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Title: Molecular dynamics simulations of membrane proteins
Authors: Baştuğ Turgut
Kuyucak, S.
Keywords: Free energy calculations
Ion channels
Molecular dynamics
Issue Date: 2012
Publisher: Springer Verlag
Abstract: Membrane proteins control the traffic across cell membranes and thereby play an essential role in cell function from transport of various solutes to immune response via molecular recognition. Because it is very difficult to determine the structures of membrane proteins experimentally, computational methods have been increasingly used to study their structure and function. Here we focus on two classes of membrane proteins-ion channels and transporters-which are responsible for the generation of action potentials in nerves, muscles, and other excitable cells. We describe how computational methods have been used to construct models for these proteins and to study the transport mechanism. The main computational tool is the molecular dynamics (MD) simulation, which can be used for everything from refinement of protein structures to free energy calculations of transport processes. We illustrate with specific examples from gramicidin and potassium channels and aspartate transporters how the function of these membrane proteins can be investigated using MD simulations. © 2012 International Union for Pure and Applied Biophysics (IUPAB) and Springer.
ISSN: 1867-2450
Appears in Collections:Malzeme Bilimi ve Nanoteknoloji Mühendisliği Bölümü / Department of Material Science & Nanotechnology Engineering
Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection

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