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Title: Structure and dynamics of protein in the permeation and gating of potassium ion channels : identifying molecular determinants and developing coarse-grained approaches
Author: Cosseddu, Salvatore M.
Awarding Body: University of Warwick
Current Institution: University of Warwick
Date of Award: 2013
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Ion channels are transmembrane proteins which allow small ions to flow across the membrane downhill along the electrochemical gradient, with high effciency and selectivity over the different ion species, and which play crucial roles in a wide range of vital physiological functions. Research on the channels selective for potassium ions have attracted a great deal of attention over the past decade. This is because of the availability of three dimensional microscopical structures and because they provide a paradigm for the study of the complex superposition of the permeation of the ions and structural rearrangements which is responsible for the regulation of the current in ion channels. In the present work a thorough study of the strong coupling between permeation and the dynamics of the protein in the potassium ion channel KcsA is presented, based on Molecular Dynamics and Metadynamics calculations, which reveals the clear links between the function and the structure of the protein. The molecular determinants for the conformational changes of the pore region have been identified and described in details. The relationship between these rearrangements and the gating process known as "C-type inactivation", found in a variety of potassium ion channels, have been investigated and a mechanism has been proposed for the process. The knowledge acquired from these investigations is finally applied to unveil the driving forces and energetics associated with the permeation and selectivity properties of KcsA channel.
Supervisor: Not available Sponsor: Engineering and Physical Sciences Research Council
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available
Keywords: QP Physiology