terminal homology (ENTH) domain that acts as a phosphatidylinositol 4,5-bisphosphate‐lipid‐targeting and membrane‐curvature‐generating element. Upon binding phosphatidylinositol 4,5‐bisphosphate, the N-terminal helix (H 0) of the ENTH domain becomes structured and aids in the aggregation of ENTH domains, which results in extensive membrane remodeling. In this article, atomistic and coarse-grained (CG) molecular dynamics (MD) simulations are used to investigate the structure and the stability of ENTH domain aggregates on lipid bilayers. EPR experiments are also reported for systems composed of different ENTH-bound membrane morphologies, including membrane vesicles as well as preformed membrane tubules. The EPR data are used to help develop a molecular model of ENTH domain aggregates on preformed lipid tubules that are then studied by CG MD simulation. The combined computational and experimental approach suggests that ENTH domains exist predominantly as monomers on vesiculated structures, while ENTH domains self-associate into dimeric structures and even higher‐order oligomers on the membrane tubes. The results emphasize that the arrangement of ENTH domain aggregates depends strongly on whether the local membrane curvature is isotropic or anisotropic. The molecular mechanism of ENTH‐domain-induced membrane vesiculation and tubulation and the implications of the epsin's role in clathrin-mediated endocytosis resulting from the interplay between ENTH domain membrane binding and ENTH domain self-association are also discussed.

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          Highlights

          ► ENTH domain plays an essential role in clathrin-mediated endocytosis. ► Membrane binding of ENTH domain is studied by a combined MD and EPR approach. ► A CG ENTH model for CG MD simulations is developed. ► ENTH-bound membrane tubules and vesicles are studied via CG MD simulations. ► The arrangement of ENTH domains highly correlates with local membrane curvature.

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          A unified formulation of the constant temperature molecular dynamics methods

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            BAR domains as sensors of membrane curvature: the amphiphysin BAR structure.

            The BAR (Bin/amphiphysin/Rvs) domain is the most conserved feature in amphiphysins from yeast to human and is also found in endophilins and nadrins. We solved the structure of the Drosophila amphiphysin BAR domain. It is a crescent-shaped dimer that binds preferentially to highly curved negatively charged membranes. With its N-terminal amphipathic helix and BAR domain (N-BAR), amphiphysin can drive membrane curvature in vitro and in vivo. The structure is similar to that of arfaptin2, which we find also binds and tubulates membranes. From this, we predict that BAR domains are in many protein families, including sorting nexins, centaurins, and oligophrenins. The universal and minimal BAR domain is a dimerization, membrane-binding, and curvature-sensing module.
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              Deriving effective mesoscale potentials from atomistic simulations.

              We demonstrate how an iterative method for potential inversion from distribution functions developed for simple liquid systems can be generalized to polymer systems. It uses the differences in the potentials of mean force between the distribution functions generated from a guessed potential and the true distribution functions to improve the effective potential successively. The optimization algorithm is very powerful: convergence is reached for every trial function in few iterations. As an extensive test case we coarse-grained an atomistic all-atom model of polyisoprene (PI) using a 13:1 reduction of the degrees of freedom. This procedure was performed for PI solutions as well as for a PI melt. Comparisons of the obtained force fields are drawn. They prove that it is not possible to use a single force field for different concentration regimes. Copyright 2003 Wiley Periodicals, Inc.
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                Author and article information

                Journal
                J Mol Biol
                J. Mol. Biol
                Journal of Molecular Biology
                Elsevier
                0022-2836
                1089-8638
                09 November 2012
                09 November 2012
                : 423
                : 5
                : 800-817
                Affiliations
                [1 ]Department of Chemistry, Institute of Biophysical Dynamics, James Franck Institute, and Computation Institute, University of Chicago, 5735S Ellis Avenue, Chicago, IL 60637, USA
                [2 ]Zilkha Neurogenetic Institute, University of Southern California, 1501 San Pablo Street, Los Angeles, CA 90033, USA
                [3 ]Department of Physics and Astrophysics, and Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
                [4 ]MRC Laboratory of Molecular Biology, University of Cambridge, Hills Road, Cambridge CB2 2QH, UK
                Author notes
                [†]

                C.-L.L. and C.C.J. contributed equally to this work.

                Article
                YJMBI63783
                10.1016/j.jmb.2012.08.010
                3682188
                22922484
                3c9fbc8e-306e-4d19-8aba-45671821a810
                © 2012 Elsevier Ltd.

                This document may be redistributed and reused, subject to certain conditions.

                History
                : 31 May 2012
                : 13 August 2012
                : 16 August 2012
                Categories
                Article

                Molecular biology
                cme, clathrin-mediated endocytosis,enth, epsin n-terminal homology,molecular dynamics,rt, room temperature,epsin,has, hybrid analytical systematic,amphipathic helix binding,membrane remodeling,n-bar, n-terminal bin/amphiphysin/rvs-homology,md, molecular dynamics,em, electron microscopy,cg, coarse-grained,pmf, potential of mean force,enth domain,pip2, phosphatidylinositol 4,5-bisphosphate

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