Kinesin-1 (D. melanogaster)
Created by Heather Stuck
Kinesin-1, represented by PDB ID 2Y5W, is a motor protein used in transporting cargo, such as organelles, throughout the cell. Protein 2Y5W, specifically, is the motor domain aspect of Kinesin-1 found in Drosophila Melanogaster.1 Since the motility of kinesins requires a substantial amount of ATP during its anterograde transport, it is crucial for these proteins to travel only when needed for transporting cargo. Kinsein-1 prevents this waste through autoinhibition.2
Kinesin-1 includes a motor domain dimer whose monomer heavy chain units, chains A and B, are connected via a coiled-coil made up of two alpha helices. Each of these monomers also binds a magnesium-ADP complex.3 While the secondary structure of these motor domains, composed of eleven α-helices and fourteen β-strands, is highly conserved within the kinesin family, it is the tail and neck domains that affect the specifics of the protein’s functionality.4 The prominence of the neck linker to the motility function of kinesins is supported in the “fast kinesin” found in Neurospora crassa, PDB ID of 1GOJ. The neck region of this protein is virtually nonexistent. This very small region allows the heads of the protein to rotate quicker, increasing the speed of transportation, and giving it its name of “fast kinesin.” Just like Kinesin-1, this protein’s movement is powered off of ATP hydrolysis. In addition, the region of homology (95% identical) within the amino acid sequence is found in the same “kinesin motor domain, kinesin heavy chain, or KIF5-like subgroup” section.5 These homologs show the correlation between these kinesins’ structure and their function in transport. Despite being from different organisms,both use ATP hydrolysis to power the power stroke of their neck links during such movement.
During the transport of cargo along microtubules, Kinesin-1 has a free motor domain dimer conformation, which allows for the docking and undocking of the neck linkage, in addition to the dissociation of ADP. In this conformation, the dimer is only united by this singular coiled-coil linkage.6 Under highly ionic conditions, the motor domains obtain a more extended conformation while, under physiological conditions, the domains are more compact.7 In order to preserve ATP when cargo transportation is not required, Kinesin-1 undergoes autoinhibition. During this, a second cross linkage, involving the Ser181 residue of each domain, is formed by the binding of one tail domain to the two motor domains.8 Tail domains both favor the binding of ADP to kinesin and their own attachment to ADP bound kinesin motor domains.9 The dual linkage causes the motor domains to angle more inward, impeding protein movement. Since the mechanism, causing the change in motility function, does not alter or block the binding sites of nucleotides or microtubules, the effects of an allosteric site or steric hindrance are negated as possible mechanisms. It is most likely that this conformation change, by the additional linkage, restricts the movement of the motor domains by inhibiting the release of ADP, therefore preventing any movement along the microtubule, since the power strokes of the neck linkages are eliminated.10 Due to the high energy costs of ATP formation, this mechanism allows a cell to function more effectively, only undergoing ATP hydrolysis when anterograde transport is necessary.11
The binding of the tail domain to the motor domains is only permitted due to specific functionally important residues. The hydrogen bond between the Lys944 residue of the tail and the Asp185 residue of the motor domain, the hydrophobic interactions between the tail domain’s Ile942, Ile946, and the individual motor domains’ Phe123, Ile126, and Phe135, in addition to the C-H-π cooperation between the pyrrolidine ring of Pro945 with Phe179.12 The amino acid sequence of the tail domain is essentially symmetrical around the important Lys944 residue allowing the tail domain to bind to the β4 of both motor domain monomers.13 Varying between an expanded or linear structure, the tail domain is an extension to the eight stranded β sheet of a monomer. Although this is the wild-type form of the protein, mutagens have been added to support the identified protein structure. When Asp185 was replaced with Asn and His136 was replaced with Glu, the tail domain did not bind as well with the motor domains.14 Altering the residues most likely affects the hydrogen bonds formed between the tail and motor domains decreasing their binding affinity. The influence of both the discussed Lys944 residue and experimental mutations, shows the impact an amino acid sequence can have on a proteins conformation and sequentially its function.
This structural information of Kinesin-1, found in Drosophila Melanogaster, validates the protein’s function as a motor protein and how its primary, seconday, and tertiary structures contribute to efficiency in doing so.