Membrane channel protein, function molecular model

Standard molecular mechanics (MM) force fields have been developed that provide a good description of protein structure and dynamics,21 but they cannot be used to model chemical reactions. Molecular dynamics simulations are very important in simulations of protein folding and unfolding,22 an area in which they complement experiments and aid in interpretation of experimental data.23 Molecular dynamics simulations are also important in drug design applications,24 and particularly in studies of protein conformational changes,25,26 simulations of the structure and function of ion channels and other membrane proteins,27-29 and in studies of biological macromolecular assemblies such as F-l-ATPase.30... 

Plate 29 Structure of membrane proteins. Membrane peptides often self assemble into controlled oligomerie forms to make molecular selective channels whose structure can be very difficult to resolve at the molecular level by most methods, although solid state NMR methods can make a contribution to their functional and structural description. Here the pentameric funnel-Hke bundle of the M2-peptide from the nicotinic acedy choline receptor has been resolved from NMR studies of oriented M2 peptides in lipid bilayers. The funnel has a wide mouth at the N-terminal, intracellular side of the pore. The pore lining residues has also been modelled and distances between residues in the channel estimated. The a-carbon backbone is in cyan, acidic residues in red and basic residues in blue, polar residues in yellow and lipophilic residues in purple. (Figure adapted from Opella et al., (1999) Nature St. Biology, 6 374-379). See Membranes Studied by NMR Spectroscopy. 

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