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Is there some way to experimentally determine the density distribution of Kinesin and Dynein in a Neuron? Fluorescence labeling would be impossible(?) as GFP markers would probably alter the motor dynamics. Any ideas? Or do any studies exist which looked into this topic?

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I have next to no knowledge of this area, but I do know that Peter Baas has done extensive studies of Kinesin-5 in neuronal growth cones during development. I mention that in the off chance that some of his imaging techniques might be helpful to you. –  jonsca Jul 2 at 12:31
    
Are you sure that GFP tagged motors don't function properly in these two cases? I'm almost certain I've seen motors tagged before. –  leonardo Jul 2 at 12:51

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It is possible to tag molecular motors with fluorescent proteins. It may impede with its movement but as this paper describes, a variant can be created that doesn't have cargo binding ability.

Constitutively active kinesin motors can be generated by truncations that remove autoinhibitory and cargo-binding regions of the polypeptide. For this work, we generated KHC(1-560) (Figure 1A), a dimeric motor that has been well characterized in vitro and in vivo [16],[18],[19]. KHC(1-560) motors were tagged with three tandem copies of monomeric Citrine (mCit), a variant of enhanced yellow fluorescent protein (FP) (Figure 1A), and expressed in COS cells (Figure 1B). Single Kinesin-1 motors were tracked in live cells using a modified TIRF microscope (Figure 1C) in which the angle of illumination was varied to enable deeper imaging as described [17]

However, if your objective is just to determine the density distribution of Kinesin and Dynein in a Neuron, you can simply fix the cells and do IHC staining for the motor proteins followed by high resolution imaging.

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