Folding motor domains

In spite of the gross conformational differences between the Ned dimers, there are only minor differences between the individual motor domains. The overall fold of the motor domain is very similar to that of kinesin-1 and other N-type motors. Major differences are (1) The N-terminal lobe of Ned is enlarged (+9 amino acids) compared with rat kinesin-1. The additional residues are located between /11b and /11c (the L2 finger ). This, however, does not result in a simple elongation of the /1-hairpin as in HsKSP and in M-type motors (see below). In fact, the tip of the L2 finger is rather broadened and forms a short a-helix. (2) Loop L5, the insert in the P-loop helix z 2. is quite short (approximately eight residues compared with 12 in rat kinesin-1), due to three residues that are missing in the primary structure of DmNcd. (3) Switch-1 helix z.3 is short and loop L9, the linker between z.3 and / 6 that includes the switch-1... 

Many experiments have been carried out by using this setup the stretching of single DNA molecules, the unfolding of RNA molecules or proteins, and the translocation of molecular motors (Fig. 2). Here we focus our attention on force experiments where mechanical work can be exerted on the molecule and nonequilibrium fluctuations are measured. The most successful studies along this line of research are the stretching of small domain molecules such as RNA [83] or protein motifs [84]. Small RNA domains consist of a few tens of nucleotides folded into a secondary structure that is further stabilized by tertiary interactions. Because an RNA molecule is too small to be manipulated with micron-sized beads, it has to be inserted between molecular handles. These act as polymer spacers that avoid nonspecific interactions between the bead and the molecule as well as the contact between the two beads. 

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