Despite more than 40 years of investigation since the discovery of dynein [Gibbons, I. R. and Rowe, A. J. (1965). Science149, 424-426] our understanding of how this microtubule-based motor generates force and movement remains frustratingly incomplete at the atomic level. Electron microscopy (EM) has played a major role in establishing dynein's complex architecture and its nucleotide-dependent conformational changes. In this chapter we review recent structural studies and describe in detail negative stain EM and computational single-particle image processing techniques that have been used to investigate dynein. We describe studies of both Chlamydomonas flagellar inner arm dynein-c and recombinant cytoplasmic dynein from Dictyostelium. We also detail methods for locating green fluorescent protein (GFP) and blue fluorescent protein (BFP) tags inserted at specific locations within the dynein motor, which can be used to map subdomains and conformational changes.
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